Emergence of livestock-associated MRSA in the Egyptian Nile Delta that carry the exfoliative toxin gene etA: a case for enhanced surveillance.

Background: 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 until, in 2016, CC15-MRSA were described from Saudi Arabia that carried a SCCmec V element also comprising the fusidic acid resistance gene, fusC. Henceforth, this strain has spread across Gulf states and Egypt infecting or colonizing both, humans and livestock.

Methods: DNA-microarray-based typing was performed on 134 MRSA isolates collected from livestock and farmers in the Nile Delta region of Egypt in 2022. Isolates with conspicuous toxin gene carriage were sequenced applying Oxford Nanopore Technology.

Results: Twenty-eight out of 134 isolates 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. Sequencing confirmed the presence of etA 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 genes mecA, fusC and aacA-aphD (encoding beta-lactam, fusidic acid and gentamicin/tobramycin resistance), isolates also harboured aadD, lnu(A), tet(K) (for tobramycin, lincosamide and tetracycline resistance) as well as beta-lactamase and cadmium resistance operons on a plasmid. They showed a conspicuous recombination affecting the hsdS/M operon associated with the set/ssl-locus (νSaα). This, and the identity of the composite SCCmec-[V + fusC] element, suggest descent from the etA-negative strain previously observed in Gulf states and Egypt.

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/Ritter´s disease in Egypt or in people with relevant travel history.