Intermediately virulent Rhodococcus equi isolates from pigs in Slovenia: discovery of new plasmid types and assessment of genetic diversity by pulsed-field gel electrophoresis

The presence of large plasmids in 30 Rhodococcus equi strains isolated from pig lymph nodes with granulomatous changes was investigated. Plasmid DNAs were isolated and digested with the restriction endonucleases BamHI, EcoRI, EcoT22I and HindIII for detailed comparison and estimation of plasmid sizes. A total of nine isolates were identified as intermediately virulent (VapB-positive), harbouring large plasmids of type 5 (n = 5) and four new variants that we tentatively designated as type 19 (n = 1), 20 (n = 1), 21 (n = 1) and 24 (n = 1). All isolates were subjected to genotyping with pulsed-field gel electrophoresis (PFGE). High genetic diversity was observed: 21 distinct genotypes were detected; five were found in multiple isolates and the others were unique. Isolates of the same plasmid type exhibited different PFGE profiles and vice versa. In a few cases, multiple strains from certain farms were analysed, the majority of which exhibited diverse PFGE profiles. Our findings demonstrate the presence of a wide variety of R. equi strains even in small confined environments such as farms. This is the first molecular epidemiology study of intermediately virulent R. equi isolates from Slovenian pigs.