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EU Research on Antimicrobial Resistance

EU projects 2007-2010

Project information

Health &life sciences

E U R O P E A NCOMMISSION

Research & Innovation

KI-30-11-027-E

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Drug-resistant infections are becoming ever more prevalent, both in hospitals and within the community, and are making the treatment of infectious diseases increasingly difficult. This brochure summarises research projects funded by the European Union’s Seventh Framework Programme (FP7) from 2007-2010 in an effort to combat antimicrobial resistance. EU funding in this area covers a broad range of microorganisms including bacteria, viruses, protozoa and fungi.

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doi:10.2777/48721

EuropEan Commission

Directorate-General for Research and Innovation

Directorate Health

Unit Infectious Diseases and Public Health

http://ec.europa.eu/research/health/infectious-diseases/anim.html

Contact: Rachida Ghalouci

European Commission

Office CDMA 02/155

B-1049 Brussels

Tel. (32-2) 29-64826

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European Commission

Eu research on antimicrobial resistanceEu projects 2007-2010

Luxembourg: Publications Office of the European Union

2011 — 148 pp. — 14,8 x 21 cm

ISBN 978-92-79-19646-1doi 10.2777/48721


EUROPEAN COMMISSION

2011



Edited by Dr. Maria Siomos

TABLE OF CONTENTS

LEGAL NOTICE

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ForewordIntroductIon

Projects:

Bacterial infectionsAeroPAtHAntiPathoGndIVInoceLLnABAtIVIcArePneuMoPneuMoPAtHconcordPILGrIMtrocAr HYPerdIFFFASt-Xdr-detecttB PAn-netantiresdevAPreSBIoHYPodebugItPArProHIBItSAturnteMPotest-Qc

Viral infectionsAntIFLucAtAFLu.orFLucureFludrugStrategyFLu-PHArMSILVercHAIn

Protozoan infectionscrIMALddIMALActreSchagasepinetKALAdruG-r

fungal infectionsSYBArIS

IndeX oF ProjectSIndeX oF coordInAtorS

68

101216202428323640444852566064687276808488

929498

102106110114118

122124128132136

140142

146146

5

Foreword

to increase the competitiveness of European health-related industries and businesses.

The research projects described represent important efforts in the fight against AMR and will serve as an important resource as Europe gears up its efforts to addressing the Grand Challenges of the future.

prioritised research in this field over several Framework Programmes. The research projects funded have a variety of complementary aims, including the development of novel therapeutics, clinical trials to define the optimal use of existing antimicrobial drugs, the development of targeted diagnostics, basic research on pathogens and monitoring the spread of resistance. This strong commitment continues in the 2011 Health Work Programme of the Seventh Framework Programme (FP7), in which AMR is a priority area. In addition, the EU hosts an annual European Antibiotic Awareness Day on 18 November to highlight the threat of AMR.

This brochure showcases EU-funded AMR research projects from 2007-2010. These projects address the full scope of AMR, including bacterial, viral, protozoan and fungal infections. EU-funded research brings together excellent teams of researchers from EU Member States and FP7 Associated Countries, as well as from International Cooperation Partner Countries (ICPC). Project partners come from universities, research centres, hospitals, small and medium-sized enterprises (SMEs), large industry and patient organisations, and cooperate in ambitious projects that can often only be undertaken with their combined expertise and resources. The knowledge generated by FP7 health research projects on AMR and other topics not only contributes to improving human health but also stimulates innovation, and aims

7Foreword

FOREWORD

Antimicrobial resistance (AMR) is a major obstacle to the treatment of infectious diseases worldwide. The global human burden posed by drug-resistant infections is difficult to quantify, but we have reason to fear that it may be enormous. In the European Union (EU) alone, the additional burden posed by resistance every year, focusing only on a limited group of health care-associated bacterial infections, is in the range of 2.5 million hospital days, 25 000 deaths and economic losses on the order of €1.5 billion due to extra health care costs and productivity losses.

AMR is prevalent in a wide array of microorganisms, including bacteria, viruses, protozoa and fungi. For example, there is wide-spread resistance to earlier generation antimalarial drugs in most malaria-endemic countries, and resistance to anti-retroviral drugs is of growing concern for the treatment of HIV/AIDS. In the case of tuberculosis, multi-drug resistant and even extensively drug-resistant bacterial strains have emerged, with high mortality rates. Faced with the extent of AMR, and the dwindling number of effective antimicrobials, the World Health Organization (WHO) has stated that it considers AMR to be one of the greatest threats to human health and will focus its 2011 World Health Day on antimicrobial resistance and its global spread.

The EU has been strongly committed to combating AMR since 1999, and has

6

IntroductIon

pathogens, such as those that cause HIV/AIDS and malaria. As it is likely that even such meas-ures will not be able to prevent the emergence of AMR entirely but rather just delay it, it is of paramount importance that new drugs and, particularly, new classes of drugs be continu-ously developed. Related to this, is the crucial question of whether there is a limit to how many more drugs and drug classes, that are both ef-ficacious and safe for patients, can be devel-oped against a particular pathogen. Vaccine development and the introduction of measures to increase hygiene to reduce the incidence of infectious diseases are, thus, essential comple-mentary strategies for mitigating AMR.

The epidemic proportions of many drug-resistant infections around the world serve as a stark warn-ing that to prevent a post-antimicrobial era, and the ensuing devastating consequences, it is im-perative that resources are mobilised for research targeted at containing and preventing AMR. The European Union’s Seventh Framework Programme (FP7, 2007-2013) is currently funding over 30 research projects on AMR in diverse pathogens, with a total budget of around €150 million. These projects are summarised in this brochure. It should be noted that ongoing projects funded under the Sixth Framework Programme (FP6, 2003-2006) are not included. The projects, most of which ad-dress human infections, have been grouped into four sections according to the type of pathogen under investigation, namely bacteria, viruses, pro-tozoa or fungi. About one third of the projects deal with drug discovery, while other issues cov-ered include the development of diagnostics, the effects of antimicrobial use, controlling and moni-toring the spread of AMR, and basic research on pathogens.

9

ContaCts:Dr. Line Matthiessen-GuyaderHead of Unit Infectious Diseases and Public HealthDirectorate-General for Research and InnovationEuropean CommissionEmail: [email protected]

Dr. anna LonnrothDeputy Head of UnitInfectious Diseases and Public HealthDirectorate-General for Research and InnovationEuropean CommissionEmail: [email protected]

Dr. arjon van HengelScientific OfficerInfectious Diseases and Public HealthDirectorate-General for Research and InnovationEuropean CommissionEmail: [email protected]

IntroductIon

INTRODuCTION

The discovery and development of antimicrobi-als, during the 20th century, revolutionised the treatment of infectious diseases. The ability to use antimicrobials against infections caused by microorganisms introduced the golden age of antimicrobials and led to the notion that pre-mature death due to infectious diseases would become a thing of the past. However, the intro-duction of antimicrobials into clinical practice has invariably led to the evolution of antimi-crobial-resistant pathogens, thus rendering the drugs concerned ineffective for the treatment of the infection. Antimicrobial resistance (AMR) is increasing morbidity and mortality due to infectious diseases worldwide. The problem is exacerbated in resource-poor countries as well as in immuno-compromised individuals, such as those harbouring HIV. AMR is a major prob-lem for a wide range of infectious diseases, including the poverty-related diseases HIV/AIDS, tuberculosis and malaria, as well as for many multi-drug-resistant bacterial, viral, pro-tozoan and fungal infections. In some cases, ‘superbugs’ have developed that are resistant to practically all available drugs.

AMR has been observed following the introduc-tion of every antimicrobial agent into clinical practice. For example, resistance of the bac-terium Staphylococcus aureus to penicillin was encountered in hospitals in the mid-1940s, only a few years after the introduction of penicillin. AMR was initially observed in hospital-acquired infections but soon also became widespread in community-acquired infections. The causes

of AMR are complex. On the one hand, AMR is inherent in nature as many antibiotics are produced by naturally-occurring fungi or bac-teria and such antibiotic-producing organisms usually also encode corresponding resistance genes in their genome, so as not to be sus-ceptible to the antimicrobial compounds that they produce. Furthermore, microorganisms are able to evolve, through genetic variation and epigenetic mechanisms, in response to selective pressures. The current extensive use of antimicrobials in medicine and agriculture constitutes a vast selective pressure for the evo-lution of antimicrobial-resistant pathogens. In the context of AMR, horizontal transfer of genes from one organism to another is an important driver as many of the known resistance genes are found on genetic elements, such as plas-mids and transposons that can be transferred between the same or different species.

A multifaceted approach is needed to contain and combat AMR, including the prudent use of existing antimicrobials, the use of combination therapies, the development of new antimicrobi-als and vaccine development. The prudent use of antimicrobials encompasses many issues, ranging from restricting the use of antimicrobi-als in agriculture to only administering an anti-microbial when effective and necessary in med-ical practice. The latter requires that pathogens and their drug susceptibility be rapidly and ac-curately identified prior to the implementation of treatment regimens. Microbial genomics offers unprecedented opportunities for developing molecular diagnostic tools to reach this goal. Related to the prudent use of antimicrobials is the use of combination therapies as this slows the pace of development of AMR in some

8

BACTERIALINFECTIONS

BacterIal InFectIonS 11BacterIal InFectIonS10

BacterIal InFectIonS

Aim

To apply modern structural proteomics, molecular biology, computational chemistry and screening technologies to identify novel drug targets, as well as generate hit and lead compounds.

Results

•Fundamentalinformationonessential gene products in Gram-negative bacteria and elucidation of structure–function relationships for a series of bacterial proteins.

•Identificationofnovelinhibitorsofselectedtargets and a genome-wide assessment of druggability.

PotentiAl APPlicAtions

Development of new antimicrobial therapies.

Key words:Gram-negative, pathogen, Pseudomonas aeruginosa, gene knockout, virtual screening, high-throughput screening, fragment screening, structural proteomics, ligand binding

13BacterIal InFectIonS

summARy

The project aims to support antimicrobial drug development by studying the molecular biology of Gram-negative bacteria using the pathogen model Pseudomonas aeruginosa, and developing ligands and inhibitors (hit and lead compounds) with the potential to underpin the discovery of improved therapies for Gram-negative infections. The research covers five distinct areas: (1) experi-mental validation and identification of novel targets using gene knockouts in P. aeruginosa; (2) cloning and characterisation as well as biochemical and structural biology analysis of the novel targets; (3) a directed search for ligands/inhibitors of the validated antimicrobial drug targets by virtual screening and assessment of druggability, and high-throughput screening of a subset of targets; (4) characterisation of drug target–ligand/inhibitor interactions using biochemical and crystallographic studies, computational modelling, followed by design and modelling to enhance binding proper-ties; (5) initial biological testing for efficacy against Gram-negative bacteria.

PRoblem

The prevalence of infections caused by Gram-negative pathogens coupled to increased drug resistance requires that novel antimicrobial therapies against such pathogens be developed.

12

Acronym:Contract number:

EC contribution:Duration:

Starting date:Funding scheme:

AEROPATH223461 EUR 4 591 46348 months01/11/2008 Focused research project

www.aeropath.eu

IDENTIFICATION, ChARACTERISATION AND ExpLOITATION OF NOvEL

GRAm-NEGATIvE DRuG TARGETS


Coordinator

Prof. William HunterCollege of Life SciencesUniversity of DundeeDow St.Dundee DD1 5EHUnited KingdomE-mail:[email protected]

Partners

Prof. Mahavir SinghLIONEX Diagnostics & Therapeutics Braunschweig, Germany

Prof. Gunter SchneiderKarolinska InstituteStockholm, Sweden

Prof. Jim NaismithUniversity of St. AndrewsSt. Andrews, United Kingdom

Dr. Marko Maringer mfd Diagnostics GmbHWendelsheim, Germany


and the rest of the world, new and effective anti-microbial agents against Gram-negative bacteria are especially needed.

Aim

The project aims to advance knowledge about the biological processes and mecha-nisms related to infection in Gram-negative bacteria as well as to identify new drug targets or combinations of targets in Gram-negative bacteria, and potential drugs (hit compounds).

Results

Identification and validation of novel drug targets in Gram-negative bacteria as well as hit compounds against these targets displaying antimicrobial activity.


Development of a new class of anti-infective drugs against Gram-negative bacteria.

Key words:interactomics, computational biology,structural biology, clinical microbiology,target discovery, drug discovery, antibody technology


summARy

Multi-drug-resistant bacterial infections are in-creasing at an alarming rate in community and nosocomial settings in both developing and de-veloped countries. The few antimicrobial agents that have been launched over the past decade (e.g. linezolid, daptomycin) are active against Gram-positive bacteria. To tackle the problem of multi-drug-resistant Gram-negative bacterial patho-gens, the project proposes a novel strategy for the discovery of new antimicrobial drug targets in a number of Gram-negative bacteria. This strategy is based on a comparative, system-level analysis of molecular processes involved in pathogenic-ity, drug resistance, cell division and/or growth of selected pathogenic Gram-negative bacteria through a combination of computational biology, interactome discovery, in vivo protein-blocking and structural biology techniques. This comparative analysis will permit the discovery of new potential drug targets, relevant to both species-specific and broad-spectrum antimicrobial strategies. The project will also pursue the identification of novel antibacterial compounds acting against previously validated targets by screening purpose-specific libraries of products derived from natural resources and from synthetic compounds.

PRoblem

Due to the increasing emergence and spread of antimicrobial drug-resistant pathogens in Europe

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AntiPathoGN223101 EUR 5 943 961 48 months01/02/2009 Focused research project

www.antipathogn.eu

IDENTIFICATION AND vALIDATION OF NOvEL DRuG TARGETS

IN GRAm-NEGATIvE BACTERIABy GLOBAL SEARCh:

A TRANS-SySTEm AppROACh


Coordinator

Prof. Xavier DauraInstitute of Biotechnology and BiomedicineUniversitat Autònoma de Barcelona08193 Bellaterra, SpainE-mail: [email protected]

Partners

Prof. Patrick AloyFundació Privada Institut de Recerca Biomèdica IRBBarcelona, Spain

Dr. José M. MasInfocienciaBarcelona, Spain

Dr. Víctor de LorenzoMicrobiontaTres Cantos, Spain

Dr. Dirk UllmannProteros BiostructuresMartinsried, Germany

Dr. Marc StadlerInterMed DiscoveryDortmund, Germany

Dr. Laurent VuillardBio-XtalMarseille, France

Prof. Jordi VilaFundació Clínic per a la Recerca BiomèdicaBarcelona, Spain

Dr. Manfred KoeglDeutsches KrebsforschungszentrumHeidelberg, Germany

Dr. Judith Farrés MarischAnaxomics BiotechBarcelona, Spain


PRoblem

Bacterial antibiotic resistance.

Aim

To curb the proliferation and viability of Gram-negative pathogens by inhibiting a basic essential function of bacteria, namely cell division.

Results

The project will progress beyond the state-of-the-art in antimicrobial research by incorporating frontline technology into the knowledge on the Gram-negative division process to design and run screening as-says, and validate the resultant hits. Progress will be maximised by building compound collections for screening tailored to divisome and septum targets. Lead improvement will also be performed on selected hits.


•Antibioticdiscovery.•Treatmentofinfectiousdisease.

Key words:anti-infectives, septation, Gram-negatives, synthetic scaffolds, evolutionary genetic chemistry, protein interactions, nucleotide-binding sites, peptidoglycan, molecular dynamics, e. coli


summARy

The project aims to identify novel Gram-negative targets by exploiting the components of the divi-some, their activities and interactions. Selective assays for screening will be designed with the aim of obtaining a new class of antimicrobials: compounds that block bacterial division. New medicines to attack Gram-negative pathogens would decrease the burden of infectious disease and have a beneficial social and economic impact in Europe and beyond. Cell division is an essential and still underexploited process with excellent properties to yield new inhibitors of infection by blocking the proliferation of pathogens. Inhibitors directed against bacterial division targets, that are not present in eukaryotic cells, will be both effective and innocuous to humans and animals. In addition, as many of their structures will be based on interac-tion domains and synthetic scaffolds, they would be expected to generate resistance at levels lower than for antibiotics. The project will apply existing and new knowledge on the molecular biology of Gram-negative cell division as well as novel analytical (nanodiscs), bioinformatic (molecular dynamics), structural (membrane protein crystals) and imaging (lanthanide staining) tools to exploit, in the test tube, the structures and interactions of targets in the divisome and the septum. Potent systematic screening assays will be developed and used to select compounds specifically tailored to inhibit the division of Gram-negatives (not precluding broad-spectrum compounds). Secondary activity and cell assays, based on the properties of bacte-rial division, will be generated to validate hits and advance them to leads. The medicinal properties of selected leads will be improved.

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DIVINOCELL223431 EUR 5 956 086 48 months01/03/2009 Focused research project

www.cnb.csic.es/~ divinocell/

ExpLOITING GRAm-NEGATIvE CELL DIvISION TARGETS IN

ThE TEST TuBE TO OBTAIN ANTImICROBIAL COmpOuNDS


Coordinator

Prof. Miguel VicenteCentro Nacional de BiotecnologíaC/ Darwin No. 3CSIC Campus de Cantoblanco28049 MadridSpainE-mail: [email protected]

Partners

Prof. Paulino Gómez-PuertasBiomol-Informatics SLMadrid, Spain

Dr. Veronique ArluisonCNRSParis, France

Dr. Sanne JensenEvolva BiotechFrederiksberg C, Denmark

Dr. Jan LöweMRC Laboratory of Molecular BiologyCambridge, United Kingdom

Prof. Jeffery ErringtonDemuris LtdNewcastle upon Tyne, United Kingdom

Dr. Octavio MonasterioUniversidad de ChileSantiago, Chile

Dr. Waldemar VollmerUniversity of Newcastle upon TyneNewcastle upon Tyne, United Kingdom

Dr. Tanneke den BlaauwenUniversity of AmsterdamAmsterdam, The Netherlands

Gábor NémethVichem Chemie Research LtdBudapest, Hungary

Dr. Sjouke LuirinkVrije Universiteit AmsterdamAmsterdam, The Netherlands


various classes of potent antimicrobial drugs have been developed in the past 80 years, which have considerably improved the management of infectious diseases. This golden age of antibiotics engendered such optimism that it was commonly thought that bacterial infections would be rapidly eliminated as a cause of mortality. Unfortunately, bacterial resistance to all classes of antibiot-ics soon appeared. Heavy antibiotic use and person-to-person spread of bacteria have greatly increased antibiotic resistance, and this problem is continually increasing in severity.

