Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies

Siew Woh Choo; Shusruto Rishik; Wei Yee Wee

doi:10.1099/mgen.0.000495

Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies

Siew Woh Choo, Shusruto Rishik, Wei Yee Wee

Malaysia Sch of Science

Research output: Contribution to journal › Article › Research › peer-review

7 Citations (Scopus)

Abstract

Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum. Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum, supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Sub-species 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.

Original language	English
Article number	000495
Number of pages	12
Journal	Microbial Genomics
Volume	6
Issue number	12
DOIs	https://doi.org/10.1099/mgen.0.000495
Publication status	Published - Dec 2020

Keywords

Bacterial defence genes
Comparative genomics
DN/dS
Genomic islands
M. abscessus
M. immunogenum
Non-tuberculous mycobacteria
Rapidly growing mycobacteria
Subspecies
Taxonomy
Virulence

Access to Document

10.1099/mgen.0.000495Licence: CC BY

344978165-oaFinal published version, 3.78 MBLicence: CC BY

Cite this

@article{7d55f6b980864281aec9be1f1e2b225b,

title = "Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies",

abstract = "Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum. Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum, supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Sub-species 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.",

keywords = "Bacterial defence genes, Comparative genomics, DN/dS, Genomic islands, M. abscessus, M. immunogenum, Non-tuberculous mycobacteria, Rapidly growing mycobacteria, Subspecies, Taxonomy, Virulence",

author = "Choo, {Siew Woh} and Shusruto Rishik and Wee, {Wei Yee}",

note = "Funding Information: This work was funded by the high-level talent recruitment programme for academic and research platform construction (Reference Number: 5000105) from Wenzhou-Kean University. Publisher Copyright: {\textcopyright} 2020 The Authors. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2020",

month = dec,

doi = "10.1099/mgen.0.000495",

language = "English",

volume = "6",

journal = "Microbial Genomics",

issn = "2057-5858",

publisher = "Microbiology Society",

number = "12",

}

TY - JOUR

T1 - Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies

AU - Choo, Siew Woh

AU - Rishik, Shusruto

AU - Wee, Wei Yee

N1 - Funding Information: This work was funded by the high-level talent recruitment programme for academic and research platform construction (Reference Number: 5000105) from Wenzhou-Kean University. Publisher Copyright: © 2020 The Authors. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2020/12

Y1 - 2020/12

N2 - Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum. Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum, supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Sub-species 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.

AB - Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum. Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum, supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Sub-species 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.

KW - Bacterial defence genes

KW - Comparative genomics

KW - DN/dS

KW - Genomic islands

KW - M. abscessus

KW - M. immunogenum

KW - Non-tuberculous mycobacteria

KW - Rapidly growing mycobacteria

KW - Subspecies

KW - Taxonomy

KW - Virulence

UR - http://www.scopus.com/inward/record.url?scp=85099007264&partnerID=8YFLogxK

U2 - 10.1099/mgen.0.000495

DO - 10.1099/mgen.0.000495

M3 - Article

C2 - 33295861

AN - SCOPUS:85099007264

SN - 2057-5858

VL - 6

JO - Microbial Genomics

JF - Microbial Genomics

IS - 12

M1 - 000495

ER -

Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies

Abstract

Keywords

Access to Document

Other files and links

Cite this