Genomic Insights into Methicillin-Resistant Staphylococcus aureus Type t899 Isolates Belonging to Different Sequence Types.

Methicillin-resistant (MRSA) presenting type t899 is commonly associated with sequence type 9 (ST9) but is also increasingly linked to ST398. This study provides genomic insight into the diversity of t899 isolates using core genome multilocus sequence typing (cgMLST), single nucleotide polymorphism (SNP)-based phylogeny, and the description of selected antimicrobial resistance and virulence markers. The SNP-based phylogenic tree showed that isolates sharing the same type (t899) but different STs highly diverged in their core and accessory genomes, revealing discriminant antimicrobial resistance (AMR) and virulence markers. Our results highlighted the idea that in a surveillance context where only typing is used, an additional multiplex PCR for the detection of the (M), , and genes would be valuable in helping distinguish ST9 from ST398 isolates on a routine basis. This study showed the genetic diversity and population structure of presenting the same type, t899, but belonging to different STs. Our findings revealed that these isolates vary deeply in their core and accessory genomes, contrary to what is regularly inferred from studies using typing only. Given that identical types can be associated with different STs and that typing only is not appropriate for isolates that have undergone major recombination events which include the passage of the gene (such as in t899-positive MRSA), the combination of both MLST and typing methods is recommended. However, typing alone is still largely used in surveillance studies and basic characterization. Our data suggest that additional markers, such as (M), , and genes, could be implemented in an easy and inexpensive manner in order to identify lineages with a higher accuracy.