Aim

Using P. aeruginosa and B. cenocepacia as Gram-negative model organisms, the project aims to:

•Identifynovelantibacterialandantibiotic re-sensitivisation targets in antibiotic-resistant strains using genomics approaches.

•Validatethesetargetsinstrainsofvarious clinical origin using a number of in vitro and in vivo disease models.

•Inhibitthetargetsbyoptimisedlead compounds from synthetic and natural sources.

Results

The project will generate two alternative types of antibacterials that may escape the extensive mechanisms of bacterial resistance. These are: (1) conventional antibacterials as far as their chemi-cal features and direct effects on their targets are concerned, but novel in terms of mechanism of action; and (2) non-conventional antibacterials,

such as antisense oligomers, which primarily act on the expression of the target and not on its function. The combined efforts are expected to result in a panel of new drugs for the treatment of P. aeruginosa infections in patients with cystic fibrosis and other high-risk patient groups. Fur-thermore, the knowledge generated will facilitate identification of new targets for the development of antimicrobial drugs in other bacterial pathogens, especially other Gram-negative bacteria, such as B. cenocepacia.


•Developmentofnoveltechnologiesand protocols which will be used for novel antibacterial drug discovery.

•Identificationofnoveldrugsagainstmultiresistant P. aeruginosa, B. cenocepacia and other Gram-negative bacteria with sufficient potential for further pre-clinical development.

Key words:Gram-negative bacteria, antimicrobial resistance, novel drug targets, lead compounds, antibacterials, Pseudomonas aeruginosa, Burkholderia cenocepacia


summARy

Despite the advent of antibiotics, infectious diseases retain a prominent position as a major worldwide cause of morbidity and mortality. This problem has worsened with the emergence of multi-antibiotic-resistant bacteria and the failure of pharmaceutical company drug discovery programmes to design antibiotics with truly novel modes of action. The project aims to generate new strategies leading to the identification and validation of novel tar-gets for antimicrobials using the Gram-negatives, Pseudomonas aeruginosa and Burkholderia ceno-cepacia, as model organisms, as they cause high morbidity and mortality worldwide. The versatility of these model bacteria will enable the results obtained to be extrapolated to other important bacterial pathogens. The extensive involvement of SMEs in this consortium will enable the selec-tion of lead compounds against the identified targets from their large libraries of natural and synthetic chemicals which, after validation, will establish the basis for the development of new classes of antibacterial drugs. This will result in a reduction in the incidence of disease caused by these organisms, with a direct positive impact on the quality of life and life expectancy of high-risk patient populations.

PRoblem

The considerable difficulty in resolving P. aeruginosa infections and those caused by other Gram-negative pathogens, such as B. cenocepacia, is thought to reflect the worldwide increasing occurrence of antibiotic-resistant strains. To combat infections,

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NABATIVI223670 EUR 5 506 000 48 months01/02/2009 Focused research project

www.nabativi.org

NOvEL AppROAChES TO BACTERIAL TARGET

IDENTIFICATION, vALIDATION AND INhIBITION


Coordinator

Dr. Alessandra BragonziFondazione Centro San RaffaeleVia Olgettina 6020132 MilanItalyE-mail: [email protected]

Partners

Dr. Miguel Cámara University of NottinghamNottingham, United Kingdom

Prof. Gerd DöringEberhard Karls University of TübingenTübingen, Germany

Dr. Björn KullActar ABStockholm, Sweden

Prof. John RobinsonUniversity of ZurichZurich, Switzerland

Dr. Giovanni BertoniUniversità degli Studi di MilanoMilan, Italy

Do Quoc-TuanGreenpharma S.A. Orléans, France

Prof. Peter E. NielsenUniversity of Copenhagen Copenhagen, Denmark

Dr. Daniel ObrechtPolyphor AGAllschwil, Switzerland


idly decrease a few months after immunisation, and finally no immunological memory develops. Polysaccharide–protein conjugates have an overall higher efficacy, but are expensive and complicated to produce. Moreover, serotype replacement may lead to the spread of serotypes not covered by the vaccines. Antibiotic consumption has led to a gradually increasing pneumococcal resistance against penicillin and cephalosporins, and to the emergence of multi-drug-resistant strains. These strains pose a particular and increasing problem for the treatment of pneumococcal meningitis. Since the entry of hydrophilic antibacterials (penicillin, cephalosporins, carbapenems, glycopeptides) into CNS compartments is poor, pharmacokinetic and pharmacodynamic aspects of antibiotics in the CNS compartments have to be considered. From a pharmacokinetic viewpoint, the ideal antibiotic to treat CNS infections possesses moderate lipophilicity, low molecular weight and a low binding to serum proteins. In addition to this, increasing the bacte-ricidal activity of antibiotics in vivo by adjunctive compounds appears to be promising.

Aim

The overall aim is to develop novel therapeutic and vaccine strategies to combat antibiotic resist-ance in S. pneumoniae through:

•Epidemiologystudiesofdrugresistanceand vaccine pressure replacement of S. pneumoniae.

•Analysisofhost–pathogeninteractionsand identification of potential therapeutic targets and vaccine candidates.

•Developmentofimprovedvaccineandintervention strategies.

exPected Results

Knowledge will be generated based on epidemi-ology and host–pathogen interaction in order to control diseases caused by antibiotic-resistant strains of S. pneumoniae. Molecular approaches will be used for the development of a new generation of antimicrobials and for a novel polysaccharide–glycolipid conjugate pneumococcal vaccine.


Scientific and technological knowledge essential for the improvement of current strategies for treatment and prevention of diseases caused by antibiotic-resistant pneumococci.

Key words:antibiotic resistance, S. pneumoniae, epidemiology, host–pathogen interaction, virulence mechanisms, vaccine


summARy

Diseases caused by Streptococcus pneumoniae are a major public health problem all over the world. Children, the elderly and immuno-compromised individuals are at highest risk of contracting pneumococcal diseases. Despite the availabil-ity of a large number of antibiotics, mortality and morbidity due to S. pneumoniae infections remain high. This is due to increasing antibiotic resistance among pneumococcal strains, and the fact that the current vaccine, though effective for certain serotypes, leads to serotype replacement. New intervention strategies, especially against antibiotic-resistant S. pneumoniae strains, must be developed. The major objectives of this project are: (1) monitoring prevalent S. pneumoniae serotypes and their resistance profiles in different countries; (2) analysis of host–pathogen interac-tions and identification of potential therapeutic targets and vaccine candidates; (3) providing a basis for the development of improved vaccine and intervention strategies.

PRoblem

There are currently two ways to limit the burden of pneumococcal infection: prevention by vaccina-tion and treatment with antibiotics. Vaccination of children is performed with a polysaccharide–protein conjugate, while vaccination of adults is based on the use of a 23-valent polysaccharide vaccine. Polysaccharide vaccines in young infants are poorly immunogenic, antibody levels rap-

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CAREPNEUMO223111 EUR 2 999 999 36 months01/03/2009 Focused research project

www.helmholtz-hzi.de/ en/carepneumo/home/

COmBATING ANTIBIOTIC RESISTANT pNEumOCOCCI By NOvEL STRATEGIES BASED ON in vivo AND in vitro hOST–

pAThOGEN INTERACTIONS


Coordinator

Prof. Gursharan ChhatwalDepartment of Microbial PathogenesisHelmholtz-Zentrum für InfektionsforschungInhoffenstraße 738124 BraunschweigGermanyE-mail: [email protected]

Partners

Dr. Mark van der LindenUniversitätsklinikum AachenAachen, Germany

Prof. Nicholas LegakisNational and Kapodistrian University of AthensAthens, Greece

Dr. Ewa SadowyNational Medicines InstituteWarsaw, Poland

Prof. Mário RamirezInstituto de Medicina MolecularLisbon, Portugal

Dr. Horacio Angel LopardoHospital de Pediatria SAMIC

Prof. Dr. Juan P. GarrahanBuenos Aires, Argentina

Prof. Anuradha ChakrabortiPostgraduate Institute of Medical Education and ResearchChandigarh, India

Prof. Timothy MitchellUniversity of GlasgowGlasgow, United Kingdom

Dr. Juan HermosoConsejo Superior de Investigaciones CientificasMadrid, Spain

Dr. Jesús Sanz-MoralesUniversidad Miguel Hernandez de ElcheElche, Spain

Prof. Regine LandmannUniversity Hospital BaselBasel, Switzerland

Prof. Yaffa Mizrachi NebenzahlProtea Vaccine Technologies LtdKiryat Shmona, Israel

Prof. Sven HammerschmidtErnst-Moritz-Arndt University of GreifswaldGreifswald, Germany


and disease pneumococcal isolates will be used to challenge in vivo and in vitro models, followed by integrated management and analysis of the data with a new semantic web bioinformatic infrastructure.

PRoblem

S. pneumoniae is a major pathogen and is respon-sible for high rates of disease, death and permanent injury. Pneumococcal disease can affect any age group but especially at risk are the very young and the elderly, those with compromised immune systems through illness or medical treatment, or those with chronic illness. Vaccination and antibiotics remain the main weapons against pneumococcal disease. Pneumococcal disease has traditionally been treated with penicillins. However, treatment has become more difficult due to an increasing resistance to antibiotics.

Aim

Through a systems approach to host–pneumococcal interaction, the project aims to identify the most important and consistently involved host and pneumococcal factors.

Results

Identification of new targets for vaccination, diagnosis and treatment of pneumococcal disease.


Targets for diagnosis, therapy, enhancement of host defence and prophylaxis.

Key words:pneumococcus, virulence, genomics, antibiotic resistance, epidemiology, systems biology, models of infection, genetics


summARy

The project is a fundamental, comprehensive study of host–pathogen interactions during infection with Streptococcus pneumoniae. The expectation is that the basic knowledge gained from this work will provide new targets for vaccination, diagnosis and treatment. The project is divided into six parts: (1) the molecular epidemiology of antibiotic-resistant pneumococci; (2) the genetic basis of disease susceptibility in the human host and in mice; (3) molecular aspects of virulence and host response in animal models of pneumococcal carriage and disease; (4) molecular aspects of virulence and host response in human cell culture systems; (5) pneumococcal cell biology to determine the role of central metabolic processes and the link to virulence; and (6) integrated bioinformatics and data management. It is accepted that the outcome of pneumococcal infection is determined by the interplay of both host and pathogen attributes. Pneumococcal isolates vary in the repertoire of genes that they possess. Hence, the contribution of an individual factor to the infectious process may vary according to the other host and pathogen factors that are present. To date, a reductionist approach has often been taken to the study of infection, considering the contribution of each virulence factor or host factor in isolation. Conse-quently, in searching for targets for antimicrobial therapy or for enhancement of host defence, the contribution of individual factors may be inac-curately estimated. The project, rather than using targeted mutagenesis to create strains of different phenotypes for testing, will take a systems biol-ogy approach with a checkerboard experimental design. Panels of resistant/non-resistant carriage

32




PNEUMOPATH222983 EUR 2 999 839 36 months01/03/2009 Focused research project

www.pneumopath.org

A COmpREhENSIvE DISSECTION OF

pNEumOCOCCAL–hOST INTERACTIONS


Coordinator

Prof. Peter AndrewUniversity of LeicesterMaurice Shock BuildingUniversity RoadLeicester LE1 9HNUnited KingdomE-mail: [email protected]

Partners

Dr. Jean-Pierre ClaverysCNRS-Université Paul SabatierToulouse, France

Prof. Peter HermansRadboud University Nijmegen Medical CentreNijmegen, The Netherlands

Prof. Birgitta Henriques-NormarkSwedish Institute for Infectious Disease ControlSolna, Sweden

Dr. Ingileif JonsdottirdeCODE geneticsReykjavik, Iceland

Prof. Marco OggioniUniversità degli Studi di SienaSiena, Italy

Prof. Regine HakenbeckTechnical University of KaiserslauternKaiserslautern, Germany

Prof. Herminia de LencastreUniversidade Nova de LisboaOeiras, Portugal

Prof. Oscar KuipersUniversity of GroningenHaren, The Netherlands

Dr. Nicholas LindleyInstitut National des Sciences AppliqueesToulouse, France

Prof. Jonas Almeida Instituto de Engenharia de Sistemas e ComputadoresLisbon, Portugal

Dr. Andreas Meinke Intercell AGVienna, Austria

Dr. Paul DennyMRC Mammalian Genetics UnitHarwell, United Kingdom

Prof. Staffan NormarkKarolinska InstituteStockholm, Sweden

Dr. Herman GroenIQ CorporationGroningen, The Netherlands


epidemiology as well as specific recommendations or testable hypotheses for human and veterinary clinical practice. The potential of intervention strategies to combat CA- and FA-MRSA will be determined.

PRoblem

MRSA is emerging as a community-associated pathogen, which includes the farm environment. The change in epidemiological and microbiologi-cal characteristics will provide new challenges for infection control practices in hospitals. Multiresistant and highly epidemic CA-MRSA clones have spread in otherwise healthy individuals in the USA as well as in several European countries. Furthermore, FA-MRSA can cause serious infection in animals. There is limited information about the genetic determinants and metabolic changes responsible for the enhanced epidemicity of the CA- and FA-MRSA strains, and there are no strategies for controlling the spread of these pathogens.

Aim

The aim of the project is to explain the ecologi-cal success of CA- and FA-MRSA in contrast to HA-MRSA, in order that effective strategies to control the spread of CA- and FA-MRSA can be developed.

exPected Results

•AcollectionofepidemiologicallyrelevantCA- and FA-MRSA isolates.

•Identificationandcharacterisationofthemost important epidemic clones.

•InsightsintotheevolutionofCA-andFA-MRSA in the context of the whole population of S. aureus.

•Identificationofnovelmobilegeneticelements and virulence factors.

•Identificationofproteinsthatmaybeusedfor vaccination.

•Identificationofrelevantgeneticdifferences between CA- and FA-MRSA compared to HA-MRSA.

•Identificationofregulatorypathwaysinvolved in adaptation to the community environment.

•Developmentofanex vivo porcine skin model, in particular for the study of FA-MRSA.

•Mathematicalmodelsthatdescribetheepidemiology of CA- and FA-MRSA, and that can be used to predict the outcome of interventions.

•Validatedprotocolsforphage-mediatedtreatment of animals, which in the future may be extended to humans.


summARy

Methicillin-resistant Staphylococcus aureus (MRSA) was, until recently, confined to hospitals (HA-MRSA). However, community- and farm-associated MRSA (CA- and FA-MRSA), which are epidemiologically distinct, are an important cause of infection, against which there are no effective strategies. To gain insight into the complex epidemiology of CA- and FA-MRSA, and to obtain contemporary isolates, small-scale surveillance studies will be performed among: (1) patients in the 20 most populous EU countries; (2) pigs from farms in major pig-exporting countries; and (3) calves in important veal-calf-raising countries. Genomics data for CA-MRSA is limited, and non-existent for FA-MRSA. The successful adaptation of MRSA to a new environment implies the acquisition of novel genetic determinants or the differential expression of native genes. Only two CA-MRSA isolates have been fully sequenced and the UMCU has sequenced an FA-MRSA isolate. Whole genome sequencing, comparative genome hybridisation and transcriptomics will be used to understand the genetic adaptations of MRSA in the community environment. The contribution of putative virulence factors to pathogenicity will be studied by the construction of knockout mutants and complementation experiments. The mutant strains will be tested in relevant in vitro and ex vivo models to establish the precise physiological role of the putative virulence determinants. Nowadays, mathematical modelling is an important tool for managing infection control. A few models exist that evaluate measures to reduce transmission of HA-MRSA or CA-MRSA in jails. However, no models are available for FA-MRSA. Modelling will provide both fundamental insights into MRSA

36




CONCORD222718 EUR 2 994 192 36 months01/01/2009 Focused research project

www.concord-mrsa.eu

CONTROL OF COmmuNITy-ACquIRED mRSA: RATIONALE

AND DEvELOpmENT OF COuNTERACTIONS

BacterIal InFectIonS 39


•Thedevelopmentofspecificdiagnosticassays for CA-MRSA and FA-MRSA strains.

•Developmentofvaccines.•Interventionstrategiesbasedon

mathematical modelling with regard to human and veterinary medicine to prevent the spread of CA- and FA-MRSA.

•Phage-mediatedinterventiontoreducethe number of MRSA bacteria carried by either humans or animals.

Key words:community-associated MRSA, farm-associated MRSA, MRSA, methicillin resistance, phage therapy, whole genome sequencing, comparative genomics, microarray, transcriptomics, mathematical modelling, population structure, virulence, Staphylococcus aureus

BacterIal InFectIonS38

Coordinator

Dr. Ad FluitDepartment of Medical MicrobiologyUniversity Medical Center UtrechtHeidelberglaan 1003584 CX UtrechtThe NetherlandsE-mail: [email protected]

Partners

Dr. Gerard LinaUniversite Claude Bernard Lyon 1Lyon, France

Dr. Herminia de LencastreUniversidade Nova de LisboaOeiras, Portugal

Dr. J.A. WagenaarUniversity of UtrechtUtrecht, The Netherlands

Dr. Mark WoolhouseUniversity of EdinburghEdinburgh, United Kingdom

Dr. Waleria HryniewiczNational Medicines InstituteWarsaw, Poland

Dr. Frank AarestrupTechnical University of DenmarkCopenhagen V, Denmark

Dr. Floyd WittinkUniversity of AmsterdamAmsterdam, The Netherlands

Dr. John Nicholas HousbyNovolytics LimitedCoventry, United Kingdom


teria. The focus will be on the MRSA ST398 strain, an animal-adapted, zoonotic, resistant pathogen that causes colonisation and infection in humans in community and health care settings.

exPected Results

Epidemiological and physiological studies of MRSA ST398 will be undertaken. Molecular approaches will be used in comparable animal models as well as in humans in community and health care settings to: (1) investigate/explore the biology and ecology of MRSA ST398; (2) identify and characterise factors determining the transmission pathways and risk from animal to hu-man and between humans; (3) establish genetic differences, host-range and virulence of adhesive and non-adhesive strains as well as differences between ST398 and other MRSA strains; (4) identify specific genes for the development of new rapid tests to identify specific MRSA strains; (5) provide a technology testing platform for developing and assessing decolonisation and environmental sani-tation approaches; (6) integrate results in policy and practice guidelines.


Facilitation of rapid and cost-effective measures to combat emerging resistant strains in order to prevent and eradicate community and nosocomial infec-tions for better protection of citizens and patients in Europe and beyond.

