© 2018 Mayo Foundation for Medical Education and Research

A New E-POC-h for the Lab:Changing Paradigms for Microbiology

Robin Patel, M.D.Professor of Medicine and Microbiology

Mayo Clinic, Rochester MNpatel.robin@mayo.edu

Conflict of Interest Disclosure I am a member of an Advisory Board, consultant or equivalent with a commercial organization.

Company/OrganizationCuretis, Qvella, St. Jude, Beckman Coulter, Morgan Stainley, Heraeus Medical GmbH, CORMATRIX, Specific Technologies, Diaxonit, Selux Dx,

GenMark Diagnostics, LBT Innovations Ltd, PathoQuest and Genentec

DetailsMonies are paid to Mayo Clinic

I have received a grant(s) from a commercial organization paid to me or to my institution.Company/OrganizationCD Diagnostics, BioFire, Curetis, Merck, Hutchinson Biofilm Medical Solutions, Accelerate Diagnostics, Allergan, and The Medicines Company

I have received an honorarium from a commercial organization.Company/OrganizationNBME, Up-to-Date and the Infectious Disease Board Review Course

I hold a patent for a product referred to in the CME/CPD program or that is marked by a commercial organization.Company/OrganizationDr. Patel has a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by

Samsung to Mayo Clinic, and a patent on an anti-biofilm substance issued.

I am currently participating in or have participated in a clinical trial.Company/OrganizationRAPIDS/GN

DetailsAccelerate Diagnostics

Objectives• By the end of this session, participants

should be able to: • Summarize American Academy of Microbiology’s

Report on POC Testing in Microbiology: “Changing Diagnostic Paradigms for Microbiology”

• Identify key considerations relevant to Canadian microbiology laboratories

© 2018 Mayo Foundation for Medical Education and Research

www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology

COLLOQUIUM STEERING COMMITTEE

Melissa B. Miller, Ph.D. Chair University of North Carolina at Chapel Hill

Karen C. Carroll, M.D.

Johns Hopkins University School of Medicine

Nathan A. Ledeboer, Ph.D.

Medical College of Wisconsin

Kenneth Bahk, Ph.D.

Three Lakes Partners

Keith Klugman, M.D., Ph.D.

Bill and Melinda Gates Foundation

PARTICIPANTS

Edina Avdic, PharmD, M.B.A

The Johns Hopkins Hospital

Nancy E. Cornish, M.D.

Centers for Disease Control and Prevention

Jeanne Mumford, M.T. (ASCP)

Johns Hopkins Medicine

Tobias Barker, M.D.

CVS Health

Scott Cunningham, M.S., M.T. (ASCP), S.M.

Mayo Clinic

Daniel D. Rhoads, M.D.

Case Western Reserve University

Steve Beuchaw, M.B.A.

Morgan Stanley

Charlotte A. Gaydos, M.S., M.P.H., Dr.P.H.

Johns Hopkins University

Kristian Roth, Ph.D.

Food and Drug Administration

Carey-Ann Burham, Ph.D.

Washington University at St. Louis

School of Medicine

Albeto Gutierrez, Ph.D.

Food and Drug Administration

Paul Schreckenberger, M.S., Ph.D.

Loyola University Chicago

Sheldon Campbell, M.D., Ph.D.

Yale School of Medicine

Alexander J. McAdam, M.D., Ph.D.

Boston Children’s Hospital

Fred C. Tenover, Ph.D.

Cepheid

Dan Wattendorf, M.D.

Bill and Melinda Gates Foundation

ACADEMY STAFF ASM Leadership

Marina Moses, M.S., Dr.P.H.

Director

Isabel Hinestrosa

Board of Governors Program Assistant

Stefano Bertuzzi, Ph.D, M.P.H.

Chief Executive Officer

Virginia Dolen

Program Manager

Daniel Peniston

Colloquium and Outreach Program Assistant

Rationale• Low-complexity, rapid, accurate infectious diseases

diagnostics performed on demand close to patient• Deliver timely results to inform diagnosis & treatment

• Near-patient/point-of-care testing increases access to efficient diagnostic testing across many settings• Rapidly advancing field

• Clinical Laboratory Improvement Amendments (CLIA)-waived NAATs performed outside of laboratories by non-laboratorians produce equivalent results to more-complex, gold standard laboratory assays

