Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital

Abstract

<i>Klebsiella pneumoniae</i> has emerged as an important nosocomial pathogen, with whole-genome sequencing (WGS) significantly improving our ability to characterize associated outbreaks. Our study sought to perform a genome-wide analysis of multiclonal <i>K. pneumoniae</i> isolates (<i>n</i>=39; 23 patients) producing extended spectrum beta-lactamases and/or carbapenemases sourced between 2011 and 2016 in a Portuguese tertiary-care hospital. All isolates showed resistance to third-generation cephalosporins and six isolates (five patients) were also carbapenem resistant. Genome-wide-based phylogenetic analysis revealed a topology representing ongoing dissemination of three main sequence-type (ST) clades (ST15, ST147 and ST307) and transmission across different wards, compatible with missing links that can take the form of undetected colonized patients. Two carbapenemase-coding genes were detected: <i>blaKPC-3</i>, located on a <i>Tn4401d</i> transposon, and <i>blaGES-5</i> on a novel class 3 integron. Additionally, four genes coding for ESBLs (<i>blaBEL-1</i>, <i>blaCTX-M-8</i>, <i>blaCTX-M-15</i> and <i>blaCTX-M-32</i>) were also detected. ESBL horizontal dissemination across five clades is highlighted by the similar genetic environments of <i>blaCTX-M-15</i> gene upstream of IS<i>Ecp1</i> on a <i>Tn3</i>-like transposon. Overall, this study provides a high-resolution genome-wide perspective on the epidemiology of ESBL and carbapenemase-producing <i>K. pneumoniae</i> in a healthcare setting while contributing for the adoption of appropriate intervention and prevention strategies.