Complete Genome Sequence and Analysis of a ST573 Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus SauR3 Clinical Isolate from Terengganu, Malaysia

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a World Health Organization-listed priority pathogen. Scarce genomic data are available for MRSA isolates from Malaysia. Here, we present the complete genome sequence of a multidrug-resistant MRSA strain SauR3, isolated from the blood of a 6-year-old patient hospitalized in Terengganu, Malaysia, in 2016. S. aureus SauR3 was resistant to five antimicrobial classes comprising nine antibiotics. The genome was sequenced on the Illumina and Oxford Nanopore platforms and hybrid assembly was performed to obtain its complete genome sequence. The SauR3 genome consists of a circular chromosome of 2,800,017 bp and three plasmids designated pSauR3-1 (42,928 bp), pSauR3-2 (3011 bp), and pSauR3-3 (2473 bp). SauR3 belongs to sequence type 573 (ST573), a rarely reported sequence type of the staphylococcal clonal complex 1 (CC1) lineage, and harbors a variant of the staphylococcal cassette chromosome mec (SCCmec) type V (5C2&5) element which also contains the aac(6′)-aph(2″) aminoglycoside-resistance genes. pSauR3-1 harbors several antibiotic resistance genes in a 14,095 bp genomic island (GI), previously reported in the chromosome of other staphylococci. pSauR3-2 is cryptic, whereas pSauR3-3 encodes the ermC gene that mediates inducible resistance to macrolide-lincosamide-streptogramin B (iMLSB). The SauR3 genome can potentially be used as a reference genome for other ST573 isolates.

Whole genome sequencing of methicillin-resistant Staphylococcus aureus clinical isolates from Terengganu, Malaysia, indicates the predominance of the EMRSA-15 (ST22-SCCmec IV) clone

“…dfrG was also found in two other ST772 isolates that were obtained from HSNZ previously (KT/Y21 in 2009 and SAZ_16 in 2013). We recently reported the complete genome sequence of one of the ST573 isolates, SauR3 (CP098727), by hybrid assembly of Illumina and Oxford Nanopore sequence reads 14 . SauR3 carried a 42.9 kb plasmid (pSauR3-1) with an approximately 14 kb genomic island containing resistance genes including the bla operon in a full-length Tn 552 , mphC , msrA , SAT-4 , and aadE-aph(3’’)-IIIa .…”

“…Besides, SauR3 also harbored the small, 2.5 kb RepL-type plasmid encoding ermC (designated pSauR3-3) which was responsible for its inducible iMLS B phenotype. Another interesting feature of the SauR3 genome is the presence of a SCC mec type V (5C2&5) variant which also encodes the aac(6’)-aph(2’’) aminoglycoside-resistance genes flanked by IS 431 14 . However, tracing the presence of such genetic features in the other isolates of ST573 (SauR90 and SauR169) was not possible using short-read sequences alone.…”

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

“…We tried to minimize this by closing the gaps in between contigs through PCR and conventional Sanger sequencing (see Section 3.5 ) whenever possible, but the validation of the assembled large plasmid sequences would typically require long-read sequencing using either the Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) platforms, which are higher in cost [ 127 , 128 ]. We have recently done so for one of the MRSA isolates, SauR3, and hybrid assembly of the Illumina and ONT reads validated the presence of three plasmids in the isolate [ 129 ].…”

Phenotyphic Identification and Distribution of Methicillin Resistant Staphylococcus aureus from Clinical Samples in Some Selected Hospital Laboratories in Sokoto, Sokoto State, Nigeria

“…Several researches were carried out and some are still going on Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus (MRSA) globally as the circulating gene is on rise in different hospital settings (Al-Trad et al, 2023;Dierikx et al, 2023;Nwabuife et al, 2023…”