PulseNet Gestalt John Besser Minnesota Department of Health
Questions I Was sked to ddress How are epidemiologic investigations affected by 2 nd enzyme data? re investigations delayed until results are available? Does delay affect the outcome of investigations? re resources wasted if 2 nd enzymes later reveal that multiple patterns were found and therefore a common source is less likely? How often are epi clusters found that do not correlate with PFGE 2 enzyme clusters? re further investigations conducted or additional lab testing done (3 rd enzyme, MLV for salmonella)? What happens if no epi links can be found for 2 enzyme clusters? What effect does the inclusion of unrelated cases have on epi analyses such as hypothesis generation, odds ratio, etc?
Implications of the Two Enzyme Policy Sensitivity, specificity, and significance issues Public health/regulatory action Practical implications
PulseNet Gestalt ge stalt or Ge stalt ( P ) Pronunciation Key (gshtält, -shtôlt, -stält, -stôlt) n. pl. ge stalts or ge stalt en (-shtältn, -shtôltn, -stältn, -stôltn) physical, biological, psychological, or symbolic configuration or pattern of elements so unified as a whole that its properties cannot be derived from a simple summation of its parts.
Specificity Sensitivity discrimination The use of 2 enzymes increases subtype specificity
Direct Contact with Primary Reservoir
Transmission via Vehicle
Ingredient in Product amplification
Person-To-Person Transmission
Secondary Transmission
Person-To-Pet Transmission
Multiple Transmission Routes
Multiple Transmission Routes Environment Patron illness Contaminated product Workers Other foods
Multiple Transmission Routes 12 Number of Cases 10 8 6 4 2 J FMMJJ SONDJ FMMJ JSOND J FMMJ J SOND JFMMJ JSOND
PFGE Case Definition
Goal: Identification of transmission event Method: marker for short-term evolutionary relationships minutes 0 15 30 45 60
conjugation transduction transformation mutation Via transposons plasmids integrons phage transcription errors
Subtyping (for hypothesis generating and testing): Refines the case definition to increase signal:noise
Refining the Case Definition One enzyme PFGE match Outbreakassociated
Refining the Case Definition Tenover criteria Outbreakassociated
Refining the Case Definition One enzyme PFGE match Outbreakassociated
Refining the Case Definition Two enzyme PFGE match Outbreakassociated
Refining the Case Definition Ten enzyme match Outbreakassociated
inflection point Type II error Type II error significance specificity of case definition
Specificity Sensitivity discrimination (Example: Bacteria not identified at all) ll inclusive ll isolates identical
Specificity Sensitivity (Example: Every isolate completely sequenced) ll exclusive ll isolates different discrimination
Gram Rxn genus species Tenover group subtype subtype, 2 enz Specificity Sensitivity discrimination
inflection point Type II error Type II error significance specificity of case definition
Gram Rxn genus species Tenover group subtype subtype, 2 enz Specificity Sensitivity discrimination How much discrimination is the right amount of discrimination?
It Depends On. The question you re trying to answer Prevalence of exposure Prevalence / type of agent Number of cases Other factors which contribute to specificity of case definition
Question: What is the vehicle for illnesses in a recognized outbreak?
Question: re two recognized outbreaks connected?
Question: What is the extent of an outbreak?
Question: Is there a clonal relationship between strains in different locations? Case Definition: Y. pestis isolated (biovar orientalis) from different geographic areas Burma India Indonesia US Vietnam Courtesy Kristy Kubota, CDC; ICEID Poster k2006
Question: Is their a common source for a cluster of cases?
For hypothesis generating and testing: In general, more subtype specificity is better..to a point
Factors That ffect the Need for Specificity Prevalence of exposure Prevalence / type of agent Number of cases
Odds Ratio exp+ exp- case C control B D OR = D CB
Prevalence of Exposure exp+ exp- case C control B D OR = D C B Odds ratio: inversely proportional to odds ratio
Low Prevalence Exposure case control exp+ exp- C B D Example: my mother s fruit cocktail surprise OR = D CB Consequence: less cases needed to reach significance
High Prevalence Exposure case control exp+ B Example: tomato consumption exp- C D OR = D CB Consequence: more cases needed to reach significance
Specific Exposure Definition case control exp+ exp- C B D Example: tomato consumption, supplier X OR = D CB Consequence: less cases needed to reach significance
Specificity and ssociation Exposure: tomatoes Case: S. Montevideo Control: not ill Exposed Not Exposed controls cases
Specificity and ssociation Exposure: tomatoes Case: S. Montevideo Control: not ill Case Control Exposed 6 3 Not Exposed 5 4 controls odds ratio = 1.6 cases
Specificity and ssociation Exposure: source tomatoes Case: S. Montevideo Control: not ill Tomato source Tomato source B Store X Store Y controls cases
Specificity and ssociation Exposure: source tomatoes Case: S. Montevideo Control: not ill Case Control Exposed 5 1 Not Exposed 6 6 controls odds ratio = 5 cases
Refining the EXPOSURE information: Increases signal noise ratio
exp+ case control B exp- C D OR = D CB
Case Classification exp+ Outbreak case control B exp- C C D Non-outbreak exp+ exp- C
Exposure Ratio Outbreak case control exp+ B exp- C C D Non-outbreak Ratio = specificity of case definition exp+ exp- C ffected by.. Prevalence of agent Specificity of agent definition Other case definitions
exp+ Outbreak Exposure Ratio case control B exp- C C D Non-outbreak exp+ exp- C
