First Outbreak of NDM-1-Producing Klebsiella pneumoniae ST11 in a Portuguese Hospital Centre during the COVID-19 Pandemic

New Delhi metallo-β-lactamase (NDM) carbapenemase has been considered a global threat due to its worldwide widespread in recent years. In Portugal, a very low number of infections with NDM-producing Enterobacterales has been reported. A total of 52 strains from 40 patients and 1 environmental sample isolated during COVID-19 pandemic were included in this study. Wholegenome sequencing (WGS) was performed on 20 carbapenemase-producing strains, including 17 NDM-1-producing ST11-KL105 lineage strains, one NDM-1-producing ST58 strain and one KPC-3-producing ST147 strain, recovered from a total of 19 patients. Of interest, also one NDM-1-producing ST11-KL105 was collected from the hospital environment. Genome-wide phylogenetic analysis revealed an ongoing dissemination of NDM-1-producing ST11 strains ( = 18) with the same genetic features seen across multiple wards. Furthermore, the ST58 strain, collected from a patient rectal swab that was also colonised with a strain, also showed the IncFIA plasmid replicon and the gene (preceded by IS30 and followed by genes , , , , and ). The is part of Tn identical to those reported in Poland, Italy and India. The ST147-KL64 strain has the genetic environment Tn isoform. In conclusion, herein we report the molecular epidemiology, resistome, virulome and mobilome of the first NDM-1 carbapenemase outbreak caused by ST11-KL105 lineage during the COVID-19 pandemic in Portugal. Moreover, the outbreak strains characterised included seventeen different patients (infected and colonised) and one environmental sample which also emphasises the role of commensal and hospital environment strains in the dissemination of the outbreak.