Genomic Insights Into the Complex: An Update.

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ID: 91123
2019
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Abstract
Only very recently, has it been proposed that the hitherto existing subtypes (I-VI) should be elevated, each, to a species rank. Consequently, the former subtypes have been denominated as (former type I), (II), (III), (V), and (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, , and genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, a monophyletic origin, and overlapping phenotypes, our findings support the recognition of the complex (MKC), accommodating all -derived species and . None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of . To distinguish, most reliably, between the MKC species, and between and in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the -derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug.
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jagielski2019genomicfrontiers Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Tomasz Jagielski, Paulina Borówka, Zofia Bakuła, Jakub Lach, Błażej Marciniak, Anna Brzostek, Jarosław Dziadek, Mikołaj Dziurzyński, Lian Pennings, Jakko van Ingen, Manca Žolnir-Dovč, Dominik Strapagiel
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Journal Frontiers in microbiology
Year 2019
DOI
10.3389/fmicb.2019.02918
URL
Keywords
taxonomy whole genome sequencing non-tuberculous mycobacteria (ntm) mycobacterium kansasii complex mycobacterium ostraviense sp. nov.

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