Key words:infection control, nosocomial infection, antimicrobial resistance, Staphylococcus aureus


summARy

Methicillin-resistant Staphylococcus aureus (MRSA) is of increasing concern both as a community- and hospital-acquired infection. The project will provide novel control measures for the accelerated iden-tification and control of resistant bacteria initially emerging from animals, in order to prevent and eradicate community-acquired and nosocomial infections. A deeper understanding of the factors affecting the pathogen–host interaction of resistant bacteria at the molecular as well as the population level will lead to new and more effective control measures against nosocomial infection.

PRoblem

Since 2005, the MRSA ST398 clone has been spreading both in livestock populations and in occupationally-exposed people, resulting in hu-man infection and disease in several European countries.

Aim

The key objective of the project is to provide a range of novel control measures for the accelerated identification and control of emerging resistant bac-

40




PILGRIM223050 EUR 2 993 824 36 months01/01/2009 Focused research project

www.fp7-pilgrim.eu

pREvENTING COmmuNITy AND NOSOCOmIAL SpREAD AND INFECTION WITh mRSA ST 398 - INSTRumENTS FOR

ACCELERATED CONTROL AND INTEGRATED RISk mANAGEmENT OF ANTImICROBIAL RESISTANCE


Coordinator

Prof. Katharina StärkRoyal Veterinary College Hawkshead LaneNorth Mymms AL9 7TAUnited KingdomE-mail: [email protected]

Partners

Prof. Andreas VossRadboud University Nijmegen Medical CentreNijmegen, The Netherlands Dr. Luca GuardabassiUniversity of CopenhagenCopenhagen, Denmark

Prof. Olivier DenisUniversité libre de Bruxelles - Hopital Erasme Brussels, Belgium

Prof. Henri VerbrughErasmus MCRotterdam, The Netherlands

Dr. Jodi LindsaySt. George’s Hospital Medical SchoolLondon, United Kingdom

Dr. Arjen van de GiessenRijksinstituut voor Volksgezondheid en MilieuBilthoven, The Netherlands

Dr. Robert SkovStatens Serum InstitutCopenhagen, Denmark

Dr. Josef KrysaVysoka Skola Chemicko-Technologicka V Praze Prague, Czech Republic

Prof. Patrick ButayeCentrum voor Onderzoek in de Diergeneeskunden en AgrochemieBrussels, Belgium

Dr. Duarte TitoAguacure LimitedBangor, United Kingdom

Dr. Jeanette MüllerAccelopment AG Zurich, Switzerland


with high efficiency among hospitalised patients or to produce severe or invasive infections or the ability to efficiently colonise human hosts over long periods of time. MRSA, VRE, ESMAC-BL-producing Enterobacteriaceae, multi-drug-resistant P. aeruginosa and a. baumannii are the paradigm of resistant bacteria. The selection of the most appropriate strategies to control the dissemination of these microorganisms is under debate, largely because of the lack of a definition of the specific traits of the epidemic strains.

Aim

To define genotypic or phenotypic traits of highly virulent multiresistant strains of MRSA, VRE, ESMAC-BL-producing Enterobacteriaceae, multi-drug-resistant P. aeruginosa and a. baumannii for the better design of control strategies. There are three main questions that we would like to answer:

1. Are certain resistant strains more epidemic than others? Are certain strains more prone to persist in the human environment? If so, why?

2. Do epidemic and persistent strains have specific virulence, physiological, colonisa-tion or transmission-facilitating traits that non-epidemic strains do not have?

3. What is the origin and mechanism of ac-quisition of these fitness-increasing traits in resistant bacteria? Might the elucidation of such mechanisms provide new insights for prediction and intervention?


•Toolsformonitoringthespreadofkeycommunity and nosocomial pathogens.

•Scientificbasisforanearlywarningsystem when isolates of a particular epidemicity appear in community and nosocomial settings.

•Aknowledgebaseforcombatingepidemicity and virulence, to characterise specific genetic elements carrying genes encoding ESCMAC-BL.

•Identificationofpotentialreservoirsofantibiotic resistance genes amongst community and nosocomial pathogens involving multi-drug resistance.

Key words:methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococcus spp., extended-spectrum, metallo- and acquired AmpC beta-lactamase-producing Enterobacteriaceae, multi-drug-resistant, Pseudomonas aeruginosa, acinetobacter baumannii


summARy

The project will investigate the epidemiology of new, highly virulent, multiresistant strains of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococcus spp. (VRE), extended-spectrum, metallo- and acquired AmpC beta-lactamase (ESMAC-BL)-producing Entero-bacteriaceae, multi-drug-resistant Pseudomonas aeruginosa and acinetobacter baumannii. The three major aims are: (1) definition of the major high-risk resistant clones; (2) investigation of spe-cific traits associated with virulence, transmission, persistence and resistance of epidemic clones in comparison with non-epidemic clones as well as resistance determinants and their genetic location in horizontal gene transfer units and their genetic environment; (3) development of bioinformatics tools to fully exploit the genomics data and allow the rapid identification of resistant strains with heightened epidemic potential.

PRoblem

The health care systems of most European countries are based on a continuum from acute care hospitals, through other health care facilities to the community. This framework provides the perfect opportunity for the wide-spread dissemination of high-risk resist-ant clones or genetic-resistant elements. High-risk resistant clones are bacterial clones that have: (1) mechanisms of resistance to antibiotics of critical clinical importance; (2) the ability to be transmitted

44




TROCAR223031 EUR 2 999 444 36 months01/01/2009 Focused research project

www.trocarproject.eu

TRANSLATION RESEARCh ON COmBATINGANTImICROBIAL

RESISTANCE


Coordinator

Prof. Jordi VilaDepartment of Clinical MicrobiologyInstitut d’Investigacions Biomèdiques August Pi i SunyerVillarroel 170Barcelona 08036SpainE-mail: [email protected]

Partners

Prof. Herminia de LecanstreUniversidade Nova de LisboaOeiras, Portugal

Prof. Roland LeclercqUniversite de Caen Basse-NormandieCaen, France

Prof. Alkiviadis VatopoulosNational School of Public HealthAthens, Greece

Dr. Jaana Vuopio-VarkilaNational Public Health InstituteHelsinki, Finland

Prof. Gian-Maria RossoliniUniversità degli Studi di Siena Siena, Italy

Prof. Hajo GrundmanUniversity Medical Center Groningen Groningen, The Netherlands

Dr. Karin WernerEuropean Society of Clinical Microbiology and Infectious DiseasesBasel, Switzerland

Prof. Patrice NordmannUniversité Paris Sud XILe Kremlin Bicêtre, France

Dr. Edward FeilUniversity of BathBath, United Kingdom

Prof. Wolfgang WitteRobert Koch InstituteWernigerode, Germany

Dr. David LivermoreHealth Protection AgencyLondon, United Kingdom

Rafael CantónFundación para la Investigación Biomédica del Hospital Universitario Ramón y CajalMadrid, Spain

Dr. Ana María Blanco Sánchez Sistemas Genomicos SLPaterna, Spain


the community. By June 2007, the presence of this strain had been reported in over 200 hospitals in 13 European countries. The physiological factor(s) responsible for the spread of these strains are un-known. Indeed, aside from the toxins, the identity of c. difficile virulence factors is in general unknown. This has largely been a consequence of a lack of effective gene knockout technologies for functional genomic studies.

Aim

The overall objective of the project is to determine the physiological factors that cause hypervirulence in c. difficile, to provide crucial information for both the development of more informed tests for diagnosis and epidemiological studies, and the formulation of more effective countermeasures for infection control and disease management. To establish the basis of hypervirulence, 027-associated genes which encode products hypothesised to be involved in pathogenesis will be systematically inactivated, and their effects on virulence assessed using infection models. The genes to be targeted will be chosen based on comparative genomic studies, in which hypervirulent strains are compared to ‘standard’ strains. To identify potential reservoirs of infection, the prevalence of the identified hypervirulence traits in the human and animal population will be determined by undertaking epidemiological studies. Special attention will be paid to the wider human population to gauge the prevalence of community-acquired c. difficile.

Results

ClosTron gene knockout technology will be used to identify the genes which are required for c. difficile infection and disease progression. This will lead to the identification of those physiological factors that cause hypervirulence. Once identified and their role in disease established, rational countermeasures may be devised. While the focus to date has been on hospital-acquired disease and type 027 strains, there is mounting evidence that community-acquired c. difficile is becoming an increasing problem, as is the incidence of the disease in animals. The project will establish the relationships between these strains and determine whether they act as a reservoir for hypervirulence traits. Moreover, the project will establish the relationships between health care-associated, community and animal strains to ascertain whether they share common hypervirulence traits.


•Selection/derivationofmoremeaningfuldiagnostic tests. Such tests would alert health authorities to the presence of hypervirulent strains and ensure implementation of appropriate infection control measures.

•Provisionofurgentlyneededinsightintotherole of animals as a reservoir of infection and a better appreciation of the importance of community-acquired c. difficile disease.

•Identificationoffactorsmostimportantincolo-nisation/adherence will llow the development of more effective protective vaccine(s).

•Identificationofthemostimportantvirulencefactors should provide rational targets for the development of therapeutic drugs.


summARy

Since the turn of the new millennium, there has been a dramatic rise in the incidence of clostridium difficile. It is currently the most frequently occurring health care-associated infection, killing over seven times as many people in the UK as MRSA in 2007. A number of reasons have been suggested for this increase, ranging from improvements in reporting procedures, the increasing age of the population and, therefore, the number at risk, lower standards of hygiene and overcrowding in hospitals. A further significant factor has been the emergence of so called ‘hypervirulent’ strains, typified by ribotype 027. The physiological basis of hypervirulence is poorly understood due to an absence of mutational tools for functional genomic studies. The develop-ment of the revolutionary “ClosTron” gene knockout technology by the University of Nottingham allows systematic inactivation of genes to assess the effects on virulence. Identification of the determinants that are required for infection and disease progres-sion will permit the development of more rational countermeasures against c. difficile.

PRoblem

c. difficile is wreaking havoc within European health systems due to the emergence of hyperviru-lent strains, responsible for more severe disease, higher relapse rates, increased mortality and greater resistance to antibiotics. Hypervirulent 027 strains were first reported in Canada in 2003. Since their arrival in Europe, they have rapidly spread across

48




HYPERDIFF223585 EUR 2 992 181 36 months01/11/2008 Focused research project

www.clostridium-difficile.com

ThE phySIOLOGICAL BASIS OF hypERvIRuLENCE IN Clostridium diffiCile:

A pREREquISITE FOR EFFECTIvE INFECTION CONTROL


Key words:clostridium difficile, hypervirulence, epidemiology, physiology, health care-associated infection, prevention, vaccine


Coordinator

Prof. Nigel MintonCentre for Biomolecular SciencesThe University of NottinghamUniversity ParkNottingham NG7 2RDUnited KingdomE-mail: [email protected]

Partners

Prof. Maja RupnikInstitute of Public Health MariborMaribor, Slovenia

Dr. Paola MastrantonioIstituto Superiore di SanitàRome, Italy

Prof. Anne CollignonUniversité Paris Sud XIChâtenay-Malabry, France

Dr. Ed KuijperLeiden University Medical CentreLeiden, The Netherlands

Prof. Christoph von Eichel-StreibertgcBIOMICS GmbHMainz, Germany

Prof. Peter MullanyUniversity College LondonLondon, United Kingdom


is that they only detect resistance to these two drugs. Sequencing DNA of PCR-amplified prod-ucts has been the most widely used method; it is accurate and reliable and it has become the reference standard for mutation detection in M. tuberculosis. However, it would be rather difficult to implement DNA sequencing routinely for detection of drug resistance to several drugs, such as those responsible for MDR- and XDR-TB simultaneously, since it would involve multiple reactions for each isolate, thus increasing cost.

Aims And exPected Results

The project is developing a system for fast and simultaneous detection of MDR and XDR strains based on a rapid phenotypic assay and a geno-typic test. Colorimetric methods, which have been previously validated by the group for first-line drug susceptibility testing, will be set up for key second-line drugs involved in XDR-TB. The molecular method will be based on a modification of the novel technol-ogy, detection of immobilised amplified product in a one phase system. This versatile molecular approach will be further improved and set up for the detection of MDR strains. The developed tools will then be validated in different settings and prospectively evaluated in target populations. The project will contribute to the currently avail-able tools for rapid detection of drug-resistant TB and will introduce new tools for the detection of the highly lethal XDR-TB. It will also contribute to knowledge on the mechanisms of M. tuberculosis resistance to second-line anti-TB drugs. The project will develop and test a double approach for the simultaneous detection of MDR-TB and XDR-TB in clinical isolates of M. tuberculosis in a first phase, and directly on sputum specimens once the fast

phenotypic colorimetric assay and the molecular test have been completely developed.


The fast phenotypic colorimetric assay will allow simultaneous detection of MDR and XDR TB in both M. tuberculosis isolates and sputum samples. The new molecular test will be able to detect MDR-TB and identify molecular markers of XDR-TB. After validation of the assays and evaluation in target populations, they could become alternative and innovative methods to rapidly detect MDR- and XDR-TB, and could be implemented in low-resource countries.

Key words:tuberculosis, drug resistance, MDR, XDR, rapid methods


summARy

The HIV/AIDS pandemic and the emergence of drug resistance are hindering the control of tuberculosis (TB). Multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis, defined as strains resistant to (at least) isoniazid and rifampicin, the most valuable drugs for treatment of the disease, have emerged. More recently, the appearance of extensively drug-resistant (XDR) strains has been reported. These strains, in addition to being MDR, are also resistant to key second-line drugs. Patients, especially HIV patients, harbouring XDR strains, have virtually no treatment options. Detection of drug resistance in M. tuberculosis has traditionally been based on the detection of M. tuberculosis growth on solid media, which requires several weeks to give results. Newer automated culture systems, although accurate and reliable, have been mainly evaluated for first-line anti-TB drugs and, due to their high cost, remain out of reach for most TB laboratories in middle- and low-income countries. Molecular assays have also been proposed for the detection of drug resistance in M. tuberculosis. They follow a two-step procedure with nucleic acid amplification by the polymerase chain reaction (PCR) and subsequent identifica-tion of specific mutations known to be associated with drug resistance. Two commercially available tests are based on hybridisation of amplified DNA from cultured isolates or sputum samples to several probes immobilised on a nitrocellulose strip covering the core region of rpoB for detecting resistance to RIF or katG, and inhA for detecting resistance to INH. The limitation of these assays

52




FAST-XDR-DETECT201690 EUR 2 695 565 48 months01/02/2008 Focused research project

https://room. projectcoordinator.net/ ~oligocolor

DEvELOpmENT OF A TWO-AppROACh pLATE SySTEm FOR ThE FAST AND SImuLTANEOuS

DETECTION OF mDR AND xDRm. tuberCulosis


Coordinator

Dr. Juan Carlos Palomino Prince Leopold Institute of Tropical MedicineNationalestraat 155Antwerp 2000BelgiumE-mail: [email protected]

Partners

Dr. Helmut BlockerHelmholtz-Zentrum für InfektionsforschungBraunschweig, Germany

Dr. Sven HoffnerSwedish Institute for Infectious Disease ControlSolna, Sweden

Prof. Mahavir SinghLionex GmbHBraunschweig, Germany

Dr. Girts SkendersInfectology Center of LatviaRiga, Latvia

Patricia Del PortilloCorporacion CorpogenBogota, Colombia

Dr. Viviana RitaccoAdministracion Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. MalbranBuenos Aires, Argentina

Dr. Nora MorcilloHospital CetrangoloBuenos Aires, Argentina


ated to address the contribution of different genetic backgrounds and/or different sensitivity patterns in the same genetic background to stress, in terms of survival and transcriptional response, and the ‘cost’ in terms of bacterial fitness in acquisition of the MDR phenotype. The development of a panel of M. tuberculosis strains monoresistant to selected second-line drugs is a major step in the strategy, in that it will establish a clear reference for all EU laboratories to guarantee the accuracy of clinical laboratory analysis of MDR-TB and XDR-TB cases, thus enhancing European surveillance and individual clinical management. The project will have a sig-nificant impact on TB research, including:

•Understandingtheriskfactors(includingHIV co-infection) for MDR-TB and poly-drug resistance, the nature of the transmission routes at the molecular level and the mutations associated with the development of XDR-TB.

•Rapiddiagnosisofdrug-resistantTBandof infectivity of MDR patients already undergoing therapy.

•EstablishmentofanintegratednetworkofMDR-TB sites across the EU supported by a common training curriculum.

Basic research will provide the identification of novel mutations involved in the drug-resistant phenotype (in particular for second-line and recently-introduced drugs used in MDR-TB and XDR-TB treatment).


•EstablishmentofaEuropeanintegratedand inter-dependent network for basic science and clinical research.

•DevelopmentofaEuropeanclinicalandmolecular web database for a sensitive early warning system for TB outbreak detection.

•Developmentofnewrapiddiagnosticsystems for the detection of MDR-TB and XDR-TB in cultures and primary diagnostic specimens.

•EstablishmentofanintegratednetworkofMDR-TB sites.

•Developmentofacommontrainingcurriculum for laboratory and clinical staff.

•Implementationofasystemofexternalquality assurance for drug susceptibility for first- and second-line anti-TB drugs.

Key words:multi-drug-resistant tuberculosis, extensively drug-resistant tuberculosis, molecular diagnosis, markers of resistance


summARy

As strains resistant to available anti-tuberculosis (TB) drugs have emerged, drug-resistant Mycobacterium tuberculosis strains have become a serious threat to TB control worldwide. Over 400 000 new cases of multi-drug-resistant TB (MDR-TB) occur each year and the prevalence of MDR-TB cases in the world today may approach or exceed 1 million. Recent studies have revealed the presence not only of MDR-TB but also of what has come to be called extensively drug-resistant tuberculosis (XDR-TB). The global threat of XDR-TB has major implications for public health and particularly for HIV control because of the extreme vulnerability of these patients to TB, especially XDR-TB.


