Abstract
Oxacillin-resistant Staphylococcus lugdunensis (ORSL) is considered a life-threatening isolate in healthcare settings. Among ORSL clones, ST6-SCCmec II strains are associated with an endemic spread in hospitals. We analyzed the complete genome of ORSL CGMH-SL118, a representative strain. Results revealed that this strain contained three MGEs (two prophages and one plasmid) other than the SCCmec II element, which showed remarkable differences in genome organization compared to the reference strains from NCBI. Eight multidrug-resistant genes were identified. All but blaZ were carried by MGEs, such as the SCCmec II element [mecA, ant (9)-Ia, and ermA] and the prophage φSPbeta [aac (6')-aph (2'), aph (3')-III, and ant (6)-Ia], indicating that MGEs carrying multidrug-resistant genes may be important for ST6 strains. The prophage φSPbeta contains sasX gene, which was responsible for the pathogenesis of Staphylococcus aureus. A phage-mediated resistant island containing fusB (SlRIfusB-118) was found near φSPbeta, which was highly homologous to type III SeRIfusB-5907 of Staphylococcus epidermidis. In contrast to previous studies, over 20% of ST6 isolates showed a fusidic acid-resistant phenotype, suggesting that phage-mediated intraspecies transmission of resistant islands may become an important issue for ST6 strains. Sixty-eight clinical isolates of ST6 Staphylococcus lugdunensis (50 OSSL, oxacillin-sensitive S. lugdunensis, and 18 ORSL, including CGMH-SL118) collected from various types of specimens in the hospital were studied. Among these isolates in this study, ORSL showed similar drug-resistant genes and phenotypes as CGMH-SL118. The comparative genomic analyses highlight the contribution of MGEs in the development and dissemination of antimicrobial resistance in ST6 strains, suggesting that resistance determinants and virulence factors encoded by MGEs provide a survival advantage for successful colonization and spread in healthcare settings.
Highlights
Staphylococcus lugdunensis was considered a commensal coagulase-negative staphylococcal species (CoNS) until the emergence of nosocomial infections, after which it became an important pathogen (Yeh et al, 2015)
Epidemiological surveillance showed that most clinical isolates of S. lugdunensis belonged to OSSL, and only a few isolates belonged to Oxacillin-resistant Staphylococcus lugdunensis (ORSL) (McHardy et al, 2017)
Among the ORSL clinical isolates, SCCmec V strains were the most frequently isolated strains, yet our previous studies showed that some isolates belonging to SCCmec II were the strains possibly involved in the endemic transmission, which makes them important in the hospital environment (Cheng et al, 2015; Yeh et al, 2015)
Summary
Staphylococcus lugdunensis was considered a commensal coagulase-negative staphylococcal species (CoNS) until the emergence of nosocomial infections, after which it became an important pathogen (Yeh et al, 2015). Our previous investigation identified an endemic spreading in northern Taiwan caused by a group of SCCmec II, ST6 strains (Cheng et al, 2015) Further characterization of their SCCmec cassette structure revealed similarities with S. aureus, which suggested that ORSL may act as an interspecies for SCCmec transfer to S. aureus in hospitals (Chang et al, 2019). Staphylococcus lugdunensis N920143 was one of the earlier strains that provided complete genome sequence and information about virulence factors, few MGEs were found in this strain compared to S. aureus (Heilbronner et al, 2011). The present study demonstrated that SCCmec II and ST6 strains contained unique MGEs encoding a putative virulence factor and antimicrobial resistance genes, which may be responsible for its endemic spread
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