diagnostic needs in antimicrobial resistance · find: ten years of advancing diagnostics 2 sleeping...

Diagnostic Needs in Antimicrobial Resistance

29 February 2016

FIND: Ten years of advancing diagnostics

2

Sleeping

sickness

TB

Malaria

Catalyzing Development Enabling UptakeEnsuring proper use

to drive Impact

11 new tests launched;

from biomarkers

to validation

WHO pre-qualification

and policyCases detected/

lives saved

1 2 3

RDT to support HAT

elimination

16 sub-Saharan African countries

committed to introducing new tools

and informing WHO policy

Within 24m expect increase in

coverage to ~75%, and major

reduction in incidence

Automated molecular tool, LPA

and LCx for MDR-TB control

Shaped process for policy on use as

WHO partner for trials; Xpert

implemented in 100 countries in 1 year

MDR-TB detection has doubled, stronger

lab networks at core of TB control today

(e.g., >90% of MDR-TB in India

diagnosed with new tools after training

of >4,000 lab workers)

LAMP WHO recommended and

used for surveillance in pre-

elimination settings

4-fold increase in RDT use, resulting in

significant cost savings to health

systems

Safe blood transfer device &

increased use of good-quality

RDTs

http://sdgln.com/files/blood-donation-3739.gif

http://sdgln.com/files/blood-donation-3739.gif

Our disease programmes:

Tuberculosis Malaria

Neglected

Tropical

Diseases

Hepatitis C

HIV

Acute Febrile

IllnessConnectivity

Outbreak

surveillance

Our cross-cutting programmes:

3

Our technology development programmes:

Technology

Scouting

Support for

Success

FIND Portfolio



Neglected

Tropical

Diseases

Hepatitis C

HIV

Acute Febrile

IllnessConnectivity

Outbreak

surveillance


4


Technology

Scouting

Support for

Success

AMR

FIND Portfolio



Neglected

Tropical

Diseases

Hepatitis C

HIV

Acute Febrile

IllnessConnectivity

Outbreak

surveillance


5


Technology

Scouting

Support for

Success

AMR

AMR AMR

AMR

FIND Portfolio

Product portfolio targets global community

needs

TB

Ma

lari

aH

CV

/HIV

NT

Ds

Cro

ss-c

utt

ing

th

em

es

QUANTUMDX Q-POC

QIAGEN TB Detection

SOMALOGIC Triage test

PROTEINLOGIC Triage test

BMGFLAM TB detection

SD (Alere) LAM in sputum

EIKEN High-throughput LAMP

ATOMOHCV rapid test

NWGHF/ ORTHOCore antigen test

BD Microimager

PATH High-sensitivity RDT

CEPHEID Xpert Ultra, Xtend XDR

HAINFluorotype

CEPHEID Xpert stool

CEPHEID Xpert for HCV

CITRISCellscope

MICROCOATRecombinant proteins

ALEREQ

NIPRO LPA PZA

EPISTEM Genedrive MTB/RIF

MICROCOATPositive control Wells

LPA WHO review

USTAR EasyNAT TB

MOLBIO Truenat MTB

HAIN GenoType MTBDRsl

Sequencing WHO review

YD DIAGNOSTICSREBA-MTB

CEPHEID Xpert MTB/RIF

HAIN LPA (1st line)

EIKEN LAMP Kit

BD Liquid Culture and DST

TAUNS Rapid Speciation

ZEISS LED microscopy

SD (Alere) HAT-Malaria combo test

KALON Elisa test for VL, CL, PKDL

EIKEN LAMP (congenital inf.)

EIKENBU LAMP

CODICILE HAT staging test & test of

cure

EIKEN LAMP for reference lab

SD (Alere) HAT RDT (2nd gen.)

