Insights on the Emergence of Mycobacterium tuberculosis from the Analysis of Mycobacterium kansasii

Advance Access publication February Insights on the Emergence of Mycobacterium tuberculosis from the Analysis of Mycobacterium kansasii Joyce Wang 1 2 Fiona McIntosh 0 1 Nicolas Radomski 0 1 Ken Dewar 6 Roxane Simeone 5 Jost Enninga 4 Roland Brosch 5 Eduardo P. Rocha 3 Fre de ric J. Veyrier 1 8 Marcel A. Behr 1 2 7 0 Research Institute of the McGill University Health Centre , Montreal, Que bec , Canada 1 McGill International TB Centre , Montreal, Que bec , Canada 2 Department of Microbiology and Immunology, McGill University , Montreal, Que bec , Canada 3 Microbial Evolutionary Genomics Unit, Institut Pasteur , Paris , France 4 Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur , Paris , France 5 Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur , Paris , France 6 McGill University and Ge nome Qu e bec Innovation Center , Montreal, Que bec , Canada 7 Department of Medicine, McGill University , Montreal, Que bec , Canada 8 INRS-Institut Armand-Frappier , Laval, Que bec , Canada By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium tuberculosis. Yet, although both organisms cause pulmonary disease, M. tuberculosis is a global health menace, whereas M. kansasii is an opportunistic pathogen. To illuminate the differences between these organisms, we have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478) and conducted side-by-side in vitro and in vivo investigations of these two organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise comparisons reveal conserved and discordant genes and genomic regions. A notable example of genomic conservation is the virulence locus ESX-1, which is intact and functional in the low-virulence M. kansasii, potentially mediating phagosomal disruption. Differences between these organisms include a decreased predicted metabolic capacity, an increased proportion of toxin-antitoxin genes, and the acquisition of M. tuberculosis-specific genes in the pathogen since their common ancestor. Consistent with their distinct epidemiologic profiles, following infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3 weeks. Together, these data suggest that M. kansasii can serve as an image of the environmental ancestor of M. tuberculosis before its emergence as a professional pathogen, and can be used as a model organism to study the switch from an environmental opportunistic pathogen to a professional host-restricted pathogen. mycobacteria; phylogeny; comparative genomics; virulence; Mycobacterium kansasii Introduction First identified in 1953 as the yellow bacillus (Pollak and Buhler 1953), Mycobacterium kansasii is an acid-fast bacterium that can cause a pulmonary disease in immunocompromised individuals and those with underlying pulmonary conditions such as chronic obstructive pulmonary disease and silicosis (Lillo et al. 1990; Corbett et al. 1999; Canueto-Quintero et al. 2003; Griffith et al. 2007). This disease resembles that caused by Mycobacterium tuberculosis in that patients experience similar symptoms (chest pain, productive cough, and weight loss), with comparable radiographic features (Evans, Colville, et al. 1996; Evans, Crisp, et al. 1996; Ellis 2004) and both infections can be treated with standard antituberculosis agents (Griffith et al. 2007). However, The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. although tuberculosis (TB) is a global pandemic (World Health Organization 2013), M. kansasii infections are uncommon in the general population (Good and Snider 1982; Marras et al. 2007; Cassidy et al. 2009), and human-to-human M. kansasii transmission, if any, has rarely been documented (Davies 1994; Ricketts et al. 2014). The absence of transmission of M. kansasii infection in humans marks an evolutionary deadend for this environmental organism, a scenario also described in Legionella, an accidental pathogen, and animalhuman zoonotic pathogens such as Campylobacter jejuni and Salmonella enterica (Sokurenko et al. 2006; Sanchez-Buso et al. 2014). Unlike M. kansasii, which is frequently found in aquatic environments (McSwiggan and Collins 1974; Joynson 1979; Kaustova et al. 1981; Thomson et al. 2013), the tubercle bacillus M. tuberculosis has no identified environmental reservoir. Rather, both phylogeographic and paleo-DNA studies present M. tuberculosis as a human-adapted pathogen that originated in Africa and accompanied the migrations of modern humans throughout the world (Wirth et al. 2008; Gagneux 2012; Comas et al. 2013). Despite these clear epidemiologic differences, the organisms share many similarities. Similar to M. tuberculosis, M. kansasii can grow at 37 C with growth seen after 23 weeks on Lo wensteinJensen medium (Roberts 1981). Mycobacterium kansasii is also positive for urease production, thiophene-2-carboxylic hydrazide resistance, and nitrate reduction (Roberts 1981; Tsukamura 1985), phenocopying biochemical characteristics long used for the laboratory identification of M. tuberculosis. In contrast, M. kansasii is a photochromogenic bacterium that produces carotenoid pigments against UV damage, a feature common to environmental organisms but lacking in M. tuberculosis (Tsukamura 1964; Robledo et al. 2011). Additionally, M. kansasii can utilize a much wider array of carbon and nitrogen sources to support growth than M. tuberculosis (Tsukamura et al. 1969; Tsukamura 1983), potentially capitalizing on a broader pool of nutrient sources in the environment. As more complete mycobacterial genomes become available, comparative genomic studies provide the opportunity to identify testable differences between related, but biologically distinct species. For example, the smooth tubercle bacilli, exemplified by Mycobacterium canettii, are considered to be the most closely related species to M. tuberculosis, yet a number of genetic differences have been documented between these organisms (Gutierrez et al. 2005; Fabre et al. 2010; Supply et al. 2013). The observation that M. canettii causes TB in apparently immunocompetent hosts, along with its lack of a known environmental reservoir, together suggests that the biology of M. canettii may be more similar to M. tuberculosis than their putative environmental ancestor. To elucidate the speciation of M. tuberculosis on a larger evolutionary scale, we have compared M. tuberculosis with M. kansasii. Previous analysis, using multilocus sequence analysis, has id (...truncated)