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

Abstract

Staphylococcus epidermidis has become an important nosocomial pathogen. Multidrug resistance makes S. epidermidis infections difficult to treat. The study aims to describe the genomic characteristics of methicillin-resistant S. epidermidis (MRSE) isolated from clinical sources, to comprehend the genetic basis of antibiotic resistance, virulence, and potential pathogenicity. Sixteen MRSE underwent whole-genome sequencing, and bioinformatics analyses were carried out to ascertain their resistome, virulome, mobilome, clonality, and phylogenomic relationships. In all, 75% of isolates displayed multidrug resistance and were associated with the carriage of multiple resistance genes including mecA, blaZ, tet(K), erm(A), erm(B), erm(C), dfrG, aac(6′)-aph(2′′), and cat(pC221) conferring resistance to β-lactams, tetracyclines, macrolide–lincosamide–streptogramin B, aminoglycosides, and phenicols, which were located on both plasmids and chromosomes. Their virulence profiles were evidenced by the presence of genes involved in adherence/biofilm formation (icaA, icaB, icaC, atl, ebh, and ebp), immune evasion (adsA, capC, and manA), and antiphagocytosis (rmlC, cdsA, and A). The community-acquired SCCmec type IV was the most common SCCmec type. The CoNS belonged to seven multilocus sequence types (MLSTs) and carried a diversity of mobile genetic elements such as phages, insertion sequences, and plasmids. The bacterial anti-phage defense systems clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) immunity phage system and restriction-modification system (R-M system) and the arginine catabolic mobile element (ACME) involved in immune evasion and transport of virulence genes were also found. The insertion sequence, IS256, linked with virulence, was found in 56.3% of isolates. Generally, the isolates clustered according to STs, with some similarity but also considerable variability within isolates. Whole-genome sequencing and bioinformatics analysis provide insights into the likely pathogenicity and antibiotic resistance of S. epidermidis, necessitating surveillance of this emerging pathogen.

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

“…The sequence variations observed in these plasmids were either in the non-coding sequences or the ermC upstream regulatory sequence, which will be discussed in a later section on antimicrobial resistance. The RepL plasmids appeared to have a reasonably broad host range among the Firmicutes [ 43 ] as they have been observed with a high prevalence in S. epidermidis [ 54 ] but with a much lower prevalence among Enterococcus faecalis [ 55 ]. These plasmids lack mobilization genes but a lateral transfer of these ermC small RepL plasmids between staphylococci and bacteria from different genera had been previously demonstrated.…”

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

“…The pan-genome analysis of the isolates revealed the presence of phenol-soluble modulin (PSM) genes in isolate 9SE; the PSM genes have recently been identified as significant virulence factors, most notably in aggressive strains of S. aureus [ 37 ]. The presence of the IS256 and ica genes was used as a measure of the pathogenicity of S. epidermidis [ 38 ]. The 9SE strain possessed genes associated with biofilm formation ( icaA , icaB, icaC, and icaD ), IS256, and the gene regulator ( icaR ); biofilm-forming isolates have more capacity to adhere to medical devices, thus increasing the risk of device-associated infections [ 20 ].…”

“…Although strains 14SP and 30SP lack the IS256 and ica genes, they were positive for other adhesins such as autolysin ( atl ), cell-wall-associated fibronectin-binding protein ( ebh ), elastin-binding protein ( ebp ), and Ser–Asp-rich fibrinogen-binding proteins ( sdrG ). Similarly, they were positive for other virulence factors, including cysteine protease ( sspB ), lipases ( geh and lip ), serine V8 protease ( sspA ), thermonuclease ( nuc ), and beta-hemolysin ( hlb ), which could increase their pathogenicity and differentiate them from the commensal strains [ 38 ].…”

Assessment of antibiotic use knowledge and antibiotic resistance among final year bachelors of nursing student in the university.: A cross-sectional survey

“…Another study conducted in Ghana in 2018 reported high levels of antibiotic resistance among clinical isolates, particularly for commonly prescribed antibiotics such as amoxicillin and cipro oxacin 10 Therefore, this proposed cross-sectional study aims to assess the level of knowledge of antibiotic use and antibiotic resistance among nal year university students reading Bsc.…”