Abstract
Staphylococcus caprae, Staphylococcus capitis, and Staphylococcus epidermidis belong to the “Epidermidis Cluster Group” (ECG) and are generally opportunistic pathogens. In this work, whole genome sequencing, molecular cloning and pan-genome analysis were performed to investigate the genetic characteristics of the resistance, virulence and genome structures of 69 ECG strains, including a clinical isolate (S. caprae SY333) obtained in this work. Two resistance genes (blaZ and aadD2) encoded on the plasmids pSY333-41 and pSY333-45 of S. caprae SY333 were confirmed to be functional. The bla region in ECG exhibited three distinct structures, and these chromosome- and plasmid-encoded bla operons seemed to follow two different evolutionary paths. Pan-genome analysis revealed their pan-genomes tend to be “open.” For the virulence-related factors, the genes involved in primary attachment were observed almost exclusively in S. epidermidis, while the genes associated with intercellular aggregation were observed more frequently in S. caprae and S. capitis. The type VII secretion system was present in all strains of S. caprae and some of S. epidermidis but not in S. capitis. Moreover, the isd locus (iron regulated surface determinant) was first found to be encoded on the genomes of S. caprae and S. capitis. These findings suggested that the plasmid and chromosome encoded bla operons of ECG species underwent different evolution paths, as well as they differed in the abundance of virulence genes associated with adherence, invasion, secretion system and immune evasion. Identification of isd loci in S. caprae and S. capitis indicated their ability to acquire heme as nutrient iron during infection.
Highlights
Coagulase-negative staphylococci (CoNS) commonly live on the human skin (Piette and Verschraegen, 2009; Becker et al, 2014)
The S. caprae SY333 genome consists of a circularly closed chromosome and five non-conjugative plasmids named as pSY333-92, pSY333-45, pSY333-41, pSY333-7, and pSY333-2
Staphylococcal plasmids range from just over 1.0 kb to >60.0 kb in size (Kwong et al, 2017), and the smaller plasmids generally replicate via a rolling-circle replication (RCR) mechanism that is hallmarked by the production of singlestranded intermediates during replication
Summary
Coagulase-negative staphylococci (CoNS) commonly live on the human skin (Piette and Verschraegen, 2009; Becker et al, 2014) They often caused infectious diseases in specific groups of patients, such as those with neonates, neutropenia, and so on (Ma et al, 2011; Zong et al, 2011), and infections at metastatic sites, such as joints, heart and bones. The virulence properties of CoNS species are mainly related to their ability to form biofilms and produce colonizing biomaterials (Becker et al, 2014). At present, these species are considered as important bloodstream pathogens usually with multidrug resistance (May et al, 2014). The reasons why S. caprae can cause hospital-acquired infections haven’t been fully elucidated
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