Shay Lee Chong1, Joon Liang Tan2, Yun Fong Ngeow3,4. 1. Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450, Melaka, Malaysia. 2. Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450, Melaka, Malaysia. tjl2309@hotmail.com. 3. Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, 43000, Kajang, Selangor, Malaysia. 4. Center for Research On Communincable Diseases, Universiti Tunku Abdul Rahman, Bandar Sungai Long, 43000, Kajang, Selangor, Malaysia.
Abstract
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.
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.
Authors: Stefan Kurtz; Adam Phillippy; Arthur L Delcher; Michael Smoot; Martin Shumway; Corina Antonescu; Steven L Salzberg Journal: Genome Biol Date: 2004-01-30 Impact factor: 13.583
Authors: Ben Murrell; Joel O Wertheim; Sasha Moola; Thomas Weighill; Konrad Scheffler; Sergei L Kosakovsky Pond Journal: PLoS Genet Date: 2012-07-12 Impact factor: 5.917
Authors: Taras Y Nechitaylo; Mario Sandoval-Calderón; Tobias Engl; Natalie Wielsch; Diane M Dunn; Alexander Goesmann; Erhard Strohm; Aleš Svatoš; Colin Dale; Robert B Weiss; Martin Kaltenpoth Journal: Proc Natl Acad Sci U S A Date: 2021-04-27 Impact factor: 11.205