Identification of mutations in Staphylococcus epidermidis small colony variants associated with prosthetic joint infection by direct whole genome sequencing from colonies

Background: We previously reported phenotypic characteristics of S. epidermidisIDRL-8864 and its small colony variant (SCV) counterpart, IDRL-8866, both of which were recovered from an infected shoulder arthroplasty (Diagn Microb Infect Dis 2012). The aim of this study was to assess genetic differences between the paired strains by whole genome sequencing (WGS) performed directly on colonies of each strain.

Methods: A single colony of IDRL-8864 and 5 colonies of IDRL-8866 on tripticase soy agar were independently picked and treated in TE buffer with achromopeptidase. Supernatants were used as crude DNA extracts for WGS. Library preparation for WGS was performed using Nextera XT DNA sample preparation kits followed by WGS with the Illumina MiSeq platform. De novo assembly using CLC Genomics Workbench was performed for each strain. Gene annotation was performed on the Rapid Annotations using Subsystem Technology server. The assembled contigs were submitted to CSI Phylogeny 1.1 on the Center for Genomic Epidemiology website to call single nuclear polymorphisms (SNPs). The SNPs from each gene of IDRL-8866 colonies were associated with a position of the genome of IDRL-8864, and common non-synonymous mutations determined for the 5 IDRL-8866 colonies compared with IDRL-8864. The KEGG Automated Annotation Server was used for assessing putative function of the genes with non-synonymous mutations, with reference to the genome of S. epidermidis RP62A.

Results: Compared with IDRL-8864, the number of SNPs found in the 5 IDRL-8866 colonies ranged from 11 to 31. Common non-synonymous mutations in the 5 IDRL-8866 colonies were found in gluD (nitrogen metabolism pathway); rpoB and nrdF (purine/pyrimidine metabolism pathways); coaBC (CoA synthesis pathway); yycG(heme and hemin usage pathways); and SERP0719 (cell wall synthesis).

Conclusion: Conversion of normal phenotype S. epidermidis to SCV colonies in strains from a patient with prosthetic joint infection was accompanied by non-synonymous mutations in genes related to bacterial physiological functions, which might inform the mechanism of chronic infection and the resistance to antimicrobial treatment by SCV-forming S. epidermidis. Further investigations are needed to assess whether these findings generalize to other S. epidermidis SCVs and the relationship to chronic infection.