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Exploring the plasmidome of non-tuberculous mycobacteria

M Diricks(1) N Wetzstein(2) M Merker(1) S Niemann(1)

1:Research center Borstel; 2:University Hospital Frankfurt

Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment and some species are causing rising numbers of infections in humans. Yet, it is unclear if this is due to an increase in virulence of some NTM strains or due to other factors. Plasmids for instance may play a pivotal role in transmitting virulence factors and resistance genes. However, studies focusing on these genetic elements in NTMs are scarce. Here, we determine the prevalence, characteristics and diversity of plasmids using different plasmid databases (NCBI and PLSDB). In addition, we evaluated the ability of different state-of-the-art plasmid prediction tools (plasmidspades, platon and SRST2) to reconstruct plasmids from short read sequencing data. A total of 199 complete genomes were available in NCBI for 18 clinically relevant NTM species. Among those, 60 genomes from nine species (including M. abscessus, M. avium, M. intracellulare, M. kansasii, M. fortuitum, M. lentiflavum, M. marinum, M. ulcerans and M. gordonae) harbored one up to five plasmids. The 154 NTM plasmids available in PLSDB were highly diverse with regard to length (4 kbp - 864 kbp), circularity (15% linear) and genomic content (few shared genes) but known resistance and virulence genes were typically absent. Genetically closely related plasmids were found in different NTMs, indicating that those plasmids can move across species barriers. Short sequencing reads can be used to detect the presence of known plasmids but de novo plasmid assembly remains a challenge. Overall, the results significantly broaden our knowledge of plasmids in NTMs and might facilitate further plasmidome studies.

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