Low Prevalence gent case control exp+ exp- C B D Example: Salmonella Poona OR = D CB Few misclassified cases
High Prevalence gent case control exp+ exp- C B D Example: S. Typhimurium common subtype OR = D CB Many misclassified cases
More Specific Case Definition: 2 Enzymes case control exp+ exp- C B D Example: S. Typhimurium Subtype X1, B7 OR = D CB Less misclassified cases
Specificity and ssociation Exposure: tomatoes Case: S. Montevideo Control: not ill Exposed Not Exposed controls cases
Specificity and ssociation Exposure: tomatoes Case: S. Montevideo subt. Control: not ill Exposed Not Exposed controls cases
Specificity and ssociation Exposure: tomatoes Case: S. Montevideo subt. Control: not ill Case Control Exposed 5 3 Not Exposed 1 4 controls odds ratio = 6.7 cases
Specificity and ssociation Exposure: source tomatoes Case: S. Montevideo subt. Control: not ill Case Control Exposed 5 3 Not Exposed 1 4 controls odds ratio = 6.7 cases
Specificity and ssociation Exposure: source tomatoes Case: S. Montevideo subt. Control: not ill Case Control Exposed 5 1 Not Exposed 1 6 controls odds ratio = 30 cases
Specificity and ssociation Case Definition Non-specific Case Definition Specific Exposure Non-specific OR=1.6 OR=6.7 Exposure Specific OR=5 OR=30
Timeliness of the interview exp+ exp- case C control B D OR = D CB affects the sensitivity ND specificity of exposure information
E. coli O157:H7 Subtype Surveillance; Minnesota, 2000 22 20 18 16 No. of cases 14 12 10 8 6 4 2 Jan Feb Mar pr May Jun Jul ug Sep Oct Nov Dec Month
Statistical ssociation with Consumption of Hamburger from Producer ; November- December 2000 22 22 20 20 18 18 16 16 No. of cases 14 12 10 8 No. of cases 14 12 10 8 6 6 4 4 2 2 Nov Dec Nov Dec Without PFGE OR = 1.93; p = 0.31 -NOT significant- With PFGE OR = 17.1; p = 0.005 -SIGNIFICNT-
Implications of the Two Enzyme Policy Sensitivity, specificity, and significance issues Public health/regulatory action Practical implications
E. coli O157:H7 Outbreak ssociated with Pre-packaged Salad: Whole Different Timeline MDH issues Press Release 3:29 P.M. e-mail from Seattle law firm to MDH 3:56 p.m. Contact person for outbreak posted on law firm website 4:45 p.m. Minneapolis Law Firm Star Tribune d Solicitation First lawsuit filed in Minneapolis Second lawsuit filed in Minneapolis 29 30 1 2 3 4 5 6 7 8 9 10 11 12 13 September October 2005
http://www.cnn.com/us/9708/21/beef.update/index.html
Microbial DN Fingerprinting : dependent on continuous genetic change
Question: Does the DN in a specimen match the DN in an individual? Human DN testing X Year 0 25 50
Crime investigation: 22 Odds of exposure given illness Outbreak investigation: No. of cases 20 18 16 14 12 10 8 6 1 in 200 4 2 With PFGE OR = 17.1; p = 0.005
Multi-State Salmonella Typhimurium Outbreak ssociated with Cold Stone Creamery Ice Cream gent: rare (never seen before subtype), multiple cases, multiple states Temporal relationship: 10 cases/1 week Exposure: rare ( cake batter ice cream )
Implications of the Two Enzyme Policy Sensitivity, specificity, and significance issues Public health/regulatory action Practical implications
Practical Considerations gent and exposure prevalence information is not generally available Routine real-time 2 nd enzyme assays speeds up investigation and interventions for those situations where it s needed
Practical Considerations Multiple case definitions may be needed (e.g. definitions based on 2 enzymes, 1 enzyme, and no PFGE) if the number of cases is small significance specificity of case definition
Practical Considerations I you can t use 2 nd enzyme analysis on all recommended pathogens: use for clusters of common subtypes, or when highprevalence exposures are suspected
When are 2 nd enzymes likely necessary? Exposure common rare gent common ++++ ++ rare ++ + lso recommended High consequence pathogens Multi-state clusters
Practical Considerations The 2 enzyme policy is designed to make specific agent data readily available It is NOT a required criteria for epidemiological significance!
Practical Considerations Lack of 2 enzyme data is NOT reason to delay a public health action, if a significant association is found with any other case definition
Subtype Interpretation subtype mismatch does not automatically exclude association subtype match does not guarantee association The significance of a subtype match is greater if the agent and/or exposure is rare More so than human DN fingerprinting, molecular subtype data cannot be evaluated outside epidemiological context
Practical Considerations Obtaining sensitive and specific exposure information is at least as important as agent specificity (Realtime interview, detailed, open-ended questions)
Important notes for epidemiology investigators: a Using strict case definitions based on two enzymes is useful for increasing the specificity of hypothesis generation and testing. However, since multiple PFGE strains are on occasion found among epidemiologically-linked cases, investigators should not rule out using both stringent case definitions based on two enzyme results and less stringent case definitions based on single enzyme results. b The significance of clusters is dependent on epidemiological measures. In any particular situation, second enzyme results may or may not ultimately prove to be a useful refinement of the case definition. While it is prudent for laboratories to begin second enzyme testing under these circumstances, this does NOT mean that investigators should wait for the second enzyme results before taking action. c In all cases, investigators should obtain as specific exposure information as possible, which strengthens measures of association between illness and exposure