SD (Alere)BU tests

EIKENHAT LAMP

ZEISS Primostar iLED

WHO/HARVARD UNIVERISTY Thin layer

chromatography

SD (Alere)HAT RDT

Buruli ulcer

Chagas

Leishmaniasis

HumanAfricanTrypanosomiasis

Moecular lDST

(platform agnostic)

WEHI Vivax RDT

PHILIPS Minicare

MEMED ImmunoXpertTM

CEPHEID Ebola Xpert

ALEREQ

INTEC PRODUCT One Step Ebola RDT

SENOVA Dediatest Ebola

CORGENIXReEBOVTM Antigen RDT

SDBIOSENSORSD Ebola Zaire RDT

CEA Ebola eZYSCREEN RDT

ORASURE Ebola Rapid Ag RDT

CHEMBIO DPP® Fever panel

EDAC: Implementation of

Ebola and fever tools

MULTIPLEHIA marker selection

BIORAD HIV Incidence

SEDIA HIV Incidence

Map of causes of fever

USTAR EasyNAT TB

BD SERS-HNW Fever panel

AccelerateAccess

Guide use and policy Catalyze Development Research

6

FIND is currently working with 185 partners globally

Industry

• 46 partners

Universities and ResearchInstitutes

• 44 partners

Advocacy

• 2 partners

Clinical Trial Sites

• 32 partners

Implementing partners

• 26 partners

Government/ multilateral

agencies

• 35 partners

7

- FIND logistics team designated for studies

-- Can support installation/training if company cannot

- Industry agreement templates

-- Support for product development (pre-validation)

-- Sequential laboratory field validation studies with PQ

- Protocols for immunoassay, molecular, across diseases

- Connectivity platform

-- Can support rapid data analysis and troubleshooting

Diagnostic Needs in Combating AMR in LMIC

8

1. Surveillance of AMR

2. Detection of AMR in Clinical Settings

- Routine

- Referral/Specialty

3. Prevention of AMR through Diagnosis of Acute Febrile Illness

AMR Activities at FIND

9

!

!!

!!!!!!

Anti"Microbial)Resistance!

Landscape)Analysis)of)the)State)of)AMR)Testing)Technologies)

!

!

!

Heinz!Reiske,!PhD!

! !

AMR Diagnostics Landscape Report – 2015

AMR Diagnostic Systems

• 19 molecular technologies

• 4 phenotypic drug susceptibility test systems

• 5 automated susceptibility test systems

DST assays for priority pathogensMDR Acinetobacter/Pseudomonas

Campylobacter

Candida

E. coli

MRSA

Neisseria gonorrhoeae

Streptococcus pneumoniae

Salmonella spp.

Plasmodium spp.

MDR TB / XDR TB

Emerging technologies for POC/District molecular testing

1. Surveillance of AMR

10

AMR Diagnostic Systems

• 19 molecular technologies

• 4 phenotypic drug susceptibility test systems

• 5 automated susceptibility test systems

Workflow Chemistry Menu Cost

Molecular technologies

Phenotypic DST systems

Automated susceptibility test systems

Next Gen Sequencing (NGS ) for AMR Surveillance?

DNA Extraction Amplification and Library Prep NGS Sequencing

Mutation Detection Clinical Interpretation

11

Advantages of NGS for AMR Surveillance

Culture-Free AMR Surveillance• Expands AMR surveillance into regions with no Cx facilities

• Provides direct, unbiased estimates of mixed populations

Standardized across sites

Quick

High Throughput

Suitable for automation/data sharing through connectivity and cloud-based analysis

Provide data on frequency and distribution of AMR genotypes to predict effectiveness of POC RDST and new drugs

12


13

U

C-D

avis

Next Gen Sequencing platforms

District Hospital Level

Next Gen Sequencing for Clinical Use??

• 200 genetic sequences in 24-48 hours

• Integrated benchtop automation

• Price points can be suitable by 2019

Pilot program for MDR TB"Next Generation Sequencing for Rapid

Diagnosis and Surveillance of Drug-resistant

Tuberculosis"


14

U

C-D

avis

Next Gen Sequencing platforms

District Hospital Level

Next Gen Sequencing for Clinical Use??