American Academy of Microbiology Colloquium Report

1. Reviews characteristics & applications of near-patient and POC tests for infectious diseases

2. Provides overview of considerations pertaining to their implementation, oversight, & evaluation

3. Provides recommendations

Statement of Task• Examine role near-patient testing & impact on changing diagnostic paradigms • Tests may detect identify causative organisms, biomarkers, distinguish viral vs bacterial infections, determine strain type, provide resistance information

• Automation, simplification, miniaturization ® performance outside labs • Innovative developers & financial community leveraging technology • Microbiology oversight & PT ensure tests conducted correctly & results

reported appropriately• Maintain personnel with adequate clinical microbiology expertise to assist with

decision support & performance of advanced testing • Address distribution between centralized labs & POC locations

Vocabulary• Waived testing – FDA designation diagnostic assays

deemed to be simple to perform, insignificant risk of erroneous result, reduced regulatory oversight…often performed outside lab

www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatoryAssistance/ucm393229.htm

• Nonwaived testing – FDA designation tests moderate or high complexity…performed in lab inspected by regulatory agency

• Near-patient testing – Imprecise term testing (waived or nonwaived) performed in close proximity to patients, either at POC or nearby area; typically short turnaround times & results guide immediate medical management

Point-of-Care TestingSample Definitions

• “…designed to be used at or near site where the patient is located, do not require permanent dedicated space, and are performed outside physical facilities of clinical laboratories”

www.cap.org/apps/docs/education/OnlineCourseContent/2012/LAP/Resources/Checklists/POC09252012.pdf

• “…will result in clear and actionable management decisions such as when to start treatment or to require a confırmatory test, within same clinical encounter”

Pai M et al. 2015. Microbe 10:103–7

Types of Tests• M. tuberculosis, influenza & other respiratory viruses, S.

pyogenes, C. trachomatis, N. gonorrhoeae• Antigen tests (commonly lateral-flow assays)

“…in general, lower sensitivity and specificity than nucleic acid-based tests…”

• Nucleic acid amplification tests“…may not identify clinically relevant infections (some cases)…risk contamination during nucleic acid extraction or carryover of previously amplified material, including vaccines…leakage test cartridges…performance may be impacted by mutations in RNA/DNA sequences - false negative…”

20 Minute POC Organism-Specific PCRCobas® Liat (Roche)

• Influenza A/B ± RSV, Streptococcus pyogenes• Swab used to collect specimen ® placed in liquid medium• Liquid pipetted into reaction container• Barcode scanned• Reaction container placed into instrument

Patel and Karon. J Clin Microbiol 2017;55:1984-8Uhl and Patel. J Clin Microbiol 2016:54:815

Courtesy of Roche

8-15 Minute POC Organism-Specific NAATAlere™ i Influenza A & B, Alere™ i RSV, Alere™ i Strep A

NEAR technology (Nicking Enzyme Amplification Reaction)

Courtesy of Alere

Boehme et al. N Engl J Med 2010;363:1005-15www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology

Large Multiplex “Syndromic” Panels

© 2018 Mayo Foundation for Medical Education and Research

FilmArray® Respiratory Panel EZ (RP EZ)• Viruses:

• Adenovirus, Coronavirus, Human Metapneumovirus, Human Rhinovirus/Enterovirus, Influenza A, Influenza A/H1, Influenza A/H3, Influenza A/H1-2009, Influenza B, Parainfluenza Virus, Respiratory Syncytial Virus

• Bacteria:• Bordetella pertussis, Chlamydophila pneumoniae,

Mycoplasma pneumoniae

FDA-Approved Multiplex Respiratory Panels

Ramanan et al. Clin Microbiol Rev 2018;31:1-28

Parameter FilmArray Verigene x-TAG RVP x-TAG RVP FAST NxTAG-RPP eSensor RVP ePlex

Analysis platform FilmArray system or FilmArrayTorch

Verigene system Luminex 100/200 Luminex 100/200 Luminex MAGPIX eSensor ePlex system

Acceptable specimens NP swab NP swab NP swab NP swab NP swab NP swab NP swabNumber of targets 20 16 12 8 20 14 17PathogensVirusesAdenovirus ü ü ü ü ü ü(differentiates B/E from C) üCoronavirus üCoronavirus HKU1 ü üCoronavirus NL63 ü üCoronavirus 229E ü üCoronavirus OC43 ü üHuman bocavirus üHuman metapneumovirus ü ü ü ü ü ü üInfluenza A ü ü ü ü ü ü üSubtype H1 ü ü ü ü ü ü üSubtype H3 ü ü ü ü ü ü üSubtype 2009 H1N1 ü ü ü

