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Iskalni niz: "avtor" (Dominik Strapagiel) .

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1.
Genomic insights into the Mycobacterium kansasii complex : an update
Paulina Borówka, Tomasz Jagielski, Dominik Strapagiel, Marija Žolnir-Dovč, Jakobus van Ingen, Lian Pennings, Mikołaj Dziurzyński, Jarosław Dziadek, Anna Brzostek, Błażej Marciniak, Jakub Lach, Zofia Bakuła, 2020

Povzetek: Only very recently, has it been proposed that the hitherto existing Mycobacteriumkansasii 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, amonophyletic 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 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.
Ključne besede: Mycobacteriumkansasii complex, Mycobacteriumostraviense sp. nov., non-tuberculous mycobacteria (NTM), whole genome sequencing, taxonomy
DiRROS - Objavljeno: 31.07.2020; Ogledov: 838; Prenosov: 431
.pdf Celotno besedilo (10,22 MB)

2.
Subspecies-specific sequence detection for differentiation of Mycobacterium abscessus complex
Alina Minias, Lidia Żukowska, Jakub Lach, Tomasz Jagielski, Dominik Strapagiel, Su-Young Kim, Won-Jung Koh, Heather Adam, Ruth Bittner, Sara Truden, Marija Žolnir-Dovč, Jarosław Dziadek, 2020

Povzetek: Mycobacterium abscessus complex (MABC) is a taxonomic group of rapidly growing, nontuberculous mycobacteria that are found as etiologic agents of various types of infections. They are considered as emerging human pathogens. MABC consists of 3 subspecies - M. abscessus subsp. bolletti, M. abscessus subsp. massiliense and M. abscessus subsp. abscessus. Here we present a novel method for subspecies differentiation of M. abscessus named Subspecies-Specific Sequence Detection (SSSD). This method is based on the presence of signature sequences present within the genomes of each subspecies of MABC. We tested this method against a virtual database of 1505 genome sequences of MABC. Further, we detected signature sequences of MABC in 45 microbiological samples through DNA hybridization. SSSD showed high levels of sensitivity and specificity for differentiation of subspecies of MABC, comparable to those obtained by rpoB sequence typing.
Ključne besede: Mycobacterium abscessus complex, nontuberculous mycobacteria, diagnosis
DiRROS - Objavljeno: 23.11.2020; Ogledov: 11128; Prenosov: 322
.pdf Celotno besedilo (1,23 MB)

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