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

Jonathan Asante; Bakoena A Hetsa; Daniel G Amoako; Akebe L K Abia; Linda A Bester; Sabiha Y Essack

doi:10.3389/fmicb.2021.656306

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

Front Microbiol. 2021 Aug 5:12:656306. doi: 10.3389/fmicb.2021.656306. eCollection 2021.

Authors

Jonathan Asante^{1

2}, Bakoena A Hetsa^{1

2}, Daniel G Amoako¹, Akebe L K Abia¹, Linda A Bester³, Sabiha Y Essack¹

Affiliations

¹ Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
² School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
³ Biomedical Research Unit, University of KwaZulu-Natal, Durban, 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.

Keywords: Staphylococcus epidermidis; antibiotic resistance; coagulase-negative; genomics; staphylococci; whole-genome sequencing.