Forum on Culture-Independent Diagnostics: Charting a Path for Public Health

Transcription

1 Forum on Culture-Independent Diagnostics: Charting a Path for Public Health Selected Slides John Besser CDC Enteric Diseases Laboratory Branch NCEZID/DFWED The findings and conclusions in this presentation are those of the author and do not necessarily represent the views of the Centers for Disease Control and Prevention

2 Institutions Represented Government Non-governmental organizations International partners Medical device industry Commercial laboratories Healthcare institutions Professional societies Academic institutions

3 Forum Goals Raise awareness Define the issues Stimulate applied research Start building consensus Initiate post-meeting actions

4 Bacterial Culture

5 Rapid ( Culture-Independent ; Non- Culture )Tests (Pictures of commercial products removed)

6 Crisis Danger + Opportunity

7 Forum on Culture-Independent Diagnostics: Charting a Path for Public Health Danger: Threats to infectious disease surveillance programs Opportunity: Potential solutions; benefits of action

8 Rapid / Culture-Independent Tests versus Culture

9 Rapid / Culture-Independent Tests versus Culture Culture or standard tests (e.g. microscopy) Rapid/culture independent tests Sensitivity Gold standard Low to high Specificity Interpretation of positive findings Range of pathogens detected Allows for susceptibility testing & genotyping? High Usually straightforward All pathogens allowed by growth or test conditions Yes Low to high, almost always different Significant issues Limited to specific pathogen tested Generally no

10 Demise of GC Culture Rapid NAA test: Fast (hours) Urine specimen (vs urethral swab) Includes Chlamydia trachomatis High sensitivity No susceptibility data Specimen incompatible with culture Expensive Some concerns about false positives

11 Medical reasons for laboratory testing Appropriate treatment Prevent unnecessary treatment or procedures

12 Public health reasons for surveillance / outbreak investigation Limit transmission Control underlying problems Monitor trends informed policy development

13 Impacts Patient Management Public Health Programs Requiring accurate case counts Isolate-requiring

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16 Impacts Patient Management Public Health Programs Requiring accurate case counts o Burden o Attribution o Trends Isolate-requiring

17 Estimates of Foodborne Illness

18 Cases per 100,000 persons Variability in diagnostic test performance Incidence of STEC infections in FoodNet, : 60 (36%) of 184 broths sent public health laboratories could be confirmed as Shiga toxin-positive Culture-confirmed STEC + all additional Shiga toxin-positive broths Culture-confirmed STEC + additional Shiga toxin-positive broths confirmed at Public Health Lab All culture-confirmed STEC

19 Impacts Patient Management Public Health Programs Requiring accurate case counts Isolate-requiring o Subtype-based tracking programs o Susceptibility monitoring o Subtype-based attribution studies

20 Selected Microbial Disease Agents Under Agent Public health surveillance Isolate significance Salmonella spp. Subtype, AST ++++ Shigatoxin-producing E. coli Subtype, AST ++++ Listeria monocytogenes Subtype, AST ++++ Mycobacterium tuberculosis Genotype, AST ++++ Bordetella pertussis AST +++ Neisseria meningitidis Subtype, AST +++ Legionella pneumophila Subtype (outbreaks) ++ Influenza virus Serotype, AST ++ Neisseria gonorrhea AST + Methicillin-resistant Staphylococcus aureus Surveillance Subtype (outbreaks) + Cryptococcus neoformans AST?

21 Global Meat Trade Source: Center for Global Food Issues

22 Incidence per 100,000 population Nationwide reporting began in 1912 Reported Salmonella infections in the United States, Typhoid Fever Non-typhoid Salmonellosis CDC, National surveillance data National salmonella serotype surveillance Years

23 number Salmonellosis Cases Minnesota; June October Salmonella spp. Salmonella Enteritidis

24 Incidence per 100,000 population Nationwide reporting began in 1912 Reported Salmonella infections in the United States, Typhoid Fever Non-typhoid Salmonellosis CDC, National surveillance data National salmonella serotype surveillance Years

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26 PulseNet/VetNet Electronic Communication State and Local Public health laboratories State Departments of Agriculture PFGE patterns (~50,000/yr to PulseNet) National databases E. coli pathogens Salmonella sp. and Campylobacter spp.

