Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

Abstract

22Several emerging pathogens have arisen as a result of selection pressures exerted by modern healthcare. 23Klebsiella quasipneumoniae was recently defined as a new species, yet its prevalence, niche, and propensity to 24 acquire antimicrobial resistance genes are not fully described. We have been tracking inter-and intra-species 25 transmission of the Klebsiella pneumoniae carbapenemase (KPC) gene, bla KPC , between bacteria isolated from a 26 single institution. We applied a combination of Illumina and PacBio whole-genome sequencing to identify and 27 compare K. quasipneumoniae from patients and the hospital environment over 10 and five-year periods 28respectively. There were 32 bla KPC -positive K. quasipneumoniae isolates, all of which were identified as K. 29 pneumoniae in the clinical microbiology laboratory, from eight patients and 11 sink drains, with evidence for 30 seven separate bla KPC plasmid acquisitions. Analysis of a single subclade of K. quasipneumoniae subspecies 31 quasipneumoniae (n=23 isolates) from three patients and six rooms demonstrated seeding of a sink by a patient, 32 subsequent persistence of the strain in the hospital environment, and then probable transmission to another 33 patient. Longitudinal analysis of this strain demonstrated the acquisition of two unique bla KPC plasmids and then 34 subsequent within-strain genetic rearrangement through transposition and homologous recombination. Our 35 analysis highlights the apparent molecular propensity of K. quasipneumoniae to persist in the environment as well 36as acquire carbapenemase plasmids from other species and enabled an assessment of the genetic rearrangements 37