ArticleNature medicine2016
Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis.
Article in Nature medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers, 1 of them a synthesis that pooled it.
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Who cites it
96 citing papers in PubMed, 1 synthesis or guideline pooled it, 150 citations in OpenAlex.
- Molecular clustering of patients with diabetes and pulmonary tuberculosis: A systematic review and meta-analysis.PloS one · 2017Pooled it
- Population-level genome sequencing reveals distinctmSystems · 2026Article
- Within-host pathogen population diversity predicts treatment response in Tuberculosis.medRxiv : the preprint server for health sciences · 2026Article
- Population-level genome sequencing reveals distinct Mycobacterium tuberculosis intrahost mutational trajectories in simian immunodeficiency virus co-infected and antiretroviral treated non-human primates.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- Within-Host Environmental Heterogeneity Is Associated With Phenotypic but Not Genomic Diversity in Wolbachia Endosymbionts.Environmental microbiology reports · 2026Article
- Resistance variation and bacterial interactions shape adaptation of a genetically diverse pathogen population to antibiotic therapy.The ISME journal · 2026Article
- Heteroresistance inFrontiers in cellular and infection microbiology · 2026Review
- Mycobacterium tuberculosis biology, pathogenicity and interaction with the host.Nature reviews. Microbiology · 2025Review
- Primary tuberculous mycobacterial granulomas provide a niche for superinfecting Mycobacterium abscessus.Nature communications · 2025Article
- Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex.Nature reviews. Microbiology · 2025Review
- Within-host bacterial evolution and the emergence of pathogenicity.Nature microbiology · 2025Review
- Population sequencing for phylogenetic diversity and transmission analyses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.Cell host & microbe · 2025Article
- Detection of a Mixed-Strain Infection with Drug- and Multidrug-ResistantAntibiotics (Basel, Switzerland) · 2025Article
- Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species.bioRxiv : the preprint server for biology · 2025Article
- Type VII secretion system gene mutations driving global mycobacterium tuberculosis transmission revealed by whole genomic sequence.Frontiers in cellular and infection microbiology · 2025Article
- From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance.Annual review of microbiology · 2024Review
- Molecular characteristics of drug-susceptible Mycobacterium tuberculosis clinical isolates based on treatment duration.Osong public health and research perspectives · 2024Article
- Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis across different settings.Nature communications · 2024Article
36 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
Abstract
Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.