Whole - Genome Sequence Analysis of Carbapenem Resistant Acinetobacter baumannii isolated from Medan, North Sumatera, Indonesia

Abstract

Abstract Background Acinetobacter baumannii, an opportunistic pathogen that is responsible for nosocomial infections globally, presents a formidable challenge owing to its ability to develop resistance against antibiotics. This resistance, which includes resistance to carbapenems, the last-resort antibiotics, has led to the emergence of Carbapenem-Resistant Acinetobacter baumannii (CRAB) strains. The distribution of these strains encompasses Indonesia, particularly in Medan. Investigation on its resistance can only be performed thoroughly using Whole Genome Sequencing (WGS) process. Methods The samples used in this study is 32 bacterial isolates from Murni Teguh Memorial Hospital in Medan, North Sumatra, collected between July – December 2022 and has been confirmed as A. baumannii using VITEK-2 system. Bacterial isolates are tested for carbapenem sensitivity using disc diffusion method. DNA isolation is performed using QIAamp DNA mini kit and ran through WGS process using Novaseq 6000 Illumina. Bioinformatics analysis is performed consisting of MLST, phylogenetic tree, identification of elements such as resistance genes, plasmids, insertion sequences, prophage sequences, and CRISPR/Cas system sequences. Results 58 resistance genes and several mutations were identified. The majority of these genes exert their influence on resistance through efflux pump mechanisms. All the carbapenem-resistant isolates showing co-occurrence of blaOXA-23 and blaOXA-51 family genes. MLST analysis revealed that out of the 30 isolates, 27 were identified as A. baumannii and were further divided into 7 distinct Sequence Types (STs), with the majority belonging to ST 2 and ST 1. Furthermore, the analysis uncovered the presence of novel STs, specifically assigned as ST-Past 2456 and ST-Oxf 3213. Aside from resistance genes, 20 plasmids, 89 insertion sequences, 20 prophage sequences, and 1 CRISPR/Cas system identified in this research. Conclusion WGS analysis of A. baumannii isolates from Medan reveals the presence of several resistance determinants that can contribute to the high resistance levels observed in these isolates. Comparative analysis with global isolates indicates that the majority of isolates belong to globally recognized lineages with high resistance levels. Along with the discovery of the new ST in this study, the information obtained is expected to assist other researchers in further studies related to A. baumannii and its resistance to antimicrobials.