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

Abstract

Staphylococcus aureus (S. aureus) ST22 is considered a clinically important clone because an epidemic strain EMRSA-15 belongs to ST22, and several outbreaks of this clone have been documented worldwide. We performed genomic analysis of an S. aureus strain Lr2 ST22 from Pakistan and determined comparative analysis with other ST22 strains. The genomic data show that Lr2 belongs to spa-type t2986 and harbors staphylococcal cassette chromosome mec (SCCmec) type IVa(2B), one complete plasmid, and seven prophages or prophage-like elements. The strain harbors several prophage-associated virulence factors, including Panton–Valentine leukocidin (PVL) and toxic shock syndrome toxin (TSST). The single nucleotide polymorphism (SNPs)-based phylogenetic relationship inferred from whole genome and core genome revealed that strain Lr2 exhibits the nearest identities to a South African community-acquired methicillin-resistant S. aureus (CA-MRSA) ST22 strain and makes a separate clade with an Indian CA-MRSA ST22 strain. Although most ST22 strains carry blaZ, mecA, and mutations in gyrA, the Lr2 strain does not have the blaZ gene but, unlike other ST22 strains, carries the antibiotic resistance genes erm(C) and aac(6′)-Ie-aph(2″)-Ia. Among ST22 strains analyzed, only the strain Lr2 possesses both PVL and TSST genes. The functional annotation of genes unique to Lr2 revealed that mobilome is the third-largest Cluster of Orthologous Genes (COGs) category, which encodes genes associated with prophages and transposons. This possibly makes methicillin-resistant S. aureus (MRSA) Lr2 ST22 strain highly virulent, and this study would improve the knowledge of MRSA ST22 strains in Pakistan. However, further studies are needed on a large collection of MRSA to comprehend the genomic epidemiology and evolution of this clone in Pakistan.

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

“…However, in the present study, only a total of 21 isolates (23.9%) harbored the lukED genes, which were distributed among various sequence types (ST1: n = 5, ST88: n = 1, ST239: n = 2, ST672: n = 10, ST1178: n = 1, ST7879: n = 1, ST7883: n = 1). In addition, the lukED genes were not found in the ST22 isolates, which was consistent with a previous study 52 . Despite recent findings which described the emergence of hypervirulent ST22 strains carrying both PVL and tst genes 53 , 54 , the HSNZ ST22 isolates notably lacked these virulence factors.…”

Antibiotic Susceptibility Profiling of Human Pathogenic Staphylococcus aureus Strains Using Whole Genome Sequencing and Genome-Scale Annotation Approaches

“…Recently, El-Deeb et al [ 73 ] analyzed the whole genome of nine methicillin-resistant staphylococci (MRS) collected in Eastern Province, Saudi Arabia, and they found that only isolate SA1 recovered from goat’s milk had the PVL toxin gene and the Staphylococcus enterotoxin B gene seb . Ullah et al [ 70 ] conducted a genomic investigation of an S. aureus strain isolated from Pakistan and discovered that the strain has many prophage-associated virulence factors, including PVL and toxic shock syndrome toxin (TSST). Additionally, all 52 isolates of S. aureus isolated from the vascular accesses in hemodialysis patients at Assiout University Hospitals were negative for the PVL gene [ 74 ].…”

“…Each row represents the aligned sample. Panton-Valentine leukocidin (PVL) toxin is a virulence factor in S. aureus associated with deep skin and soft-tissue infections (furunculosis, cutaneous abscesses, and severe necrotizing pneumonia) [68][69][70]. In 1932, Panton and Valentine defined the PVL as a virulence factor in the family of synergohymenotropic toxins in S. aureus [71].…”

Genomic Analysis of Antibiotics Resistance in Pathogens

“…This collection also gathers papers on antibiotic resistance of some of the major emerging infections pathogens such as Mycobacteroides abscessus [ 3 ], Klebsiella pneumoniae [ 4 , 5 ], Salmonella sp. [ 6 , 7 ], Francisella tularensis [ 8 ], Acinetobacter baumannii [ 9 , 10 ], or Pseudomonas aeruginosa [ 11 ] and other human pathogens such as Neisseria gonorrhoea [ 12 ], Staphylococcus aureus [ 13 ], or Escherichia coli [ 14 ]. Most of them are high-priority pathogens [ 15 ], according to the National Institute of Allergy and Infectious Diseases, and are globally and medically important pathogens.…”

“…It has been classified as a globally and medically important human and foodborne pathogen [ 16 ], and methicillin resistance has been a major challenge to treatment and patient science. Ullah et al have performed a comparative genomic analysis of a highly virulent methicillin-resistant S. aureus (MRSA) of a Pakistan clone [ 13 ].…”