The project addresses critical issues involved in the spread of MDR-TB, i.e. early detection of drug resistance cases through rapid identification, drug susceptibility testing and effective treatment. Of particular importance is the development of ef-fective, standardised training on TB management, improved tools to better understand MDR/XDR epi-demiology and the standardisation of microbiology methodology needed for the correct management of drug-resistant TB cases. The integration of basic science, focusing research on the characterisation of molecular mechanisms of drug resistance and the effective contribution of the mutation to the therapy outcome, will permit the introduction of novel and more effective diagnostic tools, and will likely provide new targets for drug development. A transcriptional regulatory network of M. tuberculosis will be gener-

56




TB PAN-NET223681 EUR 10 998 270 60 months01/01/2009 Large-scale integrating project

www.tbpannet.org

pAN-EuROpEAN NETWORk FOR STuDy AND CLINICAL mANAGEmENT OF DRuG RESISTANT TuBERCuLOSIS


Dr. Manca Zolnir-DovcNRL Slovenia – University Clinic of Respiratory and Allergic DiseasesGolnik, Slovenia

Dr. Leen RigoutsPrince Leopold Institute of Tropical MedicineAntwerp, Belgium

Dr. Ionela Sorina MunteanSPF Brasov – Pneumophtisiology Hospital BrasovBrasov, Romania

Dr. Cristina PopaI-M.NASTA – ‘Marius Nasta’ Institute of Pneumology Bucharest, Romania

Dr. Philip SupplyInstitut Pasteur de LilleLille, France

Dr. Hanna Kristiina SoiniNational Institute for Health and WelfareTurku, Finland

Dr. Maryse Fauville-DufauxScientific Institute of Public Health Brussels, Belgium

Prof. Zofia ZwolskaNational Tuberculosis and Lung Diseases Research InstituteWarsaw, Poland

Dr. Maria Laura GennaroUniversity of Medicine and Dentistry of New JerseyNewark, USA


Coordinator

Dr. Maria Daniela Cirillo Università Vita-Salute San RaffaeleVia Olgettina 58Milan 20132ItalyE-mail: [email protected]

Partners

Prof. Francis DrobniewskiUniversity of LondonLondon, United Kingdom Dr. Sabine Ruesch-GerdesForschungszentrum Borstel Borstel, Germany

Dr. Christoph LangeForschungszentrum BorstelBorstel, Germany

Dr. Giovanni Battista MiglioriFondazione Salvatore MaugeriTradate, Italy

Dr. Andrea GoriAzienda Ospedaliera S. Gerardo di MonzaMonza, Italy

Tania SeverinEuropean Respiratory SocietyLausanne, Switzerland

Dr. Mark PerkinsFoundation for Innovative New DiagnosticsGeneva, Switzerland

Prof. Sven HoffnerSwedish Institute for Communicable Disease ControlSolna, Sweden

Dr. Vibeke Østergaard ThomsenStatens Serum InstitutCopenhagen, Denmark

Dr. Vera Katalinic-JankovicCroatian National Institute of Public HealthZagreb, Croatia

Prof. Gianni PozziUniversità degli Studi di SienaSiena, Italy

Dr. Vera AllerheiligenHain Lifescience GmbHNehren, Germany

Dr. Jelena StorozenkoInfectology Center of LatviaRiga, Latvia

Dr. Luca Vincenzo Di MaioGuido Montessori CompanyRome, Italy

Dr. Manfrid DanilovitšTartu University HospitalTartu, Estonia

Dr. Edita DavidavičienėNational Tuberculosis and Infectious Diseases University HospitalVilnius, Lithuania

Dr. Petras StakenasUniversity of VilniusVilnius, Lithuania

Dr. Turid MannsåkerNorwegian Institute of Public HealthOslo, Norway


by an organism and we will investigate this in a number of clinically-important organisms.

PRoblem

Antibiotic resistance is recognised as being one of the major medical problems facing mankind and measures to prevent the increase in antibiotic-resistant organisms require knowledge of both the genesis of antibiotic resistance and its dissemina-tion. The problem of antibiotic resistance affects almost every bacterial species for which treatment with antibiotics is available. Furthermore, in recent years, resistance to several antibiotic classes has developed in some species, resulting in the oc-currence of multi-drug-resistant bacterial strains, also known as superbugs. The occurrence of superbugs is associated with treatment failures, higher morbidity and mortality, and increased cost. Consequently, the therapeutic options for some infections are limited, especially in developing countries, where second- and third-line antibiotics are unavailable or unaffordable. In Europe, it has long been recognised that antibiotic resistance is a multifaceted threat to the health of the European population. All European countries are seeing a steady decrease in antibiotic effectiveness. This trend is likely to become more pronounced because of increasing antimicrobial use in emerging market communities, travel and migration.

Aim

•Theprojectwillstudytheimpactofdifferentantibiotics in selecting resistance among pathogenic and commensal members of the indigenous microbiota of humans.

exPected Results

•Knowledgeofthedynamicsofresistanceemergence at a variety of body sites during the administration of a range of antibiotics frequently used in Europe.

•Informationonthecompositionoftheentire microbial communities inhabiting the oral cavity and colon, and the effect of antibiotic administration on these communities.

•Identificationoftheresistancedeterminantsin those antibiotic-resistant isolates that emerge during the administration of different classes of antibiotics.

•Informationontheemergenceandpersistence of resistance determinants following the administration of several different classes of antibiotics.

•Developmentofimprovedmicroarraysforthe identification of resistance determinants in Gram-negative and Gram-positive bacteria.

•Informationontheentirecomplementofresistance determinants (the resistome) in the oral and faecal microbiota, and the effect of antibiotic administration on these.


The results of the project will enable governments and health care providers to formulate strategies to combat antibiotic-resistant bacteria in Europe. The new microarrays developed during the project will be very useful in diagnostic laboratories to rapidly determine which antibiotics would be ineffective against a disease-causing organism in a particular individual. Additionally, the microarrays will be


summARy

The objective of the project is to study the impact of different antibiotics on the prevalence of resistant bacteria in the human host. We will use culture-based and culture-independent approaches to investigate the impact of four different types of antibiotics (with different modes of action, antimi-crobial spectra and pharmacokinetic properties) on the emergence of antibiotic-resistant organisms and their persistence at several body sites. Disruption of the indigenous microbiota is recognised as an important factor in the persistence and transmis-sion of antibiotic-resistant organisms. Thus, we will study the ecological impact of antibiotics on the indigenous microbiota. Using microarrays, we will then identify the genes responsible for resistance in the antibiotic-resistant organisms isolated. The genetic elements involved in resistance transfer by a number of these organisms will also be determined. We will use 454 pyrosequencing to determine the full complement of resistance genes (the ‘resistome’) present in cultivable and not-yet-cultivated members of the oral and faecal microbiota, and the effect on these resistomes on antibiotic administration. Another important aspect of the dynamics and transmission of resistance is the fitness cost associated with resistance acquisition

60




antiresdev241446 EUR 5 368 088 36 months 01/11/2009 Focused research project

www.ucl.ac.uk/antiresdev

ThE EFFECTS OF ANTIBIOTIC ADmINISTRATION ON ThE

EmERGENCE AND pERSISTENCE OF ANTIBIOTIC-RESISTANT

BACTERIA IN humANS AND ON ThE COmpOSITION OF ThE INDIGENOuS mICROBIOTAS AT

vARIOuS BODy SITES


useful in surveillance studies of antibiotic resistance. The project will enable a better understanding of the molecular mechanisms underlying the spread of mobile genetic elements and this will help in the development of means of preventing or reducing horizontal gene transfer and the dissemination of resistance.

Key words:antibiotic resistance, genetic determinants, microarrays, fitness cost, ecology, resistome, pyrosequencing, indigenous microbiota, metagenomics


Coordinator

Prof. Michael WilsonDivision of Microbial DiseasesUCL Eastman Dental InstituteUniversity College London256 Grays Inn RoadLondon WC1X 8LDUnited KingdomE-mail: [email protected]

Partners

Prof. Carl Erik Nord Karolinska InstituteStockholm, Sweden

Prof. Gianni PozziUniversità degli Studi di SienaSiena, Italy

Dr. Nadine McCallumUniversity of ZurichZurich, Switzerland

Dr. Vincent Perreten University of BerneBerne, Switzerland

Prof. Cornelius Knabbe Robert Bosch Gesellschaft für Medizinische ForschungStuttgart, Germany

Dr. Muna AnjumVeterinary Laboratories AgencyAddlestone, Surrey, United Kingdom

Prof. Wim CrielaardVrije Universiteit AmsterdamAmsterdam, The Netherlands

Prof. Anthony CoatesHelperby Therapeutics LimitedLondon, United Kingdom

Dr. Bart KeijserNederlandse Organisatie voor Toegepast-Natuurwetenschappelijk Onderzoek - TNODelft, The Netherlands


•Determiningthepatternsofprescribingantibiotics by primary care physicians in each participating country.

•Assessingthecompatibilityofprescriptionpatterns and resistance patterns. The results will be related to relevant guidelines of the nine participating countries (focusing on syndromes and diseases mainly caused by S. aureus and S. pneumoniae), in order to formulate evidence-based treatment guidelines.

exPected Results

•Anoverviewofalloftheliteratureregarding the relationship between antibiotic consumption and outpatient resistance patterns.

•ResistancepatternsfornineEuropeancountries of S. aureus and S. pneumoniae. These will be collected by taking nose swabs of patients (N = 4000 per country, a total of 36 000) visiting a primary care practice for a non-infectious disease.

•Dataonallantibioticprescriptionsforthepast 5 years will be extracted from the practice data systems of the participating general practitioners.

•Aninventoryandevaluationofnationalprimary care treatment guidelines. An integrated multilevel design will be used to assess the appropriateness of prescribing antibiotics at a European and national level.


Evidence-based recommendations for national primary care treatment guidelines.

Key words:antibiotic resistance, primary care, antibiotic prescribing, evidence-based guidelines


summARy

Bacterial resistance to antibiotics is a major public health problem. The project is being carried out in nine European countries, and collects data on antibiotic resistance patterns and antibiotic prescrip-tions in a primary care setting. This information will be used to formulate recommendations for evidence-based antibiotic treatment guidelines in primary health care in Europe.

PRoblem

Antibiotic resistance patterns vary considerably across Europe and data on resistance and pre-scription patterns for outpatients are lacking. This is important as this is the setting in which over 90% of all antibiotics are prescribed.

Aim

The project aims to assess the appropriateness of prescribing antibiotics in primary care by:

•Providingaliteraturereviewabouttheassociation between the consumption of antibiotics and antibiotic resistance patterns in the community.

•EstablishingthepatternofresistanceofStaphylococcus aureus and Streptococcus pneumoniae isolated from nasal mucous swab samples in healthy persons consulting their primary care physician.

64




APRES223083EUR 2 809 51148 months01/10/2009 Focused research project

www.nivel.eu/apres

ThE AppROpRIATENESS OF pRESCRIBING ANTIBIOTICS IN pRImARy hEALTh CARE IN EuROpE WITh RESpECT

TO ANTIBIOTIC RESISTANCE


Coordinator

Prof. François SchellevisNetherlands Institute for Health Services ResearchP.O. Box 15683500 BN UtrechtThe NetherlandsE-mail: [email protected]

Partners

Prof. Michael PringleUniversity of NottinghamNottingham, United Kingdom

Dr. Ellen StobberinghUniversity of MaastrichtMaastricht, The Netherlands

Prof. Herman GoossensUniversity of AntwerpenWilrijk, Belgium

Dr. Douglas FlemingRoyal College of General PractitionersBirmingham, United Kingdom

Dr. Andrea Poppelier Société Française de Médecine Générale St. Porchaire, France

Prof. Milica KatićUniversity of ZagrebZagreb, Croatia

Brigitte Daniel-MayrKrankenhaus der Elisabethinen LinzLinz, Austria

Dr. Andrew LoveringNorth Bristol NHS TrustBristol, United Kingdom

Kathryn HoffmannMedical University of ViennaVienna, Austria

Dr. Bonaventura BolíbarIDIAP Jordi GolBarcelona, Spain Prof. Imre RurikUniversity of DebrecenDebrecen, Hungary

Prof. Frank BuntinxCatholic University of LeuvenLeuven, Belgium

Prof. Sigvard MölstadJönköping County CouncilJönköping, Sweden


Key words:biocide, antibiotic resistance, human pathogen


summARy

Biocides have been in use for hundreds of years for antisepsis, disinfection and preservation. Despite this widespread and ever increasing use, most bacterial and fungal species remain susceptible to biocides. The dramatic increase and spread of resistance to antibiotics linked to reports of co- and cross-resistance between antibiotics and biocides led to speculation about the potential hazard of biocide use. The project will use a high throughput screening approach on collections of thousands of well characterised microorganisms and an interactive web-based data analysis platform. Phenotypic screening for reduced susceptibility to biocides, detection of novel resistance genes and mobile elements, and screening for their molecular epidemiology and metagenomics will be accom-panied by methodological innovation for testing risk evaluation and registration of biocides.

Aim

The overarching question which the project aims to address is whether the use of biocides has contributed to the development and spread of clinically significant antibiotic resistance in human pathogens.


Provision of solid data and analysis to direct future issuing of guidelines for safe environmental, medi-cal and industrial use of biocides.

68




BIOHYPO227258EUR 4 300 00036 months01/06/2009 Focused research project

www.sites.google.com/ site/biohypo/home

CONFRONTING ThE CLINICAL RELEvANCE OF BIOCIDE INDuCED

ANTIBIOTIC RESISTANCE


Coordinator

Prof. Marco OggioniPoliclinico Le ScotteUniversità degli Studi di Siena53100 SienaItalyE-mail: [email protected]

PartiCiPants

Dr. Ian MorrisseyQuotient Bioresearch LimitedFordham, United Kingdom

Lucilla BaldassarriIstituto Superiore di SanitàRome, Italy

Prof. Jonas AlmeidaUniversidade Técnica de LisboaLisbon, Portugal

Prof. Ülkü YetişMiddle East Technical UniversityAnkara, Turkey

Hans-Joachim RödgerLysoform Dr. Hans Rosemann GmbHBerlin, Germany

Pilar VisaBiolab Española S.L.Barcelona, Spain

Dr. Jose-Luis MartínezCentro Nacional de BiotecnologiaMadrid, Spain

Dr. Ayse KalkanciGazi UniversityAnkara, Turkey


Dr. Diego MoraUniversità di MilanoMilan, Italy

Dr. Stephen LeibUniversity of BernBern Switzerland

Dr. Carlo VitiUniversità di FirenzeFlorence, Italy

Dr. Marina ElliAAT – Advanced Analytical Technologies SRLPiacenza, Italy


tions and antimicrobial resistance across Europe, it has become clear that wide variability in pre-ventive practices and outcomes across European countries exists, indicating considerable leeway for improvement.

Aim

To address the challenges of improving antibiotic therapy and reducing antimicrobial resistance, the project will make use of data that are already routinely collected and stored in electronic clinical information systems (CISs) in hospitals and primary care clinics. Today however, this occurs in widely differing systems. The challenge is to establish the coherent and systematic exchange of a rich data set, harmonised across the project sites and their CIS systems. This data set will include information about patients and their illness situations, pathogens and drug treatments.

Results

The project will contribute to achieving world-leading levels of patient safety and optimised medical interventions. The learn–predict–prevent approach embodied in the knowledge base and the decision support system of the project will con-tribute to effective and automated risk prediction. Further expected outcomes are:

•CISsofparticipatingEuropeanhospitals,industry and their clients are updated with project knowledge.

•Newknowledgewillbemadeavailableataglobal level, preferably through a European or global disease control centre/public authority, and/or through open source services

•New,advancedICTapplicationsandinnovations will be marketed in the following domains: virtualisation of clinical data repository information, advanced multimodal data mining techniques on text, image and distributed storage, use of machine reasoning related to real point of care patient data.

•Adistributedmedicalknowledgerepository integrated with domain knowledge coming from external sources (guidelines and scientific evidence).

•Innovativeanduser-friendlyknowledgerepresentation paradigms for both clinicians and IT experts.


Examples of applications benefiting from the project’s research include:

•Computerisedphysicianorderentrysystems, integrated with, for example, drug databases and/or clinical decision support systems.

•Adversedrugeventreportingsolutions,and hospital-wide CISs, health database systems or electronic health record systems.

•Integrationofknowledgetranslationanddecision support into hospital and general practitioner practice systems.

Key words:information technology, antimicrobial resistance, clinical information system


summARy

Improving the quality of health care and patient safety are priority health policy goals globally. Despite half a century of antibiotic use, re-emerging and new infectious diseases, partially caused by the rise of antimicrobial resistance, have become important problems. This increasing prevalence of resistance results in escalating health care costs, increased morbidity and mortality and the (re-) emergence of potentially untreatable conditions. The project is developing an IT framework to allow health care systems to better address these emergent problems and improve their management. In the context of infectious diseases, the project detects patient safety-related patterns and trends, acquires new knowledge through advanced data mining, and uses this knowledge for better decision-making on the optimal treatment for infectious diseases, thereby improving the quality of health care.

PRoblem

The rapid development of antimicrobial resistance, and the spread of nosocomial and other infections are major concerns. The impact of this phenom-enon is most apparent in hospitals. However, community-based practice is not immune, due to the frequency and rapidity of patient transfers between the two sectors and citizen mobility. Hence, epidemics are a regular occurrence and may spread between continents. Examples of such epidemics are methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci or multiresistant tuberculosis. In addition, as a result of the efforts made in harmonising data on infec-

72




DebugIT217139EUR 6 410 00048 months01/01/2008 Large-scale integrating project

www.debugit.eu

DETECTING AND ELImINATING BACTERIA

uSING INFORmATION TEChNOLOGy


Partners

Dr. Christian LovisLes Hôpitaux Universitaires de GenèveGeneva, Switzerland

Dr. Alexandros KalousisUniversity of GenevaGeneva, Switzerland

Dr. Daniel KarlssonLinköping UniversityLinköping, Sweden

Dr. Karl Stroetmannempirica Gesellschaft für Kommunikations- und Technologieforschung mbHBonn, Germany

Prof. Dipak KalraUniversity College LondonLondon, United Kingdom

Dr. Marie-Christine JaulentINSERMParis, France

Dr. Stefan SchulzUniversitätsklinikum FreiburgFreiburg, Germany

Dr. Dimitris IakovidisTechnologiko Expedeftiko Idrima LamiasLamia, Greece

Milan RuzickaInternetový Pristup Ke Zdravotním Informacím PacientaPrague, Czech Republic

Coordinator

Dr. Dirk ColaertAgfa Healthcare NVSeptestraat 272640 MortselBelgium E-mail: [email protected]


Dr. Orlin GyurovGama Sofia Ltd.Sofia, Bulgaria

Dr. Philipp DaumkeAverbis GmbHFreiburg, Germany

Dr. Patrick RuchHaute Ecole Spécialisée de Suisse OccidentaleDelémont, Switzerland

Lukas NemecMD ACCESS ASPrague, Czech Republic


Aim

The main aim of the project is to describe and predict the dynamics of antibiotic resistance development at the level of the drug target, the microbe and the host. At the present time, we do not know how to reduce or reverse the develop-ment of resistance, since current knowledge about the mechanisms and evolutionary constraints that drive the emergence and survival of resistant strains is scarce. In addition, the severe lack of knowledge means that we do not know how the various parts of the puzzle fit together, i.e. how do we connect antibiotic use patterns, bacte-rial resistance mechanisms, bacterial physiology and fitness, bacterial survival within a host and bacterial spread between hosts. The project aims to generate the knowledge needed to answer this question by developing novel conceptual and experimental approaches. In addition, we intend to explore several approaches, both with regard to new principles for rationally choosing drug targets and drugs with minimised risk of resistance development.

exPected Results

The obtained results will have general biological implications with regard to molecular evolution and bacterial adaptation, virulence and transmission as well as several medically relevant applications. The results will include:

•Parametervaluesformostofthebacterialfactors expected to be important for resistance development.

