Whole Genome Sequencing of Methicillin-Resistant Staphylococcus epidermidis Clinical Isolates Reveals Variable Composite SCCmec ACME among Different STs in a Tertiary Care Hospital in Oman.

Zaaima Al-Jabri,Amal Al-Hinai,Atika Al-Bimani,Meher Rizvi,Zahra Al-Shabibi,Ammar Al-Shabibi

doi:10.3390/microorganisms9091824

Abstract

Staphylococcus epidermidis has been recently recognized as an emerging nosocomial pathogen. There are concerns over the increasing virulence potential of this commensal due to the capabilities of transferring mobile genetic elements to Staphylococcus aureus through staphylococcal chromosomal cassette (SCCmec) and the closely related arginine catabolic mobile element (ACME) and the copper and mercury resistance island (COMER). The potential pathogenicity of S. epidermidis, particularly from blood stream infections, has been poorly investigated. In this study, 24 S. epidermidis isolated from blood stream infections from Oman were investigated using whole genome sequence analysis. Core genome phylogenetic trees revealed one third of the isolates belong to the multidrug resistance ST-2. Genomic analysis unraveled a common occurrence of SCCmec type IV and ACME element predominantly type I arranged in a composite island. The genetic composition of ACME was highly variable among isolates of same or different STs. The COMER-like island was absent in all of our isolates. Reduced copper susceptibility was observed among isolates of ST-2 and ACME type I, followed by ACME type V. In conclusion, in this work, we identify a prevalent occurrence of highly variable ACME elements in different hospital STs of S. epidermidis in Oman, thus strongly suggesting the hypothesis that ACME types evolved from closely related STs.

Highlights

Staphylococcus epidermidis, despite being a member of the skin normal flora, has been increasingly associated with bacteremias, skin and soft tissue infections, and deviceassociated infections [1,2]
The methicillin-resistant S. epidermidis (MRSE) lineage mostly belonged to three groups: two clusters of sequence type-2 (ST-2), and one ST-23 [4], supporting the concerns raised in numerous smaller scale and local studies that S. epidermidis is a dominant reservoir of multidrug resistance genes through horizontal gene transfer (HGT) [4,5]
Emerging strain USA300 in North America as well as S. epidermidis ATCC 12228 harbor two mobile genetic elements—the arginine catabolic mobile element (ACME) and the copper and mercury resistance island (COMER), which are closely related to SCCmec forming composite islands [6,7]

Summary

Introduction

Staphylococcus epidermidis, despite being a member of the skin normal flora, has been increasingly associated with bacteremias, skin and soft tissue infections, and deviceassociated infections [1,2]. A collection of 283 S. epidermidis whole genome sequences of a worldwide data set were analyzed to validate the distribution of the composite Staphylococcus aureus chromosomal cassette elements (SCCmec) elements [3]. The MRSA emerging strain USA300 in North America as well as S. epidermidis ATCC 12228 harbor two mobile genetic elements—the arginine catabolic mobile element (ACME) and the copper and mercury resistance island (COMER), which are closely related to SCCmec forming composite islands [6,7]. The mosaic composition of ACME elements is attributed to the Microorganisms 2021, 9, 1824. Five main types of ACME have been identified in S. epidermidis so far, based on the presence and or absence of three main operons, namely arc, opp, and kdp, as with different flanking DRs [10,11]

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