Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain

Abstract

The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicolan = 1; K. pneumoniaen = 2) and Tn4401d isoform (K. pneumoniaen = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.

Phenotypic and Molecular Characterization of Commensal, Community-Acquired and Nosocomial Klebsiella spp.

“…In contrast, 9 out of the 10 Klebsiella isolates from the NICU were MDR, thus supporting the situation of nosocomial outbreak. In addition, the NICU bla CTX-M-15 -producing K. pneumoniae K12-9 and the commensal K. quasipneumoniae MV91-24 isolates exhibited resistance to imipenem, thus indicating the wide dispersion of carbapenemases, either combined with ESBL or not, among different environments, a fact that has been described previously [42,43].…”

An Update on Wastewater Multi-Resistant Bacteria: Identification of Clinical Pathogens Such as Escherichia coli O25b:H4-B2-ST131-Producing CTX-M-15 ESBL and KPC-3 Carbapenemase-Producing Klebsiella oxytoca

“…Klebsiella pneumoniae (Kp) is the causative agent of severe infections, including wound infections, bloodstream infections, meningitis, and pneumonia [ 28 ]. It is an increasingly resistant pathogen that has shown the ability to express diverse mechanisms, making the species multi-resistant to several clinical antimicrobial classes [ 3 ]. Ambler class B metallo-β-lactamases are a worldwide, increasingly distributed class, and represent a major treatment problem due to not being inhibited by any beta-lactamase inhibitor [ 4 , 9 , 14 ].…”

“…Ambler class B metallo-β-lactamases are a worldwide, increasingly distributed class, and represent a major treatment problem due to not being inhibited by any beta-lactamase inhibitor [ 4 , 9 , 14 ]. In Portugal, the Ambler class A KPC-3 is the most frequent carbapenemase described in healthcare-associated infections [ 2 , 3 , 28 , 46 ]. In this work, we describe a KPC-3 producing K. oxytoca , a rod-shaped bacterium that is closely related to K. pneumoniae , with bla KPC-3 included in a transposon Tn4401 isoform b, mobile genetic element (MGE), which can favor horizontal dissemination capacity [ 28 ].…”

“…The primers used to amplify the bla OXA - genes were 5′-GTACTAATCAAAGTGTGAA-3′ and 5′-TTCCCCTAACATGAATTTGT-3′. Studies of the genetic structure surrounding the bla KPC-3 gene, in order to identify the Tn3-based transposon, Tn4401 , were undertaken as previously described [ 3 ].…”

“…According to Sanderson et al 2016 [ 1 ], antibiotic resistance genes (ARGs) should be considered a biological contaminant of emerging concern, considering that they are able to transfer, through genetic processes, to multiple types of organisms and over long distances. Increasing resistance to antibiotics has led to the investigation of different origins, such as wastewater treatment plants (WWTPs), which have long been considered to be reservoirs of bacterial resistance [ 2 , 3 ]. Although multidrug-resistant (MDR) bacteria are ubiquitous in the environment, WWTPs are a key source of antibiotic resistance determinants outside hospitals, potentially providing a selective pressure for multidrug resistance [ 4 , 5 ].…”