NDM-1 carbapenemase resistance gene vehicles emergent on distinct plasmid backbones from the IncL/M family

Abstract

Objectives To assess the genetic contexts surrounding blaNDM-1 genes carried on IncM plasmids harboured by six carbapenemase-producing Enterobacterales (CPE) isolates referred to the UK Health Security Agency’s Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit. Methods Between 2014 and 2018, the AMRHAI Reference Unit undertook WGS of CPE isolates using Illumina NGS. Nanopore sequencing was used for selected isolates and publicly available plasmid references were downloaded. Analysis of incRNA, which encodes the antisense RNA regulating plasmidic repA gene expression, was performed and bioinformatics tools were used to analyse whole plasmid sequences. Results Of 894 NDM-positive isolates of Enterobacterales, 44 NDM-1-positive isolates of five different species (Citrobacter spp., Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca) encoded the IncRNA locus of IncM2 plasmids. Long-read sequencing of six diverse isolates revealed related IncM2, NDM-1-encoding plasmids. Plasmid ‘backbone’ areas were conserved and contrasted with highly variable resistance regions. Sub-groupings of IncM2 plasmids encoding blaNDM-1 were detected; one sub-group occurred in five different health regions of England in every year. The diversity of NDM-1-encoding resistance gene integrons and transposons and their insertions sites in the plasmids indicated that NDM-1 has been acquired repeatedly by IncM2 variants. Conclusions The use of sequencing helped inform: (i) a wide geographical distribution of isolates encoding NDM-1 on emergent IncM2 plasmids; (ii) variant plasmids have acquired NDM-1 separately; and (iii) dynamic arrangements and evolution of the resistance elements in this plasmid group. The geographical and temporal distribution of IncM2 plasmids that encode NDM-1 highlights them as a public health threat that requires ongoing monitoring.

A Broad-Host-Range Plasmid Outbreak: Dynamics of IncL/M Plasmids Transferring Carbapenemase Genes

“…Interestingly, this plasmid was found in another E. coli isolate of different sequence type (ST2350) collected from a human screening rectal sample, also in a South-East England hospital in 2018. A nearly identical plasmid, pKp_SE1_NDM (accession number: CM010662), was identified in K. pneumoniae (ST534) isolated from a human rectal sample in the same hospital in 2017 [ 13 ], suggesting that this specific plasmid variant could have been transmitting locally between different Enterobacterales species between 2017 and 2018.…”

“…In a previous study, clinical isolates of five different species ( E. coli , Enterobacter cloacae , Citrobacter sp. , K. pneumoniae and Klebsiella oxytoca ) isolated across the UK were found to harbour closely related IncM2 plasmids carrying bla NDM-1 , suggesting inter-species horizontal gene transfer [ 13 ]. Representative isolates from that study were included here to quantify the threat posed by these emergent NDM-1 plasmids in comparison with the globally disseminated OXA-48 plasmids.…”

“…When the influence of the donor background was discarded by using E. coli MG1655 as the donor ( Figure 2 B), all IncM2 NDM-1-harbouring plasmids conjugated at homogeneous frequencies (between 10 −2 and 10 −3 ), highlighting the similarities between their plasmid backbone [ 13 ]. pCTX-M-3 plasmid was added as a control IncM2 plasmid with a different cargo ( bla CTX-M-3 ) and its conjugation frequency was ~10 −2 .…”

“…Since then, it has been reported in numerous Gram-negative bacterial species and transmissible plasmids around the world, including IncN, IncA/C, IncF, IncH and IncL/M incompatibility groups [ 12 ]. In particular, a recent study performed in the UK, which analysed the sequence of 44 NDM-1-positive isolates belonging to five different bacterial species, suggested that the bla NDM-1 gene has been recently acquired on multiple occasions by IncL/M plasmids in geographically widespread isolates [ 13 ].…”

Prevalence of Class 1 integron in disease-causing carbapenem-resistantEscherichia coliin a tertiary hospital in Kathmandu, Nepal

“…34 So the co-occurrence on NDM-1 with intI1 as well as with other OXA variants is concerning as they can transfer the antibiotic resistant trait by moving between species. 34, 36 Additionally, the presence of the VIM gene, though only found in three isolates (6.2%) in our study, is interesting as there are only few studies reporting VIM presence in Enterobacteriaceae particularly Klebsiella pneumoniae, Escherichia coli and Enterobacter spp. 35 But most importantly, literature suggests that both of these amber class B carbapenemase-encoding genes are associated with integrons and are basically integrated into the gene cassette, 36 so their 100% prevalence within the integron-positive isolates in this study is relevant.…”