Molecular Epidemiology of Mycobacterium tuberculosis Across 3 Distinct Geographic Sites in South Africa

作者：Theresa Ryckman, Lincoln Hopkins, Linrui Tang, Patrick Biché, Mbali Mohlamonyane, Matshidiso Morolo, Bareng A. S. Nonyane, Khatija Ahmed, Neil Martinson, Colleen F. Hanrahan, Shaheed Vally Omar, Barun Mathema, David W. Dowdy · 发表于：The Journal of Infectious Diseases · 年份：2025 · DOI：10.1093/infdis/jiaf326 · 被引用次数：2 · 研究领域：Tuberculosis Research and Epidemiology、Diagnosis and treatment of tuberculosis、Mycobacterium research and diagnosis

BACKGROUND: Whole genome sequence data can generate insights about Mycobacterium tuberculosis (Mtb) transmission. We used whole genome sequencing and linked epidemiology data from a recent randomized trial to characterize Mtb relatedness across 3 geographically distinct South African sites. METHODS: We sequenced culture isolates from participants with culture-positive tuberculosis in the Kharituwe study, which evaluated household contact investigation strategies in 1 urban and 2 rural sites. We adapted a previous bioinformatic pipeline to clean, extract, and filter Mtb reads; perform reference alignment; calculate single-nucleotide polymorphism (SNP) distances between isolates; and group isolates into clusters linked by recent transmission based on 3 SNP-based cutoffs. Sequence data were linked to individual data on demographics and risk factors. We analyzed clustering across and within study sites and used log-binomial regression to assess characteristics associated with clustering. RESULTS: At a cutoff of 12 SNPs, 213 of 714 sequenced isolates passing quality control filters were clustered. While only 3 of 45 pairs included participants from different sites, the majority of clusters with ≥4 participants included representation from at least 2 sites. Expanding to a 20-SNP cutoff revealed a large cluster containing 10% of isolates, with urban/rural representation mirroring that of all the isolates (61% urban, 39% rural). Participants from the urban site, TB household contacts...