Investigation of the Species Distribution of Tissue Invasive Klebsiella Pneumoniae Complex in A New York Hospital System Using Whole Genome Sequencing

Abstract BACKGROUND: Current research indicates that Klebsiella pneumoniae is a complex of closely related organisms (K. pneumoniae sensu stricto, K. quasipneumoniae, K. variicola, K. quasivariicola, and K. africana). There is a paucity of research into the distribution of K. pneumoniae complex members in clinical specimens and the pathogenic potential of complex members other than K. pneumoniae sensu stricto.METHODS: To assess the rates and characteristics of different K. pneumoniae complex members in our 886 bed tertiary care facility in Rochester, New York, we performed whole genome sequencing using the Illumina MiSeq on all inpatient, sterile-source isolates identified by routine culture work-up as K. pneumoniae from October 2018 - October 2019 (n=35). We additionally sequenced all K. pneumoniae liver isolates available in our collection, spanning 2017-2019 (n=12). Analyses were focused on delineating complex members, detection of antibiotic resistance genes, and gene clusters associated with hypervirulent phenotypes.RESULTS: In the yearlong collection of 35 K. pneumoniae complex isolates, we found that 92.4% were K. pneumoniae sensu stricto (n=32), 5.7% were K. quasipneumoniae (n=2), and 2.9% were K. variicola (n=1). In the liver isolate collection, one additional K. variicola was identified. Both K. quasipneumoniae isolates and one K. variicola isolate were from liver. One K. quasipneumoniae isolate was a phenotypic and genotypic extended spectrum beta-lactamase producer. All other K. quasipneumoniae and K. variicola isolates were resistant only to ampicillin. Five K. pneumoniae sensu stricto isolates were identified which carried genes associated with hypervirulence. No K. quasipneumoniae or K. variicola carried any hypervirulence associated genes.CONCLUSIONS: The rates of K. pneumoniae sensu stricto, K. quasipneumoniae, and K. variicola observed in this study are consistent with those observed internationally and in blood isolates. Interestingly, all of our K. quasipneumoniae isolates were isolated from liver abscesses. Genetic loci associated with hypervirulence appear to be restricted to K. pneumoniae sensu stricto.