Influenza B ü ü ü ü ü ü üParainfluenza 1 ü ü ü ü ü üParainfluenza 2 ü ü ü ü ü üParainfluenza 3 ü ü ü ü ü üParainfluenza 4 ü ü ü üRespiratory syncytial virus ü üRespiratory syncytial virus A ü ü ü ü üRespiratory syncytial virus B ü ü ü ü ü

Rhinovirus/enterovirus ü ü ü ü ü ü üBacteriaChlamydophila pneumoniae ü ü üMycoplasma pneumoniae ü ü üBordetella pertussis ü üBordetella parapertussis/Bordetella bronchiseptica üBordetella holmesii üThroughput Scalable Low Medium Medium High Medium ScalableTime to result 1 hour ~2-3 hours ~8 hours ~6 hours ~4 hours ~6 hours ~1.5 hours

The acceptable specimen type for all panels is nasopharyngeal swab. RVP, respiratory virus panel; RPP, respiratory pathogen panel.

CuretisUnyvero Lower Respiratory Tract Panel

Courtesy of Curetis

FDA-Approved Multiplex Gastrointestinal Panels

Ramanan et al. Clin Microbiol Rev 2018;31:1-28

Verigene EP Luminex GPP BioFire GIPAnalysis platform Nanosphere Verigene System MAGPIX or Luminex 100/200 System FilmArray system or FilmArray TorchAcceptable specimens Stool in Cary Blair Fresh stool or in Cary Blair Stool in Cary BlairNumber of targets 8 14 22PathogensBacteriaCampylobacter species ü ü üSalmonella species ü ü üShigella species/Enteroinvasive E. coli ü ü üVibrio species ü ü üYersinia enterocolitica ü üEscherichia coli 0157 ü üEnterotoxigenic E. coli ü üEnteropathogenic E. coli üEnteroaggregative E. coli üPlesiomonas shigelloides üToxinsstx1/stx2 (Shiga toxin-producing E. coli) ü ü üClostridium difficile (toxin A/B) ü üVirusesNorovirus GI/GII ü ü üRotavirus A ü ü üAstrovirus üAdenovirus 40/41 ü üSapovirus üParasitesCryptosporidium species ü üEntamoeba histolytica ü üGiardia lamblia ü üCyclospora cayetanensis üThroughput Scalable (1-32) 24 Scalable (1-12)Time to result < 2 hours ~5 hours ~1 hour

FDA-Approved Multiplex PCR Assay for Spinal FluidFilmArray Meningitis/Encephalitis PanelViruses Bacteria Fungi Features

Cytomegalovirus Escherichia coli K1 Cryptococcus neoformans/gattii

Acceptable specimens: CSF

Enterovirus Haemophilus influenzae Throughput: 1

Herpes simplex virus 1 Listeria monocytogenes Time to results: ~1 hour

Herpes simplex virus 2 Neisseria meningitidis

Human herpes virus 6 Streptococcus agalactiae

Human parechovirus Streptococcus pneumoniae

Varicella zoster virusLiesman et al. J Clin Microbiol 2018;56:e01927-17

Syndromic Panels• Thoughtfully developed

• Clinical utility each pathogen considered • Sensitivity & specificity may vary between panels &

individual molecular tests• Concern about indiscriminate deployment, when

nuanced approach to testing needed• Professional judgment may be required to determine

when panel approach warranted & to interpret results

Laboratory Testing for Infectious Causes of Diarrhea

Ramanan et al. Clin Microbiol Rev 2018;31:1-28

Syndromic Panel Considerations Pharyngitis

• Most common bacterial cause acute pharyngitis = Streptococcus pyogenes (GAS)® Antibiotic

• Other causes• Groups C & G streptococci, Mycoplasma pneumoniae, viruses,

Fusobacterium necrophorum

• Testing for multiple targets simultaneously could allow more rapid determination of cause of pharyngitis• Initiate antibiotic treatment for GAS; or• Inform patient infected by agent for which antibiotics not warranted

Benefits• Provide information quickly, allowing provider to make

treatment decision when patient seen (rather than requiring follow-up visit)

• In regions where infectious diseases testing unavailable, provide information to inform diagnosis and treatment

• Improve healthcare facility use (reduced patient wait time, resources to follow up on laboratory-based results)

• Decrease exposure to other contagious patients• Home-collected specimens, obviate office/ED visit • Increase patient satisfaction

