Mode and dynamics of vanA-type vancomycin-resistancedissemination in Dutch hospitals

Background: Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and especially to vancomycin, a first-line antibiotic to treat infections with multidrug-resistant Gram-positive pathogens, has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or Tn1546 transposition between different genomic locations. Here, we reconstructed all nested genetic elements (clone, plasmid,transposon) to study how the dissemination of vanA-type vancomycin-resistance occurred in Dutch hospitals (2012-2015). Methods: We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterisation was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. This allowed determining all nested genomic elements (clone, plasmid and transposon) involved in the dissemination of the vanA gene cluster. Next, we conducted an "all vs. all" pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid or Tn1546 spread accounted for the dissemination of vanA resistance. Results: The 309 VRE isolates belonged to 18 different SCs of which SC13 (n = 102, 33%), SC17 (n = 52,16.8%) and SC18 (n = 42, 13.6%) were predominant. We identified seven different plasmid types bearing the vanA gene cluster, four of which were highly similar (identity ~99%, coverage ~84%) to previously described complete plasmid sequences. We estimated that clonal dissemination contributed most (~45%) to the spread of vancomycin-resistance in Dutch hospitals, followed by Tn1546 mobilisation (~12%) and plasmid dissemination (~6%). Conclusions: The dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of Tn1546 transposition and/or plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides one of the first quantitative assessments to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type vancomycin-resistance cluster.