27 Pathogen Specific Surveillance

28 Exploiting the True Potential of Agent- Based Surveillance Informational trace-backs Enhanced exposure-gathering, laboratory, communication, and analysis methods

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31 Current PulseNet Methods (PFGE and MLVA) are Isolate-Dependent (Note: so is whole genome sequencing, and most other methods being considered)

32 Hazards of Inaction

33 O104 H4,templateId=raw,property=publicatio nfile.pdf/ehec_o104_h4.pdf

34 Crisis Danger + Opportunity

35 Successful Adaption to Culture Demise

36 General Strategies to Address Issue Short-term: Preserve isolates Longer-term: Develop cultureindependent pathogen characterization methods Very long-term: paradigm shifting technologies

37 Tomorrow s Breakout Sessions Short term Longer term Very long term A. Regulatory and Device Industry Strategies B. Clinical and Public Health Practice C. Strategies (1) including cultureindependent pathogen characterization assay development D. Strategies (2) same as (1) plus susceptibility surveillance E. Novel approaches, known but unproven technologies or processes

38 Reflex Culture Follow-up culture automatically initiated when positive culture independent-based laboratory test results are observed. (possible when the specimen collected is compatible with culture)

39 Short-term: Preserve isolates Work with medical industry to make new tests compatible with public health needs Change criteria for medical device licensure? Make reflex culture reimbursable? Modify State reporting rules Develop isolate recovery capacity for PHLs Sentinel culture-based surveillance?

40 Longer-term: Develop culture-independent pathogen characterization methods Identify ID/subtype/virulence targets for direct molecular detection New testing strategies (Point-of-care? Public health labs? Reference labs?) Develop global consensus

41 Bacteria in Human Stools Up to bacteria/ml; ~500 species Bacteroides fragilis Clostridium putrificum Streptococcus sp. (S. equinus) Bacteroides vulgatus Clostridium sp. (C. cadaveris) Streptococcus sp. (S. pyogenes) Bacteroides eggerthii Clostridium difficile Enterococcus faecalis Bacteroides sp. (B. fragilis) Eubacterium tenue Enterococcus gallinarum Bacteroides sp. (B. thetaiotaomicron) Clostridium bifermentans Lactobacillus acidophilus Bacteroides sp. (B. vulgatus) Clostridium sp. (C. sordellii) Weissella kandleri Bacteroides sp. (B. eggerthii) Peptostreptococcus (P. anaerobius) Lactobacillus fermentum Bacteroides sp. (B. uniformis) Fusobacterium nucleatumd Vagococcus fluvialis Cytophaga xylanolytica Eubacterium plautii Bifidobacterium infantis Bacteroides distasonis Eubacterium sp. (E. cylindroides) Bifidobacterium dentium Bacteroides sp. (B. distasonis) Streptococcus sanguis Bifidobacterium sp. (B. longum) Clostridium oroticum Streptococcus oralis Bifidobacterium adolescentis Clostridium sp. (C. nexile) Streptococcus intermedius Bifidobacterium pseudolongum Ruminococcus hansenii Lactococcus lactis subsp. cremoris Escherichia coli Ruminococcus productus Streptococcus sp. (S. mitis) Carnobacterium divergens Eubacterium ventriosum Leuconostoc lactis Lactobacillus maltaromicus Clostridium sp. (C. clostridiiforme) Streptococcus sp. (S. bovis) Salmonella sp. (S. typhi) Clostridium histolyticum Streptococcus sp. (S. equi subsp. equi) Enterobacter sp. (E. aerogenes) Clostridium sp. (C. beijerinckii) Streptococcus mutans Serratia sp. (S. marcescens) Clostridium sp. (C. butyricum) Streptococcus sp. (S. sanguis) Proteus sp. (P. vulgaris) Clostridium sp. (C. perfringens) Streptococcus sp. (S. salivarius) Klebsiella sp. (K. pneumoniae)

