Jagielski Tomasz, Borówka Paulina, Bakuła Zofia, Lach Jakub, Marciniak Błażej, Brzostek Anna, Dziadek Jarosław, Dziurzyński Mikołaj, Pennings Lian, van Ingen Jakko, Žolnir-Dovč Manca, Strapagiel Dominik
Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland.
Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
Front Microbiol. 2020 Jan 15;10:2918. doi: 10.3389/fmicb.2019.02918. eCollection 2019.
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.
直到最近，才有提议将迄今存在的亚型（I - VI）各自提升到物种等级。因此，之前的亚型被命名为（原I型）、（II型）、（III型）、（V型）和（VI型）。本研究通过使用一种三管齐下的计算策略扩展了最近发表的研究结果，该策略基于比对分数 - 平均核苷酸同一性、基因组到基因组距离和核心基因组系统发育，而且样本本质上是独立的且规模更大，从而对该复合体给出了更精确和完整的描述。此外，使用了五个典型的分类标记，即16S rRNA、、和基因，以及16S - 23S rRNA基因间隔区（ITS）。这三种主要方法产生了高度一致的结果，证实了每个亚型确实代表一个独特物种的观点。这项工作不仅巩固了当前确立的五个物种的地位，还对第六个物种进行了描述，即新种，以取代之前的IV型亚型。通过显示出密切的遗传相关性、单系起源和重叠的表型，我们的研究结果支持对复合体（MKC）的认可，该复合体包含所有源自的物种和。没有一种最常用的分类标记能准确区分所有的MKC物种。同样，除了的非光致变色性外，未发现允许在该复合体内进行物种区分的物种特异性表型特征。为了最可靠地区分MKC物种，特别是区分和，应采用基于全基因组的方法。由于在源自的物种中差异1基因的毒力相关区域分布没有明显差异，这些物种各自的致病潜力只能根据它们在临床相关人群中的流行情况进行推测性评估。需要大规模的分子流行病学研究来更好地理解MKC物种的临床意义和病理生物学。药物敏感性分析结果强调了利福平在治疗MKC引起的感染中的优先地位，同时由于对乙胺丁醇的高耐药性而削弱了其使用。
