Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country
| Autor: | Matthias Egger, Marie Ballif, Hansjakob Furrer, Jean-Paul Janssens, Reno Frei, Katia Jaton, Sebastien Gagneux, Mireia Coscolla, Jan Fehr, Matthias Hoffmann, Marisa Dolina, Sara Droz, Sonia Borrell, Erik C. Böttger, Manuel Battegay, Alexandra Calmy, Thomas Bruderer, David Stucki, Lukas Fenner, Kathrin Zürcher, Jesica Mazza Stalder, Gaby E. Pfyffer, Ekkehardt Altpeter, Jacques Schrenzel, Hans L. Rieder, Hans H. Siegrist |
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| Přispěvatelé: | University of Zurich, Fenner, Lukas |
| Rok vydání: | 2016 |
| Předmět: |
Male
0301 basic medicine Epidemiology 2726 Microbiology (medical) 10234 Clinic for Infectious Diseases Switzerland/epidemiology 0302 clinical medicine Cluster Analysis 030212 general & internal medicine 610 Medicine & health ddc:616 Genetics Molecular Epidemiology biology 10179 Institute of Medical Microbiology Incidence Incidence (epidemiology) Middle Aged Mycobacterium tuberculosis/classification/genetics/isolation & purification Female 360 Social problems & social services Switzerland Adult Microbiology (medical) medicine.medical_specialty Tuberculosis Adolescent Emigrants and Immigrants Single-nucleotide polymorphism Polymorphism Single Nucleotide Mycobacterium tuberculosis Young Adult 03 medical and health sciences Internal medicine Disease Transmission Infectious medicine Humans Typing Genotyping Tuberculosis/epidemiology/microbiology/transmission business.industry Sequence Analysis DNA Odds ratio biology.organism_classification medicine.disease Confidence interval Molecular Typing 030104 developmental biology 570 Life sciences business Genome Bacterial Follow-Up Studies |
| Zdroj: | Journal of Clinical Microbiology, Vol. 54, No 7 (2016) pp. 1862-1870 |
| ISSN: | 1098-660X 0095-1137 |
| DOI: | 10.1128/jcm.00126-16 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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