The novel pseudo-compound transposon Tn7086 carries aminoglycoside resistance genes in Enterococcus faecalis

Enterococcus faecalis is a member of the human gut microbiota and a pathogen responsible for mild and severe infections. Here, genome analysis of E. faecalis strains isolated from different body sites revealed the presence of a novel family of IS1216E-flanked pseudo-compound transposons carrying aminoglycoside resistance genes and other resistance determinants. The representative element, named Tn7086, is 25,380 bp long, contains 27 ORFs and shows a mosaic structure containing (i) the macrolide–lincosamide–streptogramin resistance gene erm(B), (ii) the aminoglycoside–streptothricin resistance gene cluster ant(6′)-Ia–sat4–aph(3′)-IIIa, (iii) the gentamicin resistance determinant acc(6′)-aph(2″) and (iv) a toxin–antitoxin cassette. Tn7086 family members contain deletions and/or insertions including three DNA segments, two of which carry antimicrobial resistance genes. All elements integrate downstream of a conserved 8-bp target site within the chromosomal panE gene, located between lysR and rbgA and encoding a 2-dehydropantoate 2-reductase. Genome-wide analysis of 646 complete E. faecalis genomes showed panE disruption in 12.7% of isolates due to the presence of Tn7086 family members (10.7%) or IS1216E (2%), while an intact panE gene was found in the other genomes. Element integration produced either target-site duplication or DNA deletions, with or without the target site. PCR and sequencing analysis showed that Tn7086 and Tn7086-like elements excise from the chromosome and produce circular translocatable units at frequencies of 1.24±0.03 to 22.4±17.7 copies per 106 chromosomes. In conclusion, we describe the novel Tn7086 family of IS1216E-flanked pseudo-compound transposons in E. faecalis, which carry multiple antimicrobial resistance genes, integrate at a specific chromosomal site within panE and are capable of excision to form circular translocatable units.