Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand
The worldwide spread of carbapenem-resistant Acinetobacter baumannii (CRAB) has become a healthcare challenge for some decades. To understand its molecular epidemiology in Southern Thailand, we conducted whole-genome sequencing (WGS) of 221 CRAB clinical isolates. A comprehensive bioinformatics anal...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022000010 |
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| author | Arnon Chukamnerd Kamonnut Singkhamanan Virasakdi Chongsuvivatwong Prasit Palittapongarnpim Yohei Doi Rattanaruji Pomwised Chanida Sakunrang Kongpop Jeenkeawpiam Mingkwan Yingkajorn Sarunyou Chusri Komwit Surachat |
| author_facet | Arnon Chukamnerd Kamonnut Singkhamanan Virasakdi Chongsuvivatwong Prasit Palittapongarnpim Yohei Doi Rattanaruji Pomwised Chanida Sakunrang Kongpop Jeenkeawpiam Mingkwan Yingkajorn Sarunyou Chusri Komwit Surachat |
| author_sort | Arnon Chukamnerd |
| collection | DOAJ |
| description | The worldwide spread of carbapenem-resistant Acinetobacter baumannii (CRAB) has become a healthcare challenge for some decades. To understand its molecular epidemiology in Southern Thailand, we conducted whole-genome sequencing (WGS) of 221 CRAB clinical isolates. A comprehensive bioinformatics analysis was performed using several tools to assemble, annotate, and identify sequence types (STs), antimicrobial resistance (AMR) genes, mobile genetic elements (MGEs), and virulence genes. ST2 was the most prevalent ST in the CRAB isolates. For the detection of AMR genes, almost all CRAB isolates carried the blaOXA-23 gene, while certain isolates harbored the blaNDM-1 or blaIMP-14 genes. Also, various AMR genes were observed in these CRAB isolates, particularly aminoglycoside resistance genes (e.g., armA, aph(6)-Id, and aph(3″)-Ib), fosfomycin resistance gene (abaF), and tetracycline resistance genes (tet(B) and tet(39)). For plasmid replicon typing, RepAci1 and RepAci7 were the predominant replicons found in the CRAB isolates. Many genes encoding for virulence factors such as the ompA, adeF, pgaA, lpxA, and bfmR genes were also identified in all CRAB isolates. In conclusion, most CRAB isolates contained a mixture of AMR genes, MGEs, and virulence genes. This study provides significant information about the genetic determinants of CRAB clinical isolates that could assist the development of strategies for improved control and treatment of these infections. |
| first_indexed | 2024-04-11T05:20:33Z |
| format | Article |
| id | doaj.art-acc8a551d098480dabda45875570d3f7 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:33Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-acc8a551d098480dabda45875570d3f72022-12-24T04:51:07ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-0120545558Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern ThailandArnon Chukamnerd0Kamonnut Singkhamanan1Virasakdi Chongsuvivatwong2Prasit Palittapongarnpim3Yohei Doi4Rattanaruji Pomwised5Chanida Sakunrang6Kongpop Jeenkeawpiam7Mingkwan Yingkajorn8Sarunyou Chusri9Komwit Surachat10Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, ThailandDepartment of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, ThailandEpidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, ThailandPornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, ThailandDivision of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology, Fujita Health University, Aichi, JapanDivision of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, ThailandMolecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, ThailandMolecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, ThailandDepartment of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, ThailandDepartment of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Corresponding authors at: Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand and Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand; Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand; Corresponding authors at: Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand and Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.The worldwide spread of carbapenem-resistant Acinetobacter baumannii (CRAB) has become a healthcare challenge for some decades. To understand its molecular epidemiology in Southern Thailand, we conducted whole-genome sequencing (WGS) of 221 CRAB clinical isolates. A comprehensive bioinformatics analysis was performed using several tools to assemble, annotate, and identify sequence types (STs), antimicrobial resistance (AMR) genes, mobile genetic elements (MGEs), and virulence genes. ST2 was the most prevalent ST in the CRAB isolates. For the detection of AMR genes, almost all CRAB isolates carried the blaOXA-23 gene, while certain isolates harbored the blaNDM-1 or blaIMP-14 genes. Also, various AMR genes were observed in these CRAB isolates, particularly aminoglycoside resistance genes (e.g., armA, aph(6)-Id, and aph(3″)-Ib), fosfomycin resistance gene (abaF), and tetracycline resistance genes (tet(B) and tet(39)). For plasmid replicon typing, RepAci1 and RepAci7 were the predominant replicons found in the CRAB isolates. Many genes encoding for virulence factors such as the ompA, adeF, pgaA, lpxA, and bfmR genes were also identified in all CRAB isolates. In conclusion, most CRAB isolates contained a mixture of AMR genes, MGEs, and virulence genes. This study provides significant information about the genetic determinants of CRAB clinical isolates that could assist the development of strategies for improved control and treatment of these infections.http://www.sciencedirect.com/science/article/pii/S2001037022000010Carbapenem-resistant Acinetobacter baumannii (CRAB)Whole-genome sequencing (WGS)Bioinformatics toolSequence type (ST)Antimicrobial resistance (AMR) geneMobile genetic element (MGE) |
| spellingShingle | Arnon Chukamnerd Kamonnut Singkhamanan Virasakdi Chongsuvivatwong Prasit Palittapongarnpim Yohei Doi Rattanaruji Pomwised Chanida Sakunrang Kongpop Jeenkeawpiam Mingkwan Yingkajorn Sarunyou Chusri Komwit Surachat Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand Computational and Structural Biotechnology Journal Carbapenem-resistant Acinetobacter baumannii (CRAB) Whole-genome sequencing (WGS) Bioinformatics tool Sequence type (ST) Antimicrobial resistance (AMR) gene Mobile genetic element (MGE) |
| title | Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand |
| title_full | Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand |
| title_fullStr | Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand |
| title_full_unstemmed | Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand |
| title_short | Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand |
| title_sort | whole genome analysis of carbapenem resistant acinetobacter baumannii from clinical isolates in southern thailand |
| topic | Carbapenem-resistant Acinetobacter baumannii (CRAB) Whole-genome sequencing (WGS) Bioinformatics tool Sequence type (ST) Antimicrobial resistance (AMR) gene Mobile genetic element (MGE) |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022000010 |
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