New Tests and Technologies• Field rapidly advancing ® Future tests faster• Tests read by instrument, interfaced (¯’d interpretative errors, data

sharing)• Patient data

• As locations of care diversify & patients tested in different settings, patients may gain control of curating their EHR, perhaps in “cloud”, shared across providers

• Targets of interest• US: STIs, pharyngitis, UTIs (infection vs non-infection), CAP (viral vs bacterial)• Global: TB, HIV, malaria

• Developing countries• Access to same high-quality testing as developed countries• Call for ‘Model List of Essential Diagnostics’, similar to Model List of

Essential Medicines maintained by WHO, to include POC testsSchroeder et al. N Engl J Med 2016; 374:2511-2514

• Future: Detailed information (resistance, quantification), host biomarkers, microbiome to monitor health & predict disease risk

Diversity of Target Product Profiles, Users, and Settings Within Spectrum of POC testing

www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology

Community Pharmacies• Vaccinations, POC tests• >5% laboratories certificate of waiver ® pharmacies• Physician-pharmacist collaborative practice agreement

(CPA) delegate prescriptive authority to pharmacists for treatment of infectious diseases based on CLIA-waived tests

• Potential of POC tests in pharmacies to decrease inappropriate antibiotic usage in outpatient setting & increase patient satisfaction

Enable In-Home Testing• Patients could collect their own samples at home and either bring

specimen to laboratory or run test at home• In-home antibody tests for HIV in saliva results in 20 min

(http://www.oraquick.com/)• FDA-cleared in-home sample collection kits for HIV & hepatitis

C from fingerstick blood ® mail to lab• GAS, gonorrhea, chlamydia, influenza likely available soon

• Recommendations• Clear and concise sample collection instructions • Specific in-home collection kits for ease sample collection

Patients can Collect Own Throat Swabs

N pairs% Positive

% Concordant(95% CI)

HCW-/Self-Collection ResultsConcordant Discordant

Healthcare Worker

Self P-value - / - + / + + / - - / +

OVERALL 402 33.3 34.3 0.41 94.0 (91.3, 96.0) 254 124 10 14

First swab: Self 203 35.0 36.0 0.53 95.1 (91.2, 97.3) 126 67 4 6

First swab: Healthcareworker

199 31.7 32.7 0.59 93.0 (88.5, 95.8) 128 57 6 8

Murray et al. J Clin Microbiol 2015;53:573

Shifting Patient Flow/Reorienting Specimen Collection• Clinical workflow needs to allow quick testing & result reporting

• Convenient care clinics - <20 minutes

• Redesign workflow to realize benefits • Shift patient flow and reorient specimen collection• Begin with specimen collection ordered through triage mechanism based

on symptoms, nurse-initiated provider orders• Specimen collection at home & testing performed in clinic, ED or off-site

diagnostic testing laboratory• Telemedicine - testing performed at home, with results sent electronically

for secure interpretation and linkage to care • Results available before healthcare provider sees patient

• Prescription of antibiotics - more-directed therapy, antimicrobial stewardship

How Fast is Fast Enough?• Impact of 90-min Xpert CT/NG test

• Sample collection on patient arrival

• Only 21% patients received results before leaving• 48 min sample collection to clinical consultation

• Test turnaround time >30 min ineffective

Harding-Esch et al. Sex Transm Infect. 2017;93(6):424-9.

How Long Will Patients Wait?• Prospective cohort study• 1,356 patients - questionnaire - ?max time willing to wait

CT/NG results• 26% unwilling to wait 20 min• 129 patients tested positive

• 20 min test - immediate treatment 72% positive patients• 90 min test - immediate treatment 3% positive patients

Atkinson et al. Int J STD AIDS. 2016;27:650-5

Rapid Influenza Tests in ED

• US EDs (National Hospital Ambulatory Medical Care Survey)

• 4.2 million visits

• 42% influenza diagnoses - rapid tests

• Fewer ancillary tests (45% vs 53% visits),

• Fewer antibiotic prescriptions (11% vs 23%)

• Increased antiviral use (56% vs 19%)

Blaschke et al. Pediatric Infect Dis Soc. 2014;3:112-8

Routine POC Testing Respiratory Viruses In Adults:Open-label, Randomized Controlled Trial

• Pragmatic, parallel-group, open-label, randomized controlled trial

• 24 h of presentation to ED or acute medical unit, large UK hospital with acute respiratory illness and/or fever >37.5°C

• 720 subjects: Molecular POC test for respiratory viruses vs routine care

• ¯ Mean LOS

• POC (5.7 days [SD 6.3]) vs control group (6.8 days [7.7]); p=0.0443

• ­ Appropriate antiviral treatment of influenza-positive patients

• POC (52/57 [91%]) vs control group (24/37 [65%]); p=0.0026

• = Mean duration of antibiotics

• 301/360 (84%) POC group received antibiotics vs 294/354 (83%) controls Brendish et al. Lancet Respir Med. 2017;5:401-11.

