Examination of Staphylococcus aureus Prophages Circulating in Egypt

Abstract

Staphylococcus aureus infections are of growing concern given the increased incidence of antibiotic resistant strains. Egypt, like several other countries, has seen alarming increases in methicillin-resistant S. aureus (MRSA) infections. This species can rapidly acquire genes associated with resistance, as well as virulence factors, through mobile genetic elements, including phages. Recently, we sequenced 56 S. aureus genomes from Alexandria Main University Hospital in Alexandria, Egypt, complementing 17 S. aureus genomes publicly available from other sites in Egypt. In the current study, we found that the majority (73.6%) of these strains contain intact prophages, including Biseptimaviruses, Phietaviruses, and Triaviruses. Further investigation of these prophages revealed evidence of horizontal exchange of the integrase for two of the prophages. These Egyptian S. aureus prophages are predicted to encode numerous virulence factors, including genes associated with immune evasion and toxins, including the Panton–Valentine leukocidin (PVL)-associated genes lukF-PV/lukS-PV. Thus, prophages are likely to be a major contributor to the virulence of S. aureus strains in circulation in Egypt.

Genomic epidemiology and characterization of Staphylococcus aureus isolates from raw milk in Jiangsu, China: emerging broader host tropism strain clones ST59 and ST398

“…Except for immune escape genes, the sea gene is also present in the genome of MRSA ST59 in a prophage region of Staphy_phiNM3 type. However, similar to previous studies, S. aureus prophages rarely carried antibiotic resistance genes (Ene et al, 2021).…”

Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps

“…Prophage encoded ARGs are sparsely reported in clinically important bacteria like Acinetobacter , Pseudomonas , Escherichia [ 16–18, 67, 71 ]. Also ARGs have been occasionally reported in S. aureus prophages [ 47 ], especially in regions where inappropriate use of antibiotics is highly prevalent. Our results could not identify complete ARGs in any of the prophage regions although ARGs like tet-38, norA, blaZ, fosB were highly prevalent in these isolates [ 32 ].…”

“…Further, amino acid (aa) sequences for integrase genes were extracted from PHASTER annotations. Representative integrase sequences (Sa1int-Sa12int) were retrieved from NCBI [31, 46, 47], aligned along with query sequences using MAFFT and phylogenetic diversity was inferred using FastTree 2.1 in Geneious Prime 11.09 (ver 21.1, Biomatters Ltd. Auckland, New Zealand). All trees, unless specified, were visualized using iTOL V5 (https://itol.embl.de) [48].…”

Characteristics of Prophage Patterns and Virulence Gene Profiles among Methicillin-Resistant Staphylococcus aureus Isolates from Patients with Diabetic Foot Infections in a Referral Hospital in Tehran, Iran

“…Also, SGFa and SGFb were the dominant subtypes among the isolates, which is consistent with previous reports in Iran [15,17,18,[23][24][25] . In S. aureus strains isolated from human sources, SGF-type prophages are associated with the immune evasion cluster [26] , which includes enterotoxin A (sea) [26] , enterotoxin K [7] , enterotoxin Q (seq), beta-hemolysin (hlb), staphylokinase (sak), chemotaxis inhibitory protein, and staphylococcal complement inhibitor [26,27] . Therefore, MRSA strains isolated in the current study could be considered as reservoirs of virulence-associated genes circulating in Iran.…”