tuberculosis cluster investigations using genotyping data frank romano, mph cdc public health...
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Tuberculosis Cluster Investigations Using Genotyping Data
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Frank Romano, MPHCDC Public Health Advisor
Historical Perspective
• 1989 ACET & CDC Publishes A Strategic Plan for the Elimination of TB in the US
– Predicted incidence rate of 3.5 per 100,000 by 2000
– Predicted the elimination of TB by 2010
History (cont.)• Late 1980’s – early 1990’s: Few states
performing TB genotyping using IS6110 RFLP
• Jan. 1990–August 1993: Strain W– MDR Strain– 357 cases reported in NYC prisons and
hospitals– HIV seropositive population– 80% mortality (Duration 4–6 weeks)
• April 1996: CDC establishes the National Tuberculosis Genotyping and Surveillance Network (NTGSN)
• 1996—2000: NTGSN conducts population-based study to determine the frequency of specific strains geographically using IS6110 RFLP and Spoligotyping
• 2001: Results of study published
Use Genotype Results to Better Understand:
• spread of related strains in communities
• geographic mobility of related strains
• relatedness of strains in persons at high risk for tuberculosis
• capacity of local TB controllers to identify patients involved in outbreaks and to provide a database of DNA fingerprints for tuberculosis control activities
CDC TB Genotyping Program
• January 2004, the CDC Tuberculosis Genotyping Program was initiated to enable rapid genotyping of isolates from every patient in the USA with culture-positive tuberculosis (TB)
• The Federal Tuberculosis Task Force recommended nationwide TB genotyping in response to the Institute of Medicine report, Ending Neglect
• The TB Genotyping Program contracts with laboratories
that provide results within 10 working days using two PCR-based genotyping tests
PCR Based Testing
• Polymerase chain reaction (PCR)
• Only a small amount of culture is needed for PCR-based genotyping, and the PCR test can be completed in 1day*
*because the PCR tests are batched, the actual turn-around time from receipt of a specimen to reporting the results can be longer
CDC TB Genotyping Program
Goal: Provide nationwide rapid genotyping tests
• Two CDC-funded laboratories perform genotyping for one isolate from every culture-positive TB case in the US
• CDC funded TB programs submit isolates to regional genotyping labs
• Genotyping labs report results within 10 days
Assigned to California Lab Assigned to Michigan Lab
CDC TB Genotyping Program:Genotyping Laboratory
AssignmentsLAB
LAB
CDC Genotyping Program Laboratory Methods
Two tiered testing to maximize discriminatory power
PCR • MIRU Variable number tandem repeats of mycobacterial
interspersed repetitive units
• Spoligotyping Spacer oligonucleotide typing
IS6110-based RFLP • Done only for isolates that match by both PCR
tests• At request of CDC grantee
Comparison of Testing Methods
• IS6110RFLP- (Restriction Fragment Length Polymorphism)– Considered most discriminatory test worldwide– Disadvantages—Cost, time, need for specialized training & lab
equipment
• Spoligotype- (Spacer Oligonucleotide Typing)
– Lower Specificity than RFLP– Lower cost, rapid results
• MIRU- (Variable number tandem repeats of mycobacterial interspersed repetitive units)
– Lower Specificity than RFLP– Lower cost, rapid results
Tuberculosis Genotyping Guide
National TB Controllers Association
Centers for Disease Control and Prevention
Value of Genotyping
Identify and prevent transmission• Enhance contact investigations• Identify nontraditional settings of transmission• Facilitate identification of clusters and outbreaks
Improve clinical management • More readily identify false-positive cultures• Help distinguish between relapse and reinfection
Value of Genotyping (II)
Enhance surveillance• Evaluate prevalence of M. tuberculosis genotypes• Monitor trends in recent transmission
Evaluate prevention activities• Completeness of contact investigations• Progress toward TB elimination
CDC TB Genotyping Program
• All programs with CDC Cooperative Agreements are eligible (64)
• Program options
Selective genotyping Universal genotypingUniversal genotyping for subregion
D.C.
Aug 04
Universal
Selective
Mixed
Not enrolled
NYC
SD
TB Genotyping Programs
D.C.
June 06
Universal
Selective
Mixed
Not enrolled
NYC
SD
TB Genotyping Programs
CDC National TB Genotyping Program Update
• As of May 1, 2006, 15,573 isolates have been submitted nationally
• 439 isolates submitted from Ohio as of 7/19/2006• Ohio has 44 clusters (range 2 - 13 patients) as of
7/19/2006• Sharing genotype pattern data across jurisdictions
(Quarterly Reports from CDC)
County Genotyping Report
County Cluster Report
Genotyping Results• Interpreting genotyping results and
epidemiologic data• When to initiate a cluster investigation,
initiate (expand) an outbreak investigation, or do nothing
Epi-link: a characteristic that 2 or more TB patients share that explains where and when TB could have been transmitted between them
Interpreting Results
• Matching genotype vs. non-matching genotype
• Epi-linked vs. non-epi-linked
• Involved in same recent chain of transmission vs. not involved
Matching Genotypes
False-positive culture?
