Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications

Abstract

Acinetobacter baumannii is a highly potent nosocomial pathogen that is associated with increased in-hospital mortality. Here, we investigated the changes in molecular characteristics of carbapenem-resistant A. baumannii (CRAB) isolated from the blood samples of patients admitted to a tertiary hospital in South Korea from January 2009 to July 2015. Whole genome sequencing using the Illumina MiSeq platform and multi-locus sequence typing (MLST) were performed for 98 CRAB clinical isolates. In silico analyses for the prediction of antimicrobial resistance and virulence factor genes were performed. Plasmid sequences, including complete forms, were reconstructed from the sequence reads. Epidemiologic data were collected from the hospital database. MLST using the Oxford scheme revealed 10 sequence types of CRAB, of which ST191 was the dominant type (n = 59). Although bla OXA-23 was shared by most analysed strains, the compositions of antimicrobial resistance determinants differed among sequence types. ST447 and ST451/ST1809 with a few resistance genes were isolated during the later years of the study period. The number of virulence genes increased, while that of ST191 did not change significantly over the investigation period. Intriguingly MLST types, compositions of antimicrobial resistance genes, and virulence genes had no association with clinical outcomes of CRAB bacteraemia. In conclusion, active changes in or accumulations of antimicrobial resistance determinants and virulence genes in CRAB were not observed during the research period. Molecular characteristics of CRAB had no association with clinical outcomes of CRAB bacteraemia.

Analysis of blaCHDL Genes and Insertion Sequences Related to Carbapenem Resistance in Acinetobacter baumannii Clinical Strains Isolated in Warsaw, Poland

“…Carbapenem-resistant A. baumannii ST195 and ST208 are widespread in the world, and are dominant mainly in the Far East, e.g., in China [ 36 , 37 , 38 , 39 , 40 ]. Furthermore, the ST208/ST1806 strains have been isolated in South Korea [ 41 ].…”

Epidemiological and genomic characteristics of Acinetobacter baumannii from different infection sites using comparative genomics

“…Several studies investigated the molecular epidemiology of A. baumannii , focusing on its carbapenem resistance and virulence [ 6 – 8 ]. Few studies pay attention to the whole genome characteristics of clinical isolates from diverse infection sites.…”

Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

“…AMR prediction with ResFinder and KmerResistance showed high concordance, with most of the resistance genes identified commonly. The isolates showed a common antibiotic resistance profile reported in multidrug-resistant A. baumannii in Korea [ 32 , 42 , 43 ]. A previous study showed high concordance with ResFinder, an assembly-based tool, and KmerResistance, a read-based tool, in high-quality sequencing results, as in our study [ 26 ].…”