The Genome of Staphylococcus epidermidis O47

Abstract

The skin colonizing coagulase-negative Staphylococcus epidermidis causes nosocomial infections and is an important opportunistic and highly adaptable pathogen. To gain more insight into this species, we sequenced the genome of the biofilm positive, methicillin susceptible S. epidermidis O47 strain (hereafter O47). This strain belongs to the most frequently isolated sequence type 2. In comparison to the RP62A strain, O47 can be transformed, which makes it a preferred strain for molecular studies. S. epidermidis O47's genome has a single chromosome of about 2.5 million base pairs and no plasmid. Its oriC sequence has the same directionality as S. epidermidis RP62A, S. carnosus, S. haemolyticus, S. saprophyticus and is inverted in comparison to Staphylococcus aureus and S. epidermidis ATCC 12228. A phylogenetic analysis based on all S. epidermidis genomes currently available at GenBank revealed that O47 is closest related to DAR1907. The genome of O47 contains genes for the typical global regulatory systems known in staphylococci. In addition, it contains most of the genes encoding for the typical virulence factors for S. epidermidis but not for S. aureus with the exception of a putative hemolysin III. O47 has the typical S. epidermidis genetic islands and several mobile genetic elements, which include staphylococcal cassette chromosome (SCC) of about 54 kb length and two prophages ϕO47A and ϕO47B. However, its genome has no transposons and the smallest number of insertion sequence (IS) elements compared to the other known S. epidermidis genomes. By sequencing and analyzing the genome of O47, we provide the basis for its utilization in genetic and molecular studies of biofilm formation.

Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa

“…IS256 has been shown to facilitate genomic rearrangements in pathogenic S. epidermidis isolates ( Cabrera-Contreras et al, 2019 ). The detection of IS families IS110, IS200/IS605, and IS3 agrees with a study of Raue et al (2020) , which also found the IS family IS6 was not detected in the current study. Again, the detection of IS256 and the ica operon in isolates belonging to ST2 agrees with a study conducted in China, which analyzed S. epidermidis from community and hospital environments ( Du et al, 2013 ).…”

“…The detection of blaZ in all isolates and the regulator genes blaR and blaI may explain the resistance against penicillin and cephalosporins observed in antibiotic susceptibility tests, which is in agreement with a previous study (Cabrera-Contreras et al, 2019). S. epidermidis isolates carrying similar resistance gene profiles have been previously reported (Xu et al, 2018;Cabrera-Contreras et al, 2019;Raue et al, 2020). Generally, there was considerable agreement between resistance phenotypes and genotypes observed with ARGs affirming the phenotype, except in a few instances.…”

“…The isolates, however, cannot be dismissed as non-pathogenic, as they can deploy several other virulence factors such as immune evasion (encoded by hasC , rfbA-1 , adsA , and capC ), toxins (encoded by hlb , hlyA , and cysC1 ) anti-phagocytosis ( rmlC , cdsA , cpsA , and cpsF ), stress adaptation ( katA , katA , mntB , and sodCI ), and intracellular survival ( lplA1 ). Previous studies in S. epidermidis have reported similar biofilm/adherence-associated genes to those reported in this study, including elastin binding protein gene ebp , serine protease gene sspA , autolysin gene atlE , lipase gene geh , the cell wall-associated fibronectin-binding protein gene ebh , nuclease gene nuc , and the ica genes ( Salgueiro et al, 2017 ; Xu et al, 2018 ; Raue et al, 2020 ).…”

“…All isolates bore at least one sequence with CRISPR ( Table 3 ), 10 of which contained at least one intact prophage. In a previous study ( Raue et al, 2020 ), four candidates for CRISPR elements were found while investigating the genome of S. epidermidis O47 strain, which is biofilm-positive and methicillin-susceptible. The S. epidermidis O47 strain from that study lacked the CRISPR-associated genes just, as was observed in this study.…”

Whole-Genome Sequence of Multidrug-Resistant Methicillin-Resistant Staphylococcus epidermidis Carrying Biofilm-Associated Genes and a Unique Composite of SCCmec

“…SnapGene Viewer v.6.0.2 was used for the visualization of gene cassettes. Virulence genes were investigated using the virulence factor database (VFDB) [ 53 ], using S. epidermidis RP62A as a reference strain for comparison [ 54 ].…”