Klebsiella quasipneumoniae Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment

Abstract

Several emerging pathogens have arisen as a result of selection pressures exerted by modern health care. Klebsiella quasipneumoniae was recently defined as a new species, yet its prevalence, niche, and propensity to acquire antimicrobial resistance genes are not fully described. We have been tracking inter- and intraspecies transmission of the Klebsiella pneumoniae carbapenemase (KPC) gene, blaKPC, between bacteria isolated from a single institution. We applied a combination of Illumina and PacBio whole-genome sequencing to identify and compare K. quasipneumoniae from patients and the hospital environment over 10- and 5-year periods, respectively. There were 32 blaKPC-positive K. quasipneumoniae isolates, all of which were identified as K. pneumoniae in the clinical microbiology laboratory, from 8 patients and 11 sink drains, with evidence for seven separate blaKPC plasmid acquisitions. Analysis of a single subclade of K. quasipneumoniae subsp. quasipneumoniae (n = 23 isolates) from three patients and six rooms demonstrated seeding of a sink by a patient, subsequent persistence of the strain in the hospital environment, and then possible transmission to another patient. Longitudinal analysis of this strain demonstrated the acquisition of two unique blaKPC plasmids and then subsequent within-strain genetic rearrangement through transposition and homologous recombination. Our analysis highlights the apparent molecular propensity of K. quasipneumoniae to persist in the environment as well as acquire carbapenemase plasmids from other species and enabled an assessment of the genetic rearrangements which may facilitate horizontal transmission of carbapenemases.

Forensic genomics of a novel Klebsiella quasipneumoniae type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology

“…While K. quasipneumoniae subsp. similipneumoniae has been less widely reported and discussed than K. pneumoniae, similar to our investigation, there has been an increased recognition of K. quasipneumoniae subspecies in hospital surveys and their association with resistance genes [57,58], indicating that a comprehensive assessment of their role in AMR ecology and contribution to disease burden is required. Their underrecognition is also due to the mis-assignment of non-K. pneumoniae strains to the type species.…”

Evaluation of MASTDISCS combi Carba plus for the identification of metallo‐β‐lactamases, KPC and OXA‐48 carbapenemase genes in Enterobacteriaceae clinical isolates

“…In this study, the sensitivity and the negative predictive value of MAST‐ Carba plus for predicting MBLs and OXA‐48 production are as high as 100%, but the positive predictive value for MBLs producers is only 84·2%, indicating that it is necessary to increase the validation of MBLs strains. Since the positive predictive value of OXA‐48 is 80·0%, it should be noted that MAST‐ Carba plus (disc E) contained temocillin, and K. pneumoniae may occasionally show temocillin resistance, leading to false‐positive OXA‐48 production (Zioga et al ; Mathers et al ). In addition, the sensitivity of KPC producers is only 82·3%, indicating that the sensitivity of MAST‐ Carba plus to predict KPC production needs to be further improved (Miao et al ; Taoufik et al ).…”

Water as a Source of Antimicrobial Resistance and Healthcare-Associated Infections

“…Bacterial species from biofilm and swab samples taken from water-related devices were isolated using a variety of methods including direct inoculation onto cetrimide, MacConkey, tegritol-7, or deoxycholate agar, and centrifugation to resuspend a pellet for inoculation onto selective agar, as shown in Table 1 [ 33 , 37 , 42 , 45 , 49 ]. Five studies used additional methods such as polymerase chain reaction (PCR), matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF), VITEK-2, multiplex PCR and 16S gene sequencing to identify isolated bacterial species ( Table S1 ) [ 63 , 64 , 65 ].…”

“…The size, shape and biovolume of bacteria may influence the filterability of a sample and potentially lead to inaccurate findings, particularly if multiple species of bacteria are being investigated using the one pore diameter [ 96 ]. Alternative molecular techniques for bacterial detection such as qPCR and whole-genome sequencing (WGS) have been employed by 27 studies included in this review [ 13 , 14 , 17 , 18 , 20 , 25 , 26 , 34 , 37 , 40 , 43 , 45 , 46 , 51 , 52 , 56 , 57 , 59 , 60 , 63 , 64 , 65 , 97 , 98 , 99 , 100 , 101 ]. Molecular techniques have significant advantages such as rapid turnaround times and detection of non-culturable cells [ 102 ].…”