• 200 genetic sequences in 24-48 hours

• Integrated benchtop automation

• Price points can be suitable by 2019

Pilot program for MDR TB"Next Generation Sequencing for Rapid

Diagnosis and Surveillance of Drug-resistant

Tuberculosis"

14

Level 1/2

POC Molecular Systems

• Limited AMR menu at present

• Price points/ease of use not yet suitable

3. Fever Programme at FIND

Problem statement - AFI

~655 M cases of fever/yr in children in Africa (Gething et. al. 2013)

• ~182 M of these children with fever present to health facilities/yr

• 43% are malaria 94 M w/ non-malarial fever seek care in Africa

Fever studies in Africa and South East Asia have highlighted

the diversity of pathogens (Acestor et. al. 2012, Mayxay et. al. 2013,

Mueller et. al. 2014, D’Acremont et. al. 2015)

The lack of diagnostic guidance results in overuse of abx(Yebyo et. al. 2016)

Two broad diagnostic needs

1. Fever biomarker Abx or not?

2. Pathogen identification Esp. outbreak

surveillance

15

Fever: Current State-of-the-Art in Dx

CRP and PCT are used in HIC

• Data in LMIC are not compelling Problem specific to CRP/PCT, or more general

confounding factors?

Two commercial products in RDT format designed for use in HIC; focused on

HIC market opportunity

• FebriDx® (RPS, Sarasota, USA) – CRP + MxA

- Fair data in limited evaluations in HIC (AUC – 0.84)

- Requires fresh blood! Can only be field-tested

• ImmunoPOC™/ImmunoXpert™(MeMed, Carmel, Israel) – CRP + IP10 + TRAIL

- Good data in evaluations in HIC (AUC – 0.94)

Academic studies of several promising markers• HNL, HBP, IL-4, IL-8

• No data on performance in LMICs

• No ability to assess performance of multiple markers in combination without raw data from single population

16

Fever biomarkers – FIND workplan

• Netherlands grant – 2016-2019• TPP-driven development of a POC test using fever biomarker for clinical case management (abx or not?)

• Fever biomarker landscape analysis (FIND)• Several promising candidates with data from HIC academic studies

• Very few viable commercial products available

• None of the potential commercial options optimally tested in LMICs

• Biomarker meeting (WHO, FIND, MSF, ReACT)• Consensus on need to develop TPPs for Biomarker assays

• Consensus on need to test existing best-in-class markers in LMICs

• TPP for fever dx test based on biomarkers• FIND drafting final version with expert consensus

• Specimen bank• Evaluating global sites (>10) for participation in specimen bank for validation of new candidate fever

biomarkers

17

Connected Diagnostics Platform

The connected diagnostics platform (CDP) allows aggregation of data from multiple

Dx regardless of manufacturer.

18

CDx Platform – Web Portal

19

Connected Diagnostics - Partners

20

Thank you!

F

IND

/M

on

ne

rat

Children in the Thai-Burmese border region

EXTRA SLIDES

Molecular Testing Platforms

for use in

AMR Surveillance

Platform Detail

Attribute QIAsymphony® – QIAGEN®

AMR Menu C. difficile, VRE (vancomycin resistance), potential for menu

expansion on existing platform

Chemistry Standard real-time, multiplex level of up to 6 labeled targets/sample

Automation / Integration Sample prep, PCR assembly are automated on the same module;

manual transfer to real-time instrument automated interpretation of

results

Ease of use System not fully integrated; suitable for high complexity environment

Analytes Dual targets (both toxin A and B) for C. difficile detection.

Both type A and B vancomycin resistance targeted (vanA and vanB);

vanB detection could potentially result in false positives if harbored by

non-Enterococcus, but also an advantage if type B vancomycin

resistance is prevalent

TAT Longer than other molecular systems, but instrument throughput

allows the processing of up to 70 samples in a single run.

