Genetic diversity in monophasic (1,4,[5],12:i:- and 1,4,[5],12:-:1,2) and in non-motile (1,4,[5],12:-:-) variants of Salmonella enterica S. Typhimurium

Abstract

Monophasic variants of Salmonella enterica serotype Typhimurium, lacking either the second phase H-antigen with the antigenic formula 1,4,[5],12:i:- or lacking the first phase H-antigen with the antigenic formula 1,4,[5],12:-:1,2, and a non-motile variant lacking both flagellar phases were phenotypically and genotypically characterised. The genetic diversity of a collection of 58 isolates of Salmonella enterica 1,4,[5],12:i:- (n=23), 1,4,[5],12:-:1,2 (n=17), 1,4,[5],12:-:- (n=18) mainly from swine, bovine and poultry sources using a novel multiplex real-time PCR to simultaneously target different classes of genes (i.e. 10 loci) was investigated in regards to antimicrobial resistance and pulsed field gel electrophoresis (PFGE) typing. The majority of the S. 1,4,[5],12:i:- strains were genotypically confirmed to be variant of serotype Typhimurium, except two mdh negative isolates. Five fljB positive S. 1,4,[5],12:i:- variants were detected and could be considered as “inconsistent” variant. Moreover, presence of the fliC and fljB amplicons in the phenotypically monophasic S. 1,4,[5],12:-:1,2 and non-motile isolates suggest that their expressions should be blocked by mutation or deletion in the promoter regions linked to the flagellar phase expression. Based on the combination of detection of the following markers: Salmonella Pathogenic Islands (SPI-2 to SPI-5), virulence plasmid (spvC), antimicrobial resistance markers (blaTEM and sul1), Salmonella Genomic island (SGI-1 left junction), the integrase from class 1 integron (intI1) and DT104 16S-23S spacer region, thirteen different genotypes were identified among the 58 isolates. All investigated isolates showed virulence potential as determined by the presence of four SPI markers, which was exhibited in the genotype A9 mainly encountered for S. 1,4,[5],12:-:1,2 isolates. In contrast, high-frequency of markers were encountered for S. 1,4,[5],12:i:- assigned to genotypes B7 gathering almost all 10 markers except SGI-1. Frequencies of SGI-1 markers typically detected in serotype Typhimurium strains differed strongly among the three variants ranging from 0% for fljB negative S. 1,4,[5],12:i:- to 58.8% for S. 1,4,[5],12:-:-. The three variants were clearly phenotypically and genotypically distinct and varied in their resistance-types as well as in their PFGE types and genotypes newly described in this study. This first study on the French collection from non human sources could suggest presence of the Spanish clone in France as well as, to a lesser extent, some “inconsistent” variants exhibiting the resistance-type AM S SSS TE previously described in different European countries.