Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains

Behra, Phani Rama Krishna; Das, Sarbashis; Pettersson, B. M. Fredrik; Shirreff, Lisa; DuCote, Tanner; Jacobsson, Karl-Gustav; Ennis, Don G.; Kirsebom, Leif A.

doi:10.1038/s41598-019-40922-x

Cited by 14 publications

(29 citation statements)

References 85 publications

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“…In contrast to the Mmuc T - Mpho T tRNA cluster, the Maub T gene cluster encompasses both tRNA and protein genes. Large tRNA gene clusters have previously been reported to be present in M. abscessus M24 (34 tRNA genes; [91]) and M. conceptionense MLE (37 tRNA genes; NCBI bioproject id PRJNA288077; see also [92]). The majority of the tRNA genes encompassing the Maub T cluster are also present in the M. abscessus M24 and M. conceptionense MLE clusters (Additional file 3: Figure S11b; Table S5).…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

et al. 2019

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Background Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum ( Mmuc ) and Mycobacterium neoaurum ( Mneo ) clade members. Results Genome sizes for Mmuc- and Mneo -clade members vary between 5.4 and 6.5 Mbps with the complete Mmuc T (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNA Ile TAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales -derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc -clade members. Conclusions Phages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc - and Mneo -clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1447-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

et al. 2019

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“…For the M. chelonae-abscessus complex, the reported number of σ factors is 17 to 19 [ 49 ]. Behra and coworkers (2019) reported three sigJ orthologs in the M. chelonae genome and four in the M. abscessus genome [ 49 ], while the absence of sigK in the M. abscessus genome was also registered [ 49 ].…”

Section: Mycobacteria Ecology: the Underlying Resilience Biologymentioning

confidence: 99%

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

et al. 2020

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Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.

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“…Mycobacterium spp. are acid‐fast, Gram‐positive, nonmotile, aerobic bacilli (Aubry et al 2017) that are associated with disease in both aquatic and terrestrial animals (Park et al 2008; Lage et al 2015; Aubry et al 2017; Behra et al 2019). Mycobacteriosis has been reported in a broad range of freshwater, marine‐water, and brackish‐water fish species (Francis‐Floyd 2011; Delghandi et al 2020), and numerous reports have highlighted outbreaks that resulted in considerable losses in cultured fish (Ashburner 1977; Hedrick et al 1987).…”

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Mycobacterium salmoniphilum and M. chelonae in Captive Populations of Chinook Salmon

et al. 2021

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Chinook Salmon Oncorhynchus tshawytscha is a keystone fish species in the Pacific Northwest. In 2019, unusual mortalities occurred in two different populations of cultured fingerlings from the same facility in California, USA. The systems consist of outdoor, enclosed, flow‐through freshwater tanks that are maintained at 18 ± 1°C. Clinical signs and gross findings were only observed in one population and included abnormal swimming, inappetence, lethargy, skin discoloration, and the presence of multifocal nodular and ulcerative skin lesions. Microscopic lesions were infrequent and consisted of severe, locally extensive granulomatous dermatitis and myositis and mild, multifocal, granulomatous branchitis, myocarditis, and hepatitis. Intracellular acid‐fast organisms were observed within areas of granulomatous myositis. Posterior kidney swabs were collected and inoculated in nutrient‐rich and selective agar media and incubated at 25°C for 2 weeks. Visibly pure bacterial colonies were observed 7–10 d postinoculation. Partial sequences of 16S rRNA initially identified the recovered bacteria as members of the genus Mycobacterium. However, marked variability was observed among Mycobacterium spp. isolates by using repetitive extragenic palindromic polymerase chain reaction fingerprinting. Amplification and sequencing of the ribosomal RNA internal transcribed spacer, 65‐kDa heat shock protein, and RNA polymerase β‐subunit gene of the cultured isolates identified M. salmoniphilum and M. chelonae, discrete members of the M. chelonae‐abscessus complex, isolated from diseased Chinook Salmon fingerlings.

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Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains

Cited by 14 publications

References 85 publications

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

Mycobacterium salmoniphilum and M. chelonae in Captive Populations of Chinook Salmon

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