Molecular Epidemiology of Tuberculosis Kathy DeRiemer, PhD, MPH School of Medicine University of California, Davis
Overview TB transmission and pathogenesis Genotyping methods Genotyping for clinical management Genotyping for TB Control Programs Future applications of genotyping
Mycobacterium tuberculosis is infectious and spreads through the air Coughing, sneezing, talking, shouting, singing.....
Mycobacterium tuberculosis Thick, lipid-rich cell wall and membrane Clonal organism, but some progeny lose chunks of DNA and become different
Restriction fragment length polymorphism (RFLP) analysis IS6110 RFLP genotyping MIRU-based genotyping Barnes PF, Cave MD. New Engl J Med 2003; 349:1149-56
Variable number tandem repeats (VNTR), 21-635 bp MIRU = mycobacterial interspersed repeat units MLVA = multiple locus VNTR analysis Sputgiesz RS, et al. J Clin Microbiol 2003; 41:4224-30
Spoligotyping IS6110 DR locus H37Rv X Spacer BCG H37Rv X Barnes PF, Cave MD. New Engl J Med 2003; 349:1149-56
Comparison of Genotyping Systems Kremer et al., 1999. J Clin Micro (37), 2609-2618
Who is Infected and Diseased? Transmission and pathogenesis Recent infection and rapid progression to disease Infection... Latency, Latent TB infection (LTBI) Reactivated disease
IS6110 RFLP of M. tuberculosis Identify unsuspected transmission Strain 4 Unsuspected transmission among Southeast Asian persons Strain 5 Unsuspected transmission among US born persons
Outbreak in a facility for AIDS patients DNA fingerprints Restriction fragment length polymorphisms (IS6110 RFLP) Unique: Reactivation of latent TB infection Clustered: Recent transmission Each vertical lane is an isolate of M. tuberculosis from a different TB patient
MIRU-VNTR Advantages Almost as discriminatory as IS6110 RFLP Automated high throughput analysis of many isolates Digital results, easy to establish and compare databases New loci identified for strains in specific geographical regions
Genotyping for Clinical Management 1. Confirm cross-contamination in the laboratory ~ 3% of patients do not have TB Cross contamination = sputum smears are negative and only one specimen is culture positive
Genotyping for Clinical Management 2. Evaluate recurrent tuberculosis Relapse of disease, caused by the same strain that caused the first episode Relapse represents treatment failure Reinfection, with a different strain of M. tuberculosis
Genotyping for Clinical Management MIRU-VNTR IS6110 RFLP Exogenous reinfection was common (61.5%) Shen G, et al. Emerg Infect Dis 2006; 12:1776-8
Genotyping for Clinical Management 3. Evaluate isolates with different patterns of drug susceptibility Cross contamination Original organism developed drug resistance during or after antituberculosis therapy Transmission of a drug-resistant strain
Transmission of drug-resistant tuberculosis in Shanghai 84% (27/32) of treated patients had primary resistance Li X, et al. J Infect Dis 2007; 195: 864-9
Genotyping for Clinical Management 4. Evaluate mixed infections Mixed infections: Shanghai, VNTR-7 loci Estimated rate: 5.6% (95% CI 3.1-9.2%) Retreatment cases New cases Non-Beijing strains Beijing strains 15.7% 4.1% 12.5% 3.5% p < 0.05 p < 0.05 Fang R, et al. Tuberculosis (Edinb.) 2008; in press
Genotyping for TB Control Programs 5. Evaluate chains of transmission Outbreak versus coincidental occurrence of a large number of cases Guide public health measures to reduce transmission of M. tuberculosis
Genotyping for TB Control Programs 6. Identification of groups at increased risk for tuberculosis Homeless shelters
Genotyping for TB Control Programs Prisoners
Genotyping for TB Control Programs Schools and day care centers
Genotyping for TB Control Programs Residences for the elderly
Genotyping for TB Control Programs Impact of HIV M. tuberculosis Acute disease infection (30%) (10% life, HIV+ 5-10% /yr) Exposure No M. tuberculosis infection Reactivation Latent (10% life, HIV+ 80%) infection (70%) (90%) Lifelong containment
Genotyping for TB Control Programs Impact of HIV Comparison of genotype clusters, San Francisco DeRiemer K, et al. Am J Respir Crit Care Med 2007; 176:936-44
Genotyping for TB Control Programs Predictors of clustering in San Francisco Cattamanchi A, et al. Int J Tuberc Lung Dis 2006; 10:297-304
Genotyping for TB Control Programs 7. Improving case finding and contact investigations Identify locations TB patients use Household versus community sites Determine who needs to be screened
Migrating Populations -75 Compared to 1960-75, four-fold increase in migration during 1990s Source: Population Action International 1994
US Tourist exports drug-resistant TB Honeymoon Greece, Italy, Czech Republic (7 airline flights) Homecoming New York to Denver Wedding - Greece
M. tuberculosis can transmit from infectious source cases to their contacts World-famous infectious TB patient TB contact (wife) wearing protective N95 respirator
Contact investigation Contacts Index case + Infected contacts Concentric circle approach
Yield of contact investigations: active TB Child contacts < 5 years 5-14 years < 15 years Adult contacts Total studies (n) 13 6 8 9 Pooled yield (95% CI) 8.5% (7.4-9.7%) 6.0% (4.7-7.5%) 7.0% (6.0-8.0%) 6.5% (5.7-7.4%) Morrison J, et al. Lancet Infect Dis 2008; in press
Yield of contact investigations: latent TB infection Child contacts < 5 years 5-14 years < 15 years Adult contacts Total studies (n) 14 7 10 7 Pooled yield (95% CI) 30.4% (28.6-32.3%) 47.9% (45.5-50.4%) 40.4% (38.7-42.2%) 64.6% (62.9-66.2%) Morrison J, et al. Lancet Infect Dis 2008; in press
Genotyping for TB Control Programs 7. Evaluation of TB programs San Francisco, California Cattamanchi A, et al. Int J Tuberc Lung Dis 2006; 10:297-304
Genotyping for TB Control Programs 7. Evaluation of TB programs San Francisco, California Cattamanchi A, et al. Int J Tuberc Lung Dis 2006; 10:297-304
Future Applications of Genotyping Surveillance genotyping: Real-time genotyping Rapid identification of outbreaks Evaluation of social networks
Genome of Mycobacterium tuberculosis Cole ST, et al. Nature 1998
Proposed evolutionary pathway of the tubercle bacilli RD = region of difference, genomic deletion BCG Ernst JD, et al. J Clin Invest 2007; 117:1738-45
Global Population Structure of M. tuberculosis Six main lineages, geographically structured Stable associations between host and pathogen Gagneux S, Small PM. Lancet Infect Dis 2007; 7(5):328-37 Gagneux S, DeRiemer K, Van T, PNAS 2006; 103:2869-73
New Paradigms: Interface of Several Fields Molecular epidemiology Microbial Pathogenesis Functional Genomics
Acknowledgments Shanghai CDC and Fudan University Dr. Jian Mei, Xin Shen, Dr. Qian Gao and many more Key Project of Chinese National Programs for Fundamental Research & Development (973 Program 2005CB523102, 2002CB51284) Chinese National Programs B63 (2006AA027423, 2006AA022328) Shanghai Key Medical Foundation (grant 5III029) Shanghai Municipal Sciences & Technology Commission (grants 05PJ14025, 05DZ22320)
Acknowledgments Stanford University Peter Small Qian Gao Anthony Tsolaki Sebastien Gagneux Bouke de Jong University of California, Davis and San Francisco Phillip Hopewell, Charles Daley National Institutes of Health Wellcome Trust