•Newunderstandingofhowdifferentlevels in the pathways leading from drug sensitivity to drug resistance and high fitness are integrated.

•Experimentalknowledgerequiredtomodel and perform risk assessments for the development and spread of antibiotic resistance.

•Knowledgebaserequiredtodevelopnovel diagnostic test systems for bacteria and compounds with a high risk of resistance development.

•Developmentandimplementationoftheuse of different approaches to measure bacterial transmission between hosts.


•Strategiestoreducetherateofresistancedevelopment by exploiting novel drug targets and drugs.

•Predictivetoolsforindustryandregulatoryagencies for pre-clinical and clinical development of novel antibiotics.

•Performanceofriskassessmentsforthedevelopment and spread of antibiotic resistance.

•Noveldiagnostictestsystemsforbacteriaand drugs with a high risk of resistance development.

Key words:infectious disease, bacteria, antibiotic resistance, virulence, fitness, transmission, mathematical modelling, mutation, plasmid


summARy

Antibiotic resistance represents a rapidly growing public health concern and economic problem both within the EU and globally. The urgency of the resistance problem makes the development of experimental and theoretical tools and methods to understand and predict (and by inference prevent) the development of antibiotic resistance a high priority. The project aims to describe and predict the dynamics of antibiotic resistance development at the level of the drug target, the microbe and the host. The obtained results will have general biological implications with regard to molecular evolution and bacterial adaptation, virulence and transmission. Most importantly, the results will generate strategies to reduce the rate of resistance development.

PRoblem

The intensive use and misuse of antibiotics have resulted in antibiotic resistance among many human pathogens. Due to the lack of industrial develop-ment of new antibiotics, there is growing concern that the loss of therapeutic options will present us with a post-antibiotic era where present and future medical advances are negated. Resistant bacteria dramatically reduce the possibilities of treating infections effectively, and increase the risk of complications and fatal outcome for patients with severe infections.

76




PAR241476 EUR 6 000 00036 months01/04/2010 Focused research project

www.imbim.uu.se/PAR/index.html

pREDICTING ANTIBIOTIC

RESISTANCE


Coordinator

Prof. Dan AnderssonDepartment of Medical Biochemistry and MicrobiologyUppsala UniversityHusargatan 3Uppsala 75123SwedenE-mail: [email protected]

Partners

Prof. Niels Frimodt-MøllerStatens Serum InstitutCopenhagen, Denmark

Prof. Fernando BaqueroHospital Ramon y CajalMadrid, Spain

Dr. Jose Luis MartinezCentro Nacional de Biotecnologia CSICMadrid, Spain

Prof. Erik BöttgerUniversity of ZurichZurich, Switzerland

Prof. Patrice CourvalinInstitute PasteurParis, France

Prof. Ian ChopraUniversity of LeedsLeeds, United Kingdom

Dr. Ivan MaticINSERMParis, France

Prof. Timothy WalshUniversity of CardiffCardiff, United Kingdom

Prof. Simon FosterUniversity of SheffieldSheffield, United Kingdom

Prof. Stephen GillespieUniversity of St. Andrew’sSt. Andrew’s, United Kingdom



the past few years. Some, but presumably not all, European countries provide comprehensive national guidelines or recommendations based on the literature. Furthermore, there is no overview about surveillance practices and HAI prevention programmes adopted and implemented by Euro-pean hospitals, and to what extent they relate to national guidelines.

Aim

The project aims at improving the understanding of European guidelines and hospital policies and practices for HAI prevention by overcoming common obstacles and hurdles for implementing evidence-based best practices, and by testing the effectiveness of two interventions to prevent catheter-related bloodstream infection as a pro-totype of HAI. Furthermore, the project aims to understand facilitating and impeding factors in the adoption and implementation of guidelines and recommendations by European hospitals.

exPected Results

The project will provide a synthesis of European HAI prevention guidelines to assess their quality and how these reflect upon HAI surveillance. Furthermore, the project will report on surveillance strategies and prevention programmes adopted and implemented by European hospitals, and what organisational, structural and other contextual fac-tors facilitate or impede such action. Finally, in a representative sample of European hospitals, the project will assess the effectiveness of a multimodal intervention strategy to reduce catheter-associated bloodstream infection. Qualitative methods will

provide deeper insight into the implementation process among the selected hospitals.


The analysis of the project is expected to produce a multidimensional image related to the perception and implementation of defined, evidence-based infection control measures and their effect on disease control outcomes among European hospitals. This comprehensive view on implementation processes will serve to support and advise clinicians, manag-ers, policy makers, researchers and professional societies about key elements in the adoption and implementation of evidence-based prevention measures and guidelines.

Key words:guidelines, evidence-based practice, infection control, bundle, multimodal, hand hygiene, catheter-associated bloodstream infection, implementation, adoption


summARy

Health care-associated infections (HAIs) are adverse events in health care delivery and are associated with increased morbidity and mortality. It is not currently known what practices have been adopted by European hospitals to prevent such events and whether they are effective. The aim of the project is to understand existing guidelines and practices to prevent HAI in European hospitals, identify factors that enable and reduce compliance with best practices, and test the effectiveness of interventions of known efficacy. The information will be synthesised to develop recommendations for the EU, policy makers, managers and medical professionals.

PRoblem

The impact of HAI is important due to its high incidence, which is associated with significant mortality and substantial extra costs for care. In the EU, the annual number of HAIs is estimated at 4 544 100, with approximately 37 000 attribut-able deaths and 16 million extra hospital days. HAI rates differ dramatically among European countries. Although some differences may be explained by the diversity in patient mix, others suggest variability of policies and practices in HAI prevention, such as differences in adoption and application of guidelines and protocols, beliefs and attitudes among health care workers, staffing patterns, available resources or barriers to implementing best practices. A remarkable expansion and proliferation of infection control publications and guidelines has occurred over

80




PROHIBIT241928 EUR 2 999 93448 months01/01/2010 Focused research project

www.prohibit.unige.ch

pREvENTION OFhOSpITAL INFECTIONS

By INTERvENTIONAND TRAINING


Coordinator

Dr. Walter ZinggUniversity of GenevaRue Gabrielle Perret-Gentil 4Geneva 14, 1211SwitzerlandE-mail: [email protected]

Partners

Prof. Hajo GrundmannRijksinstituut voor Volksgezondheid en MilieuBilthoven, The Netherlands

Prof. Petra GastmeierCharité Universitätsmedizin BerlinBerlin, Germany

Prof. Markus DettenkoferUniversitätsklinikum FreiburgFreiburg, Germany

Prof. Hervé RichetCentre Hospitalier Régional de MarseilleMarseille, France

Dr. Emese SzilágyiOrszagos Epidemiologiai KözpoontBudapest, Hungary

Prof. Piotr HeczkoJagiellonian University Medical CollegeKrakow, Poland

Dr. Alison HolmesImperial College of Science, Technology and MedicineLondon, United Kingdom

Dr. Benedetta AllegranziWorld Health OrganizationGeneva, Switzerland



elucidate the time-varying and heterogeneous role of antibiotic selection pressure on emergence and selection of AMR.

Aim

The project aims at defining strategies to improve knowledge about antibiotic selection pressure and judicious antibiotic use. One intervention study and three observational clinical studies will be conducted that will produce demonstrable improvements over previously generated evidence regarding the effect of antibiotic exposure and selection pressure on acquisition, selection and transmission of ARB within hospital and community settings. Molecular and pharmacological issues generated by the four clinical studies will also be addressed.

exPected Results

The project programme will provide a compre-hensive knowledge base on the effect of various antibiotic classes, duration of treatment, order of treatment and dosage used on AMR in the com-munity, general hospital wards and in intensive care units. These comprehensive data will be generated at the individual level for both colonised and non-colonised patients, and at the ecological (i.e. ward) level. Moreover, the project will provide data on the effects of antibiotics on resistance both at the human host level and at the bacterial level. Combining the results of epidemiological investigations with microbiological and molecu-lar studies on epidemicity, virulence and fitness of strains will provide data for action. Thus, the results will provide the basis for better treatment

decisions regarding antibiotic choices in various settings to minimise AMR, without compromising patient outcomes. This unprecedented approach will allow the development of guidelines on antibiotic use and formulary interventions at the local, regional and European level.


The gaps between scientific knowledge and cur-rent practices of misuse of antimicrobial agents are enormous. AMR represents a particular challenge because it touches upon several aspects of care, from basic knowledge to antibiotic prescribing. The continuing emergence of new resistance traits or their spread to new species and new epide-miological chains permanently challenges our ability to contain AMR. The project will address this knowledge gap through a variety of research platforms focusing on the effect of various antibiotic agents and prescribing patterns on selection and spread of ARB. The ultimate aim is, therefore, to develop an educational knowledge base for better antibiotic prescribing practices.

Key words:antimicrobial resistance, antibiotic resistant bacteria, pharmacokinetics, pharmacodynamics, microbiology, bacterial genetics, epidemiology, therapeutic drug use


summARy

The project will study the impact of antibiotic exposure on antimicrobial resistance (AMR), with a multidisciplinary approach that bridges microbiological, clinical, epidemiological and pharmacological research. The project will improve methodological standards and conduct research to better understand the impact of antibiotic use on acquisition, selection and transmission of antibiotic-resistant bacteria (ARB) in different environments, by combining state-of-the-art analyses of molecular, ecological and individual patient-level data. The proposed programme and anticipated results will help reduce the burden of AMR in Europe and guide both clinical decision-making and policy decisions in this area.

PRoblem

The project responds to an urgent need, as stated in the EU Council conclusions (June 2008) on AMR, in which the EU “stresses the need of research in the area of AMR, e.g. to increase the understanding of the mechanisms and underlying risk factors that advance the development of AMR and to increase the knowledge of the effectiveness of current and future control measures”. AMR is rampant among bacteria that cause health care- and community-acquired infections, driving up costs and increasing the difficulty of therapeutic management. To gain a handle on the factors that are propelling the problem of AMR, molecular and patient-level investigations are necessary to better

84




SATURN241796 EUR 5 999 436 60 months01/01/2010 Focused research project

www.saturn-project.eu

ImpACT OF SpECIFIC ANTIBIOTIC ThERApIES ON ThE pREvALENCE

OF humAN hOST RESISTANT BACTERIA


Coordinator

Dr. Stephan HarbarthUniversity of GenevaRue Micheli-Du-Crest 24Geneva 14, 1211SwitzerlandE-mail: [email protected]

Partners

Dr. Maciej Godycki-CwirkoUniversytet Medyczny w LodziLodz, Poland

Prof. Yehuda CarmeliThe Foundation for Medical Research Infrastructural Development and Health ServicesTel Aviv, Israel

Prof. Herman GoossensUniversity of AntwerpWilrijk, Belgium

Dr. Evelina TacconelliUniversita Cattolica del Sacro CuoreMilan, Italy

Prof. Marc BontenUniversitair Medisch Centrum UtrechtUtrecht, Netherlands

Carlos TriayARTTICParis, France

Prof. Jordi VilaConsorci Institut d’Investigacions Biomediques August Pi i SunyerBarcelona, Spain

Prof. Laurent GutmannFondation Hopital Saint JosephParis, France


Dr. Knut OhlsenJulius-Maximilians Universität WürzburgWürzburg, Germany

Dr. Biljana JovanovicClinical Center of SerbiaBelgrade, Serbia

Dr. Smaranda BoteaInstitute of Infectious Diseases

Prof. Dr. Matei BalsBucharest, Romania

Dr. Johan MoutonStichting Katholieke UniversiteitNijmegen, Netherlands


field of microbiology. For example, if microbiologi-cal POC tests are to be developed for home use, would the general public feel confident enough to actually use microbiological POC test kits at home, or alternatively, would they prefer face-to-face contact with their own general practitioner? A further problem involves building confidence in microbiological POCT technologies to facilitate the replacement of currently-accepted standard methodologies with new microbiological POCT technologies.

Aim

•Toprovideabetterunderstandingofthesocial, ethical and economic hurdles to microbiological POCT within Europe, to be achieved by gathering data from both commercial and public sources within EU member states, and by comparing and contrasting the concerns and issues raised. Suggestions as to how these problems may be solved will also be provided.

•Tosetupastandardbacterialarchivethat will: (1) allow manufacturers of microbiology POCT technologies to set up standardised small- to medium-scale pre-evaluation studies; and (2) allow clinical hospitals to validate and quality control their own use of microbiological POCT kits, including comparison against their current standard testing methodologies. The archive will comprise several hundred bacterial isolates representing the most frequent bacterial species associated with current (and future) priority diseases, including antibiotic-resistant and sensitive phenotypes of clinically-relevant bacterial

species, collected from all over the world, and including category 3 pathogens.

•Toprovideastandardsoftwarepackagethat will accompany the bacterial archive, which will allow clinical hospitals (intra- and inter-laboratory testing), manufacturers of microbiological POC tests, as well as other interested parties to determine the sensitivity, specificity, reproducibility, etc. of parameters of their own microbiological POC tests.

exPected Results

The project will allow an informed, European-wide assessment to be made of the clinical needs and hurdles to the implementation of microbiological POCT, identifying the strategies necessary to increase confidence and uptake of POCT meth-odologies within clinical hospitals and amongst the general public. International harmonisation of POCT development and quality control testing will be promoted by the provision of an archive of clinically-relevant bacterial isolates and ac-companying comparison software.


•Generalandstate-specificrecommendations regarding the steps necessary to close the gap between current POCT technologies and their uptake in the microbiological health care field.

•Adoptionofastandardandinternationally-recognised quality control archive and accompanying comparison software.


summARy

The project will help fill the current gap between microbiological point-of-care testing (POCT) tech-nologies and the actual clinical need/uptake of testing protocols and kits that have been based upon these technologies. Presently, POCT meth-odologies are being adopted at a faster rate in other health care-related fields, for example clinical chemistry, than in microbiology. The project will identify specific problems, opinions and issues related to the implementation of microbiological POCT within the European Union, and provide suggestions on how to increase microbiologi-cal POCT uptake within EU member states. To increase confidence in microbiological POCT technologies, a standard archive of bacterial isolates and accompanying software will be developed to encourage harmonisation and standardisation for the development and quality control of microbiological POCT technologies within POCT-developing industries, as well as within POCT end-user laboratories.

PRoblem

POCT procedures are gaining momentum in many fields of health care, for example, for the measurement of blood glucose levels, or blood gas and electrolyte testing. However, a gap currently exists between the realisation of POCT technologies and actual clinical need within the

88




TEMPOtest-QC241742 EUR 3 064 573 36 months01/02/2010 Focused research project

AN INTEGRATED TOOL-kIT FOR ThE CLINICAL EvALuATION OF

mICROBIAL DETECTION AND ANTIBIOTIC SuSCEpTIBILITy pOINT-OF-CARE TESTING

TEChNOLOGIES

www.tempotest-qc.eu


Coordinator

Dr. John HaysErasmus MCDepartment of Medical Microbiology and Infectious Diseases‘s Gravendijkwal 230Rotterdam 3015CEThe NetherlandsE-mail: [email protected]

Partners

Dr. Albert BosConsultatie Implementatie Technisch Beheer B.V.Zutphen, The Netherlands

Prof. Gian-Maria RossoliniUniversità degli Studi di SienaSiena, Italy

Prof. Patrice NordmannUniversité Paris-Sud XI Le Kremlin-Bicetre, France

Prof. Youri GlupczynskiCatholic University of LeuvenYvoir, Belgium

Dr. William MacKayQuality Control for Molecular DiagnosticsGlasgow, United Kingdom


Key words:point-of-care testing, antimicrobial resistance, survey, quality control, comparison software

vIRALINFECTIONS

VIral InFectIonS 93VIral InFectIonS92

treatments generally target viral components, the project focuses on host cell factors to interfere with virus replication. The concept of drugs targeting human factors, established in the treatment of other diseases, has not yet been fully explored for treatment of viral infections, despite bearing compelling advantages over conventional antiviral therapies: (1) avoidance of viral escape mutants and (2) broad coverage against unprecedented viral variants. This promising, novel approach, which inhibits factors temporarily dispensable for the host but essential for virus replication, will open the route to alternative treatment options for com-bating influenza with the potential to complement currently available strategies and overcome their limitations, such as resistance and viral variability. The project will build upon an existing repertoire of indirect antiviral targets. We will identify and select validated host cell targets, druggable lead compounds (kinase and non-kinase inhibitors) against them, refine them into clinically applicable drugs, and perform pre-clinical assessments. In addition, crucial host cell functions not targeted by conventional drugs will be explored using therapeutic RNAi. As an extension of the EU-funded studies, the consortium will subsequently pursue, using private funds, the implementation of phase I and II clinical trials.

exPected Results

•Proofofprinciplethatinfluenzainfectioncan be efficiently treated by targeting human determinants at either the protein or RNA level using small molecule or siRNA inhibitors, respectively.

•Anovel therapeuticstrategy tocombatinfluenza virus infections by more reliable (avoidance of resistance) and more versatile (broad intra-species spectrum) means.

•Anefficientin vivo strategy for siRNA delivery into influenza virus-susceptible cells.

•Patentablehitandleadcompoundswithproven efficient prevention of acute viral infection in influenza animal models devoid of triggering risk of viral resistance.

•Pre-clinicallyassesseddrugs.•Analternativetreatmentoptionforviral

strains resistant to currently available anti-influenza drugs.


