GENOME SEQUENCING OF A MULTIDRUG-RESISTANT STAPHYLOCOCCUS CAPITIS SCAR194 CLINICAL ISOLATE FROM TERENGGANU, MALAYSIA, REVEALED THE PRESENCE OF A 30.7 KB RESISTANCE PLASMID

Abstract

Intro: Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) that mainly causes bloodstream infections, especially in neonatal intensive care units (NICUs). However, very little is known regarding the characteristics of this pathogen from Malaysia. Here, we present the genome sequence analysis of a methicillin-resistant S. capitis ScaR194 from Terengganu, Malaysia. Methods: S. capitis ScaR194 was isolated from the pus of a 70-year old male patient in Hospital Sultanah Nur Zahirah, the main tertiary hospital in Terengganu in 2019. Antimicrobial susceptibility was determined by disk diffusion and genome sequencing was performed on an Illumina HiSeq platform with assembly using UniCycler v0.4.8. Findings: S. capitis ScaR194 was resistant to seven antibiotics from five antimicrobial classes and was thus, multidrug resistant (MDR). ScaR194 also displayed the macrolide-streptogramin B (MS) phenotype. The assembled genome size of ScaR194 was 2,590,732 bp over 38 contigs. ScaR194 carried the mecA methicillin-resistance gene which was found in a possible SCCmec type V(5C2) element as well as a blaZ β-lactamase gene. Genome analysis also revealed the presence of a 30,743 bp plasmid designated pScaR194-1 which encoded a plasmid replication initiation (replicase) gene of the rep39 family with a RepA_N domain. Plasmid pScaR194-1 harboured the msrA, mupA and aph(2’’)- aac(6’) genes which confer resistance to macrolides, mupirocin, and gentamicin, respectively, along with the czcD and copAZ heavy metal resistance genes. Fifteen virulence genes mediating cellular adherence (atl, ebp, icaA, icaB, icaC, icaR and sdrC), immune evasion (adsA, capB, capC and manA), encoding lytic enzymes (geh, lip and nuc), and toxin (hlb) were found in the chromosome of ScaR194. Conclusion: Genome analysis of multidrug-resistant S. capitis ScaR194 led to the identification of a 30.7 kb RepA_N plasmid that encoded multiple antibiotic and heavy metal resistance. To our knowledge, this is the first genome description of a clinical S. capitis isolate from Malaysia.