Molecular Epidemiology ofMycobacterium tuberculosisBarry N. Kreiswirth, PhDDirector, PHRI TB Center                  Prese...
Slow grower; doubles 24hrs; 3-4 weeks to culture3-4 weeks for susceptibility testingHighly transmissible; requires BL3 fac...
TB Statistics  2 billion infected (1/3 world population)  8-9 million new cases each year  1.6 million deaths per year ...
HIV and Multidrug Resistance                 HIV and Tuberculosis Co-infection of M.tb and HIV a deadly-duet 11% co-infe...
M. tuberculosis Genome – H37RvGenome size (bp): 4,411,5323,959 predicted ORFs (90.8%)2,441 attributed functions  912 conse...
Comparative Sequence Analysis  M. tuberculosis genome is highly conserved  M. tuberculosis is a monomorphic species  Sy...
A new evolutionary scenario for the   Mycobacterium tuberculosis complex.Brosch R, Gordon SV, Marmiesse M, Brodin P,    Bu...
Evolution of the Mtb Complex  Brochet et al, PNAS, 2002
Molecular Tools - Genotyping Methods        Primary Genotyping Method    IS6110            Southern blot hybridization  ...
Genotyping Targets to Discriminate M. tuberculosis                                     Strain 210                         ...
Biology of IS6110 Unique to M. tuberculosis complex Copy number from 1 - 26 insertions Insertions dispersed around geno...
Insertion Sequence IS6110
IS6110 DNA Fingerprinting Standardized Methodology Southern blot hybridization PvuII restriction digest Common right-s...
DNA Fingerprints of M. tuberculosis Strains
Searching the Database for Strain W4
SRO Outbreak in San Francisco
Genotyping Data – Public Health Issues Evaluate nosocomial and community transmission Evaluate suspected cases of labor...
TREATING TUBERCULOSIS
The last TB drug, ethambutol, was discovered in1968 at “Wyeth”                                  PyrazinamideStreptomycin  ...
Antimycobacterial Agents    First Line Drugs       Second Line Drugs   Streptomycin        Ethionamide   Isoniazid     ...
Current therapy for tuberculosis disease                                 Advantages:        2HRZE/4HR                    ...
Drug Resistant M. tuberculosisMultidrug Resistance (MDR)    Resistance to at least isoniazid (INH) and rifampin    (RIF)Mu...
Cure Rates for MDR-TB and XDR-TB   MDR-TB cure rate 1993-8: 94%  (fluoroquinolones & surgery were critical  variables)   M...
DRUG SUSCEPTIBILITY TESTING
Mycobacteriology testing in the clinical laboratory It is not the black sheep of the lab - - - It is the pig!
METHODS Middlebrook 7H10 or 7H11 agar – Incorporate drug Middlebrook 7H10 or 7H11 agar - E-test Lowenstein-Jensen slant...
Genotyping Drug Resistance Nearly all drug resistance target genes identified With two exceptions, non-synonymous  mutat...
Drug Resistance Target Genes
Rifampin Resistance & rpoB MutationsWT: CTG AGC CAA TTC ATG GAC CAG AAC CCG CTG TCG GGG TTG ACC CAC AAG CGC CGA CTG TCG GC...
Fluoroquinolone Resistance and gyrA MutationsWild Type:    CAC GGC CAC GCG TCG ATC TAC GAC AGC CTGResistance:   CAC GGC CA...
Genotyping Drug Resistance        Advantages                        Challenges   Speed                           Bypass ...
Genotyping Drug ResistanceHain reverse hybridization line probe assay (HainLifescience, Nehren, Germany) Multiplex PCR an...
Tuberculosis in New York City
AIDS
168th Street Men’s Shelter – March, 1992
W Strain MDR Outbreak in NYC January 1990 - August 1993 43 Months - 8,021 Cases 357 Patients with W strain tuberculosis...
Outbreak of the Multidrug Resistant “W” Tuberculosis Clone
W MDR Outbreak: 1990-1993   Isoniazid (100%)        katG - 315:AGC>ACA; Ser>Thr   Rifampin (100%)         rpoB - 526:CAC...
W MDR OUTBREAK: 1993-1999             W34             W31       W40       W12             W25       W1             W1     ...
Creating Extremely Drug Resistant W StrainsMunsiff et al., JID 2003:188;356
XDR-TB OUTBREAK IN                    AN HIV-POSITIVE                 POPULATION IN SOUTH                        AFRICA15 ...
