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

• Published in: Frontiers in microbiology 2021-08, Vol.12, p.656306-656306
• Main Authors: Asante, Jonathan, Hetsa, Bakoena A., Amoako, Daniel G., Abia, Akebe L. K., Bester, Linda A., Essack, Sabiha Y.
• Format: Article
• Language: English
• Subjects: antibiotic resistance; coagulase-negative; genomics; Microbiology; staphylococci; Staphylococcus epidermidis; whole-genome sequencing
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2021.656306

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 SCC mec type IV was the most common SCC mec 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.