TBGenotyping Information Management System TBGIMS

1
TB-Genotyping Information Management System
(TB-GIMS)
Smita G. Chatterjee Research Epidemiologist Divi
sion of Tuberculosis Elimination National Center
for HIV/AIDS, Viral Hepatitis, STD, and TB
Prevention April 30, 2009
The findings and conclusions in this presentation
have not been formally disseminated by CDC and
should not be construed to represent any agency
determination or policy
SAFER HEALTHIER PEOPLE
2
Overview

• Genotype updates
• TB-GIMS updates
• Aberration detection system

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Genotyping Updates
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National TB Genotyping Service (1)

• Over 43, 542 isolates genotyped as of February
  09
• Universal genotyping coverage nationally 86
  (2007)
• Renewed 5 year contracts with California and
  Michigan genotype laboratories

5
National TB Genotyping Service (2)

• Launch of expanded genotype testing (MIRU2)
• Additional 12 loci MIRU
• Will add discriminatory power
• Some large clusters will be divided into smaller
  components, each of which may represent true
  clusters
• Additional MIRU2 requests for historical
  isolates, as is now done for RFLP

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MIRU-VNTR12 ? MIRU-VNTR 24
miru02
miru39
miru04
miru40
miru10
miru31
miru16
miru27
miru26
miru24
miru20
miru23
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New Cluster Naming Conventions
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TB Genotyping Information Management System
(TB-GIMS) Updates
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Goals of TB-GIMS

• Improve access and dissemination of genotyping
  information
• Create a standard database that local programs
  can use to track isolates, receive and update
  genotyping information, manage and use
  surveillance-linked genotype information
• Design of TB-GIMS
• 1. role-based access
• 2. role-based features

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Access to Data
Administrators
Super User
Potential TB-GIMS Users
Standard User
Restricted User
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Role Based Access

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Role Based Features

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TB-GIMS Home Page
Under Development
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Search Genotyping Results
Under Development
15
Genotype Results
Under Development
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Search Surveillance Records
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Surveillance Records
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Laboratory Role Edit isolates
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Laboratory Role Edit isolates
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TB-GIMS Generate Reports
Under Development
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National Distribution Report
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Surveillance Report
NYC
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Epidemiologic Curve Report
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County Distribution Report
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Video Clip

• Our very own Martin participating in TB-GIMS
  pilot usability testing in January 2009

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TB-GIMS Timeline

• Usability testing completed
• TB-GIMS user group conference calls
• began February 2009
• Pilot testing begins June 2009
• Roll out begins Winter 2009 2010

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Pilot TestingJune - August 2009

• Simulation exercise with super users from 5 east
  coast and 5 west coast state programs and labs,
  genotyping labs and CDC
• Additional pilot testing of 20 standard and 20
  restricted access users
• Analyses and user input on prioritizing decisions
  for incorporation in revision and roll out in
  winter 2009-2010

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Next Steps

• Mapping
• Dynamic queries/reports
• Field tests
• Usability tests and feedback
• Training
• Aberration Detection

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Aberration Detection
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How do you define an outbreak?

• . . . the occurrence, in a community or
  region, of cases of an illness clearly in excess
  of normal expectancy . . .
• . . . number of cases needed varies according
  to agent, size and type of population exposed,
  time, and place of occurrence.
• - JM Last (1988). Dictionary of Epidemiology

Log Likelihood Ratio (LLR)
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Measures of Geospatial Concentration

• Log-Likelihood Ratio (LLR) measures the
  difference between the observed and the expected
  geospatial concentration
• Weighted by case count
• Log transformed
• Widely studied in statistics
• Used by SaTScan software system

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Log-Likelihood Ratio Derivation
N abcd
LLR alog(Obs_in/Exp) clog(Obs_out/Exp)
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Assessing the Sensitivity of LLR to determine a
threshold for alerts

• By expert opinion
• By known outbreak

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By Expert OpinionState Cluster Prioritization
(N66)
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By Known OutbreakDistribution of PCR06800
(CA_384) in U.S.
Spoligotype 777737774020771 MIRU 225326153323
Total isolates 39 CA isolates 36 (92) as
of Feb 2009
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By Radius of Outbreak
LLR 32.6
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Potential Aberration Detection Alert
N 17
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Distribution of PCR01328 (CA_089) in U.S.
Spoligotype 776377777760751 MIRU 333325153222
Total isolates 126 CA isolates 57 (45) as
of Feb 2009
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By Radius of Outbreak
LLR 17.8
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Potential Aberration Detection Alert
N 21
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Ongoing Developments

• Time Indicators
• Risk factors for increased transmission
• Incarceration drug use homelessness
• Severity of disease
• Age lt 5 years HIV infection drug resistance
• Decreased risk of recent transmission
• Immigration to U.S. lt2 years before diagnosis
• TBESCs Task Order 26 Improving the utilization
  and integration of TB genotyping into routine TB
  program practice

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Contact Information
Smita Chatterjee 404 639 2135
Schatterjee_at_cdc.gov Lauren Cowan 404 639
1481 Lcowan_at_cdc.gov Thomas Navin 404 639
5300 Tnavin_at_cdc.gov
TBGenotyping_at_cdc.gov
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Relative Risk as a Measure of Geospatial
Concentration
Relative Risk (a/ab) / (c/cd)
197
44
Relationship of LLR and RR
LLR alog(RR) (ac)log(Obs_out/Exp)