The innovative drugs developed by the project will have great therapeutic potential against influenza virus infections. This novel generation of drugs promises to preclude the development of viral resistance and to ensure efficacy against upcoming pandemic influenza strains. Moreover, this novel antiviral therapeutic strategy also generates ample new perspectives for the treatment of acute viral infections other than influenza.

Key words:influenza, virus infection, host-targeted therapy, small molecule inhibitor, drug design, therapeutic RNAi

95VIral InFectIonS

summARy

The project aims towards the development of innovative drugs against influenza virus infec-tions based on a novel concept that precludes the development of viral resistance and ensures efficacy against upcoming pandemic influenza strains. While traditional anti-influenza treatments generally target viral factors, the project aims to develop drugs that interfere with host cell factors. This approach is thought to be advantageous regarding: (1) avoidance of viral escape mutants and (2) broad coverage against unprecedented viral variants.

PRoblem

Despite vaccination and currently available antiviral drugs, influenza virus infections still have a huge impact on human health worldwide. In light of the risk posed by seasonal infections and also the recurring threat of influenza virus pandemics, there is an acute need to develop effective and lasting drugs. The current panel of preventive and therapeutic measures against influenza virus infections rests on: (1) active vaccination and (2) the use of conventional anti-viral drugs. Both strategies have their intrinsic limitations owing to the high variability of influenza viruses.

Aim

Viral replication uses the machinery and metabo-lism of host cells and, thus, depends on multiple host cell factors. While traditional anti-influenza

94




ANTIFLU259842 EUR 5 999 998 75 months01/04/2011 Focused research project

INNOvATIvE ANTI-INFLuENzA DRuGS

ExCLuDING vIRAL ESCApE

VIral InFectIonS

97VIral InFectIonS

Coordinator

Prof. Thomas MeyerMax Planck Institute for Infection BiologyCharitéplatz 110117 BerlinGermanyE-mail: [email protected]

Partners

Prof. György KériVichem Chemie Research LtdBudapest, Hungary

Prof. Jørgen KjemsAarhus UniversityAarhus, Denmark

Dr. Bert KleblLead Discovery Center GmbHDortmund, Germany

Dr. Marc LecuitInstitut PasteurParis, France

Bruno CucinelliARTTIC Paris, France

Dr. Ivana SurovaBioTest s.r.o.Konarovice, Czech Republic

Prof. Wendy Barclay Imperial College of Science, Technology and MedicineLondon, United Kingdom

Dr. Jesper WengelRibotask ApSOdense, Denmark

Prof. Oded LivnahHebrew University Jerusalem, Israel

Dr. Jens von KriesLeibniz Institut für Molekulare PharmakologieBerlin, Germany

96 VIral InFectIonS

PRoblem

Influenza is a leading cause of morbidity, mortal-ity and economic loss. The influenza pandemic in 1918 (the Spanish flu) is estimated to have killed more than 30 million people worldwide. The avian H5N1 influenza, which originated in Hong Kong in 1997, has already infected over 100 humans and shows a lethality of over 50%. There is concern that a mutated form of this virus may lead to a new pandemic. Prevention and treatment of influenza rely on inactivated vac-cines and antiviral agents. Although vaccines are considered to be the best option for controlling influenza, at least six months are needed to produce vaccines based on the surface glycoproteins of an epidemic virus strain. The efficacy of antiviral drugs, such as Amantadine and Rimantadine, is limited due to their inapplicability to influenza B viruses and to the rapid emergence and transmission of drug-resistant variants. Synthesis of NA inhibitors, such as Oseltamivir, was a significant milestone in antiviral influenza therapy. The active centre among all influenza viruses makes it the potential target of Oseltamivir that would offer protection against any influenza virus that might emerge in humans. However, Oseltamivir supply is a problem. The relative production processes are expensive, complicated and not environmentally friendly. Although catalysis can sometimes solve difficult synthetic problems, Oseltamivir derivatives cannot be prepared in a single metal catalytic reaction. In the case of a pandemic episode or dangerous mutation, Europe, China and the entire world will face the problem of preparing NA inhibitors in a relatively short period of time.

Aim

The aim is to achieve new, innovative, simple and straightforward synthetic routes for enhancing the availability and supply of NA inhibitors. The project addresses this target through the objective of preparing difficult and highly challenging NA inhibitors. The five main tasks are: (1) synthesis of modified catalysts for an organocatalytic domino reaction, scaling up of the reaction, testing the new catalyst in the established domino reactions aiming at the production of new cyclohexene derivatives, and manipulation of the derivatives for practical and rapid access to newly designed NA drug candidates; (2) use of the catalysts in the design of new organocatalytic domino reactions and synthesis of cyclic compounds via domino reactions; (3) preparation of a new NA inhibitor through the use of organocatalytic domino reac-tions; (4) testing the new NA inhibitor with cell lines, animals and viruses; and (5) testing the newly prepared inhibitor against influenza viruses in silico, in vitro and in vivo.

exPected Results

•ProposalofnewNAinhibitorsforscreening against flu viruses.

•Defininganewstrategyfororganocatalytic, highly economical domino reactions.

•Decreasingcostsandminimisationof problems related to the supply of Oseltamivir and Oseltamivir derivatives.

•Contributingtosolvingtheproblemofavian flu where it has developed (Hong Kong and China).

99VIral InFectIonS

summARy

Despite widespread immunisation, influenza kills thousands of people, and costs Europe, the USA and Asia enormous amounts of money in health care expenses and productivity losses. Small-molecule antiviral agents represent a novel opportunity for effective prevention of and therapy for flu. Inhibitors of neuraminidase (NA), an essential enzyme for viral replication in all three classes of influenza viruses, have recently been found. Two of these inhibitors have reached the market, namely Zanamivir and Oseltamivir phosphate. The recent health concerns related to avian flu have increased the demand for stockpiles of NA inhibitors, both as a frontline therapy against a possible flu pandemic and as a preventive agent. Natural sources of shikimic acid are scarce and increasing demand has put pressure on developing new routes that do not involve complex natural products. There is a need to simplify the synthetic processes and make them cheaper in order to find new drug candidates, cut drug costs and improve availability as well as efficiency, and new chemical syntheses are necessary. The project proposes a new domino reaction based on an organocatalytic approach to the synthesis of new Tamiflu derivatives. The chemistry involved in this project is easy to perform and can be adapted to the industrial context. Moreover, new chemical structures will be prepared and evaluated as potential drugs against virulent and mutated flu viruses.

98




CATAFLU.OR201431 EUR 2 300 000 36 months01/04/2008 Focused research project

ORGANOCATALyTIC AppROAChES TOWARDS EASy SyNThESIzED, ECONOmICAL

AND hIGh yIELDING OSELTAmIvIR DERIvATIvES

VIral InFectIonS

www.catafluor.eu

101VIral InFectIonS


The action may have a profound long-term effect in contributing to solving problems related to the supply of Oseltamivir derivatives experienced by European industries and European countries during the crisis of the Asian flu.

Key words:influenza, Tamiflu, neuraminidase inhibitors, influenza pandemic, shikimic acid, Oseltamivir phosphate, new drugs, organocatalysis

100

Coordinator

Prof. Pier Giorgio CozziDepartment of Chemistry ‘Giacomo Ciamician’Alma Mater Studiorum - Università di BolognaVia F. Selmi 240126 BolognaItalyE-mail: [email protected]

Partners

Prof. Stefan TomaComenius UniversityBratislava, Slovakia

Dr. Axel Jacobi von WangelinUniversity of CologneCologne, Germany

Prof. Gui LuSun Yat-Sen UniversityGuangzhou, China

Dr. Yue Ming LiHong Kong Polytechnic UniversityHunghom, Kowloon, Hong Kong, China

Prof. Kristiina WähäläUniversity of HelsinkiHelsinki, Finland

Dr. Roman FišeraSynkola, S.R.O.Bratislava, Slovakia

VIral InFectIonS

developed each year. There are a few antiviral drugs that are currently on the market; however, their therapeutic potential is restricted through the rapid appearance of drug-resistant viruses during treatment. Thus, the need for novel effective drugs against influenza is evident.

Aim

We aim to develop a novel broad-spectrum antiviral therapeutic against the influenza virus that is less prone to development of resistance.

exPected Results

We aim to develop an antiviral drug candidate with proven efficacy against the influenza virus that has successfully undergone pre-clinical test-ing phases, and is ready to enter a phase 1 clinical trial.


Treatment of influenza virus infection.

Key words:influenza, antiviral drug

103VIral InFectIonS

summARy

The project aims to develop an innovative, first-in-class therapeutic against influenza, targeting the replication core of the virion which is a major contributor to viral virulence. The high level of conservation combined with slow mutation rates of the target region should result in therapeutics with broad viral strain specificity associated with a reduced risk for developing resistance. The project builds on two successful EU-FP7 drug discovery projects, FLUINHIBIT and FluDrugStrategy, both targeting specific but different protein–protein interactions with small molecule inhibitors. The lead candidates from these two projects will be developed synergistically through lead optimisation and pre-clinical development phases, with the final objective of delivering one or more drug candidates suitable for entering clinical development.

PRoblem

Influenza viruses cause a highly contagious respiratory disease in both humans and animals. Typically, influenza spreads worldwide in sea-sonal epidemics, resulting in an estimated 3 to 5 million cases of severe illness and 250 000 to 500 000 deaths annually. In addition to these seasonal epidemics, there have been several pandemics since the early 1900s, where highly virulent strains emerged, the most devastating being the Spanish flu of 1918, which caused 20–40 million deaths globally. Vaccination is currently the primary means of controlling the spread of influenza virus infections but due to the virus’s notorious ability to mutate, new vaccines must be

102




FLUCURE259972 EUR 5 982 600 48 months01/10/2010 Focused research project

DEvELOpmENT OF NOvEL ANTIvIRAL DRuGS AGAINST

INFLuENzA

VIral InFectIonS

www.vironova.com

105VIral InFectIonS

Coordinator

Dr. Heather Marshall-Heyman Vironova ABGävlegatan 2211330 StockholmSwedenE-mail: [email protected]

Partners

Prof. Helena DanielsonBeatica ABUppsala, Sweden

Dr. Ulrich KesslerPike Pharma GmbHZurich, Switzerland

Prof. Martin SchwemmleUniversitätsklinikum FreiburgFreiburg, Germany

Prof. Lilia VitevaBulgarian Academy of SciencesSofia, Bulgaria

Dr. Iwan de EschVrije Universiteit AmsterdamAmsterdam, The Netherlands

Dr. Gintautas ZvirblisUniversity of VilniusVilnius, Lithuania

Dr. Reiner ClassPharmacelsus GmbHSaarbrücken, Germany

Prof. Maurizio BottaUniversità degli Studi di SienaSiena, Italy

104 VIral InFectIonS

PRoblem

Vaccination is the main clinical approach to protecting against influenza infection. However, the epitopes on the surface of the influenza virus change rapidly, which means that a new vaccine must be developed each year. Thus, we are al-ways one year behind, employing the vaccines raised against the previous season’s prevalent viral strains and hoping that this year’s prevalent strains are not too different. This approach means that the efficacy of current vaccines fluctuates greatly. For example, in 1997, this efficacy was only 50%, whereas in 1998 it was 86%. There are also two classes of antiviral medication that can be effective in the prophylaxis and treatment of influenza. These are inhibitors of neuraminidase and of M2 ion channels. However, the influenza virus can develop resistance to these standard antiviral drugs, and during the 2005/06 influenza season, the US Centers for Disease Control and Prevention recommended against treatment with M2 ion channel inhibitors. This project instead focuses on antivirals which inhibit virus maturation. This is a novel class of antivirals and is of interest for three important reasons: (1) the targets for this class of antivirals are mainly protein–protein con-tacts between the virus structural proteins; (2) the target protein is highly conserved among different viruses within the same family which could result in broad-range antivirals; and (3) development of drug resistance to this type of antiviral is less likely since this would affect protein–protein interactions that are critical for overall virus particle integrity and survival.

Aim

The project aims to produce a novel class of maturation-inhibiting antiviral drug candidates against the Influenza A virus. We have chosen a systematic approach that is rapid and efficient, and offers unique opportunities to define lead compounds against novel targets for antiviral therapy.

exPected Results

The project is expected to deliver maturation-inhibiting lead compounds against the Influenza A virus. This will include the identification of substances that inhibit maturation and/or alter the structure of the influenza virus, as well as a description of the mechanisms of action of these compounds. The work will develop methods to screen fragments directed against the target protein of the Influenza A virus as well as molecular models for the protein target and in silico screening, and will determine the pharmacologically-relevant properties of the lead compounds. The work will also optimise the algorithm for detection and characterisation of influenza virions in electron micrographs.


A broad-range antiviral lead compound that is insensitive to virus mutation.

Key words:drug discovery, maturation inhibitors, Influenza A virus, image analysis

107VIral InFectIonS

summARy

During the last century, three influenza pandemics occurred, and the threat of a new influenza pandemic has become imminent. A new pandemic would indicate that the influenza virus had undergone major changes, such as antigenic reassortment. Current treatments are unlikely to be effective, and new vaccines and antiviral agents will be essential to combat such an outbreak. The project aims to develop a new class of antiviral drug candidates. The target protein is highly conserved among hu-man strains of the virus as well as strains infecting other species, including birds. This would indicate that its rate of mutation is considerably lower than those of the surface proteins (i.e. haemagglutinin, neuraminidase and the M2 ion channel) upon which the currently available antiviral drugs act. The target is also involved in a variety of important viral and cellular processes. We will design and synthesise molecules that either inhibit or, conversely, stabilise protein–protein interactions, so that either the formation of virus particles is prevented or release of viral genetic material does not occur. The project combines knowledge-based design and synthesis of compounds with unique patented image analysis and mathematical algorithm software to find and develop these new types of potential antiviral molecules. The methodology allows for rapid discovery of lead molecules. Key molecules with optimal binding kinetics to the target protein will be designed and synthesised, then analysed and tested in two separate experimental systems for their effect on the virus structure and matura-tion process.

106




FluDrugStrategy202033 EUR 1 498 396 30 months01/03/2008 Focused research project

COmBATING INFLuENzA uSING

A NOvEL ANTIvIRAL STRATEGy

VIral InFectIonS

www.fludrugstrategy.com

109VIral InFectIonS

Coordinator

Dr. HeatherMarshall-Heyman Vironova ABGävlegatan 2211330 StockholmSwedenE-mail: [email protected]

Partners

Prof. Helena DanielsonBeactica ABUppsala, Sweden

Prof. Peter StaeheliUniversitätsklinikum FreiburgFreiburg, Germany

Prof. Nicolina StambolievaBulgarian Academy of SciencesSofia, Bulgaria

Dr. Iwan de EschVrije Universiteit AmsterdamAmsterdam, The Netherlands

108 VIral InFectIonS

flu, and, thus, could have an enormous impact on public health as well as on the competitiveness of the European pharmaceutical sector.

PRoblem

In recent years, the serious threat posed by the influenza virus to worldwide public health has been highlighted by, firstly, the ongoing low level trans-mission to humans of the highly pathogenic avian H5N1 strain (63% mortality in infected humans) and secondly, of the unexpected emergence in 2009 of a novel pandemic strain A/H1N1 that rapidly spread around the entire world. While the impact of the 2009 pandemic was fortunately milder than foreseen, under less fortunate circumstances (e.g. mutation to a more virulent form, resistance to Tamiflu), the delay in generating and deploying a vaccine could have been catastrophically costly in terms of human lives and societal disruption. It is now widely acknowledged that to bridge the period before a new vaccine becomes available and to treat severe cases, as well as to counter the problem of viral resistance, a wider choice of anti-influenza drugs is required.

Aim

The primary aim is to develop novel inhibitors tar-geting the influenza viral polymerase and advance a lead candidate into clinical development. In particular, we will target the unique cap-snatching mechanism of transcription of the polymerase, for which two specific active sites in two discrete domains exist, the cap-binding domain and the endonuclease domain. To achieve the objective, three integrated programmes will be pursued:

•Acomprehensivemedicinalchemistryprogramme.

•Aprogrammetodeterminethein vitro and in vivo efficacy of a selected set of promising compounds.

•Aprogrammetopursuepre-clinicalandclinical development of a selected drug candidate.

exPected Results

The project aims to complete a phase 1a clini-cal trial for at least one lead anti-polymerase compound. Since neither pandemic nor seasonal influenza adhere to national borders and readily spread to the most remote human habitats, the envisaged novel therapeutics will, without doubt, significantly contribute to the ability of mankind to combat the unpredictability of influenza viruses and their mutations, and benefit universal health and well being.


New anti-influenza drug options for advanced clinical development and new tools, assays and diagnostics for influenza academic and medical research.