Equipment and reagent

resource requirements

Reagents must be shipped and stored frozen; lab infrastructure

required to maintain instrument and process waste

Est. cost (USD) >$200,000

Platform GeneXpert ® - Cepheid®

AMR Menu C. difficile, VRE (vancomycin resistance), MRSA, M. tuberculosis drug

resistance, Carbapenem resistance (CE marked only)

Chemistry Standard real-time, multiplex level of up to 6 labeled targets/sample

Automation / Integration Sample prep and PCR are automated and fully integrated; automated

interpretation of results

Ease of use System fully integrated; suitable for moderate complexity environment;

mfr. performs yearly calibration; external controls run separately from

patient samples per individual lab procedures

Analytes Single target (toxin B, tcdB) for C. difficile detection in one version of the assay,

additional assay version includes C. difficile virulence markers (cdtB and tcdC

D117)

Type A and B vancomycin resistance targeted (vanA and vanB) (type A only in

US); vanB detection could potentially result in false positives if harbored by

non-Enterococcus, but also an advantage if type B vancomycin resistance is

prevalent

SCCmec/attB junction, some assay versions include mecA and spaA; those

lacking mecA have the potential to score empty cassette MRSA strains as

MRSA

rpoB for MTB complex and rif. resistance

TAT Rapid run time, but throughput limited on single module versions. Higher

throughput modules of the platform exist, multi-module platforms are

random access.

Equipment and reagent resource

requirements

Reagents can be shipped and stored at room temp for some assays,

other require refrigeration.

Attribute NucliSENS easyQ® - bioMérieux ®

AMR Menu MRSA, Carbapenem resistance (KPC)

Chemistry Isothermal amplification, fluorescent probe detection, multiplex level

of at least 3 distinctly labeled targets

Automation / Integration Sample prep and PCR set-up are manual; software interpretation of

results

Ease of use System not fully integrated, user required to perform instrument

maintenance; suitable for high complexity environment

Analytes SCCmec cassette junction and the mecA gene

blaKPC gene

TAT 48 sample throughput, run time is comparable to most other

molecular platforms. However, hands on time longer and maximum

sample throughput is smaller than other comparable systems.





Est. cost (USD) $50,000

Platform Quidel® / LyraTM direct real-time PCR assays

AMR Menu C. difficile

Chemistry Standard real-time, multiplex level of 4 – 6 distinctly labeled targets

depending on real-time PRC platform used (SmartCycler® and 7500

up to 4, QuantStudioTM up to 6)

Automation / Integration Sample prep and PCR set-up and results interpretation are manual

Ease of use System not fully integrated, user required to perform instrument

maintenance; suitable for high complexity environment.

Crude lysate sample prep is simpler than other manual sample prep

reagents that purify nucleic acid; straightforward assembly of

reactions

Validation on multiple real-time PCR platforms provides flexibility to

end-user

Analytes Dual targets (both toxin A and B) for C. difficile detection.

TAT 96 sample format in kit, with reagents aliquoted to accommodate

blocs of 12 samples. Sample prep is more rapid than standard

nucleic acid purification systems; PCR thermal protocol faster than

comparable real-time PCR assays



Reagents stored 2 – 8 C; sample prep reagents stored at room temp;

lab infrastructure required to maintain instrument and process waste

Est. cost (USD) $65,000 - $80,000

Platform Quidel® / AmpliVue®


Chemistry Helicase dependent amplification, isothermal; multiplex level of up to

3 targets, possibly more

Automation / Integration Sample prep and amplification set-up and results interpretation are

manual

Ease of use System not integrated, but assay steps are simple and laboratory

does not require real-time PCR platforms; can use assay with general

laboratory equipment; suitable for moderate complexity environment.


reagents that purify nucleic acid; straightforward assembly of

reactions

Analytes Single target (toxin A) for C. difficile detection

TAT Single sample to result assay; crude lysis and amplification are rapid

if single sample throughput is all that is required



Reagents can be stored 2 – 8 C. Used consumables discarded as

biohazard waste

Est. cost (USD) Cost of consumable plus $2,500 - $5,000 in ancillary equipment

Platform Meridian Bioscience® / illumigene®


Chemistry LAMP, isothermal; multiplex level of up to 2 targets (each target is in a

separate module); ability to detect single target/module limits assay

menu

Automation / Integration Sample prep and amplification set-up and results interpretation are

manual

Ease of use System not integrated, but assay steps are simple (2 min hands-on

time); laboratory does require instrumentation provided by the mfr for

usage; suitable for moderate complexity environment.


reagents that purify nucleic acid; pre-made master mixes allow rapid

and straightforward assembly of reactions

Analytes Single target (toxin A) for C. difficile detection

TAT Rapid sample to result assay; crude lysis and amplification are rapid

and instrumentation accommodates up to ten samples at a time



Reagents can be stored at room temp

External controls stored at 2 – 8 C.

