THE ACCESSORY GENOME OF VANCOMYCIN-RESISTANT ENTEROCOCCI AND ITS ROLE IN ANTIMICROBIAL RESISTANCE
Vancomycin-resistant enterococci (VRE) are a major cause of bloodstream infections in severely ill and immunocompromised patients. Up to 80% of these resistant infections are associated with E. faecium— which also possess resistance to many other commonly-used antimicrobials—leaving clinicians with limited treatment options. These organisms possess high rates of genomic variation and recombination through the acquisition of genetic information, including resistance genes, comprising the accessory genome. Thus, studying the pan-genome is of paramount importance to dissect the E. faecium population structure and allow for full characterization of acquired resistance and virulence genes. E. faecium bloodstream isolates (n=162) were collected through “The Vancomycin Resistant Outcomes Study (VENOUS),” a prospective cohort study of VRE bloodstream infection outcomes in adult patients at participating institutions—a general hospital system and major cancer center (Houston, TX) and a general hospital system in Detroit, MI. Preliminary data was generated using the Illumina MiSeq platform, which was used for initial phylogenomic analyses and gain/loss events of clinically-relevant genes. Long-read
sequencing data was generated for a subset of 20 isolates, and multiple bioinformatics tools were utilized to assess the diversity and location of antimicrobial resistance (AMR) genes and mobile genetic elements (MGEs) comprising the accessory genome. Of the 20 isolates on which long-read sequencing was performed, 12/20 (60%) contained plasmids harboring the entirety of the vanA operon. These plasmids were variable in size, and there were a wide variety of mobile genetic elements mediating the insertion of the vanA operon into these plasmids. The pan-genome of E. faecium displays incredible diversity and plasticity, indicating that traditional methods of characterization such as MLST, may not be ideal for this organism. MGEs are ubiquitous in E. faecium clinical strains, and they facilitate the transmission of a wide variety of AMR and virulence genes that are associated with complicated, multidrug-resistant infections. Mechanisms of AMR transmissibility are neither conserved nor predictable, but there are patterns associated with antibiotic and immune selection and pressure. Further analyses are needed to fully characterize the repertoire of MGEs associated with both AMR and virulence and to produce higher-resolution analyses of longitudinal genomic changes in cases of persistent bacteremia.