Suspected false-positives are a priority• need to stop treatment for falsely
diagnosed patients as soon as possible
False-Positive CulturesClinical Picture
• Health care provider or clinical lab is suspicious
• patient had only 1 positive culture out of 1 or multiple specimens collected
• patient asymptomatic for TB• patient’s chest radiograph not consistent
with TB• patient has another confirmed diagnosis
to explain symptoms
False-Positive Cultures
Laboratory• specimens were processed in the same
laboratory on the same day
• isolates were collected in the same hospital or clinic within 3 days
• PCR genotyping pattern matches the laboratory control strains (H37rv or H37ra) or laboratory proficiency specimens
False-Positive Cultures
False-positive result confirmed:• identify which patients actually have TB
and which patients were misdiagnosed
• alert the health care providers so they can correctly diagnose and treat the misdiagnosed patients
• alert the laboratory so the cause of the false-positive culture can be determined and corrected
Matching Genotypes
Patients Epi-linked prior to genotyping
Interpretation:• probably involved in same chain of recent
transmission• RFLP confirmation or cluster investigation
not needed• may determine that an outbreak
investigation is needed
Outbreak Investigations
• An increase in the expected number of cases
• Transmission continues despite adequate control efforts by the TB program
• The contact investigation has grown to a size that requires additional outside help
Cluster OH_009
• 11 Hamilton County cases + 1 Kentucky case
• CDC currently assisting with investigation in Indiana
1
3 1
12
4
Number of isolates as of 06/30/2006n = 55IN = 61.8% of isolates(Note: 1 case in Florida matches on spoligotype and is missing MIRU but is linked epidemiologically)
2
34
3
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2
3
Matching Genotypes
Patients have possible epi-links• are there 3+ people in the cluster?• are there high-risk people in the cluster?
If yes, request RFLP for confirmation• if RFLP does not confirm match, no
further investigation needed• if RFLP confirms match, consider doing
a cluster investigation
High-risk Patients
• live in congregate settings
• are infected with HIV or have other immunocompromising conditions
• are children
• have cavitation on chest radiographs
• have MDR TB
• are homeless
Cluster Investigations
Should only be done when needed• can be labor intensive• detailed cluster investigation protocols
and data collection forms are available from CDC
• review information previously collected to determine if additional information is needed–may need to interview patients again
Prioritizing Cluster Investigations
1. suspected false positive culture2. cluster of 3+ high-risk persons w/ possible epi-links3. cluster of 2 high-risk persons w/ possible epi-links4. cluster of 3+ low-risk persons w/ possible epi-links5. cluster of 2 low-risk persons w/ possible epi-links6. cluster of high-risk persons with no epi-links7. cluster of low-risk persons with no epi-links
Matching Genotypes
Patients have no epi-links identified, but are involved in same chain of recent transmission
Interpretation: Failure to identify known epi-links due to -
• inadequate contact investigation• transmission from casual contact
Matching Genotypes
Patients not epi-linked and not involved in same chain of recent transmission
Interpretation: Matching genotypes with no recent transmission due to -
• transmission of endemic strain• large outbreak in the past• false positive culture(s)• laboratory error
Non-matching Genotypes
Patients epi-linked and involved in same chain of recent transmission
Interpretation: non-matching genotypes with no recent transmission due to -
• genotypes that changed slightly over time
• co-infection with >1 strain of M. tb
• laboratory error
Non-matching Genotypes
Patients epi-linked and not involved in same chain of recent transmission
Interpretation: • misleading epi-links identified
Non-matching Genotypes
Patients not epi-linked
Interpretation: • no evidence of recent transmission
Large Clusters
As clusters grow in size, it becomes easier to:
• identify epi-links
• identify an endemic strain
Deciding What To Do
Making the correct decision depends upon having complete and accurate data from a variety of sources
• patient interviews
• contact investigations
• laboratory results
• medical records
Questions????
0
25000
50000
75000
100000
125000
150000
0 50 100 150 200 250 300 350 400 450 500 550 600Size (nt)
Dye
Sign
al
60
68.64
7080
90
100 120
137.51
140 160 180
190
200
217.80
219.08
220
231.54
232.63
233.70
238.82
240
259.06
260 280 300 320 340 360
362.75
363.99
365.38
380 400 420 440 460480 500
520 540 560 580 600 620
Definitions
Selective Genotyping: The process of submitting only selected high priority M tuberculosis isolates for genotyping
Universal Genotyping: The process of submitting all M tuberculosis isolates for genotyping
DefinitionsGenotype: The designation that results from one or more of the three genotyping techniques used for M tuberculosis: Spoligotyping, MIRU analysis, and IS6110-based RFLP
Genotyping: Also referred to as DNA fingerprinting. A laboratory approach that provides a description of the genetic makeup and relatedness of M. tuberculosis isolates
Cluster: A genotyping cluster is two or more M tuberculosis isolates that share matching genotypes
An epidemiologic cluster is two or more persons with TB who share epidemiologic links
Laboratory Contact Person
Kevin Sohner, B.S.Ohio Dept. of Health Laboratories
Special Microbiology Section8995 E. Main St., Bldg. 22Reynoldsburg, OH 43068
phone: (614) 644-4668fax: (614) 644-4412
e-mail: [email protected]
CDC WebBoard and Contact Information
• NTCA/CDC TB Genotyping Working Group: Tom Navin, MD at [email protected]
• Guide, application instructions and updates for CDC TB Genotyping Program: http://web-tb.forum.cdc.gov Guide (printed copy): Alan Schley at [email protected]