Est. cost (USD) $8,000

Platform Roche / LightCycler® 480

AMR Menu MRSA, VRE

Chemistry Standard real-time, multiplex level of up to 6 distinctly labeled targets

Automation / Integration Manual option for sample prep and reaction assembly; user loads

assembled PCR onto the LightCycler®; results interpreted by the

instrument software

Automated option, sample prep and PCR assembly are on the same

module; manual transfer to real-time instrument automated

interpretation of results

Ease of use System not fully integrated, however reagents are packaged in ready-

to-use format making manual reaction assembly straightforward

Manual and automated options of system provide lab with flexibility

based on throughput needs

Analytes Right extremity (RE) of the SCCmec/orfX junction for MRSA

vanA and vanB, vanB2/3 for VRE; vanB detection could potentially

result in false positives if harbored by non-Enterococcus, but also an

advantage if type B vancomycin resistance is prevalent

TAT Rapid thermal cycling (throughputs up to 30 samples) compared to

similar platforms; maximum sample throughput is lower than other

comparable systems.



Reagents can be stored frozen; lab infrastructure required to maintain

instrument and process waste


Platform Roche / cobas® 4800 system

AMR Menu MRSA/MSSA


Automation / Integration Sample prep and reaction assembly are on the sample module and

integrated with the real-time PCR instrument; user manually transfers

assembled PCR plate to the thermal cycler

Ease of use System integrated, reagents are load and go; system may not be

suitable for low sample throughput needs

Analytes Right extremity (RE) of the SCCmec/orfX junction for MRSA

cpe gene of Staphylococcus aureus (species-specific marker)

TAT Rapid turn around for up to 94 samples compared to other similar

integrated platforms



PCR reagents can be stored at 2 – 8C, extraction reagents at room

temp; lab infrastructure required to maintain instrument and process

waste


Platform ELITech

AMR Menu MRSA/MSSA


on Applied Biosystems® 7500

Automation / Integration Sample prep is automated on separate module; user manually

assembles PCR and loads onto the thermal cycler. User manually

exports results to a software application to interpret results

Ease of use System not integrated, user required to perform instrument

maintenance; suitable for high complexity environment

Hands on time is longer than comparable systems, other comparable

systems offer automated PCR assembly and module integration

Analytes Staphylococcus aureus ldh1 gene (species-specific marker) and

mecA gene (methicillin resistance); potential for false positive results

if mixed flora sample contains MSSA and MR-CoNS

TAT Turn around is standard for similar thermal cyclers and other systems

with the same level of automation.





Platform AdvanDx / XpressFISH®

AMR Menu MRSA (mecA, does not directly detect MRSA)

Chemistry PNA hybridization probes for FISH, multiplex level for FISH in general

is 2-3 distinctly labeled targets

Automation / Integration Manual process for sample fixation, probe hybridization and

microscopy

Ease of use Steps are relatively straightforward but require familiarity with

preparing slides and performing microscopic analysis. Additional

systems required to determine species.

Analytes mecA gene (methicillin resistance)

TAT Turn around is standard for similar FISH assays. Time savings comes

from eliminating blood culture work ups.



Reagents can be stored at 2 – 8C

Est. cost (USD) Cost of fluorescent microscope and ancillary lab equipment $15,000

- $100,000

Platform Great Basin Scientific / Portrait Analyzer


Chemistry Isothermal HDA of target nucleic acids; biotinylated oligonucleotides

binding to anti-biotin/HRP conjugates; colorimetric substrate within

macroarray , multiplex level of up to 64 distinct results

Automation / Integration Sample prep and amplification are automated and fully integrated;

automated interpretation of results

Ease of use System fully integrated; suitable for moderate complexity

environment; external controls run separately from patient samples

per individual lab procedures

Analytes Single target (toxin B, tcdB) for C. difficile

TAT Rapid run time, but throughput limited to one sample at a time.



