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pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence

Nature Microbiology volume 1, Article number: 15019 (2016) Cite this article

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Abstract

Mycobacterium tuberculosis is a major, globally spread, aerosol-transmitted human pathogen, thought to have evolved by clonal expansion from a Mycobacterium canettii-like progenitor. In contrast, extant M. canettii strains are rare, genetically diverse, and geographically restricted mycobacteria of only marginal epidemiological importance. Here, we show that the contrasting evolutionary success of these two groups is linked to loss of lipooligosaccharide biosynthesis and subsequent morphotype changes. Spontaneous smooth-to-rough M. canettii variants were found to be mutated in the polyketide-synthase-encoding pks5 locus and deficient in lipooligosaccharide synthesis, a phenotype restored by complementation. Importantly, these rough variants showed an altered host–pathogen interaction and increased virulence in cellular- and animal-infection models. In one variant, lipooligosaccharide deficiency occurred via homologous recombination between two pks5 genes and removal of the intervening acyltransferase-encoding gene. The resulting single pks5 configuration is similar to that fixed in M. tuberculosis, which is known to lack lipooligosaccharides. Our results suggest that pks5-recombination-mediated bacterial surface remodelling increased virulence, driving evolution from putative generalist mycobacteria towards professional pathogens of mammalian hosts.

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Figure 1: Comparison of pks5 genomic region of various mycobacterial strains.
Figure 2: Complementation of morphology phenotypes of R variants.
Figure 3: PFGE and Southern hybridization analyses with PCR-derived probes binding either in a conserved domain of pks5 or within the pap gene.
Figure 4: Deficient LOS production in rough morphotypes.
Figure 5: Morphotype-associated differences in host–pathogen interaction.
Figure 6: Scheme showing supposed molecular key events in mycobacterial evolution from the recombinogenic M. canettii strain pool of putative environmental origin, towards professional pathogens of mammalian hosts evolved by clonal expansion of one emerging sublineage.

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Acknowledgements

The authors thank T. Seemann for initial help with NeighborNet analysis, and H. Pouseele for help with mapping and SNP analysis. The authors also thank I. Rosenkrands and G. Delogu for providing polyclonal anti-SigA antibodies and vector pMV10-25, respectively, and K. Sébastien for expert assistance in animal care in the biosafety-A3 facilities. The authors acknowledge support from a European Community grant (no. 260872), the EU-EFPIA Innovative Medicines Initiative (grant no. 115337), the Agence National de Recherche (ANR-14-JAMR-001-02) and the Fondation pour la Recherche Médicale FRM (DEQ20090515399 and DEQ20130326471). High-throughput sequencing was performed on the Genomics Platform, a member of the ‘France Génomique’ consortium (ANR10-INBS-09-08). R.B. is a member of the LabEx consortium IBEID at the Institut Pasteur. F.L.-C. was supported by the French Region Ile-de-France (Domaine d'Intérêt Majeur Maladies Infectieuses et Emergentes) PhD programme. E.C.B. was supported by a stipend from the Pasteur–Paris University (PPU) International PhD programme and the Institut Carnot Pasteur Maladies Infectieuses.

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Authors and Affiliations

  1. Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75015, Paris, France

    Eva C. Boritsch, Wafa Frigui, Alessandro Cascioferro, Alexandre Pawlik, Fabien Le Chevalier, Mickael Orgeur, Laleh Majlessi & Roland Brosch

  2. CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 31000, Toulouse, France

    Wladimir Malaga, Gilles Etienne, Françoise Laval, Mamadou Daffé & Christophe Guilhot

  3. Université de Toulouse, UPS, IPBS, 31000, Toulouse, France

    Wladimir Malaga, Gilles Etienne, Françoise Laval, Mamadou Daffé & Christophe Guilhot

  4. University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France

    Fabien Le Chevalier

  5. Institut Pasteur, PF1-Plate-Forme Génomique, Paris, France

    Laurence Ma & Christiane Bouchier

  6. Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia

    Timothy P. Stinear

  7. Inserm U1019, CNRS UMR8204, Université de Lille, Institut Pasteur de Lille, Center for Infection and Immunity, 59000, Lille, France

    Philip Supply

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Contributions

E.C.B., C.G., L. Majlessi and R.B. designed the study. E.C.B., W.F., F.L.C. and A.P. performed mycobacterial phenotypic assays and/or infection experiments. E.C.B., A.C. and R.B. established genetic constructs. W.M., G.E., F.L., M.D. and C.G. generated and/or analysed mycobacterial lipid and lipooligosaccharide profiles. E.C.B., L.Ma, C.B., M.O., T.P.S. and P.S. generated and/or analysed sequence data. E.C.B and L.Majlessi conducted and analysed immune assays. E.C.B., T.P.S., P.S., C.G. and R.B. wrote the manuscript, with comments from all authors.

Corresponding authors

Correspondence to Christophe Guilhot or Roland Brosch.

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Competing interests

P.S. is a consultant for Genoscreen. All other authors declare no competing financial interests.

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Supplementary Information

Supplementary Figures 1–13, Tables 1–5, Note, References and raw data (gels, blots and TLCs). (PDF 9240 kb)

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Boritsch, E., Frigui, W., Cascioferro, A. et al. pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence. Nat Microbiol 1, 15019 (2016). https://doi.org/10.1038/nmicrobiol.2015.19

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