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

Abstract Background Acinetobacter baumannii is a common nosocomial pathogen that poses a huge threat to global health. Owing to the severity of A. baumannii infections, it became necessary to investigate the epidemiological characteristics of A. baumannii in Chinese hospitals and ascertain the reasons for the high antibiotic resistance rate and severe infections. This study aimed to investigate the epidemiologic and genetic characteristics of A. baumannii isolated from patients with hospital acquired pneumonia (HAP), bloodstream infection (BSI) and urinary tract infection (UTI) in China and uncover potential mechanisms for multi-drug resistance using whole genome sequencing. Results All isolates were classified into one of two primary clades. Clonal complex 208 (CC208) mainly consisted of ST195 (32%) and ST208 (24.6%). CC208 and non-CC208 isolates had carbapenem resistance rates of 96.2% and 9.1%, respectively. UTI isolates possessed the greatest number of unique genes enriched in 'Replication, recombination, and repair' and ‘Amino acid transport and metabolism’ although the numbers of genes specific to HAP-isolates were fewer. No specific virulence gene was identified when comparing isolates from the three infection sites, but most isolates possessed virulence factors related to polysaccharide biosynthesis, capsular polysaccharide synthesis and motility. ABGRI1 antibiotic resistance islands were responsible for streptomycin, tetracycline and sulfonate resistance. The blaOXA−23 gene was the most probable cause for carbapenem resistance, although the blaOXA−66 gene with nonsynonymous SNPs (F82L, I129L) was not. Conclusions Our study illustrates epidemiological and genomic characteristics of A. baumannii from HAP, BSI and UTI in China and reveals possible molecular mechanisms of multi-drug resistance. The differential resistance, virulence and genetic features provide supportive evidence for the diverse sites of infection caused by A. baumannii.