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

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a priority nosocomial pathogen with plasmids playing a crucial role in its genetic adaptability, particularly in the acquisition and spread of antimicrobial resistance. In this study, the genome sequences of 79 MSRA clinical isolates from Terengganu, Malaysia, (obtained between 2016 and 2020) along with an additional 15 Malaysian MRSA genomes from GenBank were analyzed for their plasmid content. The majority (90%, 85/94) of the Malaysian MRSA isolates harbored 1–4 plasmids each. In total, 189 plasmid sequences were identified ranging in size from 2.3 kb to ca. 58 kb, spanning all seven distinctive plasmid replication initiator (replicase) types. Resistance genes (either to antimicrobials, heavy metals, and/or biocides) were found in 74% (140/189) of these plasmids. Small plasmids (<5 kb) were predominant (63.5%, 120/189) with a RepL replicase plasmid harboring the ermC gene that confers resistance to macrolides, lincosamides, and streptogramin B (MLSB) identified in 63 MRSA isolates. A low carriage of conjugative plasmids was observed (n = 2), but the majority (64.5%, 122/189) of the non-conjugative plasmids have mobilizable potential. The results obtained enabled us to gain a rare view of the plasmidomic landscape of Malaysian MRSA isolates and reinforces their importance in the evolution of this pathogen.

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

“…ermC was detected in the ST22 isolates at a high frequency ( n = 60). This gene is located on a small RepL-type plasmid (2.4–2.7 kb) in the ST22 isolates 13 as well as other isolates. The cat gene that mediates resistance to chloramphenicol was identified only in four isolates of ST22 (Fig.…”

“…SauR165 (ST22 cat -positive isolate) carried more resistance genes ( n = 14) compared to other ST22 isolates ( n = 7–10). SauR165 was found to harbor a 28.6 kb RepA_N-type plasmid, pSauR165-1, which encode six antibiotic resistance genes including cat , tetK , ant(4’’)-Ib , aac(6’)-Ie-aph(2’’)-Ia , lnuA and qacA , along with the cadDX cadmium resistance genes 13 .…”

“…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. Nevertheless, both SauR90 and SauR169 did not harbor the ermC -encoding RepL-type plasmid and displayed the MS phenotype 13 .…”

“…The findings revealed that SauR156 (the only ST9 isolate) carried 18 resistance genes, including some genes that were not found in other STs such as ermB , lnuB , lsaE , and fexA . Furthermore, an 11.3 kb PriCT_1 plasmid (pSauR156-1), which encodes ermB , tetL , and aadD was detected in SauR156 13 .…”

“…Similar to ST22 isolates, the ST672 isolates also appeared to be more susceptible to antimicrobials, with resistance genes detected in the range of nine to ten genes. Nine of the ten ST672 isolates harbored the blaZ gene in the 6,545 bp transposon Tn 552 which was encoded on a 20.7 kb plasmid that was highly similar to pMW2, a 20,654 bp Rep_3-type plasmid initially described in MRSA strain MW2 isolated in USA in 1998 13 , 15 . The sole blaZ -negative ST672 isolate, SauR248, was plasmid-free.…”