Abstract
Staphylococcus epidermidis is found naturally on the skin but is a common cause of persistent orthopaedic device-related infections (ODRIs). This study used a pan-genome and gene-by-gene approach to analyse the clonality of whole genome sequences (WGS) of 115 S. epidermidis isolates from 55 patients with persistent ODRIs. Analysis of the 522 gene core genome revealed that the isolates clustered into three clades, and MLST analysis showed that 83% of the isolates belonged to clonal complex 2 (CC2). Analysis also found 13 isolate pairs had different MLST types and less than 70% similarity within the genes; hence, these were defined as re-infection by a different S. epidermidis strain. Comparison of allelic diversity in the remaining 102 isolates (49 patients) revealed that 6 patients had microevolved infections (>7 allele differences), and only 37 patients (77 isolates) had a ‘true’ persistent infection. Analysis of the core genomes of isolate pairs from 37 patients found 110/841 genes had variations; mainly in metabolism associated genes. The accessory genome consisted of 2936 genes; with an average size of 1515 genes. To conclude, this study demonstrates the advantage of using WGS for identifying the accuracy of a persistent infection diagnosis. Hence, persistent infections can be defined as ‘true’ persistent infections if the core genome of paired isolates has ≤7 allele differences; microevolved persistent infection if the paired isolates have >7 allele differences but same MLST type; and polyclonal if they are the same species but a different MLST type.
Highlights
Persistent orthopaedic device-related infections (ODRIs) are a major clinical problem due to their chronic persistence and recalcitrance to antibiotics
It has been suggested that in-host adaptation influences the diversity within S. aureus [6,7] and S. epidermidis [4,8] from the skin and infected sites; there is a paucity of data on collections of persistent prosthetic joint infection (PJI) and fracture-related infection (FRI) isolates
A threshold of ≤7 allele differences was used to define 37 patients (77 isolates) as ‘true’ persistent infections, while 12 patients (25 isolates) had a microevolved persistent infection. This 75% incidence of persistent infection is comparable to the 71% that Galdbart et al [24] calculated from examining the diversity in PJI caused by 54 S. epidermidis isolates from 14 patients using pulse-field gel electrophoresis (PFGE)
Summary
Persistent orthopaedic device-related infections (ODRIs) are a major clinical problem due to their chronic persistence and recalcitrance to antibiotics. Whole genome sequencing has shown that commensal and clinical S. epidermidis comprise highly diverse assemblages of related strains [3,4]. Isolates that are closely related genetically can display different phenotypes that may allow some of them to make the transition from the skin environment to implant-associated infections [4,5]. A previous study has shown high variability in biofilm phenotypes in isolates from commensal and infection sources, and a correlation between genotypic groupings (clade, clonal complex and sequence type) and known biofilm-associated genes, indicating widespread acquisition and mobility of these genes between lineages [3]. To analyse the clonality of isolates during persistent S. epidermidis infections (up to 428 days), the WGS of 115 S. epidermidis isolates from 55 patients with persistent PJIs or FRI were examined
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