Whole genome sequencing of Acinetobacter baumannii clinical isolates from Terengganu, Malaysia (2017 – 2018) revealed the predominance of the multidrug resistance ST2, GC2 lineage

Din, N.S., Mohd Rani, Farahiyah, Ismail, S., Rahman, N.I.A., Othman, N., Abdullah, F.H., Cleary, David, Clarke, Stuart C. and Yeo, C.C. (2022) Whole genome sequencing of Acinetobacter baumannii clinical isolates from Terengganu, Malaysia (2017 – 2018) revealed the predominance of the multidrug resistance ST2, GC2 lineage. (Submitted)

Abstract

Introduction: cinetobacter baumannii is a Gram-negative coccobacillus that has become a major nosocomial pathogen and a common isolate in Malaysian hospitals. One of the features that enabled A. baumannii to gain clinical prominence is its remarkable ability to rapidly acquire and develop resistance to nearly all classes of antibiotics. In this study, whole genome sequencing was carried out on thirty-six A. baumannii clinical isolates from Hospital Sultanah Nur Zahirah, the main tertiary hospital in Terengganu, Malaysia, from the years 2017 and 2018.

Methods: antimicrobial resistance profiles of the A. baumannii isolates were determined by disk diffusion. Whole genome sequencing was performed on the Illumina platform and the sequences were assembled using UniCycler.

Findings: majority of the isolates (n = 30) were carbapenem as well as multidrug resistant (MDR; i.e., resistant towards three of more antimicrobial classes). The sequence type 2 (ST2) of the A. baumannii Global Clone 2 (GC2) lineage was predominant (n = 27) and all ST2 isolates were MDR. Phylogenetic analysis indicated that these ST2 isolates were very closely related. Nearly all the MDR isolates (n = 29) harboured the blaOXA-23 acquired carbapenemase gene with the remaining one MDR isolate, A. baumannii AC1839 harbouring two acquired carbapenemase genes, blaOXA-58, and blaNDM-1. AC1839 was however typed as ST1278/ST515 and was not of the GC2 lineage. Several MDR isolates also harboured broad spectrum β-lactamases with more than half (n = 19) carrying
the blaTEM-1D gene and two MDR isolates harbouring the blaCARB-5-like gene. Majority of the isolates (n = 34) harboured the Acinetobacter-derived single-variant cephalosporinase gene, blaADC25, which is likely responsible for cephalosporin resistance. Resistance genes for aminoglycosides, macrolides, sulphonomides, and tetracyclines were also identified from the genome sequences of these A. baumannii isolates.

Conclusion: whole genome sequencing has revealed that the multidrug-resistant ST2 clone harbouring the acquired blaOXA-23 carbapenemase gene is the predominant A. baumannii clone in Terengganu.

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Contributors

Author: David Cleary

Author: Stuart C. Clarke

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