Gradual loss of mobile genetic element in S.aureus USA300 in a closed hospital niche

Our French national reference laboratory was requested to determine the epidemiological link between 19 Staphylococcus aureus isolates (MSSA and MRSA) obtained from patients and healthcare workers in a long-term hospital, following the death of a nurse from pneumonia presumed to be associated with the drainage of a patient with an active infection. WGS sequencing was performed for all isolates for virulome and resistome determination and phylogenetic relationships. The analysis revealed that 12 strains belonged to the North American ST8 USA300 lineage which is the predominant methicillin-resistant S. aureus (MRSA) in the United States and northern South America but is less prevalent in Europe. The strains are typically described as belonging to the clonal complex 8 (CC8), and possessing several MGE: the PVL encoding bacteriophage ?Sa2USA, the staphylococcal chromosomal cassette mecIVa (SCCmecIVa) and the locus referred to as the arginine catabolic mobile element (ACME). Indeed, four out of the 19 strains possessed all the typical characteristics of this USA300 lineage. However, one strain did not carry SCCmec, six did not have the ACME element and two did not carry ?Sa2USA. The topology of the phylogenetic tree and phylodynamic analysis suggest the entry of the ancestral USA300 harboring all three MGE in the long-term care structure to have occurred 2 to 3 years earlier. As long term hospital facility may represent a relatively closed ecosystem we conclude that this loss of MGE is a phenomenon of niche specialisation, in this case constituted in an original way by a care institution.