A genetic cluster of MDR Enterobacter cloacae complex ST78 harbouring a plasmid containing blaVIM-1 and mcr-9 in the Netherlands

Abstract

Background Carbapenemases produced by Enterobacterales are often encoded by genes on transferable plasmids and represent a major healthcare problem, especially if the plasmids contain additional antibiotic resistance genes. As part of Dutch national surveillance, 50 medical microbiological laboratories submit their Enterobacterales isolates suspected of carbapenemase production to the National Institute for Public Health and the Environment for characterization. All isolates for which carbapenemase production is confirmed are subjected to next-generation sequencing. Objectives To study the molecular characteristics of a genetic cluster of Enterobacter cloacae complex isolates collected in Dutch national surveillance in the period 2015–20 in the Netherlands. Methods Short- and long-read genome sequencing was used in combination with MLST and pan-genome MLST (pgMLST) analyses. Automated antimicrobial susceptibility testing (AST), the Etest for meropenem and the broth microdilution test for colistin were performed. The carbapenem inactivation method was used to assess carbapenemase production. Results pgMLST revealed that nine E. cloacae complex isolates from three different hospitals in the Netherlands differed by <20 alleles and grouped in a genetic cluster termed EclCluster-013. Seven isolates were submitted by one hospital in 2016–20. EclCluster-013 isolates produced carbapenemase and were from ST78, a globally disseminated lineage. EclCluster-013 isolates harboured a 316 078 bp IncH12 plasmid carrying the blaVIM-1 carbapenemase and the novel mcr-9 colistin resistance gene along with genes encoding resistance to different antibiotic classes. AST showed that EclCluster-013 isolates were MDR, but susceptible to meropenem (<2 mg/L) and colistin (<2 mg/L). Conclusions The EclCluster-013 reported here represents an MDR E. cloacae complex ST78 strain containing an IncH12 plasmid carrying both the blaVIM-1 carbapenemase and the mcr-9 colistin resistance gene.

Epidemiology of carbapenem-resistant and carbapenemase-producing Enterobacterales in the Netherlands 2017–2019

“…Genetic clusters were identified for E. coli , K. pneumoniae complex and Citrobacter freundii using whole genome multi-locus sequence typing (wgMLST), and for Enterobacter cloacae complex using pan-genome multi-locus sequence typing (pgMLST) [ 15 ]. Isolates were considered part of a genetic cluster if their allelic distance was ≤ 25 alleles for E. coli or ≤ 20 alleles for K. pneumoniae complex, E. cloacae complex and C. freundii [ 15 , 16 ]. Clusters were included only if they contained ≥ 2 isolates originating from ≥ 2 persons.…”

First reported detection of the mobile colistin resistance genes,mcr-8 andmcr-9, in the Irish environment

“…However, while the qse B and qse C genes have been detected in colistin resistant isolates previously (Cha et al, 2020; Ding et al, 2021; Yuan et al, 2019), in our study, despite the presence of these genes in plasmid pB18161 they were not associated with phenotypic colistin resistance. Similarly, others have also reported on isolates remaining susceptible to colistin despite the presence of this system, leading to the belief that there may be other unidentified factors associated with the expression of mcr -9 and induction of colistin resistance (Hendrickx et al, 2021; Kananizadeh et al, 2020; Ribeiro et al, 2021). Overall, although the mcr -9 gene is a phosphoethanolamine transferase and is similar in ways to other mcr genes, it does not seem to be as concerning as, in general, it does not appear to mediate phenotypic resistance to colistin.…”

“…With regards to the genetic environment, similar to our findings, many reports to date have indicated the presence of the IS 5 family element IS 903 upstream of the mcr -9 gene, while downstream, they have been generally flanked by IS 1 (IS 1R ) or IS 6 (IS 26 and IS 15DII ) elements (Ai et al ., 2021; Biggel et al ., 2022; Diaconu et al ., 2021; Hendrickx et al ., 2021; Kamathewatta et al ., 2020; Ribeiro et al ., 2021; Tyson et al ., 2020). This highlights the potential involvement of IS 1 , IS 5 and IS 6 family elements in the mobilisation of the mcr -9 gene.…”

Antimicrobial Resistance and Biofilms Underlying Catheter-Related Bloodstream Coinfection by Enterobacter cloacae Complex and Candida parapsilosis

“…The multi-resistant and biofilm-forming E. cloacae complex isolates belong to the category of high-risk sources of nosocomial BSI [ 10 , 11 ]. The pathogenic potential of these bacteria increases their ability to spread resistance determinants through conjugative plasmids, not only within E. cloacae species, but also among other members of the Enterobacteriaceae family [ 12 , 13 ]. The yeast C. parapsilosis is the most common source of BSI among Candida spp.…”