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Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country.

  • Stucki D Swiss Tropical and Public Health Institute, Basel, Switzerland.
  • Ballif M Swiss Tropical and Public Health Institute, Basel, Switzerland.
  • Egger M Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
  • Furrer H Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland.
  • Altpeter E Division of Communicable Diseases, Federal Office of Public Health, Bern, Switzerland.
  • Battegay M Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
  • Droz S Mycobacteriology Unit, Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
  • Bruderer T Center for Laboratory Medicine, St. Gallen, Switzerland.
  • Coscolla M Swiss Tropical and Public Health Institute, Basel, Switzerland.
  • Borrell S Swiss Tropical and Public Health Institute, Basel, Switzerland.
  • Zürcher K Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
  • Janssens JP Division of Pneumology, University Hospital Geneva, Geneva, Switzerland.
  • Calmy A Division of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland.
  • Mazza Stalder J Division of Pneumology, University Hospital Lausanne, Lausanne, Switzerland.
  • Jaton K Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland.
  • Rieder HL Epidemiology, Biostatistics, and Prevention Institute, University of Zürich, Zürich, Switzerland.
  • Pfyffer GE Department of Medical Microbiology, Luzerner Kantonsspital, Lucerne, Switzerland.
  • Siegrist HH ADMed Microbiology, La Chaux-de-Fonds, Switzerland.
  • Hoffmann M Division of Infectious Diseases, Kantonsspital St. Gallen, St. Gallen, Switzerland.
  • Fehr J University Hospital Zürich and University of Zürich, Zürich, Switzerland.
  • Dolina M Servizio di Microbiologia EOLAB, Bellinzona, Switzerland.
  • Frei R Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.
  • Schrenzel J Laboratory of Bacteriology, University Hospitals of Geneva, Geneva, Switzerland.
  • Böttger EC Institute of Medical Microbiology, National Center for Mycobacteria, University of Zürich, Zürich, Switzerland.
  • Gagneux S Swiss Tropical and Public Health Institute, Basel, Switzerland.
  • Fenner L Swiss Tropical and Public Health Institute, Basel, Switzerland lukas.fenner@ispm.unibe.ch.
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  • 2016-05-20
Published in:
  • Journal of clinical microbiology. - 2016
Adolescent
Adult
Cluster Analysis
Disease Transmission, Infectious
Emigrants and Immigrants
Female
Follow-Up Studies
Genome, Bacterial
Humans
Incidence
Male
Middle Aged
Molecular Epidemiology
Molecular Typing
Mycobacterium tuberculosis
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Switzerland
Tuberculosis
Young Adult
English Immigrants from regions with a high incidence of tuberculosis (TB) are a risk group for TB in low-incidence countries such as Switzerland. In a previous analysis of a nationwide collection of 520 Mycobacterium tuberculosis isolates from 2000 to 2008, we identified 35 clusters comprising 90 patients based on standard genotyping (24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat [MIRU-VNTR] typing and spoligotyping). Here, we used whole-genome sequencing (WGS) to revisit these transmission clusters. Genome-based transmission clusters were defined as isolate pairs separated by ≤12 single nucleotide polymorphisms (SNPs). WGS confirmed 17/35 (49%) MIRU-VNTR typing clusters; the other 18 clusters contained pairs separated by >12 SNPs. Most transmission clusters (3/4) of Swiss-born patients were confirmed by WGS, as opposed to 25% (4/16) of the clusters involving only foreign-born patients. The overall clustering proportion was 17% (90 patients; 95% confidence interval [CI], 14 to 21%) by standard genotyping but only 8% (43 patients; 95% CI, 6 to 11%) by WGS. The clustering proportion was 17% (67/401; 95% CI, 13 to 21%) by standard genotyping and 7% (26/401; 95% CI, 4 to 9%) by WGS among foreign-born patients and 19% (23/119; 95% CI, 13 to 28%) and 14% (17/119; 95% CI, 9 to 22%), respectively, among Swiss-born patients. Using weighted logistic regression, we found weak evidence of an association between birth origin and transmission (adjusted odds ratio of 2.2 and 95% CI of 0.9 to 5.5 comparing Swiss-born patients to others). In conclusion, standard genotyping overestimated recent TB transmission in Switzerland compared to WGS, particularly among immigrants from regions with a high TB incidence, where genetically closely related strains often predominate. We recommend the use of WGS to identify transmission clusters in settings with a low incidence of TB.
Language
  • English
Open access status
bronze
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/269554
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