42 Culture-Independent Subtyping/Virulence Assays: Targets Conserved primer sites Variable primer site train/species A B characterize Variable region Scoring Allele -Different sequence -Different size (MLVA) Presence/Absence -Amplicon produced -No amplicon C

43 Opportunities Faster results (better exposure recall, faster intervention) Wider understanding of disease causation Opportunity for global consensus on new methods

44 Opportunity for Global Consensus

45 The Surveillance Process Laboratory Reporting Takes Time Patient Eats Contaminated Food Stool Sample Collected 1 3 days Contact with health care system: 1 5 days Diagnosis: 1 3 days Shipping: 0 7 days Patient Becomes Ill Salmonella Identified Public Health Laboratory Receives Sample Serotyping & DNA fingerprinting: 2 10 days Case Confirmed as Part of Outbreak

46 Cladistic Methods -- More Flexible Case Definitions

47 Virulence Factors in Shiga toxin-producing E. coli (STEC) Virulence factor Gene Location Shiga toxin (stx) Intimin (eae) Enterohemolysin (EhxA, HlyA) Non-LEE effectors (nle) Saa adhesin Subtilase More (STEC autoagglutinating adhesin) Phage PAI (LEE) Plasmid (po157) PAI s Plasmid Plasmid Courtesy of P. Gerner-Smidt

48 STEC Detection and Genotyping Assay Targets and timeline for assay development O26 O103 O45 O91 O103 O111 O113 O121 O128 O145 O157 H2 H7 H8 H11 H19 H21 H25 H28 stx1 stx1a stx1b stx2 stx2a stx2b stx2c stx2d stx2e stx2f stx2g stx2h LEE Z5110 eae OI-122 Z4321 Mod 1 OI-122 Z4326 Mod 2 OI-122 Z4332 Mod 3 OI-122 Z4333 Mod 3 ehx espp katp cldt subab saa iha SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP ID phoe ID rpob/ uida Summer 2011 Fall 2011 Fall 2012

49 Culture-Independent Subtyping/Virulence Assays: Potential Issues Sensitivity Different assays needed for each pathogen? Suitable targets may not exist for all pathogens

50 (human disease monitoring portion) GISP-like sentinel surveillance? Combination of molecular screening and sentinel surveillance?

51 Very Long-term: Paradigm-shifting Technologies or Processes Single cell isolation and sequencing; mass MS screening, others? Metagenomics Other ways of conducting surveillance and outbreak detection?

52 Metagenomic Approach Sequence selected targets (e.g. 16S, 18S rrna) Deep sequencing (all genetic material in sample) Assemble and identify contigs Extract and analyze sequences of interest

53 Etiology of Acute Gastroenteritis in the U.S. unknown 82% viruses 67% Total Cases known agents 18% parasites 3% bacteria 30% Known Etiology

54 What is Being Done? This Meeting Workgroups (CDC, APHL, CSTE) CDC Genomics project DTRA/DOD/CDC Metagenomics project Much more needed

55 Summary: Culture Independent Diagnostics Impact High probability, high impact issue Risks of inaction and benefits of change are significant

56 CULTURE-INDEPENDENT DIAGNOSTICS FORUM: MEETING PLANNING WORKGROUP Marc Allard Robyn Atkinson John Besser Cheryl Bopp Brenda Brown Eric Brown Al Demaria Michael Farrell Patricia Fields Collette Fitzgerald Peter Gerner-Smidt Jane Getchell Patricia Griffin Thomas Hammack Vincent Hill Kristin Holt Tim F. Jones Maria Karlsson Patrick Kwan Hugh Maguire Barbara Mahon Beth McGlinchey Stephen Morse Steven Musser Michele Parsons Efrain Ribot Shari Shea Kirk Smith Nancy Strockbine Deborah Talkington Cheryl Tarr Robert Tauxe Eija Trees Jean Whichard Ian Williams