![]() ![]() This disease is endemic in the United States and is a problem worldwide due to the severe economic consequences to dairy cattle as well as goat and sheep industries. avium subspecies paratuberculosis ( Map), which is the causative agent of Johne’s disease in cattle, sheep and other ruminant animals. However, through genome sequencing, differences have been identified and highlighted, especially for M. The MAC are all closely related genetically and thus it can be difficult to distinguish which species/subspecies are the cause in human infections. avium infections in humans manifest in three different forms: lymphadenitis ( Christensen and Koeppe, 2010), disseminated ( Ohkusu et al., 2004), or the most common, pulmonary ( Inderlied et al., 1993 Tran and Han, 2014). avium have recently been confirmed by calculating average nucleotide identity (ANI) and genome-to-genome distance pairwise values ( Tortoli et al., 2019). These include: avium, hominissuis, paratuberculosis, and silvaticum. avium, which are the focus of this study. There currently exist four subspecies within M. The Mycobacterium avium complex (MAC) comprises three species which include M. These genomes provide a more complete and detailed comparison of these subspecies strains as well as a blueprint for how genetic diversity originated. A total of 80% Map genes belonged to the Map core genome, while only 40% of non- Map genes belonged to the non- Map core genome. Finally, core and pangenomes were developed for Map and non- Map strains. ![]() SNP analysis and genome organization analyses repeatedly demonstrated the conserved nature of Map versus the mosaic nature of non- Map M. The Telford strain clustered with Maa strains as an intermediate between Map type II and Mah. The most evolutionarily distinct Map strain was an ovine strain, designated Telford, which had >1,000 SNPs and showed large rearrangements compared to the bovine type II strains. avium subspecies could be divided into two major sub-divisions, with the Map type II (bovine strains) clustering tightly on one end of a phylogenetic spectrum and Mah strains clustering more loosely together on the other end. Comparing recombination events along with the larger genome size and variance observed among Mycobacterium avium subspecies avium ( Maa) and Mycobacterium avium subspecies hominissuis ( Mah) strains (collectively termed non- Map) suggests horizontal gene transfer occurs in non- Map, but not in Map strains. The Mycobacterium avium subspecies paratuberculosis ( Map) genome size and organization was remarkably consistent, averaging 4.8 Mb with a variance of only 29.6 kb among the 13 strains. Each genome was confirmed to be classified correctly based on SNP genotyping, nucleotide identity and presence/absence of repetitive elements or other typing methods. These genomes represent strains from around the world and provided a unique opportunity to examine genome dynamics in this species. avium genomes had been annotated as RefSeq genomes, facilitating direct comparisons. At the inception of this study, twenty-eight M. Mycobacterium avium comprises four subspecies that contain both human and veterinary pathogens.
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