Inferring a Population Structure for Staphylococcus epidermidis from Multilocus Sequence Typing Data

Abstract

Despite its importance as a human pathogen, information on population structure and global epidemiology of Staphylococcus epidermidis is scarce and the relative importance of the mechanisms contributing to clonal diversification is unknown. In this study, we addressed these issues by analyzing a representative collection of S. epidermidis isolates from diverse geographic and clinical origins using multilocus sequence typing (MLST). Additionally, we characterized the mobile element (SCCmec) carrying the genetic determinant of methicillin resistance. The 217 S. epidermidis isolates from our collection were split by MLST into 74 types, suggesting a high level of genetic diversity. Analysis of MLST data using the eBURST algorithm revealed the existence of nine epidemic clonal lineages that were disseminated worldwide. One single clonal lineage (clonal complex 2) comprised 74% of the isolates, whereas the remaining isolates were clustered into 8 minor clonal lineages and 13 singletons. According to our evolutionary model, SCCmec was acquired at least 56 times by S. epidermidis. Although geographic dissemination of S. epidermidis strains and the value of the index of association between the alleles, 0.2898 (P < 0.05), support the clonality of S. epidermidis species, examination of the sequence changes at MLST loci during clonal diversification showed that recombination gives rise to new alleles approximately twice as frequently as point mutations. We suggest that S. epidermidis has a population with an epidemic structure, in which nine clones have emerged upon a recombining background and evolved quickly through frequent transfer of genetic mobile elements, including SCCmec.

Comparative Epidemiology of Staphylococcus epidermidis Isolates from Patients with Catheter-Related Bacteremia and from Healthy Volunteers

“…This large genetic variability is in accordance with previous studies conducted on the genetic diversity of S. epidermidis in the hospital environment and/or in the community (27)(28)(29). However, these two distinct populations were found to be phylogenetically related, as MLST (a typing method designed to study long-term global epidemiology and population structure) revealed that all but three STs (ST73 and two new STs, close to ST19 and ST86, respectively) clustered into a unique CC that corresponds to the major CC, CC7 (previously CC2), described by Miragaia and coworkers (8,29). CRBSI S. epidermidis isolates were more resistant to antibiotics than commensal strains obtained from the skin of healthy volunteers, which is in concordance with other studies (29).…”

“…Additionally, half of the MSSE isolates seemed to carry remnants of SCCmec. All of these factors indicate that the loss and acquisition of mobile genetic elements in S. epidermidis are probably extremely frequent, even in the community setting (8).…”

“…However, when the eBURST analysis was rerun with a less stringent group definition (minimum number of identical loci for group definition of 5), all but three STs (ST73 and the two new STs) clustered into a single CC, corresponding to the CC2 described by Miragaia et al (8).…”

“…The most predominant of these lineages, clonal complex 2 (CC2), is composed of a large number of sequence types (STs), due to an unusually high rate of recombination within the lineage (8). One of these STs, ST2, was recognized as representing the majority of methicillin-resistant S. epidermidis (MRSE) clinical strains (9,10).…”

16S rRNA gene-based identification of bacteria in postoperative endophthalmitis by PCR- Denaturing Gradient Gel Electrophoresis (PCR-DGGE) fingerprinting

“…Another explanation for intraspecies heterogeneity could be that S. pneumoniae (18) and S. epidermidis (14) are considered microorganisms with a high level of genetic diversity.…”