Author(s): Perdigão, João ; Modesto, Ana ; Pereira, A. L. ; Neto, O. ; Matos, V. ; Godinho, A. ; Phelan, Jody ; Charleston, James ; Spadar, Anton ; Sessions, Paola Florez de ; Hibberd, Martin ; Campino, Susana ; Costa, A. ; Fernandes, F. ; Ferreira, F. ; Correia, A. B. ; Gonçalves, Luisa ; Clark, Taane G. ; Duarte, Aida
Date: 2021
Persistent ID: http://hdl.handle.net/10400.26/59236
Origin: Egas Moniz - Cooperativa de Ensino Superior, CRL
Subject(s): ESBL; KPC; CTX-M; Gram-negative; Portugal
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.
