Staphylococcus sciuriC2865 from a distinct subspecies cluster as reservoir of the novel transferable trimethoprim resistance gene,dfrE,and adaptation driving mobile elements

Abstract

Four methicillin-resistant Staphylococcus sciuri (MRSS) strains isolated from stranded dogs showed trimethoprim (TMP) resistance, while all staphylococcal TMP resistant dihydrofolate reductase genes ( dfr ) were negative. An in-depth whole-genome-sequencing approach on strain C2865 was followed for resistome and mobilome profiling, and for comparative genomics with S. sciuri group available genomes. Lack of species host tropism was observed, with MRSS C2865 placed at a separate sub-branch within S. sciuri species, close to the average nucleotide identity to be considered a different species (95-96%). S. sciuri proved a pronounced accessory genome (73% of genes), while MRSS C2865 distinctively harboured the highest total gene number and highest number of unique genes, with 75% associated to the recognised mobilome . A novel multidrug resistance mosaic plasmid (pUR2865-34) with several adaptive, mobilization ( oriT mimic) and segregational stability (Type Ib par system) traits and two small single resistance plasmids were identified. Plasmid pUR2865-34 enclosed a novel staphylococcal TMP resistance gene, named dfrE , which shared highest identity with dfr of soil-related Paenibacillus anaericanus (68%). DfrE conferred high-level TMP resistance in S. aureus and Escherichia coli . Database searches revealed that dfrE was formerly denoted ( dfr_like ) in an Exiguobacterium spp. from a fish-farm sediment and that was present but unnoticed in several staphylococcal and one macrococcal genomes with different epidemiological backgrounds. Novel chromosomal site-specific mobile islands with resourceful traits were identified, including a multidrug-resistant SCC mec cassette lacking cassette chromosome recombinase (Ccr) genes, a staphylococcal pathogenicity island of the SaPI4 family, and three unrelated siphoviridae prophages, two of which enclosed recombinases with the conserved Ccr-motif. We reveal a novel staphylococcal TMP resistance dfrE gene already present in diverse bacterial backgrounds. We confirm the ubiquity, high genome plasticity and low host tropism of S. sciuri highlighting its role as a resourceful reservoir for evolutionary novel features contributing to its extraordinary versatility and adaptability.

Mobile antimicrobial resistance genes in probiotics

“…36 Out of the Enterococcus faecalis deriving genes, dfrE was first identified in E. faecalis, 37 but according to a recent study it is not exclusive to this species anymore. 38 The genes efrA and efrB have been described in E. faecalis and E. faecium. 39,40 Gene emeA has only been identified in E. faecalis so far.…”

The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE , Spread Unnoticed

“…Antimicrobial resistance (AMR) genes. AMR genes formerly detected in MRSS C2865 (see Table S1 in reference 85 ) were blasted against the WGS of strain C2865. Contig(s) were manually checked for redundant dhfr genes and for additional resistance genes of interest.…”

“…Excision ability of chromosomally located MGEs. Potential excision and circularization of selected chromosomally located mobile elements, in addition to detection of the resultant chromosomal region after excision, were tested by specific inverse and conventional PCR, respectively (supplemental material; see Table S1 in reference 85 ).…”

“…Primers were designed for the detection of the TMP resistance dfrE gene, the biofilm formation ica -locus ( ica ADBC) variant genes, and the ica -locus repressor ( icaR ) (see Table S1 in reference 85 ). For the dfrE gene, primers designed enclosed the Dhfr superfamily domain region (Cd-Search PF00186).…”

Natural phage communities crosslink different species within the genus Staphylococcus

“…Ultimately, we appraised those phages' potential to incorporate foreign genetic material. For this, we transformed a natural S. sciuri plasmid pUR2865 34 (3.83 kb) conferring chloramphenicol resistance into S. epidermidis S414. This strain was chosen as donor, as it was infected by most sequenced phages (26) and by members of the Sipho-and Herelleviridae.…”