Genetic relatedness and molecular characterization of multi-drug resistant acinetobacter baumannii. (2019)

Abstract

Acinetobacter baumannii is a Gram-negative organism associated with a broad range of severe nosocomial infections and linked to prolonged hospital stay of immunocompromised patients. We used whole-genome sequencing (WGS) to characterize 41 isolates of A. baumannii collected from a hospital in Lebanon. Resistance profiles were determined through antibiotic susceptibility testing (AST) and confirmed by the detection of resistance genes in the sequenced genomes. The plasmid content was analyzed both in silico and using the Acinetobacter baumannii – PCR based replicon typing (AB-PBRT) method. Multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome SNP analysis were performed to investigate the possibility of an outbreak scenario and the relatedness between the isolates. Most of the isolates (95%; n=39) were resistant to cephalosporins, quinolones, aminoglycosides as well as to carbapenems, and were accordingly classified as being extensive drug resistant (XDR) and were referred to as carbapenem resistant Acinetobacter baumannii (CRAB). in silico analysis revealed the presence of 20 different resistance determinants each conferring resistance to one of the following: minoglycosides, β-lactams, sulfonamides, tetracyclines, or Macrolide-Lincosamide-Streptogramin (MLS). Gr2 (90%; n=37) and Gr6 (70.7%; n=29) plasmids were detected in 93% (n=38) of the isolates. ST- 636 (48.7%; n=20), ST-2 (24.4%; n=10), ST-2-like (21.9%; n=9), ST- 396 (2.5%; n=1) and ST-388 (2.5%; n=1) were the only detected sequence types. All ST-636 isolates carried blaOXA-66 and blaOXA-72, whereas ST-2 and ST-2-like isolates carried blaOXA-66 and blaOXA-23. To our knowledge, this is the first comprehensive wholegenome based characterization of CRAB associated with nosocomial infections in Lebanon, as well as in the Middle East. Our findings revealed that the studied MDR A. baumannii isolates were circulating in the hospital and were linked to two separate outbreaks during the same period infecting several immunocompromised patients and representing a leading cause of mortality.