Jan 2005 – March 2006 1,539 TB Diagnosed 542 Culture Positive Cases     168 MDR Cases      53 XDR Cases      52 / 53 Died ...
XDR-TB OUTBREAK IN AN HIV-POSITIVE   POPULATION IN SOUTH AFRICA        IS6110 Fingerprint
WHO ESTIMATES: 25,000 CASES OF XDR-TB EMERGING EVERY YEAR
 As we learned in NYC during our HIV – MDR outbreak, it will take strong political will, dedicated medical and public hea...
Case Studies
Identity Crisis8/5/05: patient KD admitted to hospital “A” with  diagnosis of suspected pulmonary tuberculosis     X-ray ...
DNA Fingerprint of the M. tuberculosis from patient KD
Identity Crisis   4/5/06 Patient CB admitted to hospital “B” with    diagnosis of suspected pulmonary tuberculosis      ...
1 2        JI strains isolated      from patient “CB/KD”             1. 2005             2. 2006
Molecular Epidemiology of Mycobacterium tuberculosis-Barry Kreiswirth PhD
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Molecular Epidemiology of Mycobacterium tuberculosis-Barry Kreiswirth PhD

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Eastern PA Branch-ASM, 41st Annual Symposium, November 17, 2011

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Molecular Epidemiology of Mycobacterium tuberculosis-Barry Kreiswirth PhD

  1. 1. Molecular Epidemiology ofMycobacterium tuberculosisBarry N. Kreiswirth, PhDDirector, PHRI TB Center Presented at the 41st Annual Symposium“Global Movement of Infectious Pathogens and Improved Laboratory Detection” Eastern PA Branch-American Society for Microbiology November 17, 2011 Thomas Jefferson University, Philadelphia
  2. 2. Slow grower; doubles 24hrs; 3-4 weeks to culture3-4 weeks for susceptibility testingHighly transmissible; requires BL3 facilities
  3. 3. TB Statistics  2 billion infected (1/3 world population)  8-9 million new cases each year  1.6 million deaths per year (25% of all preventable deaths)  This means 4, 000 deaths each day, a death every 20 seconds  85% of the mortality in developing countries2008 WHO report on TB
  4. 4. HIV and Multidrug Resistance HIV and Tuberculosis Co-infection of M.tb and HIV a deadly-duet 11% co-infected (range from 1% to over 60%) Reactivation of tuberculosis or rapid progression to disease are markers for HIV Multidrug Resistance (INH & RIF) Multidrug resistance is emerging in virtually every country 425,000 new MDR cases annually Estimated 50 million infected with MDR
  5. 5. M. tuberculosis Genome – H37RvGenome size (bp): 4,411,5323,959 predicted ORFs (90.8%)2,441 attributed functions 912 conserved hypotheticals 606 unkonwns
  6. 6. Comparative Sequence Analysis  M. tuberculosis genome is highly conserved  M. tuberculosis is a monomorphic species  Synonymous base pair changes are rare  M. tuberculosis “young” human pathogen  M. tuberculosis evolved from M. bovis
  7. 7. A new evolutionary scenario for the Mycobacterium tuberculosis complex.Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, Garnier T,Gutierrez C, Hewinson G, Kremer K, Parsons LM, Pym AS, Samper S, van Soolingen D, Cole ST. Proc Natl Acad Sci U S A 2002 Mar 19;99(6):3684-9
  8. 8. Evolution of the Mtb Complex Brochet et al, PNAS, 2002
  9. 9. Molecular Tools - Genotyping Methods Primary Genotyping Method  IS6110 Southern blot hybridization  Secondary Genotyping Methods  Spoligotyping Binary typing, DR region  PGRS Southern blot hybridization  VNTR, MIRU PCR, multiple targets  IS6110 mapping Southern blot hybridization  DNA sequencing Resistance targets, SNP  Array analysis Deletion mapping
  10. 10. Genotyping Targets to Discriminate M. tuberculosis Strain 210 Strain HN5Barnes et al. NEJM – 2003;349:1149
