Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany

Abstract

The emergence of carbapenemase-producing Enterobacteriaceae limits therapeutic options and presents a major public health problem. Resistances to carbapenems are mostly conveyed by metallo-beta-lactamases (MBL) including VIM, which are often encoded on resistance plasmids. We characterized four VIM-positive isolates that were obtained as part of a routine diagnostic screening from two laboratories in north-eastern Germany between June and August 2020. Whole-genome sequencing was performed to address (a) phylogenetic properties, (b) plasmid content, and (c) resistance gene carriage. In addition, we performed phenotypic antibiotic and mercury resistance analyses. The genomic analysis revealed three different bacterial species including C. freundii, E. coli and K. oxytoca with four different sequence types. All isolates were geno- and phenotypically multidrug-resistant (MDR) and the phenotypic profile was explained by the underlying resistance gene content. Three isolates of four carried nearly identical VIM-1-resistance plasmids, which in addition encoded a mercury resistance operon and showed some similarity to two publicly available plasmid sequences from sources other than the two laboratories above. Our results highlight the circulation of a nearly identical IncN-type VIM-1-resistance plasmid in different Enterobacteriaceae in north-eastern Germany.

Keywords: Enterobacteriaceae; IncN; VIM; mercury; resistance.

Figure 1

BLAST comparison of plasmid 1 (pPBIO2728_VIM-1). The genomes from this study (three inner circles) and sequences from a public genome (E. coli E-124-4, NCBI accession NZ_PDDP00000000.1) and two plasmids (E. coli ECONIH1 plasmid pKPC-629, NCBI accession CP009862.1; E. coli R178 plasmid pRH-R178, NCBI accession HG530658.1) (three outer rings) were compared by BLAST (-task megablast -evalue 1e-10 -dust no). Concentric rings are colored by species. The outermost ring shows coding sequences (CDS; colored according to legend) with various common IncN sequence features (e.g., CUP [Conserved Upstream]-controlled genes [ccg] [29]) labelled by gene name. The asterisks denote alleles of the IncN pMLST scheme, which match ST7. Note that all isolates in this study and only E. coli E-124-4 and E. coli R178 carry the bla_VIM-1 resistance gene. The mercury resistance operon, however, was present in all analyzed sequences.

Figure 2

Synteny plot of plasmid 1 (pPBIO2728_VIM-1) of E. coli PBIO2728 (ST10) and plasmids from the NCBI nucleotide database. Note that plasmid pRH-R178 (size = 223,382 bp; NCBI accession HG530658.1) of Escherichia coli R178 is only displayed partially. For clarity, only BLAST hits with a length of at least 2% of the length of the shorter replicon in the comparison are shown (1520 bp for both comparisons). Coding sequences (CDS) are colored according to the legend. A 22,480 bp region with 100% identity is shared between the plasmids of strains PBIO2728 and R178 and resembles a transposon carrying a class 1 integron (see text and Figure 1).