Reagents can be shipped at room temperature and stored at 2 – 8C

for cartridges and room temp for extraction reagents

Est. cost (USD) Per CAP TODAY product guide, mfr provides instrument at no cost with

purchase of tests

Platform Luminex® / xTAG®

AMR Menu C. difficile, among a panel of gastrointestinal pathogens

Chemistry Standard PCR amplification followed by detection using xTAG®

technology, multiplex level is high up to 100 targets

Automation / Integration User performs manual pre-treatment of samples, followed by

automated nucleic acid extraction. The user manually assembles

PCRs and then transfers to analyzer; analyzer software interprets the

results

Ease of use System not integrated; suitable for applications where numerous

analytes tested at once in a single sample. Set up and execution

requires a great deal of hands on time.

Analytes Dual targets (both toxin A and B) for C. difficile (among analytes for

other panel members)

TAT Turn around is comparable to systems capable of similar multiplex

level.



Some assay components can be stored at 2 – 8C after first use, while

other components must be stored frozen


Platform Nanosphere / Verigene®

AMR Menu Carbapenem resistant Gram negative bacteria (among a panel of

target organisms)

Methicillin and vancomycin resistant Gram positive bacteria (among a

panel of target organisms)

C. difficile

Chemistry Standard PCR amplification followed by array hybridization using gold

nanoparticle conjugated oligos, multiplex level is high, up to at least 16

targets

Automation / Integration Automated and integrated where the , user loads instrument with assay

consumables and chemistry and adds sample to consumable; following

sample processing and PCR amplification, user transfers slide from test

cartridge to a reader; instrument software interprets results

Ease of use System integrated; suitable for moderate complexity environment

Analytes blaCTX-M, blaOXA-48, blaNDN, blaIMP, blaOXO-23, blaVIM, blaKPC (among analytes

for other panel members)

mecA, vanA, vanB (among analytes for other panel members)

C. difficile toxin A, B and binary toxin genes and a deletion in the tcdC

gene at nucleotide 117

TAT Turn around is more rapid than comparable systems capable of

similar multiplex level.



Amplification reagents stored frozen, extraction reagents stored at 2 –

8C


Platform BioFire® / FilmArray®

AMR Menu Carbapenem resistant Gram negative bacteria and methicillin and

vancomycin resistant Gram positive bacteria (among a panel of target

organisms)

C. difficile among panel of gastrointestinal pathogens

Chemistry Nested PCR and RT-PCR with fluorescent intercalation dye for

amplicon detection. Targets detected within array modules. Multiplex

level is high, up to at least 16 targets

Automation / Integration Fully integrated and automated; user loads sample and rehydrates

reagents on cartridge; this assembly subsequently loaded onto the

instrument; software provides results interpretation


Analytes blaKPC, mecA, vanA, vanB (among analytes for other panel members)

C. difficile toxin A, B genes

TAT Turn around is more rapid than comparable systems capable of

similar multiplex level.



Reagent cartridge shipped and stored at room temperature

Est. cost (USD) $50,000 - $100,000

Platform Hain Lifescience / FluoroType®

AMR Menu MRSA

Chemistry Standard real-time PCR using fluorescently labeled probes. Multiplex

level up to 2 distinctly labeled targets

Automation / Integration User performs manual extraction and PCR assembly. PCR plate

loaded into the real-time PCR instrument; software interprets results;

process not integrated.