  11. 11. Biology of IS6110 Unique to M. tuberculosis complex Copy number from 1 - 26 insertions Insertions dispersed around genome Chromosomal “hot-spots” identified Insertions stable over time Movement is a replicative process
  12. 12. Insertion Sequence IS6110
  13. 13. IS6110 DNA Fingerprinting Standardized Methodology Southern blot hybridization PvuII restriction digest Common right-side hybridization probe Common molecular weight standards Digitized patterns Pattern matching software
  14. 14. DNA Fingerprints of M. tuberculosis Strains
  15. 15. Searching the Database for Strain W4
  16. 16. SRO Outbreak in San Francisco
  17. 17. Genotyping Data – Public Health Issues Evaluate nosocomial and community transmission Evaluate suspected cases of laboratory contamination Distinguish relapse vs re-infection Genotype drug resistance genes to distinguish spread vs acquisition Distinguish recent transmission and endemic strains
  18. 18. TREATING TUBERCULOSIS
  19. 19. The last TB drug, ethambutol, was discovered in1968 at “Wyeth” PyrazinamideStreptomycin Ethionamide Capreomycin Isoniazid Kanamycin/amikacinPAS Thioacetazone Cycloserine Rifampin Ethambutol 1965 1966 1967 19681944 1946 1952 1955 1956 1957
  20. 20. Antimycobacterial Agents First Line Drugs Second Line Drugs Streptomycin  Ethionamide Isoniazid  Amikacin / Kanamycin Rifampin  Capreomycin Ethambutol  Fluoroquinolones Pyrazinamide  PAS  Cycloserine
  21. 21. Current therapy for tuberculosis disease  Advantages: 2HRZE/4HR – 100% effective – Low relapse rate (3-4%)• Induction phase: 2 – Inexpensive months isoniazid, – Universally available – Can be given intermittently rifampin, pyrazinamide, ethambutol  Disadvantages – 6 months duration – High relapse rate in some• Continuation phase: 4 subgroups (10-15%) – Adverse effects common months isoniazid, – Interactions with HIV rifampin treatment – Not useful against MDR strains
  22. 22. Drug Resistant M. tuberculosisMultidrug Resistance (MDR) Resistance to at least isoniazid (INH) and rifampin (RIF)Multidrug Resistance (Plus) Resistance to at least isoniazid and rifampin plus resistance to fluoroquinolonesExtensively Drug Resistance (XDR) Resistance to at least isoniazid and rifampin plus resistance to fluoroquinolones AND one of the second line injectable aminoglycoside drugs (amikacin, kanamycin or capreomycin)
  23. 23. Cure Rates for MDR-TB and XDR-TB MDR-TB cure rate 1993-8: 94% (fluoroquinolones & surgery were critical variables) MDR+-TB cure rate 1993-8: 60% XDR-TB cure rate 1993-8: 20%Case studies from National Jewish TB Center, Denver CO
  24. 24. DRUG SUSCEPTIBILITY TESTING
  25. 25. Mycobacteriology testing in the clinical laboratory It is not the black sheep of the lab - - - It is the pig!
  26. 26. METHODS Middlebrook 7H10 or 7H11 agar – Incorporate drug Middlebrook 7H10 or 7H11 agar - E-test Lowenstein-Jensen slants BACTEC 460 – radioactive CO2 BACTEC MGIT 960 – oxygen consumption LIMITATIONS Susceptibility requires a growing culture – 3 weeks First-line drugs tested first – 3 weeks Second-line drugs tested for MDR – 3 weeks MDR treatment delayed
  27. 27. Genotyping Drug Resistance Nearly all drug resistance target genes identified With two exceptions, non-synonymous mutations in drug resistance target genes predicts resistance Molecular approaches are able to genotype resistance in less than 24 hrs – too costly even for developed countries
  28. 28. Drug Resistance Target Genes
  29. 29. Rifampin Resistance & rpoB MutationsWT: CTG AGC CAA TTC ATG GAC CAG AAC CCG CTG TCG GGG TTG ACC CAC AAG CGC CGA CTG TCG GCG CTGRIF: CTG AGC CAA TTC ATG GAC CAG AAC CCG CTG TCG GGG TTG ACC TAC AAG CGC CGA CTG TCG GCG CTG
  30. 30. Fluoroquinolone Resistance and gyrA MutationsWild Type: CAC GGC CAC GCG TCG ATC TAC GAC AGC CTGResistance: CAC GGC CAC GCG TCG ATC TAC GGC AGC CTG
