Repository series · ncbi-prjna1257324

Emergence of livestock-associated MRSA in the Egyptian Nile Delta that carry the exfoliative toxin gene etA

Staphylococcus aureus is a common opportunistic pathogen. Methicillin-resistant strains, MRSA, carry SCCmec elements that include beta-lactam resistance genes mecA/mecC. One globally common lineage, Clonal Complex (CC) 15 failed to evolve MRSA strains until, in 2016, CC15-MRSA were described from Saudi Arabia that carried a fusidic acid resistance gene, fusC, within a SCCmec V element. Henceforth, this strain spread across Gulf states and Egypt infecting or colonizing both, humans and livestock. DNA-microarray-based typing was performed on 134 MRSA isolates collected from livestock and farmers in the Nile Delta region of Egypt in 2022. Twenty-eight out of those 134 isolates from both, humans and milk samples of small ruminants, were assigned to CC15-MRSA-[V+fusC]. Thus, this strain was the second most common MRSA strain, behind CC88-MRSA-[IV+fusC]. Twenty out of those 28 isolates harboured the gene etA, encoding exfoliative toxin A associated with Staphylococcal scalded skin syndrome (SSSS). This toxin was previously observed in CC15, but not in CC15-MRSA. Hence, two isolates were sequenced applying Oxford Nanopore Technology. This confirmed the presence of the etA gene on a sufB-integrating prophage. Based on gene content and on electron microscopic morphology after mitomycin C induction, it was assigned to the genus Phietavirus. In addition to SCCmec-borne mecA, fusC and aacA-aphD (encoding beta-lactam, fusidic acid and gentamicin/tobramycin resistance), they also harboured resistance genes aadD, lnu(A), tet(K) (for tobramycin, lincosamide and tetracycline resistance) as well as beta-lactamase and cadmium resistance operons on a plasmid. They also showed a conspicuous recombination affecting the hsdS/M operon associated with the set/ssl-locus. This, and the identity of their composite SCCmec-[V+fusC] element, suggest descent from the etA-negative strain previously observed in Gulf states and Egypt. In conclusion, we describe a novel variant of a CC15 livestock-associated MRSA strain from Egypt. Because of the presence of etA, it might be of increased virulence to humans, especially to new-borns who might also be exposed to contaminated milk. Hence, we urgently recommend surveillance of SSSS/Ritters disease in Egypt or in people with relevant travel history.