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

Klebsiella pneumoniae 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 K. pneumoniae isolates (n=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: blaKPC-3, located on a Tn4401d transposon, and blaGES-5 on a novel class 3 integron. Additionally, four genes coding for ESBLs (blaBEL-1, blaCTX-M-8, blaCTX-M-15 and blaCTX-M-32) were also detected. ESBL horizontal dissemination across five clades is highlighted by the similar genetic environments of blaCTX-M-15 gene upstream of ISEcp1 on a Tn3-like transposon. Overall, this study provides a high- resolution genome- wide perspective on the epidemiology of ESBL and carbapenemase- producing K. pneumoniae in a healthcare setting while contributing for the adoption of appropriate intervention and prevention strategies.