Vancomycin resistance in Enterococcus faecium from the Dallas, Texas area is conferred predominantly on pRUM-like plasmids

Abstract

Vancomycin-resistant E. faecium (VREfm) is a significant public health concern because of limited treatment options. Genomic surveillance can be used to monitor VREfm transmission and evolution. Genomic analysis of VREfm has not been reported for the Dallas/Fort Worth/Arlington, Texas, area, which is currently the 4th largest metropolitan area in the United States. Our study aimed to address this gap in knowledge by analyzing the genomes of 46 VREfm and one vancomycin-sensitive comparator collected during routine fecal surveillance of high-risk patients upon admission to a Dallas, Texas hospital system (August to October, 2015). 31 complete and 16 draft genome sequences were generated. The closed VREfm genomes possessed up to 12 extrachromosomal elements each. Overall, 251 closed putative plasmid sequences assigned to previously described and newly defined rep family types were obtained. Phylogenetic analysis identified 10 different sequence types (STs) among the isolates, with the most prevalent being ST17 and ST18. Strikingly, all but three of the VREfm isolates encoded vanA-type vancomycin resistance within Tn1546- like elements on a pRUM-like (rep17) plasmid backbone. Relative to a previously reported typing scheme for the vanA-encoding Tn1546, new variants of the Tn1546 were identified that harbored a combination of 7 insertion sequences (IS), including 3 novel IS elements reported in this study (ISEfa16, ISEfa17 and ISEfa18). We conclude that pRUM-like plasmids are important vectors for vancomycin resistance in the Dallas, Texas area and should be a focus of plasmid surveillance efforts. ImportanceVancomycin is an antibiotic used to treat infections caused by multidrug-resistant Gram-positive bacteria. Vancomycin resistance is common in clinical isolates of the Gram-positive pathogen Enterococcus faecium. In E. faecium, vancomycin resistance genes can be disseminated by plasmids with different host ranges and transfer efficiencies. Surveillance of resistance plasmids is critical to understanding antibiotic resistance transmission. This study analyzed the genome sequences 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. Our work suggests that the pRUM-like plasmids should continue to be studied to understand their mechanisms of maintenance, transmission, and evolution in VREfm.