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

Transcription

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

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3 Forum on Culture- Independent Diagnostics: Charting a Path for Public Health April 25-26, 2012; Atlanta, GA Sponsored by CDC, APHL, and CSTE

4 Bacterial Culture

5 Rapid ( Culture-Independent ; Non-Culture )Tests

6 Rapid / Culture-Independent Tests versus Culture

7 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

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10 Demise of GC Culture Rapid (hours) Urine specimen (vs urethral swab) Includes Chlamydia trachomatis High sensitivity/specificity No susceptibility data Specimen incompatible with culture Expensive

11 Private Health

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

13 Estimates of Foodborne Illness

14 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

15 Culture-Independent Diagnostics: Burden, Attribution, Trends Understand extent of issue Study test performance Redefine case definitions

16 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

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

18 Global Meat Trade Source: Center for Global Food Issues

19 Lopez AD, Mathers CD, Ezzati M, Jamison DT, Murray CJ. Global and regional burden of disease and risk factors, 2001: systematic analysis of population health data. Lancet May 27;367(9524): Global Mortality (low and middle income countries)* 1.Heart disease 2.Stroke 3.Lower respiratory infections U.S. 4.HIV/AIDS Significant burden 5.Fetus/newborn Societal (perinatal) cost ~$77B conditions 6.Chronic obstructive Largely pulmonary preventable disease (COPD) 7.Diarrhea 8.Tuberculosis 9.Malaria 10.Road traffic accidents

20 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

21 Ice-Cream Associated Outbreak; U.S.A.,1994 >250,000 cases 48 States

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

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24 Electronic Data Transmission Public health laboratories PFGE patterns National database at CDC

25 October 13, 2011

26 National Cluster Investigations (~30-50 followed per week)

27 2012 PulseNet-Triggered Outbreak Investigations (so far) Investigations (so far)

28 Largest U.S. Food Recalls in which PulseNet Played a Prominent Role Year Pathogen Food Amount recalled 2011 Listeria monocytogenes Cantaloupe Unknown 2011 Salmonella Heidelberg Ground turkey products >36,000,000 lbs 2010 Salmonella Enteritidis Shell eggs >500,000,000 eggs 2010 Salmonella Montevideo Ready-to-eat Italian sausage products/pepper >1,263,754 lbs 2009 E. coli O157:H7 Cookie dough 300,000 cases of product 2009 Salmonella Typhimurium Peanut butter/peanut products >3000 types of products 2008 E. coli O157:H7 Ground beef 5,300,000 Ibs 2007 Salmonella I 4,5,12:i:- Frozen pot pies Millions of pot pies 2007 E. coli O157:H7 Frozen pizza 5,000,000 pizzas 2007 E. coli O157:H7 Ground beef (3 outbreaks) 35,400,000 lbs 2006 Salmonella Tennessee Peanut butter 326,000,000 lbs 2004 Salmonella Enteritidis Raw almonds 13,000,000 lbs 2003/ 09 E. coli O157:H7 Blade Tenderized Frozen Steak 865,046 lbs 2002 Listeria monocytogenes Ready-to-eat poultry products 27,400,000 lbs 2002 E. coli O157:H7 Ground beef 18,600,000 lbs 2000 Listeria monocytogenes Ready-to-eat poultry products 16,900,000 lbs 2000 E. coli O157:H7 Ground beef 1,100,000 lbs 1998 Listeria monocytogenes Hot dogs, deli meats 35,000,000 lbs 1998/ 08 Salmonella Agona Toasted oats cereal >3,000,000 lbs 1997 E. coli O157:H7 Frozen ground beef 25,000,000 lbs Courtesy J. Besser

29 Industries Stimulated to Change by PulseNet- Triggered Investigations Peanut products Ready-to-eat & ready-to cook foods Eggs Beef Spices Leafy greens Other vegetables Tree nuts Sprouts Mellon Poultry Dog food

30 from Mike Doyle, Ph.D; CDC Public Health Grand Rounds November 2009

31 Under-appreciated Sources of Infection Salmonella in reptiles and amphibians Multiple pathogens from live bird markets Salmonella in feeder mice Salmonella from microbiology lab exposure Salmonella in baby chicks and ducks Vibrio vulnificus after fish handling Salmonella in owl pellets STEC in petting zoos Salmonella and pocket pets

32 PulseNet Cost Effectiveness Study (CIFOR; APHL; CDC)

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34 Diffuse outbreak of EHEC caused by molding meat manufactured by one factory 17 restaurant chain: 38 cases 関西エリア 236 c/t 関東エリア 84 c/t 1 新潟県 5 山口県 1 愛媛県 広島県 1 1 香川県 兵庫県 1 大阪府 2 プラン 1 ト 1 京都府長野県岐阜 奈良 群馬県 東京 埼玉県 From Dr. Kiyosu Taniguchi 原因物質の可能性の高いロット Lot:8 月 3 日製造 320 c/t レストラン 患者数

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37 Current PulseNet methods (PFGE) and Next-Generation Methods (e.g.whole-genome sequencing) are Isolate-Dependent

38 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

39 Hazards of Inaction

40 E. Coli O104:H4 Outbreak; 2011

41 Successful Adaption to Culture Demise

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

43 Short-term: Preserve isolates Modify reimbursement? Work with medical industry to make new tests compatible with public health needs Change criteria for medical device licensure? Modify State reporting rules Develop isolate recovery capacity for PHLs* Sentinel susceptibility surveillance* *Requires new $$$

44 Long-term: Develop culture-independent pathogen characterization methods Targeted sequencing/detection CDC STEC genomics project 100,000 Pathogen Genome Collaborative (UC Davis, FDA, CDC, BGI)

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

46 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 Fall 2011 Fall 2012

47 The 100K Pathogen Genome Project is a public database of food pathogen genomes that will provide a roadmap for public-private development of methods to aid in quick identification and tracking of pathogens back to their source. The 100K Pathogen Genome Project More information: BCWEIMER@UCDAVIS.EDU

48 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

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50 Very Long-term: Paradigm-shifting Technologies Single cell isolation and sequencing; MS screening, Lab-on-a-chip technology Metagenomics

51 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

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

53 CDC DTRA/DOD Metagenomics Project ( ) Proof-of-concept Evaluate sample preparation technologies, enrichment strategies Build analysis capability / capacity Develop links (MicrobeNet, Human microbiome project, 100K Pathogen Genome Project) Analyze real world samples from outbreaks of known and unknown etiology

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

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

56 Summary: Culture Independent Diagnostics Impact In this situation, it takes money to save money