Guidelines for Clinicians•Order appropriate tests• POC test preferable to

laboratory-based assay?•Result interpretation•Results in lab results section EMR

Performance Limitations• POC tests should exhibit performance similar to

equivalent laboratory-based tests• Limitations each test understood & acknowledged • Providers aware of adverse outcomes from improper

interpretation • Consider pretest probabilities of result & therefore positive predictive

value of test in specific settings

• High analytical sensitivity ® positive results due to contamination or colonization

Engineering Controls• Vital to ensure POC tests perform accurately,

reproducibly• Removing test from laboratory removes analysis

and “troubleshooting” by experienced personnel® Engineering controls needed

• Concern that controls might not be adequate in current format & that tests should be able to employ simple checks, such as inhibition controls

Reevaluation Over Time• Periodic reevaluation - disease epidemiology

changes from changing vaccination practices, emerging infections, evolving resistance, new medical and surgical interventions, etc., alongside rapid evolution of microorganisms

• Mechanism for post-approval surveillance of waived devices and removal of poorly performing POC tests from market needed

Patel and Karon. J Clin Microbiol 2017;55:1984-8

Oversight• Testing personnel without specific laboratory medicine

training, may not be accustomed or required to perform PT, quality assurance

• Potential for misuse, incorrect performance, misinterpretation of tests, especially as tests extend to nontraditional settings

• Chemical and biological safety standards• Clinical microbiology laboratory expertise should remain

component of oversight of near-patient & POC tests

Clinical Microbiology Laboratory• Additional staffing models/support to oversee competency, PT, quality• New staffing models may result in laboratory technologists transitioning from

performing testing to overseeing tests performed outside laboratory• New type of healthcare worker certified in POC testing• Most large facilities employ clinical laboratory scientists as POC coordinators • AACC: Point-of-Care Specialist certificate program• Develop specific training, with input from clinical microbiology laboratory

experts, regarding competency & PT• Central laboratory should remain responsible for monitoring environmental

contamination when NAATs used to decrease problems with false-positive results• “Swipe testing”

Oversight in Small Physician-Run Laboratories, Nonmedical Settings

• Routine oversight by clinical microbiologists unavailable• Consultants or part-time staff to review POC testing

• “Self-monitoring” electronic system that assess results from POC tests, alerts when results outside baselines

• Competent personnel review results on regular basis to ensure rapid action initiated if anomalies identified

• Site personnel monitor contamination, with consultant staff aiding with interpretation/decontamination as needed

Public Health• Reduce spread disease (reduced time to

treatment)• Reporting to public health, ideally automatically• Outbreak recognition – easier or harder?

• POC users may need to collect another specimen for public health • How? Who will pay?

• If test results sent to central repository, increase in data flow may

Data• Results linked to EMR if possible or made

accessible to patient’s provider(s)• Responsibility of test manufacturer

• Patients - increased ownership healthcare data• IT solutions to link databases to allow

portability of results

RecommendationsImplementation Oversight Evaluation• Redesign clinic workflows to

incorporate near-patient and POCtesting

• Maintain clinical microbiology laboratory expertise and oversight of infectious disease testing

• Conduct clinical outcomes and cost-effectiveness studies for near-patient and POC tests

• Promote proper interpretation of tests to avoid adverse outcomes

• Utilize competent personnel to oversee ordering, testing, and interpretation

• Evaluate near-patient and POC tests periodically and undertake regulatory action or reclassification for tests that do not meet performance standards

• Provide resources, such as training videos, to support appropriate self-collection of patient specimens

• Educate providers and patients on different types of tests

• Ensure that public health surveillance of infectious diseases is maintained

• Link near-patient and POC test results to patient’s electronic medical record (EMR)

Conclusions• Rapidly evolving field• CLIA-waived NAATs - performance characteristics similar to

standard laboratory assays• Unclear impact on patient outcomes, healthcare delivery models,

public health, health-care costs • Outcomes studies needed• Role clinical microbiology laboratories changing

• Expertise needed to ensure oversight of test selection, quality assurance, competency, PT, utilization, interpretation

• Integrate POC tests into electronic systems; automated quality monitoring