Key words:influenza virus, polymerase, structure-based drug design

111VIral InFectIonS

summARy

The 2009 H1N1 pandemic and the ongoing threat of highly pathogenic H5N1 influenza strains have focused attention worldwide on the urgent need for new, effective anti-influenza drug op-tions, particularly when the public is not protected by natural immunity or vaccination. The need is pressing since several recent circulating strains have been resistant to currently available anti-influenza drugs. We will exploit recent advances in the detailed mechanistic understanding of the structure and function of the viral polymerase, and the replication machine of the virus, to develop new drug candidates that inhibit viral replication in infected cells. The polymerase is an excellent drug target as it is highly conserved in all influenza A strains, whether of avian, swine or human origin. The focused drug design programme will start with already existing patented small molecule hits against two different polymerase active site targets and use structure-based medicinal chemistry expertise to arrive at optimised leads to enter pre-clinical studies. In parallel, a world-leading network of European academic laboratories will continue fundamental research on influenza polymerase atomic structure, cellular function and role in inter-species transmission. This is not only valuable in its own right, to improve understanding of influenza biology, but will also feed back into the drug design programme with novel assays for polymerase inhibitors, improved understanding of how the inhibitors work in the cellular context and potential resistance mechanisms, as well as providing new targets for future anti-influenza drug design. If successful, the project will provide new therapeutic opportunities to treat both seasonal and pandemic

110




FLU-PHARM 259751 EUR 5 998 757 42 months01/11/2010 Focused research project

NEW DRuGS TARGETING

INFLuENzA vIRuS pOLymERASE

VIral InFectIonS

www.flupharm.eu

113VIral InFectIonS

Coordinator

Dr. Stephen CusackEMBL Grenoble OutstationRue Jules Horowitz 638042 Grenoble cedex 9FranceE-mail: [email protected]

Partners

Dr. Dirk Classen-HoubenSavira PharmaceuticalsVienna, Austria

Prof. Rob RuigrokUniversity Joseph Fourier Grenoble IGrenoble, France

Dr. Nadia NaffakhInstitut PasteurParis, France

Prof. Hans-Dieter KlenkPhilipps University MarburgMarburg, Germany

Dr. Gülsah GabrielHeinrich-Pette-Institut für Experimentelle Virologie und Immunologie an der Universität HamburgHamburg, Germany

Prof. Juan OrtinAgencia Estatal Consejo Superior de Investigaciones CientificasMadrid, Spain

Prof. Thierry LangerPrestwick Chemical IncStrasbourg, France

Dr. Gerhard WolberInte:Ligand Software-Entwicklungs- und Consulting GmbHVienna, Austria

112

Dr. Eva VareckovaInstitute of VirologyBratislava, Slovakia

Jean-Claude van HeugenAdvanced Technology Corporation SALiége, Belgium

Dr. Volker WacheckMedical University of ViennaVienna, Austria

VIral InFectIonS

pah and Hendra virus), alphaviruses (chikungunya virus), novel human coronaviruses, noroviruses, arenaviruses (Lassa fever virus) and hantaviruses (including hantavirus with pulmonary syndrome). Expert opinion predicts that novel and potentially highly pathogenic agents will continue to emerge from the large, genetically variable natural virus pools surrounding us. We urgently need advanced levels of preparedness with which to confront and ultimately control these viral pathogens. As illustrated by the success of anti-HIV therapy (mainly in the Western world) and recent events involving the novel H1N1 influenza virus, the ability to inhibit virus rep-lication using prophylactic or therapeutic strategies could be a major cornerstone in our battle against emerging and relatively neglected viruses. Today, antiviral drugs are only available for the treatment of infections with: (1) HIV, (2) some DNA viruses (herpes viruses, hepatitis B virus, poxviruses) and (3) a small number of RNA viruses (HCV — the first selective inhibitors are expected to be approved in 2011, i.e. 22 years after the discovery of the virus), RSV and influenza virus. Decades of rigorous effort were needed to develop these drugs and specific therapy is still lacking for the treatment of infections by all other RNA viruses.

The structural and non-structural viral proteins that orchestrate the steps in the viral replicative cycle are potentially vulnerable targets for attack by appropriate ligands that interfere with their func-tionality. The virus-specific nature of these targets and functions provides the potential to limit the negative side effects of antiviral drug treatment on regular host cell processes. Leads for the majority of currently available antiviral drugs were identified by screening compound libraries in cell culture-based systems (either employing infected cells or minigenome/replicon systems) and in vitro assays

using purified viral enzymes. Increasingly, however, selective inhibitors of viral replication are derived from structure-based drug design and detailed structural knowledge of viral proteins.

Aim

The overriding aim of the project will be the discovery and development of novel strategies to inhibit viral replication, and ultimately the selective inhibition of RNA viruses.

exPected Results

•Potentialviralinhibitorsforintegrationintothe project pipeline.

•CrystalstructuresincomplexwithRNAand other ligands deposited in a public database.

•Leadinhibitorycompoundsagainstselected viruses.

•Demonstrableefficacyofnewlyidentifiedinhibitory compounds in relevant models (proof of concept).


Therapeutics for treatment of human and/or animal virus disease.

Key words:RNA viruses, replicative enzymes, viral inhibitors, antiviral therapy, viral therapeutics, emerging viruses, neglected viruses, structure-based drug design

115VIral InFectIonS

summARy

The project will focus on selected medically important RNA viruses for which the develop-ment of drugs is considered essential (“Group A: priority viruses”); other relatively neglected and/or emerging RNA viruses will be explored through careful selection of the most promising targets and antiviral compounds. New antiviral hit compounds will be discovered by state-of-the-art cell culture-based screening, screening in enzymatic assays for specific viral proteins, and by structure-based drug discovery. The hits identified by these meth-ods will be optimised with medicinal chemistry, guided by the structure of the viral target, where available. For the most promising antiviral lead compounds, proof-of-concept will be sought in small animal studies.

PRoblem

Increasing human and animal population density through urbanisation, and agricultural climate change has an impact on virus emergence and epidemiol-ogy. Over the past three decades, emerging RNA viruses have continuously gripped the world’s atten-tion, either briefly (SARS coronavirus) or continuously (human immunodeficiency virus (HIV); avian and swine influenza viruses; hepatitis C virus (HCV)). Many other RNA virus threats were identified or ‘re-discovered’, including a variety of pathogenic flaviviruses (dengue virus (DENV) and West Nile virus (WNV)), filoviruses (Ebola and Marburg viruses), emerging picornaviruses (enterovirus 71), known and emerging paramyxoviruses (respiratory syncytial virus (RSV), human metapneumovirus (hMPV), Ni-

114




SILVER 260644EUR 12 000 000 48 months01/10/2010 Large-scale integrating project

SmALL-mOLECuLE INhIBITOR LEADS vERSuS

EmERGING AND NEGLECTED RNA vIRuSES

VIral InFectIonS

117VIral InFectIonS

Prof. Martino BolognesiUniversità degli Studi di Milano Milan, Italy

Prof. Joerg RademannUniversity of LeipzigLeipzig, Germany

Dr. Arnaud MarchandCenter for Innovation and Stimulation of Drug DiscoveryLeuven, Belgium

Coordinator

Prof. Ernst GouldUnité des Virus EmergentsFaculté de Médecine TimoneUniversité de la Méditerranée – d’Aix Marseille II Bd Jean Moulin 2713005 Marseille Cedex 05FranceE-mail: [email protected]

Partners

Prof. Rolf HilgenfeldUniversity of LubeckLubeck, Germany

Prof. Johan NeytsCatholic University of LeuvenLeuven, Belgium

Prof. Eric SnijderLeiden University Medical CenterLeiden, The Netherlands

Prof. Ron FouchierErasmus MCRotterdam, The Netherlands

Dr. Hervé BourhyInstitut PasteurParis, France

Prof. Ralf BartenschlagerUniversitätsklinikum HeidelbergHeidelberg, Germany

Dr. Frank Van KuppeveldRadboud University NijmegenNijmegen, The Netherlands

Dr. Jacques RohayemRiboxx GmbHRadebeul, Germany

Dr. Jon GrimesUniversity of OxfordOxford, United Kingdom

116

Dr. Françoise DebartNational Center for Scientific ResearchMontpellier, France

Prof. Miquel CollSpanish National Research CouncilBarcelona, Spain

Dr. Gerard BricogneGlobal Phasing LimitedCambridge, United Kingdom

Dr. Ulrich KesslerPike Pharma GmbHZurich, Switzerland

Dr. Gerhard PuerstingerUniversity of InnsbruckInnsbruck, Austria

Prof. Chris MeierUniversity of HamburgHamburg, Germany

Prof. Hong LiuChinese Academy of SciencesShanghai, China

Dr. Young-Sik JungKorea Research Institute of Chemical TechnologyDaejeon, Republic of Korea

Prof. Jih-Ru HwuNational Central UniversityJhongli, Taiwan

VIral InFectIonS

•Asustainableevidencebaseforbetter control of the epidemic and management of infected individuals.

•IncorporationofHIVgenesequencedatainto national HIV reporting structures.

•Translationofclinicalevidenceintoeffective strategies to limit the emergence and transmission of HIV drug resistance into evidence-based recommendations for public health and regulatory authorities.

•Creationofalevelplayingfieldinthe European scientific landscape in HIV resistance, and in scientific and clinical expertise in the study and management of HIV drug resistance.


The identification of novel resistance mechanisms to new drugs will prevent further development and spread of anti-HIV drug resistance. The project is developing new laboratory tools to predict and measure anti-HIV drug resistance, and management strategies are being developed for reducing its impact and incidence. HIV gene sequence data will be incorporated into national HIV reporting structures and evidence-based recommendations will also be made for public health and regulatory authorities on limiting the emergence and transmis-sion of anti-HIV drug resistance.

Key words:HIV, drug resistance, surveillance, phylogenetics, policy

119VIral InFectIonS

summARy

The current European research landscape in HIV drug resistance is too fragmented to effectively contribute to the fight against the spread of anti-HIV resistance. New insights into the prevalence and transmission of HIV-resistant strains in Europe in various cohort studies and the basic underlying mechanisms causing resistance and their implica-tions for novel antiviral drugs are being developed in different networks. Structural integration of these efforts and knowledge among centres of excellence on a pan-European scale is the next crucial step. Only through a powerful pooling of knowledge, resources and tools can decisive steps against the problem of anti-HIV resistance be achieved.


The most urgent aim is to close the gaps in our current knowledge on resistance to existing drugs and to identify novel resistance mechanisms to new drugs, preventing further development and spread of HIV. Other aims include:

•Developmentandvalidationofnewandcommon laboratory tools for prediction and measurement of HIV drug resistance.

•Improvedunderstandingoftheclinicalimplications of drug resistance, with the development of optimal management strategies for transmitted and acquired HIV drug resistance, reducing the incidence and impact at population and patient level.

118




CHAIN 223131 EUR 10 000 000 60 months 01/04/2009 Large-scale integrating project

COLLABORATIvE hIv AND ANTI-hIv

DRuG RESISTANCE NETWORk

VIral InFectIonS

121VIral InFectIonS

Dr. Vicente Soriano VasquezHospital Carlos IIIMadrid, Spain

Dr. Lieven StuyverTibotec-Virco VirologyMechelen, Belgium

Prof. Maurizio ZazziEuResist Network GEIESiena, Italy

Dr. Francesca Ceccherini-SilbersteinUniversità degli Studi di Roma Tor VergataRome, Italy

Dr. Judith TorimiroCentre Interantional de Référence Chantal Biya Yaoundé, Cameroon

Coordinator

Prof. Deenan PillayCentre of VirologyUniversity College London Windeyer BuildingCleveland Street 46London W1T 4JFUnited KingdomE-mail: [email protected]

Partners

Prof. Charles BoucherErasmus MC Rotterdam, The Netherlands

Prof. Carlo PernoInforma SRLRome, Italy

Prof. Françoise Brun-VezinetAssociation de Recherche en Virologie et DermatologieParis, France

Dr. Bonaventura ClotetirsiCaixa FoundationBarcelona, Spain

Dr. Kholoud PorterMRC Clinical Trials Unit London, United Kingdom

Dr. Carlo GiaquintoPENTA FoundationPadua, Italy

Prof. Jens LundgrenUniversity of CopenhagenCopenhagen, Denmark

Prof. Genevieve CheneUniversity of Victor Segalen Bordeaux IIBordeaux, France

Prof. Antonella d’Arminio MonforteIcona FoundationMilan, Italy

120

Prof. Coumba Toure KaneUniversite Cheikh Anta Diop de DakarDakar, Senegal

Dr. Marina BobkovaRussian Academy of Medical SciencesMoscow, Russian Federation Dr. Mario PoljakUniversity of LjubljanaLjubljana, Slovenia

Dr. Diane BennetWorld Health OrganizationGeneva, Switzerland

Prof. Anders SonnerborgKarolinska InstituteStockholm, Sweden

Prof. Huldrych GünthardUniversity of ZurichZurich, Switzerland

Prof. Annemie VandammeCatholic University of LeuvenLeuven, Belgium

Dr. Osamah HamoudaRobert Koch InstituteBerlin, Germany

Dr. Ricardo CamachoInstitute of Hygiene and Tropical MedicineLisbon, Portugal

VIral InFectIonS

pROTOzOANINFECTIONS

Protozoan InFectIonS 123Protozoan InFectIonS122

researchers to resolve this problem through a logical series of meetings, conferences, workshops and dissemination strategies. The action will coordinate leading European malaria research initiatives in antimalarial drug discovery and development, coordinate the European effort with international initiatives, engage industry, provide guidance on standardisation of core requirements of regulatory drug development, contribute towards generating global priorities and prepare the European anti-malarial research agenda for the next decade. A coordinated action plan will be published and a five-year rolling review timetable will be established with quantitative endpoints mapped directly onto the action plan. An expert advisory group will be established and this group will work towards securing funding to enable the five-year review and updated timetable. The result is a coordinated, rationalised and integrated series of initiatives that are monitored and updated continuously to meet the ongoing needs of malaria drug development for the future.


The model that will be established in this coor-dination action can be applied to other disease areas, particularly (but not exclusively) in relation to neglected diseases

Key words:malaria, drugs, public private partnerships, coordination

125Protozoan InFectIonS

summARy

There are a number of European and interna-tional initiatives that are committed to antimalarial drug discovery and development, but they are fragmented and uncoordinated. This action will coordinate leading European malaria research initiatives on antimalarial drug discovery and development, integrate the European effort with international initiatives, engage industry and provide guidance on standardisation of core requirements of regulatory drug development. The goal is to contribute towards generating global priorities and preparing the European antimalarial research agenda for the next decade. Globally, antimalarial drug discovery and development initiatives are fragmented and uncoordinated, with few links between programmes. There is an urgent need for coordination, rationalisation and integration among initiatives to ensure that research priorities are identified in a systematic and transparent way, and that programmes conform to standardised and internationally acceptable methods without excessive duplication. Engage-ment with small and large industrial partners and endemic country scientists, all of whom could contribute significantly to these initiatives, is weak as are dissemination efforts.


We have brought together key organisations includ-ing the Medicines for Malaria Venture (MMV), the World Health Organization (WHO), the Gates Foundation and a number of academic malaria

124




CRIMALDDI 222948 EUR 500 000 27 months 01/02/2009 Coordination action

ThE COORDINATION, RATIONALISATION AND

INTEGRATION OF ANTImALARIAL DRuG DISCOvERy AND

DEvELOpmENT INITIATIvES

Protozoan InFectIonS

www.crimalddi.eu


Coordinator

Prof. Stephen WardLiverpool School of Tropical MedicinePembroke PlaceLiverpool L35 QAUnited KingdomE-mail: [email protected]

Partners

Dr. Solomon Nwaka World Health OrganizationGeneva, Switzerland

Dr. Ian BathurstMedicines for Malaria VentureGeneva, Switzerland

Prof. Michael LanzerUniversitätsklinikum HeidelbergHeidelberg, Germany

Prof. Donatella TaramelliUniversità degli Studi di MilanoMilan, Italy

Dr. Henri VialCNRSMontpellier, France

Prof. Christian Doerig INSERM, University of GlasgowGlasgow, United Kingdom

Prof. Simon EfangeUniversity of BueaBuea, Cameroon

Prof. Chibale KellyUniversity of Cape TownRondebosch, South Africa

126 Protozoan InFectIonS

(ACTs – artemisinin-based combination therapies). However, the use of ACTs requires careful monitor-ing as there is a significant risk of parasites also developing resistance to this new generation of drugs, leaving vulnerable communities without appropriate treatment measures.


The aim of the project is to develop and evaluate molecular tools for monitoring ACT drug resistance in selected target countries (i.e. Burkina Faso, Nigeria and Tanzania). These will preferably be based on isothermal amplification technology and will have an easy read-out system which can be implemented in routine malaria diagnosis, prefer-ably under resource-poor conditions. The possible evolution of ACT drug resistance will be monitored along with the molecular principles that confer drug resistance (these could be single nucleotide point mutations or altered gene expression). The consortium hopes, in particular, to identify alleles of candidate resistance genes associated with increased transmission success of P. falciparum after ACT treatment in completed clinical trials with endpoints at the gametocyte or infected mosquito level. The commercial value aspects of the developed tests will also be explored, with the possibility of bringing developed tools to market at affordable and competitive prices. ACT treatment trials will be conducted with transmission endpoints, and measurement will be made of the impact of resistance-associated alleles of key genes on:

•Gametocyteprevalence,densityandlongevity.

•Infectiousnessofgametocyte-positivetreated individuals to mosquitoes.

•Infectiousnessofrandomly-selectedtreatedindividuals to mosquitoes.

These activities will lead to new information on the genetic basis of ACT resistance, new tools for the diagnosis of malaria, new tools for monitoring ACT drug resistance, and new insights into the transmission of ACT-resistant parasites.


The outcome of the project will lead to improved diagnosis of malaria. The work will provide more insight into the development of drug resistance and could have wider applications in the field of malaria or other infectious diseases in general. The developed tools could be implemented in resistance surveillance studies of national malaria control programmes in disease-endemic countries. The new knowledge about the molecular basis of ACT resistance and the effect on disease transmission will have implications for adjustment of control programmes.

Key words:malaria, drug resistance, artemisinin-based combination therapy, diagnostics, molecular biology, Plasmodium, rapid tests


summARy

Malaria is the most serious parasitic disease in the world. Approximately a quarter of the world’s population is at risk of contracting the disease, and every year more than 2 million people, mainly young children in sub-Saharan Africa, die because of it. Malaria is caused by single-celled (protozoan) parasites of the genus Plasmodium. Four species can cause human disease: P. falciparum (the most important one and responsible for the majority of deaths), P. vivax, P. ovale and P. malariae. Accurate diagnosis followed by prompt and efficacious treatment is the backbone of any malaria control programme. However, both diagnosis and treatment represent huge challenges, as many laboratory tests to confirm malaria infection lack sensitivity/specificity or are difficult to perform under rural conditions. Most affordable drugs are also losing their effectiveness due to emerging resistance. Improved diagnostic tools to support the clinical suspicion of malaria are needed. In principle, molecular biology-based tools would provide the most sensitive and accurate tools for diagnosis, but their implementation in resource-poor settings is hampered due to dependency on electricity, and the cost of equipment. To circumvent resistance, the World Health Organization recommends the use of combination therapies for P. falciparum malaria, preferably those containing artemisinin derivatives

128




MALACTRES 201889 EUR 2 800 358 60 months 01/01/2008 Focused research project

muLTI-DRuG RESISTANCE IN mALARIA uNDER

COmBINATION ThERApy: ASSESSmENT OF SpECIFIC

mARkERS AND DEvELOpmENT OF INNOvATIvE, RApID AND

SImpLE DIAGNOSTICS


www.malactres.eu


Coordinator

Dr. Hendricus SchalligRoyal Tropical InstituteMeibergdreef 39Amsterdam 1105 AZThe NetherlandsE-mail: [email protected]

Partners

Dr. Colin SutherlandLondon School for Hygiene and Tropical MedicineLondon, United Kingdom

Prof. Umberto d’AlessandroPrince Leopold Institute of Tropical MedicineAntwerp, Belgium

Dr. A. van AmerongenAgrotechnology and Food Innovations BVWageningen, The Netherlands

Christopher DanksForsite Diagnostics LtdYork, United Kingdom

Dr. Ehijie EnatoUniversity of Benin CityBenin City, Nigeria

Dr. Halidou TintoCentre MurazBobo-Dioulasso, Burkina Faso

Dr. Jan Teun BousemaKilimanjaro Christian Medical CentreMoshi, Tanzania


Aim

The project aims to elucidate the epidemiology of the genetic lineages of t. cruzi, for improved under-standing and prevention of Chagas disease.

exPected Results

The project will profoundly improve our knowledge and understanding of the epidemiology of the most significant parasitic disease in the Americas. The outputs of the project will facilitate understanding the diversity of clinical manifestations and the reduction of the burden of disease:

•Techniquesforidentifyingt. cruzi lineages will be developed, improved, compared and deployed in endemic regions.

