Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital
João Perdigão, Ana Modesto, Ana L. Pereira, Oliveiro Caetano de Freitas Neto, Vítor Matos, Ana Godinho, Jody Phelan, James Charleston, Anton Spadar, Paola Flórez de Sessions, Martin L. Hibberd, Susana Campino, Ana Roberta Fusco da Costa, Fernando Montezano Fernandes, Fábio J. Ferreira, Alan Blendo Bonfim Correia, Luísa Gonçalves, Taane G. Clark, Aida Duarte
Abstract
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: bla KPC-3 , located on a Tn4401d transposon, and bla GES-5 on a novel class 3 integron. Additionally, four genes coding for ESBLs ( bla BEL-1 , bla CTX-M-8 , bla CTX-M-15 and bla CTX-M-32 ) were also detected. ESBL horizontal dissemination across five clades is highlighted by the similar genetic environments of bla CTX-M-15 gene upstream of IS Ecp1 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.