Acinetobacter baumannii is an important nosocomial pathogen of critically ill patients that has become increasingly hard to treat due to rising antibiotic resistance. Here we undertook a genome-led investigation of a carbapenem-resistant A. baumannii (CRAB) outbreak in an intensive care unit (ICU) in Brisbane.
26 CRAB isolates from 17 patients were collected between May-August 2016 and sequenced using the Illumina platform. Many of the patients displayed co-infection with Klebsiella pneumoniae, Serratia marcescens and Pseudomonas aeruginosa, which were also sequenced. Pacific Biosciences Single Molecule Real-Time (SMRT) sequencing was used to fully elucidate the genomic context of two representative isolates. Nanopore MinION sequencing was also used to investigate the feasibility of real-time sequencing analysis in the clinical setting.
All CRAB isolates were found to be sequence type (ST)1050 and differed by less than 13 core single nucleotide polymorphisms (SNPs), indicative of direct transmission within the hospital. Sequencing of historical CRAB isolates from the same hospital found no close relationship with the current CRAB outbreak, suggesting that the index case had been introduced into the hospital. Carbapenem resistance in the CRAB isolates appeared to be driven by both overexpression of the beta-lactamase OXA-23 by ISAba1 and overexpression of the chromosomal ampC by ISAba125. The CRAB isolates also carried the transposon Tn6279, conferring resistance to macrolides, aminoglycosides and chloramphenicol. Three CRAB isolates independently developed resistance to colistin during the outbreak via mutations in pmrB, questioning the use of colistin as a surgical prophylaxis. MinION sequencing of a CRAB isolate from an additional patient rapidly placed it within the outbreak cluster, but lacked the resolution to infer the precise genetic relationship with other outbreak isolates.
Overall these results demonstrate how different WGS platforms can be used in conjunction to fully characterise a nosocomial outbreak in the clinical microbiology setting.