Proposal of a new method for subtyping of Mycobacterium kansasii based upon PCR restriction enzyme analysis of the tuf gene

Bakuła, Zofia; Modrzejewska, Magdalena; Safianowska, Aleksandra; Ingen, Jakko van; Proboszcz, Małgorzata; Bielecki, Jacek; Jagielski, Tomasz

doi:10.1016/j.diagmicrobio.2015.12.009

Cited by 16 publications

(33 citation statements)

References 21 publications

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“…For genotypic identification, total DNA was purified from solid bacterial cultures with a standard extraction method described previously (Santos et al, 1992). Genotyping of M. kansasii strains was performed by PCR-RFLP analysis of the hsp65, rpoB, and tuf genes, as reported elsewhere (Telenti et al, 1993;Kim et al, 2001;Bakuła et al, 2016).…”

Section: Species Identification and Genotypingmentioning

confidence: 99%

“…Whereas, the former had type I-specific sequence of the hsp65 gene and type IIspecific sequence of the spacer region, the latter displayed type II-specific spacer sequence and a unique hsp65 gene sequence (Iwamoto and Saito, 2005). The separateness of the M. kansasii subspecies was further supported by polymorphisms at other genetic loci, including the RNA polymerase gene (rpoB) and the translational elongation factor Tu (tuf ), successfully applied for the differentiation between the subspecies I-VI (Kim et al, 2001;Bakuła et al, 2016). Noteworthy, the inter-subspecies differences have been detected at the protein level.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Insights Into the Mycobacterium kansasii Complex: An Update

et al. 2020

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Only very recently, has it been proposed that the hitherto existing Mycobacterium kansasii subtypes (I-VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (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 M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf 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 M. kansasii 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., Mycobacterium ostraviense 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 M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. 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 M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum 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 M. kansasii-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 Jagielski et al. Genomic Insights Into Mycobacterium kansasii Complex are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro 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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Section: Species Identification and Genotypingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic Insights Into the Mycobacterium kansasii Complex: An Update

et al. 2020

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“…Grouping of M. kansasii into seven genetically similar subtypes (I to VII) adds more complexity to the clinical and epidemiological relevance of M. kansasii isolations. Of the M. kansasii subtypes, type I has been isolated most frequently from human sources and involved in the causation of NTM disease (3–5). …”

Section: Genome Announcementmentioning

confidence: 99%

“…Genotyping was performed by means of PCR-restriction endonuclease analysis for the hsp65 and tuf genes, as previously described (4, 8). Illumina paired-end libraries were prepared with the Nextera XT kit, in accordance with the manufacturer’s instructions.…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequences of Mycobacterium kansasii Clinical Strains

et al. 2017

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“…Eine Studie aus Kroatien macht für die unterschiedliche Häufigkeitsverteilung pulmonaler NTM zwischen küstennahen und städtischen Gebieten auch eine unterschiedliche Wasserversorgung verantwortlich[29]. Auch wenn für M. kansasii bis heute sieben verschiedene Genotypen beschrieben wurden, so wurden aus humanen Proben mit Krankheitswert bisher fast ausschließlich Typ I (und seltener Typ II) isoliert[30,31]. In der Schweizer Studie von Taillard et al mit 114 Patienten wurde der Genotyp I in 67 % aller Isolate nachgewiesen, die Genotypen II und III-VII nur in 21 % und 8 %.…”

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