The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci

Abstract

<i>Enterococcus faecium</i> has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCC<i>mec</i> This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of <i>rlmH</i> and encoded large serine recombinases <i>ccrAB</i> similar to SCC<i>mec</i> Horizontal transfer of an ECC element termed ECC::<i>cat</i> containing a knock-in <i>cat</i> chloramphenicol resistance determinant occurred in the presence of a conjugative <i>rep</i>_pLG1 plasmid. We determined the ECC::<i>cat</i> insertion site in the 3' region of <i>rlmH</i> in the <i>E. faecium</i> recipient by long-read sequencing. ECC::<i>cat</i> also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC::<i>cat</i> and the conjugative plasmid. The <i>ccrAB_Ent</i> genes were found in 69 of 516 <i>E. faecium</i> genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by <i>attR</i> and <i>attL</i> sites of approximately 50 bp. The <i>attECC</i> sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare <i>E. faecium</i> genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in <i>E. faecium</i><b>IMPORTANCE</b><i>Enterococcus faecium</i> is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid <i>E. faecium</i> in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, <i>ccrAB</i>_Ent, large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci.