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

Nature Medicine volume 22, pages 1470–1474 (2016)Cite this article

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Abstract

Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV1. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history2,3,4,5 and in local outbreaks6,7,8, 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.

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Figure 1: Postmortem analysis of 2,693 M. tuberculosis samples from 329 sites across the bodies of 44 subjects.
Figure 2: Genomic sequencing reveals variation due to mixed infection and de novo mutation.
Figure 3: M. tuberculosis diversity within the lungs is spatially structured.
Figure 4: M. tuberculosis dissemination within lungs, between lungs and between organs follows similar dynamics.

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Acknowledgements

We thank L. Maziya, Z. Magcaba, N. Xengxe and M.J. Khumalo for their assistance with enrollment and postmortem analyses, the Edendale Hospital management and the KwaZulu-Natal Department of Health. We are grateful to M. Baym and members of the Kishony lab for helpful discussions, C. Duvallet for comments on the manuscript, and H. Chung for discussions of spatial diversity and comments on the manuscript. We thank the team at Macrogen Clinical Laboratories for their help with Illumina sequencing and I. Comas (University of Valencia) for providing the M. tuberculosis reference sequence. This work was funded in part by US National Institutes of Health grants DP2 OD006663 (T.C.) and R01-GM081617 (R.K.), F. Hoffman LaRoche, Inc. (R.K.), and European Research Council FP7 ERC grant 281891 (R.K.).

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Author notes

  1. Ted Cohen and Roy Kishony: These authors jointly directed this work.

Authors and Affiliations

  1. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA

    Tami D Lieberman, Lealia L Xiong & Roy Kishony

  2. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Tami D Lieberman

  3. Department of Internal Medicine, Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa

    Douglas Wilson

  4. Department of Infection Prevention and Control, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa

    Reshma Misra & Prashini Moodley

  5. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA

    Ted Cohen

  6. Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA

    Ted Cohen

  7. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA

    Ted Cohen

  8. Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel

    Roy Kishony

  9. Faculty of Computer Science, Technion–Israel Institute of Technology, Haifa, Israel

    Roy Kishony

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Contributions

T.C. and D.W. conceived and coordinated the study; T.D.L., D.W., T.C. and R.K. designed the study; D.W. identified eligible decedents and conducted postmortem biopsies; R.M. and P.M. processed and cultured samples, performed antibiotic sensitivity testing and extracted DNA; T.D.L. and L.L.X. prepared genomic libraries; T.D.L. and R.K. analyzed genomic data; T.D.L., D.W., T.C. and R.K. interpreted results and wrote the manuscript.

Corresponding authors

Correspondence to Ted Cohen or Roy Kishony.

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The authors declare no competing financial interests.

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Supplementary Figures 1–7, Supplementary Tables 1–3 and Supplementary Note (PDF 1595 kb)

Supplementary Table 4

All de novo mutations detected in M. tuberculosis samples grown from autopsy specimens from 44 subjects. (CSV 233 kb)

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Lieberman, T., Wilson, D., Misra, R. et al. Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis. Nat Med 22, 1470–1474 (2016). https://doi.org/10.1038/nm.4205

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