Clinically Relevant Plasmid-Host Interactions Indicate that Transcriptional and Not Genomic Modifications Ameliorate Fitness Costs of Klebsiella pneumoniae Carbapenemase-Carrying Plasmids

Abstract

The rapid dissemination of antimicrobial resistance (AMR) around the globe is largely due to mobile genetic elements, such as plasmids. They confer resistance to critically important drugs, including extended-spectrum beta-lactams, carbapenems, and colistin. Large, complex resistance plasmids have evolved alongside their host bacteria. However, much of the research on plasmid-host evolution has focused on small, simple laboratory plasmids in laboratory-adapted bacterial hosts. These and other studies have documented mutations in both host and plasmid genes which occur after plasmid introduction to ameliorate fitness costs of plasmid carriage. We describe here the impact of two naturally occurring variants of a large AMR plasmid (pKpQIL) on a globally successful pathogen. In our study, after pKpQIL plasmid introduction, no changes in coding domain sequences were observed in their natural host, Klebsiella pneumoniae. However, significant changes in chromosomal and plasmid gene expression may have allowed the bacterium to adapt to the acquisition of the AMR plasmid. We hypothesize that this was sufficient to ameliorate the associated fitness costs of plasmid carriage, as pKpQIL plasmids were maintained without selection pressure. The dogma that removal of selection pressure (e.g., antimicrobial exposure) results in plasmid loss due to bacterial fitness costs is not true for all plasmid/host combinations. We also show that pKpQIL impacted the ability of K. pneumoniae to form a biofilm, an important aspect of virulence. This study used highly relevant models to study the interaction between AMR plasmids and pathogens and revealed striking differences from results of studies done on laboratory-adapted plasmids and strains.

Different impacts of naturally occurring variants of the globally disseminated carbapenemase-encoding plasmid pKpQIL on the biology of host strains

“…Previously, we have carried out an in-depth transcriptomic profiling of K. pneumoniae ST258 carrying these two plasmids (19). The plasmids (in particular, the substituted region) affected the host transcriptomic landscape differently (19).…”

“…Previously, we have carried out an in-depth transcriptomic profiling of K. pneumoniae ST258 carrying these two plasmids (19). The plasmids (in particular, the substituted region) affected the host transcriptomic landscape differently (19). Interestingly, the K. pneumoniae Ecl8 host carrying the pKpQIL-D2 plasmid out-competed the pKpQIL-UK counterpart in pairwise competition assay; even though the latter had a higher conjugation frequency than pKpQIL-D2 (19).…”

“…Previously, our team has shown that both the pKpQIL-UK and -D2 are well adapted to their Klebsiella hosts and transcriptional changes were effected to ameliorate (if any) possible fitness cost from plasmid carriage in ST258 strains of K. pneumoniae (19). Given the identification of the -D2 variant in various species, we hypothesised that the 17.6 kb variable region within pKpQIL-D2 may provide an adaptive fitness advantage when compared with the parent plasmid, which facilitated a broader host range and increased dissemination potential than the original pKpQIL in the UK.…”

Development of CRSIPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria

“…1E). Since the majority of clinically important AMR genes are encoded on plasmids (12), the killing efficiency of PhagoCas13a was expected to be superior to that of PhagoCas9 in light of the current difficulty with the threat of Carbapenem-resistant Enterobacteriaceae (CRE) carrying resistant genes on the plasmids. Besides, previous studies have suggested that CRISPR-Cas9 is prone to unexpected genetic mutations due to its DNA-cleavage activity (13)(14)(15).…”

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones ofKlebsiella pneumoniae

“…This is particularly worrying from a hospital infection control perspective since many of the MDR clones investigated here appear well adapted to transmission and colonisation in the human population, and are frequent causes of hospital outbreaks 7,8 . Given the mounting evidence that MDR clones can carry multiple plasmids at limited fitness cost [64][65][66] and frequently exchange plasmids with other bacteria 54,55 , it seems these MDR clones may also be the perfect hosts for consolidation and onwards dissemination of MDR and virulence determinants. The greatest concern is that these determinants will be consolidated onto a single mobile genetic element; indeed mosaic Kp plasmids carrying AMR genes plus iuc and rmpA2 have already been reported in an MDR Kp clone 30 , and Escherichia coli plasmids bearing iuc, rmpA and AMR genes have been detected in Kp 27 .…”