•Ahighqualitygenomesequenceforthesecond major t. cruzi genetic lineage will be obtained.

•Methodswillbedevisedforlineage-specific diagnosis of t. cruzi infections and for detection of multiclonal infections.

•Progresswillallowthefundamentalquestion of the association between the t. cruzi genetic lineage and the clinical outcome to be tackled.

•Newinformationwillbeobtainedonthe unknown sylvatic hosts of t. cruzi IId, IIe, IIb and IIa, with an assessment of the epidemiological threat that they represent.

•Thebiologyofthegeneticlineageswillbe compared experimentally in vitro and in vivo, in terms of cell invasion, pathogenesis, congenital transmissibility and susceptibility to drug treatment.


By application of molecular tools for identification of t. cruzi lineages and local use of the methods, wider and sustained molecular epidemiological studies will be enabled in endemic regions, and comparative studies between endemic regions. The molecular methods that will be developed in this project will also provide an important means of molecular tracking of the origin of t. cruzi isolates, thus whether a European infection was imported from Central America or South America or locally acquired from transfusion of contaminated blood. Insight into drug susceptibilities and comparative pathogenesis of the genetic lineages will be relevant to improve treatment and management of cases. Identifying the role of mammalian reservoir hosts and vectors will define which are fundamentally relevant to disease transmission, and will guide the further development of control strategies. The expanded international repository of representative isolates of t. cruzi will greatly facilitate future research.

Key words:Trypanosomatidae, trypanosoma cruzi, Chagas disease, molecular epidemiology, diagnosis, pathogenesis, disease control, genomics, population genetics, phylogenetics


summARy

The focus of the project is to elucidate the epide-miology of the genetic lineages of trypanosoma cruzi, the causative agent of Chagas disease, for improved understanding and prevention of Chagas disease. Approximately 10 million people are infected with t. cruzi in Latin America and Chagas disease claims an estimated 13 000 lives annually. The project aims to: (1) improve and standardise techniques for genotyping t. cruzi; (2) improve our understanding of the population genetics of t. cruzi; (3) sequence the genome of t. cruzi line-age I; (4) develop lineage-specific immunological diagnosis; (5) conduct pilot studies to evaluate t. cruzi lineage-specific associations with clinical outcome, congenital infection, cellular infectivity and susceptibility to trypanocidal drugs. The project will contribute towards improved measures for reducing the future burden of Chagas disease.

PRoblem

t. cruzi is known to be a heterogeneous complex of organisms, predominantly clonal but with a proven capacity for genetic hybridisation. Genetic lineages have been defined, named t. cruzi I, II (a, b, c, d, e). However, understanding of their comparative biology and public health importance is fragmentary, and there are practical difficulties in simply discerning the lineages and the relation-ships between them.

132




ChagasEpiNet 223034 EUR 2 876 507 36 months 01/01/2009 Focused research project

COmpARATIvE EpIDEmIOLOGy OF

GENETIC LINEAGES OF trypanosoma Cruzi


www.ki.se/chagasepinet


Coordinator

Prof. Michael MilesLondon School of Hygiene and Tropical MedicineKeppel StreetLondon WC1E 7HTUnited KingdomE-mail: [email protected]

Partners

Prof. Philippe BuscherInstitute of Tropical MedicineAntwerp, Belgium

Prof. Yves CarlierUniversité libre de BruxellesBrussels, Belgium

Dr. Michel TibayrencL’institut de recherche pour le développementBangkok, Thailand

Prof. Bjorn AnderssonKarolinska InstituteStockholm, Sweden

Dr. Kevin TylerUniversity of East AngliaNorwich, United Kingdom

Prof. Manuel Fresno EscuderoUniversidad Autonoma de MadridMadrid, Spain

Dr. Faustino TorricoUniversidad Mayor de San SimónCochabamba, Bolivia

Dr. Hernan CarrascoUniversidad Central de VenezuelaCaracas, Venezuela

Dr. Patricio DiosqueUniversidad Nacional de SaltaSalta, Argentina

134

Dr. Ana JansenFiocruz, Instituto Oswaldo CruzRio de Janeiro, Brazil

Dr. Alejandro LuquettiUniversidade Federal de Goiás Goiânia, Brazil

Prof. Felipe GuhlUniversidad de los Andes FundacionBogota, Colombia

Prof. Aldo SolariUniversidad de ChileSantiago, Chile

Dr. Mario GrijalvaPontificia Universidad Católica del EcuadorQuito, Ecuador


emerge. Widespread over-the-counter drug sales and irrational drug prescribing further increase this risk. Moreover, the region is confronted with an expanding HIV-epidemic, and we expect to see more HIV-VL co-infections which will gener-ate major therapeutic challenges. Combination regimens for VL are under clinical development, but the drug policy will take several more years to change. Meanwhile, the effectiveness of current drugs needs to be safeguarded in order to cure patients and to sustain the control of VL. For this, the uninterrupted supply of quality drugs, the promo-tion of treatment adherence, and the monitoring of treatment effectiveness and drug resistance will be pivotal. There is a direct need for new tools to allow monitoring treatment effectiveness and drug resistance because: (1) validated methods to monitor treatment effectiveness under routine conditions do not exist; (2) there are discrepancies in assays for the assessment of drug resistance in Leishmania parasites; (3) the knowledge on mechanisms of emergence of drug resistance, its dynamics and the impact of the introduction of new drugs is poor; and (4) molecular tools for high throughput monitoring of drug resistance do not exist. Clinical and laboratory research is urgently needed to support the drug policy of the VL elimination programme.

Aim

To develop, evaluate and disseminate new tools for evaluation of drug resistance in leishmania donovani as well as innovative methodologies for routinely monitoring KA treatment effectiveness.

exPected Results

•Aninnovativeapproachforroutinelymonitoringeffectiveness of VL treatment in the health services of l. donovani-endemic areas.

•Comprehensivecollectionsofwell-documented clinical samples and parasites, including all available epidemiological information.

•Areferencegenomesequenceofl. donovani from the region that will serve as a reference for identifying markers of drug resistance and SNPs for population genetic studies.

•Upgradedandstandardisedassaysfortesting in vitro susceptibility against anti-leishmanial drugs.

•Decipheringmolecularmechanismsunderlying natural resistance against SSG and MIL, and clarifying the relation between natural resistance and clinical treatment failure.

•Validatedsimplemolecular techniques formonitoring natural resistance to SSG and MIL.


Our clinical and epidemiological work should contribute to: (1) an early identification (in clinical settings as well as in peripheral health centres) of patients at higher risk of treatment failure, and (2) a more rational therapeutic attitude. This would have a direct impact on treatment costs. By deciphering the molecular mechanisms leading to drug resistance and providing the respective detection tools, and


summARy

This project concerns the effective control of the neglected parasitic disease, Kala-Azar (KA) or visceral leishmaniasis (VL). By providing knowledge and tools relevant for monitoring the effectiveness of the few existing drugs, we will contribute to safeguarding them and establishing a basis for their longer-term and more rational use. We will use an integrated and multidisciplinary approach to develop new tools for monitoring the response to treatment and drug resistance. Molecular mechanisms leading to drug resistance will be studied and affordable tools for the detection of drug resistance will be developed, so as to be applicable in endemic countries.

PRoblem

KA has been reported in 51 countries around the world, with an annual incidence of 500 000 cases, about 90% of which occur in India, Nepal, Bangladesh, Sudan and Brazil. Early treatment is a major pillar of the current KA elimination pro-gramme, which was launched by the governments of India, Nepal and Bangladesh. The arsenal of available drugs is limited. Due to its toxicity as well as to emerging drug resistance, the former first-line drug, sodium stibogluconate (SSG), was recently replaced by miltefosine (MIL) on the Indian subcontinent, but MIL is an oral drug with a long half-life, and it is feared that resistance will rapidly

136




KALADRUG-R 222895 EUR 2 999 998 48 months 01/11/2008 Focused research project

NEW TOOLS FOR mONITORING DRuG

RESISTANCE AND TREATmENT RESpONSE IN vISCERAL

LEIShmANIASIS IN ThE INDIAN SuBCONTINENT


www.leishrisk.net/leishrisk/ Default.aspx?Menu=MenuMain&MIID=35&WPID=41&L=E


by understanding the epidemiological dynamics of its emergence and spreading, the project will sup-port control programmes relying on chemotherapy (among other methods), such as the KA elimination programme.

Key words:visceral leishmaniasis, Indian subcontinent, treatment effectiveness, drug resistance, miltefosine, antimonials, paromomycine, comparative genomics

Coordinator

Prof. Jean-Claude Dujardin Institute of Tropical MedicineNationalestraat 1552000 AntwerpBelgiumE-mail: [email protected]

Partners

Prof. Graham CoombsUniversity of StrathclydeGlasgow, United Kingdom

Prof. Louis MaesUniversity of AntwerpAntwerp, Belgium

Dr. Gabrielle SchönianUniversitätsmedizin Charité BerlinBerlin, Germany

Dr. Martin Eichner University of TübingenTübingen, Germany

Dr. Matt BerrimanWellcome Trust Sanger InstituteUnited Kingdom

Prof. Shyam SundarBanaras Hindu UniversityVaranasi, India

Dr. Suman Rijal B.P. Koirala Institute of Health SciencesDharan, Nepal

Dr. Poonam SalotraIndian Council of Medical ResearchNew Delhi, India

Prof. Syamal RoyCouncil of Scientific and Industrial ResearchCalcutta, India


FuNGALINFECTIONS

Fungal InFectIonS 141Fungal InFectIonS140

Fungal InFectIonS 143

cause of mortality in immuno-compromised patients, whose population is ever expanding through the aggressive use of cytotoxic chemotherapy, broad-spectrum antibiotics and underlying disease, such as AIDS. In addition, filamentous fungi can produce a number of allergic diseases in immuno-competent patients, unlike common aeroallergens also colonising human lung and other tissue to vari-ous degrees. As fungal pathogens are eukaryotes and, therefore, share many of their biological processes with humans, most antifungal drugs are associated with severe toxicity. No standardised vaccines exist for preventing any of the fungal infections of humans, a situation attributed both to the complexity of the pathogens involved and to their sophisticated strategies for surviving in the host and evading immune responses. Evidence has emerged that the host immune response and antifungal therapy are the major determinants of the outcome of fungal disease and act in synergy; in fact, the newest antifungal agents are immuno-modulators. Currently, the number of antifungal agents is limited and often not well tolerated, showing important secondary effects. Additionally, the number of fungal strains resistant to the most common antifungals is increasing dramatically.

Aim

The aim is to identify biomarkers of resistance to currently available treatments and to develop novel putative drug target genes and pathways in different fungi. A series of experiments will be performed, in which dendritic cells, macrophages and T lymphocytes from disease-free and immuno-compromised individuals, with and without recurrent fungal disease, are challenged with pathogenic and non-pathogenic fungal agents. We will sequence

the genomes of environmental isolates of several pathogenic subspecies and through comparative analysis will gain a better understanding of the evolution of drug resistance strategies in invasive and allergenic fungal disease. A comprehensive bar-coded S. cerevisiae gene deletion collection will be treated with a panel of existing and poten-tial antifungal drugs in order to construct models of drug resistance, and a similar strategy will be employed against a library of several thousand antifungal drug-resistant or sensitive mutants of aspergillus. The resulting comprehensive models and candidate drug-sensitive genes will be tested via specific gene knockout experiments in other fungal pathogenic species and selected targets further tested in a previously validated neutropenic mouse model.

exPected Results

•Identificationofbiomarkersofdrugsensitivity and resistance in fungal microorganisms, producing a comprehensive knowledge base of drug resistance genes for multiple safe and pathogenic species.

•Increasedunderstandingoffundamentalmechanisms of immuno-modulation by antifungal drugs in the clinical context of host–pathogen interactions.

•Identificationofgeneticsignaturesofsusceptibility and sensitivity to fungal infection in immuno-compromised and normal patients.

•Identificationofpotentialnovelcandidatemolecules for future antifungal drugs and their development for clinical trials.

Fungal InFectIonS142

summARy

The project involves a systems biology study of the specificity of response of the cell-mediated immune system to fungal microorganisms in order to investigate the genetic basis of susceptibility to fungal disease and elucidate molecular mechanisms of drug resistance in fungal pathogens. Saccha-romyces cerevisiae, a normally non-pathogenic yeast model organism, candida albicans and aspergillus fumigatus, two major recognised fungal pathogens as well as other aspergillus spp. known to be multi-drug resistant and difficult to treat will be used. The anticipated results are relevant to society in terms of reducing the burden of mortality and suffering in immuno-suppressed patients and in terms of reducing medical costs associated with treating opportunistic fungal infections. The potential economic upside for novel broad-spectrum anti-infectives is very large. The worldwide market for antifungals is currently estimated at $4 billion/year.

PRoblem

The incidence of fungal disease has risen dramati-cally in the past several decades, and this trend is exacerbated by the increased emergence and spread of antifungal drug-resistant strains of fungal pathogens. Invasive fungal infections are a major

SYBARIS 242220 EUR 4 291 161 36 months 01/11/2009 Focused research project

FINDING BIOmARkERS OF ANTI-mICROBIAL DRuG

RESISTANCE vIA A SySTEmS BIOLOGy ANALySIS OF

FuNGAL pAThOGEN INTERACTIONS WITh ThE

humAN ImmuNE SySTEm

www.sybaris-fp7.eu




Fungal InFectIonS 145


Identification of new targets for antifungal therapy. Generation of a knowledge base for drug resist-ance genes that will be a valuable resource for researchers and clinicians worldwide.

Key words:systems biology, immuno-pharmacology, antifungal resistance, functional genomics, pathway analysis, infectious fungal disease, aspergillus, candida

Coordinator

Misha KapusheskyEMBL-EBIWellcome Trust Genome CampusHinxton, Cambridge CB10 1SDUnited KingdomE-mail: [email protected]

Partners

Duccio CavalieriUniversità degli Studi di FirenzeFlorence, Italy

Dr. Paul BowyerUniversity of ManchesterManchester, United Kingdom

Dr. Manuel António da Silva SantosUniveristy of AveiroAveiro, Portugal

Dr. Philippe PierreCNRS, Centre d’Immunologie de MarseilleMarseille, France

Dr. Brian MillerAlerGenetica SLManchester, United Kingdom

Prof. Luigina RomaniUniversità degli Studi di PerugiaPerugia, Italy

Dr. Ivo Glynne GutCEA-IG – Centre National de GénotypageEvry, France

Fungal InFectIonS144

index ProjeCts

AEROPATHANTIFLUAntiPathoGNantiresdevAPRESBIOHYPOCAREPNEUMOCATAFLU.ORChagasEpiNetCHAINCONCORDCRIMALDDIDebugITDIVINOCELLFAST-XDR-DETECTFLUCUREFluDrugStrategyFLU-PHARMHYPERDIFFKALADRUG-RMALACTRESNABATIVIPARPILGRIMPNEUMOPATHPROHIBITSATURNSILVERSYBARISTB PAN-NETTEMPOtest-QCTROCAR

index Coordinators

Prof. Dan AnderssonProf. Peter AndrewDr. Alessandra BragonziProf. Gursharan ChhatwalDr. Maria Daniela CirilloDr. Dirk ColaertProf. Pier Giorgio CozziDr. Stephen CusackProf. Xavier DauraProf. Jean-Claude DujardinDr. Ad FluitProf. Ernst GouldDr. Stephan HarbarthDr. John HaysProf. William HunterMisha KapusheskyDr. Heather Marshall-HeymanProf. Thomas MeyerProf. Michael MilesProf. Nigel MintonProf. Marco OggioniDr. Juan Carlos PalominoProf. Deenan PillayDr. Hendricus SchalligProf. François SchellevisProf. Katharina StärkProf. Miguel VicenteProf. Jordi VilaProf. Stephen WardProf. Michael WilsonDr. Walter Zingg

eu reSearch on antIMIcroBIal reSIStance146

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EuropEan Commission


Directorate Health

Unit Infectious Diseases and Public Health

http://ec.europa.eu/research/health/infectious-diseases/anim.html

Contact: Rachida Ghalouci

European Commission

Office CDMA 02/155

B-1049 Brussels

Tel. (32-2) 29-64826

Fax (32-2) 29-94561

E-mail: [email protected]

How to obtain Eu publications

Free publications:

• viaEUBookshop(http://bookshop.europa.eu);• attheEuropeanCommission’srepresentationsordelegations.Youcanobtaintheircontactdetailsonthe

Internet(http://ec.europa.eu)orbysendingafaxto+3522929-42758.

priced publications:

• viaEUBookshop(http://bookshop.europa.eu);

priced subscriptions (e.g. annual series of the official Journal of the European union

and reports of cases before the Court of Justice of the European union):

• viaoneofthesalesagentsofthePublicationsOfficeoftheEuropeanUnion (http://publications.europa.eu/others/agents/index_en.htm).

European Commission

Eu research on antimicrobial resistanceEu projects 2007-2010

Luxembourg: Publications Office of the European Union

2011 — 148 pp. — 14,8 x 21 cm

ISBN 978-92-79-19646-1doi 10.2777/48721



Project information

Health &life sciences

E U R O P E A NCOMMISSION

Research & Innovation

KI-30-11-027-E

N-C

Drug-resistant infections are becoming ever more prevalent, both in hospitals and within the community, and are making the treatment of infectious diseases increasingly difficult. This brochure summarises research projects funded by the European Union’s Seventh Framework Programme (FP7) from 2007-2010 in an effort to combat antimicrobial resistance. EU funding in this area covers a broad range of microorganisms including bacteria, viruses, protozoa and fungi.

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doi:10.2777/48721

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