Genomic Analysis of Staphylococcus aureus Strains Originating from Hungarian Rabbit Farms Reinforce the Clonal Origin of Various Virulence Types

SIMPLE SUMMARY: Staphylococcosis is a major disease in both human and veterinary medicine. In commercial rabbit production, highly virulent variants cause significant economic losses. This study describes the comparative analysis of the whole genome of 51 strains sequenced by our group, and 12 sequences derived from online repositories. The investigation was based on whole-genome sequencing and whole-genome multilocus sequence typing. The typical highly virulent strains showed great similarity with ST121/t645 isolates from Italy, Spain and the UK. The most prevalent genotype in Hungary was an atypical highly virulent variant; these strains form a novel sequence type (ST5993), and belong to three different spa types (t4770, t711 and t2407). Low virulence (LV) strains grouped into two main clusters, two ST1 LV strains formed a separate cluster from the majority forming a clone-like group, despite the five different multilocus sequence typing (MLST) patterns and seven different spa types. Some strains in this survey showed genetic polymorphism on more than 50% of the examined loci, however, even within the same MLST ST group, hundreds of loci showed polymorphism, which could facilitate the very fine differentiation of the strains. ABSTRACT: Staphylococcosis is one of the most important infectious diseases in rabbit medicine, especially in commercial farming. Previous studies revealed the existence of virulent variants adapted to rabbits. Typical and atypical, highly virulent as well as low virulent variants have been isolated and reported from industrial units in all major rabbit-meat-producing countries. Preceding the research focused on detecting defined nucleotide sequences, the genome of these organisms as a whole was rarely subjected to scientific investigations. The authors sequenced 51 Staphylococcus strains originating from industrial rabbit farms in Hungary. Another 12 draft genomes of rabbit isolates were constructed from read sequences available in digital repositories, and were compared based on whole-genome multilocus sequence typing. The clonal origin of highly virulent variants is confirmed, the strains from Hungary were closely related with the strains isolated in the UK, Italy, and Spain. Atypical highly virulent strains are the most prevalent in Hungary, they form a separate clonal cluster. The low virulent strains were genetically similar, but more heterogeneous than the highly virulent (HV) and aHV strains even by the traditional MLST typing scheme. Other “non-aureus” Staphylococcus species were also identified.