Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand

Arnon Chukamnerd; Kamonnut Singkhamanan; Virasakdi Chongsuvivatwong; Prasit Palittapongarnpim; Yohei Doi; Rattanaruji Pomwised; Chanida Sakunrang; Kongpop Jeenkeawpiam; Mingkwan Yingkajorn; Sarunyou Chusri; Komwit Surachat

doi:10.1016/j.csbj.2021.12.038

Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand

Comput Struct Biotechnol J. 2022 Jan 6:20:545-558. doi: 10.1016/j.csbj.2021.12.038. eCollection 2022.

Authors

Affiliations

¹ Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
² Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
³ Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.
⁴ Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
⁵ Department of Microbiology, Fujita Health University, Aichi, Japan.
⁶ Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
⁷ Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
⁸ Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
⁹ Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
¹⁰ Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.

Abstract

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 bla _OXA-23 gene, while certain isolates harbored the bla _NDM-1 or bla _IMP-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.

Keywords: Antimicrobial resistance (AMR) gene; Bioinformatics tool; Carbapenem-resistant Acinetobacter baumannii (CRAB); Mobile genetic element (MGE); Sequence type (ST); Whole-genome sequencing (WGS).