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

Abstract

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 Klebsiella pneumoniae ST11-KL105 lineage strains, one NDM-1-producing Escherichia coli ST58 strain and one KPC-3-producing K. pneumoniae ST147 strain, recovered from a total of 19 patients. Of interest, also one NDM-1-producing K. pneumoniae ST11-KL105 was collected from the hospital environment. Genome-wide phylogenetic analysis revealed an ongoing dissemination of NDM-1-producing K. pneumoniae ST11 strains (n = 18) with the same genetic features seen across multiple wards. Furthermore, the ST58 E. coli strain, collected from a patient rectal swab that was also colonised with a K. pneumoniae strain, also showed the IncFIA plasmid replicon and the blaNDM-1 gene (preceded by IS30 and followed by genes bleMBL, trpF, dsbC, cutA, groES and groEL). The blaNDM-1 is part of Tn125-like identical to those reported in Poland, Italy and India. The blaKPC-3 K. pneumoniae ST147-KL64 strain has the genetic environment Tn4401d isoform. In conclusion, herein we report the molecular epidemiology, resistome, virulome and mobilome of the first NDM-1 carbapenemase outbreak caused by K. pneumoniae 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.

Whole-Genome Sequencing Enables Molecular Characterization of Non-Clonal Group 258 High-Risk Clones (ST13, ST17, ST147 and ST307) among Carbapenem-Resistant Klebsiella pneumoniae from a Tertiary University Hospital Centre in Portugal

“…Nevertheless, the reports in Portugal are scarce. Recently, an outbreak caused by NDM-1-producing Klebsiella pneumoniae ST11-KL105 lineage (in clinical and environmental strains) during the COVID-19 pandemic in Portugal was described [31]. However, herein we report a NDM-1-producing Klebsiella pneumoniae ST39 clone, which has been previously reported in other countries harboring the bla NDM-1 gene [32,33].…”

Emergence of a Novel NDM-5-Producing Sequence Type 4523 Klebsiella pneumoniae Strain Causing Bloodstream Infection in China

“…KPC is the dominant mechanism leading to carbapenem resistance in K. pneumoniae , as isolates harboring a bla NDM gene generate only a small proportion of CRKP. However, an outbreak of NDM-1-producing ST11 K. pneumoniae strains in a hospital center was reported in Portugal ( 16 ), which highlighted the dissemination ability of NDM-producing K. pneumoniae strains. In Enterobacterales , the bla NDM-5 gene has gradually become the main subtype of bla NDM , and most bla NDM genes are carried by the IncX3 plasmid in China, which is in the same plasmid group as pSHX180-NDM5.…”

Prevalence of Waterborne blaNDM-1 Gene Producing Carbapenem-resistant Klebsiella pneumoniae from Al-Hillah River Water, Babylon Province, Iraq

“…[7][8][9] First outbreak due to K. pneumoniae ST11producing NDM-1gene during the COVID-19 Pandemic has been particularly detected in human cases of infection in a Portuguese Hospital Centre. 10 Other report achieved by Ebomah and Okoh 11 identified K. pneumoniae harboring bla NDM-1 and bla KPC from various environmental niches like farm soil in the eastern Cape Province, South Africa. Multi-drug resistant Enterobacteriaceae carrying NDM-1gene have been recognized worldwide, with many cases linked to international travel and tourism.…”