Ease of use Lysis reagents and PCR reagents formatted as ready to use, thus

reduce some of the complexity associated with manual extraction and

PCR assembly

Analytes SCCmec-orfX junction; potential for false positives if strain is empty

cassette variant of MRSA (i.e. contains SCCmec insertion, but lacks

functional mecA gene)

TAT Turn around is comparable to similar real-time PCR systems and

assay workflows



PCR reagents stored frozen, extractions reagents stored at 2 – 8C

Est. cost (USD) $15,000 - $30,000 for instrument

Platform Hain Lifescience / GenoQuick®

AMR Menu MRSA

Chemistry Standard PCR followed by later flow hybridization to visualize PCR

products; multiplex level of at least 2 targets, more possible

depending on resolution of the lateral flow consumable

Automation / Integration User performs manual extraction and PCR assembly. PCR plate

loaded into standard thermal cycler; user then applies PCR product to

lateral flow consumable for assay readout.

Ease of use Manual process suitable for environment accustomed to molecular

testing. No specialized equipment is needed – any standard thermal

cycler will work as assay readout is a function of the consumable

provided by the mfr. However, other systems

Analytes SCCmec-orfX junction; potential for false positives if strain is empty

cassette variant of MRSA (i.e. contains SCCmec insertion, but lacks

functional mecA gene)

TAT Turn around is longer compared to similar manual PCR assay

workflows, however, no requirement for special real-time PCR platform

may be an acceptable trade off



PCR reagents stored frozen, other components stored at 2 – 8C.

Est. cost (USD) $10,000 - $25,000 for thermal cycler and ancillary equipment

Platform Hain Lifescience / DNA STRIP

AMR Menu MRSA, VRE, MDR-TB, XDR-TB, methicillin and vancomycin resistant Gram

positive organisms

Chemistry Standard PCR followed by manual hybridization reaction with colorimetric

assay readout. End-user manually interpret results based on

manufacturer’s instructions.

Automation / Integration Manual or semi-automated lysis and DNA amplification.

User performs manual hybridization reaction with colorimetric assay

readout

Ease of use Lysis reagents and PCR reagents formatted as ready to use, thus reduce

some of the complexity associated with manual extraction and PCR

assembly

System not integrated.

No specialized equipment is needed (for manual process; semi-automated

requires GenoLyse® instrument from mfr) – any standard thermal cycler

will work as assay readout is a function of the consumable provided by the

mfr. Potential for ambiguous results to confound interpretation or require

re-testing

Analytes SCCmec-orfX junction (lacks mecA detection on this test strip)

vanA, vanB, vanC1, vanC2/3 and Enterococcus species specific markers

katG, inhA, gyrA, rrs, embA, embB and embC and M. tuberculosis markers

mecA, vanA, vanB, vanC1, vanC2/3 among analytes for other panel

members

TAT Turn around is comparable to longer compared to similar manual PCR

assay workflows, however multiplex level is much higher

Equipment and reagent resource PCR reagents stored frozen, other components stored at 2 – 8C.

Platform BDTM / BD MAXTM

AMR Menu Multiple versions of MRSA or MRSA/MSSA

CRE

C. difficile


Automation / Integration Fully integrated and automated; user loads sample, reagent

cartridges and assay consumables on to the instrument; software

provides results interpretation


Analytes blaKPC, blaOXA-48, blaNDM

SCCmec cassette at orfX junction and mecA gene, some MRSA assay

versions include mecC gene and nuc gene as a S. aureus marker

C. difficile toxin B genes

TAT Turn around is longer than other fully integrated systems, but the

sample throughput is higher.



Reagent cartridge shipped and stored at room temperature


Platform Abbott / IRIDICA

AMR Menu Extensive panel of microbial pathogens, including methicillin,

vancomycin and carbapenem resistant organisms.

Chemistry Standard PCR followed by ESI/MS, multiplex level is extremely high

>700 targets

Automation / Integration Semi-automated, where user transfers between modules for

extraction, PCR and mass spec detection of amplicons; software

provides results interpretation

Ease of use System not fully integrated, suitable for high complexity environment

Analytes blaKPC, mecA, vanA, vanB (among analytes for other panel members)

TAT Turn around within one shift, but rapid considering the multiplex level



PCR reagents stored frozen, other reagents and consumables at room

temperature or refrigerated.


diagnostic needs in antimicrobial resistance · find: ten years of advancing diagnostics 2 sleeping...

Documents