Whole-genome sequencing for the characterization of resistance mechanisms and epidemiology of colistin-resistant Acinetobacter baumannii

• Published in: PloS one Vol. 17; no. 3; p. e0264335
• Main Authors: Hahm, Chorong, Chung, Hae-Sun, Lee, Miae
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.03.2022; Public Library of Science (PLoS)
• Subjects: Acinetobacter baumannii; Acinetobacter baumannii - genetics; Acinetobacter Infections - drug therapy; Acinetobacter Infections - epidemiology; Acinetobacter Infections - microbiology; Analysis; Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Antibiotic resistance; Antibiotics; Bacterial Proteins - genetics; Biology and Life Sciences; Cluster analysis; Colistin; Colistin - pharmacology; Cross Infection - drug therapy; DNA sequencing; Drug resistance; Drug Resistance, Bacterial - genetics; Epidemics; Epidemiology; Gene sequencing; Genes; Genetic aspects; Genetic relationship; Genomes; Genomic analysis; Genomics; Health care; Hospitals; Humans; Infections; Laboratories; Medical schools; Medicine; Medicine and Health Sciences; Microbial Sensitivity Tests; Mortality; Multidrug resistance; Multilocus Sequence Typing; Mutation; Next-generation sequencing; Nucleotide sequence; Nucleotide sequencing; Nucleotides; Pathogens; Patients; Polymorphism; Research and analysis methods; Single-nucleotide polymorphism; Strains (organisms); Virulence; Whole genome sequencing; South Korea; France; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0264335

Multidrug-resistant Acinetobacter baumannii is an important causal pathogen of healthcare-associated infections, and colistin-resistant strains have recently emerged owing to the increased use of colistin. Using next-generation sequencing (NGS), a single whole-genome sequencing (WGS) protocol can identify and type pathogens, analyze genetic relationships among different pathogens, predict pathogenic transmissions, and detect antibiotic resistance genes. However, only a few studies have applied NGS in studying the resistance mechanism and epidemiology of colistin-resistant A. baumannii. This study aimed to elucidate the resistance mechanism of colistin-resistant A. baumannii and analyze its molecular epidemiology through WGS. The subjects in this study were patients who visited a university hospital between 2014 and 2018. Thirty colistin-resistant strains with high minimum inhibitory concentrations were selected from various patient samples, and WGS was performed. Comparative genomic analysis was performed for the 27 colistin-resistant A. baumannii strains using a colistin-susceptible strain as the reference genome. The WGS analysis found no mutation for lpxA, lpxC, lpx D, pmrA, pmrB, and mcr1, the genes known to be associated with colistin resistance. Fifty-seven coding sequences (CDS) showed differences; they included 13 CDS with known names and functions that contained 21 genes. From the whole-genome multi-locus sequence typing (wgMLST) and single nucleotide polymorphism (SNP) analyses, two major clusters were found for the colistin-resistant A. baumannii strains. However, no differences were observed by the time of detection for each cluster, the samples, the pattern of antibiotic resistance, or the patient characteristics. In the conventional MLST following the Oxford scheme, the typing result showed ST1809, ST451, ST191, ST1837, and ST369 in the global clone 2 (GC2), without any relation with the results of wgMLST and SNP analyses. Based on the findings of the resistance gene analysis through WGS and comparative genomic analysis, the potential genes associated with colistin-resistance or CDS were examined. Furthermore, the analysis of molecular epidemiology through WGS regarding colistin-resistant A. baumannii may prove helpful in preventing infection by multidrug-resistant bacteria and controlling healthcare-associated infections.