Genomic Investigation of Methicillin-Resistant Staphylococcus aureus ST113 Strains Isolated from Tertiary Care Hospitals in Pakistan

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant and opportunistic pathogen. The emergence of new clones of MRSA in both healthcare settings and the community warrants serious attention and epidemiological surveillance. However, epidemiological data of MRSA isolates from Pakistan are limited. We performed a whole-genome-based comparative analysis of two (P10 and R46) MRSA strains isolated from two provinces of Pakistan to understand the genetic diversity, sequence type (ST), and distribution of virulence and antibiotic-resistance genes. The strains belong to ST113 and harbor the SCCmec type IV encoding mecA gene. Both the strains contain two plasmids, and three and two complete prophage sequences are present in P10 and R46, respectively. The specific antibiotic resistance determinants in P10 include two aminoglycoside-resistance genes, aph(3’)-IIIa and aad(6), a streptothrin-resistance gene sat-4, a tetracycline-resistance gene tet(K), a mupirocin-resistance gene mupA, a point mutation in fusA conferring resistance to fusidic acid, and in strain R46 a specific plasmid associated gene ant(4’)-Ib. The strains harbor many virulence factors common to MRSA. However, no Panton-Valentine leucocidin (lukF-PV/lukS-PV) or toxic shock syndrome toxin (tsst) genes were detected in any of the genomes. The phylogenetic relationship of P10 and R46 with other prevailing MRSA strains suggests that ST113 strains are closely related to ST8 strains and ST113 strains are a single-locus variant of ST8. These findings provide important information concerning the emerging MRSA clone ST113 in Pakistan and the sequenced strains can be used as reference strains for the comparative genomic analysis of other MRSA strains in Pakistan and ST113 strains globally.

A food poisoning caused by ST7 Staphylococcal aureus harboring sea gene in Hainan province, China

“…The same recombination mechanism was reported for a conjugative virulence plasmid, p15WZ-82_Vir, from a clinical Klebsiella variicola strain (Yang et al, 2020). ANT(4′)-Ib, also called aadD2, encoding an aminoglycoside 4′-O-nucleotidyltransferase was first described in Bacillus clausii and rarelly reported in S. aureus (Bozdogan et al, 2003;Ullah et al, 2021). In this study, the high prevalence of ANT (4′)-Ib, together with blaZ, tetK, and lnuA were found in ST7 food-borne and SFP strains.…”

“…ANT(4′)-Ib , also called aadD2 , encoding an aminoglycoside 4′-O-nucleotidyltransferase was first described in Bacillus clausii and rarelly reported in S. aureus ( Bozdogan et al, 2003 ; Ullah et al, 2021 ). In this study, the high prevalence of ANT (4′)-Ib, together with blaZ, tetK, and lnuA were found in ST7 food-borne and SFP strains.…”

Prevalence of mecA- and mecC-Associated Methicillin-Resistant Staphylococcus aureus in Clinical Specimens, Punjab, Pakistan

“…Further, the mecA and mecC genes were not detected in two clinical isolates in this study, although these were phenotypically and biochemically characterized as MRSA. This may indicate the need for other molecular confirmations along with conventional methods to characterize MRSA, as previously described [ 39 , 40 ]. Furthermore, it is also possible that another mutant may be circulating in our hospital-acquired MRSA.…”

Comparative Genomic Analysis of a Panton–Valentine Leukocidin-Positive ST22 Community-Acquired Methicillin-Resistant Staphylococcus aureus from Pakistan

“…Although there is a wealth of literature available on comprehensive epidemiological and molecular characterization of MRSA in the USA, Europe, and Asia, there is a scarcity of detailed genomic characterization of MRSA strains in Pakistan. According to some recent studies, Pakistan has a greater rate of MRSA infection, and the data suggest that MRSA clones are becoming more diverse [19][20][21]. The whole-genome analysis provides high resolution in both global and local outbreak investigations as well as further exploring genes associated with pathogenicity and antibiotic resistance [22].…”