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Volume 7, Issue 1

Intraspecies plasmid and genomic variation of revealed by the complete genome sequences of two clinical isolates Open Access

Abstract

is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including and , many of the less common but clinically relevant NTM species, including , still lack complete genomes to serve as a comparative reference. Well-characterized representative genomes for each NTM species are important both for investigating the pathogenic potential of NTM, as well as for use in diagnostic methods, even for species that less frequently cause human disease. Here, we report the complete genomes of two strains, isolated from two unrelated patients. Hybrid short-read and long-read sequencing and assembly, using sequence reads from Illumina and Oxford Nanopore Technologies platforms, were utilized to resolve the chromosome and plasmid sequences of each isolate. The genome of NJH_MKUB1 had 5135 coding sequences (CDSs), a circular chromosome of length 5.3 Mb and two plasmids. The genome of NJH_MKUB2 had 5957 CDSs, a circular chromosome of 6.0 Mb and five plasmids. We compared our completed genomic assemblies to four recently released draft genomes of in order to better understand intraspecies genomic conservation and variability. We also identified genes implicated in drug resistance, virulence and persistence in the chromosome and plasmids. Virulence factors encoded in the genome and in the plasmids of provide a foundation for investigating how opportunistic environmental NTM may cause disease.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): hybrid genome assembly , MinION and whole-genome sequencing
Funding
This study was supported by the:
  • National Science Foundation (Award 1743587)
    • Principle Award Recipient: JenniferR. Honda
  • Padosi Foundation
    • Principle Award Recipient: JenniferR. Honda
  • Cystic Fibrosis Foundation
    • Principle Award Recipient: MichaelStrong
  • Cystic Fibrosis Foundation
    • Principle Award Recipient: L.Elaine Epperson
  • National Science Foundation (Award 1743587)
    • Principle Award Recipient: MichaelStrong
  • National Science Foundation (Award 1743587)
    • Principle Award Recipient: L.Elaine Epperson
  • National Institutes of Health (Award 5 T15 LM009451–12)
    • Principle Award Recipient: J.R. Hendrix
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2020-12-23
2024-04-16
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Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates
M Gen 7, 000497 (2021); https://doi.org/10.1099/mgen.0.000497
/content/journal/mgen/10.1099/mgen.0.000497
/content/journal/mgen/10.1099/mgen.0.000497
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