TY - JOUR
T1 - Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand
AU - Chukamnerd, Arnon
AU - Singkhamanan, Kamonnut
AU - Chongsuvivatwong, Virasakdi
AU - Palittapongarnpim, Prasit
AU - Doi, Yohei
AU - Pomwised, Rattanaruji
AU - Sakunrang, Chanida
AU - Jeenkeawpiam, Kongpop
AU - Yingkajorn, Mingkwan
AU - Chusri, Sarunyou
AU - Surachat, Komwit
N1 - Funding Information:
The authors are grateful to the Clinical Microbiology Laboratories (CMLs) in Songklanagarind Hospital, Songkhla Hospital, Phatthalung Hospital, Satun Hospital, Trang Hospital, Pattani Hospital, and Yala Hospital for providing the CRAB isolates. We acknowledge the Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University as well as the Division of Computational Science and the Molecular Evolution and Computational Biology (MECoB) Research Unit, Faculty of Science, Prince of Songkla University for use of their research facilities. Finally, we thank Miss Parita Boonnatee for constructing some figures and Mr. Dave Patterson for English language review in this study.
Funding Information:
This research was funded by the National Science and Technology Development Agency (NSTDA), Thailand (project number: P-20–51325) and the Graduate Scholarship, Faculty of Medicine, Prince of Songkla University, Thailand (grant number: 62-012). This study was also supported by the Faculty of Science, Prince of Songkla University, Thailand (grant number: SCI64040135).
Publisher Copyright:
© 2022 The Author(s)
PY - 2022/1
Y1 - 2022/1
N2 - 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.
AB - 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.
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U2 - 10.1016/j.csbj.2021.12.038
DO - 10.1016/j.csbj.2021.12.038
M3 - Article
AN - SCOPUS:85122946452
SN - 2001-0370
VL - 20
SP - 545
EP - 558
JO - Computational and Structural Biotechnology Journal
JF - Computational and Structural Biotechnology Journal
ER -