ICE Slu van, a 94-Kilobase Mosaic Integrative Conjugative Element Conferring Interspecies Transfer of VanB-Type Glycopeptide Resistance, a Novel Bacitracin Resistance Locus, and a Toxin-Antitoxin Stabilization System

Abstract

A 94-kb integrative conjugative element (ICESluvan) transferable to Enterococcus faecium and Enterococcus faecalis from an animal isolate of Streptococcus lutetiensis consists of a mosaic of genetic fragments from different Gram-positive bacteria. A variant of ICESluvan was confirmed in S. lutetiensis from a patient. A complete Tn5382/Tn1549 with a vanB2 operon is integrated into a streptococcal ICESde3396-like region harboring a putative bacteriophage exclusion system, a putative agglutinin receptor precursor, and key components of a type IV secretion system. Moreover, ICESluvan encodes a putative MobC family mobilization protein and a relaxase and, thus, in total has all genetic components essential for conjugative transfer. A 9-kb element within Tn5382/Tn1549 encodes, among others, putative proteins similar to the TnpX site-specific recombinase in Faecalibacterium and VanZ in Paenibacillus, which may contribute to the detected low-level teicoplanin resistance. Furthermore, ICESluvan encodes a novel bacitracin resistance locus that is associated with reduced susceptibility to bacitracin when transferred to E. faecium. The expression of a streptococcal pezAT toxin-antitoxin-encoding operon of ICESluvan in S. lutetiensis, E. faecium, and E. faecalis was confirmed by reverse transcription (RT)-PCR, indicating an active toxin-antitoxin system which may contribute to stabilizing ICESluvan within new hosts. Junction PCR and DNA sequencing confirmed that ICESluvan excised to form a circular intermediate in S. lutetiensis, E. faecalis, and E. faecium. Transfer between E. faecalis cells was observed in the presence of helper plasmid pIP964. Sequence analysis of the original S. lutetiensis donor and enterococcal transconjugants showed that ICESluvan integrates in a site-specific manner into the C-terminal end of the chromosomal tRNA methyltransferase gene rumA.

Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

“…AMR genes were also found on IME integrated into rpsI, tRNALeu, and in a gene encoding an HTH-XRE regulator. Interestingly, the vanZ gene found on an IME_tRNALeu exhibits 100% of identity with the one encoded by an IME (not identified as an IME by the authors) integrated inside a Tn1549-related ICE-itself integrated into a Tn5252-related ICE-in Streptococcus lutetiensis (ICESluvan) [17,26]. This suggests a capture of this resistance gene by different genetic elements rather than clonal dissemination of MGEs carrying this gene.…”

“…The encoded VanZ protein displays only 38% of identity with the one previously described in S. suis GZ0565 [25]. However, interestingly, it shows 100% of identity with the one encoded by an IME integrated inside a Tn1549-related ICE-itself integrated with a Tn5252-related ICE-in Streptococcus lutetiensis (ICESluvan) [17,26]. These two IMEs carrying vanZ differ by their integrase and mobilization proteins (different relaxase and presence of a coupling protein only for the IME integrated into a tRNALeu gene).…”

Genomics, evolution, and molecular epidemiology of the Streptococcus bovis / Streptococcus equinus complex (SBSEC)

“…Two of these S. gallolyticus isolates contained a transferable vanB2 gene on a Tn5382-like element so far known only in enterococci (Dahl and Sundsfjord, 2003). A third of these vancomycin resistant isolates and a highly similar strain from a French patient were attributed to the species S. lutetiensis and their vancomycin resistance is encoded by a vanB gene (Bjørkeng et al, 2013). The gene is located on a 94-kb conjugative transposon Tn5382/Tn1549 accompanied by a vanZ gene, and the element is transferable to Enterococcus faecium and E. faecalis recipients.…”

Conjugative and mobilizable genomic islands in bacteria: evolution and diversity

“…Furthermore, sequence re-analysis of four ICEs from firmicutes revealed that they carry typical IMEs encoding one or two serine recombinases and a MOB but neither CP nor MPF proteins. ICE2096-RD.2 from Streptococcus pyogenes (Beres & Musser, 2007), ICESp2905 from S. pyogenes (Brenciani et al, 2011), and Tn6103 from C. difficile (Brouwer et al, 2011) carry 1, 2, and 3 IMEs, respectively, while ICESluvan, a Tn5252-related element from Streptococcus lutetiensis, carries an ICE closely related to ICE1549 that itself carries a putative IME (the 9-kb element; Bjorkeng et al, 2013). Furthermore, three types of transconjugants can be recovered from ICESp2905 transfer assays (Giovanetti et al, 2012).…”