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The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer

BACKGROUND: Mycobacteroides abscessus complex (MABC), an emerging pathogen, causes human infections resistant to multiple antibiotics. In this study, the genome data of 1,581 MABC strains were downloaded from NCBI database for phylogenetic relatedness inference, resistance profile identification and...

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Autores principales: Chong, Shay Lee, Tan, Joon Liang, Ngeow, Yun Fong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9583574/
https://www.ncbi.nlm.nih.gov/pubmed/36261788
http://dx.doi.org/10.1186/s12864-022-08941-7
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author Chong, Shay Lee
Tan, Joon Liang
Ngeow, Yun Fong
author_facet Chong, Shay Lee
Tan, Joon Liang
Ngeow, Yun Fong
author_sort Chong, Shay Lee
collection PubMed
description BACKGROUND: Mycobacteroides abscessus complex (MABC), an emerging pathogen, causes human infections resistant to multiple antibiotics. In this study, the genome data of 1,581 MABC strains were downloaded from NCBI database for phylogenetic relatedness inference, resistance profile identification and the estimation of evolutionary pressure on resistance genes in silico. RESULTS: From genes associated with resistance to 28 antibiotic classes, 395 putative proteins (ARPs) were identified, based on the information in two antibiotic resistance databases (CARD and ARG-ANNOT). The ARPs most frequently identified in MABC were those associated with resistance to multiple antibiotic classes, beta-lactams and aminoglycosides. After excluding ARPs that had undergone recombination, two ARPs were predicted to be under diversifying selection and 202 under purifying selection. This wide occurrence of purifying selection suggested that the diversity of commonly shared ARPs in MABC have been reduced to achieve stability. The unequal distribution of ARPs in members of the MABC could be due to horizontal gene transfer or ARPs pseudogenization events. Most (81.5%) of the ARPs were observed in the accessory genome and 72.2% ARPs were highly homologous to proteins associated with mobile genetic elements such as plasmids, prophages and viruses. On the other hand, with TBLASTN search, only 18 of the ARPs were identified as pseudogenes. CONCLUSION: Altogether, our results suggested an important role of horizontal gene transfer in shaping the resistome of MABC. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08941-7.
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spelling pubmed-95835742022-10-21 The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer Chong, Shay Lee Tan, Joon Liang Ngeow, Yun Fong BMC Genomics Research BACKGROUND: Mycobacteroides abscessus complex (MABC), an emerging pathogen, causes human infections resistant to multiple antibiotics. In this study, the genome data of 1,581 MABC strains were downloaded from NCBI database for phylogenetic relatedness inference, resistance profile identification and the estimation of evolutionary pressure on resistance genes in silico. RESULTS: From genes associated with resistance to 28 antibiotic classes, 395 putative proteins (ARPs) were identified, based on the information in two antibiotic resistance databases (CARD and ARG-ANNOT). The ARPs most frequently identified in MABC were those associated with resistance to multiple antibiotic classes, beta-lactams and aminoglycosides. After excluding ARPs that had undergone recombination, two ARPs were predicted to be under diversifying selection and 202 under purifying selection. This wide occurrence of purifying selection suggested that the diversity of commonly shared ARPs in MABC have been reduced to achieve stability. The unequal distribution of ARPs in members of the MABC could be due to horizontal gene transfer or ARPs pseudogenization events. Most (81.5%) of the ARPs were observed in the accessory genome and 72.2% ARPs were highly homologous to proteins associated with mobile genetic elements such as plasmids, prophages and viruses. On the other hand, with TBLASTN search, only 18 of the ARPs were identified as pseudogenes. CONCLUSION: Altogether, our results suggested an important role of horizontal gene transfer in shaping the resistome of MABC. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08941-7. BioMed Central 2022-10-20 /pmc/articles/PMC9583574/ /pubmed/36261788 http://dx.doi.org/10.1186/s12864-022-08941-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Chong, Shay Lee
Tan, Joon Liang
Ngeow, Yun Fong
The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer
title The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer
title_full The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer
title_fullStr The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer
title_full_unstemmed The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer
title_short The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer
title_sort resistomes of mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9583574/
https://www.ncbi.nlm.nih.gov/pubmed/36261788
http://dx.doi.org/10.1186/s12864-022-08941-7
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