First comparative genomic characterization of the MSSA ST398 lineage detected in aquaculture and other reservoirs.

ST398 can cause diseases in several different animals. In this study we analyzed ten ST398 previously collected in three different reservoirs in Portugal (humans, gilthead seabream from aquaculture and dolphin from a zoo). Strains tested against sixteen antibiotics, by disk diffusion or minimum inhibitory concentration, showed decreased susceptibility to benzylpenicillin (all strains from gilthead seabream and dolphin) and to erythromycin with an iMLS phenotype (nine strains), and susceptibility to cefoxitin (methicillin-susceptible , MSSA). All strains from aquaculture belonged to the same type, t2383, whereas strains from the dolphin and humans belonged to type t571. A more detailed analysis using single nucleotide polymorphisms (SNPs)-based tree and a heat map, showed that all strains from aquaculture origin were highly related with each other and the strains from dolphin and humans were more distinct, although they were very similar in ARG, VF and MGE content. Mutations F3I and A100V in gene and D278E and E291D in gene were identified in nine fosfomycin susceptible strains. The gene was also detected in six of the seven animal strains. The study of the genetic environment of -type (found in nine strains) allowed the identification of MGE (rep13-type plasmids and IS-type), presumably involved in the mobilization of this gene. All strains showed genes encoding efflux pumps from major facilitator superfamily (e.g., , -type and /-type), ATP-binding cassettes (ABC; ) and multidrug and toxic compound extrusion (MATE; /-type) families, all associated to decreased susceptibility to antibiotics/disinfectants. Moreover, genes related with tolerance to heavy metals (), and several VF (e.g., , , // and ) were also identified. Insertion sequences, prophages, and plasmids made up the mobilome, some of them associated with ARG, VF and genes related with tolerance to heavy metals. This study highlights that ST398 can be a reservoir of several ARG, heavy metals resistance genes and VF, which are essential in the adaption and survival of the bacterium in the different environments and an active agent in its dissemination. It makes an important contribution to understanding the extent of the spread of antimicrobial resistance, as well as the virulome, mobilome and resistome of this dangerous lineage.