  31. 31. Genotyping Drug Resistance Advantages Challenges Speed  Bypass culturing Resistance genes identified  Infectious & Contaminated No synonymous mutations  Cost Mutation predicts resistance  Sensitivity / Specificity  Simplicity  Flexibility
  32. 32. Genotyping Drug ResistanceHain reverse hybridization line probe assay (HainLifescience, Nehren, Germany) Multiplex PCR and reverse hybridization Identifies major mutations in rpoB, katG and inhA – Detects MDR Demonstrated with specimens and cultureCepheid (Sunnyvale, CA) PCR and molecular beacon detection Detection of rpoB – surrogate for MDR Closed system with primary specimensAbbott’s Ibis, PLEX ID (Abbott Park, IL) Multiplex PCR and mass spectrometry Detection platform able to detect XDR Not evaluated with primary specimens
  33. 33. Tuberculosis in New York City
  34. 34. AIDS
  35. 35. 168th Street Men’s Shelter – March, 1992
  36. 36. W Strain MDR Outbreak in NYC January 1990 - August 1993 43 Months - 8,021 Cases 357 Patients with W strain tuberculosis Spread in NYC hospitals and state prisons All resistant to first line drugs 86% HIV infected; >90% Mortality 160 Patients identified since study 22 Patients identified outside of NYC Bifani et al., JAMA 1996:275;452. Munsiff et al., JID 2003:188;356.
  37. 37. Outbreak of the Multidrug Resistant “W” Tuberculosis Clone
  38. 38. W MDR Outbreak: 1990-1993 Isoniazid (100%) katG - 315:AGC>ACA; Ser>Thr Rifampin (100%) rpoB - 526:CAC>TAC; His>Tyr Streptomycin (100%) rpsL - 43:AAG>AGG: Lys>Arg Ethambutol (100%) embB - 306:ATG>GTG; Met>Val Pyrazinamide (55%) pncA - 139:ACC>GCC; Thr>Ala Kanamycin (92%) rrs - nucleotide 1400 Fluoroquinolones (0%)
  39. 39. W MDR OUTBREAK: 1993-1999 W34 W31 W40 W12 W25 W1 W1 W W
  40. 40. Creating Extremely Drug Resistant W StrainsMunsiff et al., JID 2003:188;356
  41. 41. XDR-TB OUTBREAK IN AN HIV-POSITIVE POPULATION IN SOUTH AFRICA15 YEARS LATER
  42. 42. Jan 2005 – March 2006 1,539 TB Diagnosed 542 Culture Positive Cases 168 MDR Cases 53 XDR Cases 52 / 53 Died 44 Patients tested: All HIV+MEDIAN SURVIVAL OF 16 DAYS FROM THE TIME OF DIAGNOSIS
  43. 43. XDR-TB OUTBREAK IN AN HIV-POSITIVE POPULATION IN SOUTH AFRICA IS6110 Fingerprint
  44. 44. WHO ESTIMATES: 25,000 CASES OF XDR-TB EMERGING EVERY YEAR
  45. 45.  As we learned in NYC during our HIV – MDR outbreak, it will take strong political will, dedicated medical and public health teams and a great deal of money to deal with this emerging epidemic – If not, XDR and all its baggage will appear at your doorsteps
  46. 46. Case Studies
  47. 47. Identity Crisis8/5/05: patient KD admitted to hospital “A” with diagnosis of suspected pulmonary tuberculosis  X-ray abnormal; sputum smear positive  Culture positive; resistant to INH8/10/05: patient threatens to leave hospital AMA  No health officer restraining order requested  1:1 monitoring in place8/11/05: patient leaves hospital AMA  Numerous attempts to locate patient prove futile  Fictitious identity and locating information provided to hospital by patient  Case filed as lost to follow-up
  48. 48. DNA Fingerprint of the M. tuberculosis from patient KD
  49. 49. Identity Crisis 4/5/06 Patient CB admitted to hospital “B” with diagnosis of suspected pulmonary tuberculosis  X-ray abnormal; sputum smear positive  Culture positive; resistant to INH, EMB, and PZA 4/6/06 patient threatens to leave hospital AMA  Patient uncooperative; Legal intervention requested  Health Officer hospital restraining order served  Despite completely different demographic information subtle physical similarities existed between patients KD and CB  CB denies any knowledge of KD
  50. 50. 1 2 JI strains isolated from patient “CB/KD” 1. 2005 2. 2006
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