Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis

• Published in: Nature medicine Vol. 22; no. 12; pp. 1470 - 1474
• Main Authors: Lieberman, Tami D, Wilson, Douglas, Misra, Reshma, Xiong, Lealia L, Moodley, Prashini, Cohen, Ted, Kishony, Roy
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2016; Nature Publishing Group
• Subjects: 631/181/2474; 631/326/107; 631/326/325/2482; 692/308/174; 692/699/255/1856; Adult; Aged; Autopsies; Autopsy; Bacteria; Bacteriological Techniques; Biodiversity; Biomedicine; Cancer Research; Coinfection - microbiology; DNA, Bacterial - genetics; Female; Genetic aspects; Genetic diversity; Genetic Variation; Genomics; HIV; HIV Infections - complications; Human immunodeficiency virus; Humans; Infectious Diseases; Lentivirus; letter; Liver - microbiology; Lung - microbiology; Lymph Nodes - microbiology; Male; Metabolic Diseases; Middle Aged; Molecular Medicine; Mycobacterium tuberculosis; Mycobacterium tuberculosis - genetics; Neurosciences; Outbreaks; Pathogens; Phylogeny; Polymorphism, Single Nucleotide; Retroviridae; South Africa; Spleen - microbiology; Tuberculosis; Tuberculosis - complications; Tuberculosis - microbiology; Tuberculosis, Hepatic - complications; Tuberculosis, Hepatic - microbiology; Tuberculosis, Lymph Node - complications; Tuberculosis, Lymph Node - microbiology; Tuberculosis, Pulmonary - complications; Tuberculosis, Pulmonary - microbiology; Tuberculosis, Splenic - complications; Tuberculosis, Splenic - microbiology; South Africa
• DOI: 10.1038/nm.4205
• ISSN: 1078-8956

Genomic analysis of Mycobacterium tuberculosis in postmortem biopsies provides a window into intrahost diversification of a disseminated pathogen. Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV 1 . Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history 2 , 3 , 4 , 5 and in local outbreaks 6 , 7 , 8 , 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.