Comparative Genomic Analysis of a Multidrug-Resistant Staphylococcus hominis ShoR14 Clinical Isolate from Terengganu, Malaysia, Led to the Discovery of Novel Mobile Genetic Elements

Abstract

Staphylococcus hominis is a coagulase-negative Staphylococcus (CoNS) commensal capable of causing serious systemic infections in humans. The emergence of multidrug-resistant S. hominis strains is of concern but little is known about the characteristics of this organism, particularly from Malaysia. Here, we present the comparative genome analysis of S. hominis ShoR14, a multidrug-resistant, methicillin-resistant blood isolate from Terengganu, Malaysia. Genomic DNA of S. hominis ShoR14 was sequenced on the Illumina platform and assembled using Unicycler v0.4.8. ShoR14 belonged to sequence type (ST) 1 which is the most prevalent ST of the S. hominis subsp. hominis. Comparative genomic analysis with closely related strains in the database with complete genome sequences, led to the discovery of a novel variant of the staphylococcal chromosome cassette mec (SCCmec) type VIII element harboring the mecA methicillin-resistance gene in ShoR14 and its possible carriage of a SCCfus element that encodes the fusidic acid resistance gene (fusC). Up to seven possible ShoR14 plasmid contigs were identified, three of which harbored resistance genes for tetracycline (tetK), chloramphenicol (catA7), macrolides, lincosamides, and streptogramin B (ermC). Additionally, we report the discovery of a novel mercury-resistant transposon, Tn7456, other genomic islands, and prophages which make up the S. hominis mobilome.

Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Hospitalized Newborn Infants

“…WGS and bioinformatics analysis were carried out as described in [ 33 ]. Genomic DNA was extracted using a Presto™ Mini gDNA Bacteria Kit (Geneaid Biotech Ltd., Taiwan) based on the manufacturer’s instructions with the addition of a lysostaphin (Sigma-Aldrich, Saint Louis, MO, USA) digestion step.…”

WGS Data Collections: How Do Genomic Databases Transform Medicine?

“…The collections such as the Comprehensive Antibiotic Resistance Database (CARD) or the Virulence Factor Database (VFDB) are used to identify the genes responsible for drug-resistance or virulence and characterise local pathogens. It was done recently in the case of multidrug-resistant Staphylococcus hominis isolated in Malaysia [107].…”