Molecular characterization of vancomycin-resistant Enterococcus faecium isolates collected from the Dallas, Texas area

Abstract

Molecular characterization was performed for 46 vancomycin-resistant E. faecium (VREfm) isolates and one vancomycin-sensitive comparator obtained during routine fecal surveillance of high-risk patients from a Dallas, Texas area hospital system. Hybrid assemblies of long (Oxford Nanopore Technology) and short (Illumina) sequence reads enabled the generation of 31 complete and 16 draft high quality genome sequences. The VREfm isolates possessed up to 12 plasmids each. A total of 251 closed plasmid sequences, assigned to 12 previously described and 9 newly defined rep family types, were obtained. Phylogenetic analysis clustered the Dallas isolates into genomic Clade A1, including 10 different sequence types (STs), the most prevalent ones being ST17 and ST18. VREfm isolates with the novel sequence type ST1703 were also identified. All but three of the VREfm isolates encoded vanA-type vancomycin resistance within Tn1546-like elements on a pRUM-like plasmid backbone. New variants of the Tn1546 were described that harbored a combination of 7 insertion sequences (IS) including 3 novel IS elements reported in this study (ISEfa16, ISEfa17 and ISEfa18). The pRUM-like plasmids carrying the Tn1546 were grouped into 4 sub-groups based on the replication and stability modules of the plasmid backbone. Overall, we conclude that the VREfm isolates analyzed in our collection are representative of other global VanA-type VREfm in that they belong to the Clade A1 lineage, but they possess novel arrangements of the Tn1546-like elements and the vanA operon, which have evolved independently of the pRUM-like backbone. Importance Vancomycin is a broad-spectrum antibiotic used to treat infections caused by multi-drug resistant Gram-positive bacteria. However, vancomycin resistance is predominant for Enterococcus faecium and therefore infections with VREfm have few treatment options. The vancomycin resistance genes are encoded on a transposon, which can be disseminated by different plasmids with different host ranges and transferring efficiencies. The presence of resistance genes within a broad host range plasmid can generate a wide variety of resistant bacteria very quickly. Therefore, surveillance of resistance plasmids is critical. This study provided a comprehensive analysis of VREfm collected from the Dallas, Texas area, with particular focus on the mobile elements associated with vancomycin resistance genes. We find that a single plasmid family, the pRUM-like family, is associated with vancomycin resistance in the majority of isolates sampled.