Genomic insights into Salmonella Rissen from Thailand: Prophage substitution in phase 2 flagellar-encoding region and hotspot of multidrug resistance genes in the chromosome.

Salmonella Rissen (6,7,14:f,g:-) has recently emerged in Thailand; a high prevalence of multidrug resistance (MDR) has been reported. S. Rissen is a monophasic serotype, lacking phase 1 or phase 2 flagellin, and its biphasic ancestor remains unknown. In this study, pangenome SNP analysis was performed on 119 Salmonella serotypes (i.e., 325 genomes) that share antigens with S. Rissen, including those with the 6,7,14 O antigen, f,g phase 1 flagellin antigen, or the absence of phase 2 antigen, as well as those in closely related clades. Although the biphasic ancestor of S. Rissen was not determined, all 109 Thai S. Rissen isolates belong to S. Rissen lineage A, which shares a most recent common ancestor (MRCA) with another monophasic serotype, S. Oranienburg lineage G; the antigenic formula (6,7,14:m,t:[z57]; [z57]), however, indicates that some rare S. Oranienburg isolates are biphasic. Thai S. Rissen isolates not only lack the phase 2 flagellin gene, fljB, but the entire fljAB-hin region is replaced by a SEN8-like prophage. However, unlike MDR Salmonella Typhimurium monophasic variant, 4,[5],12:i:- in which AMR genes replace the fljAB-hin region, AMR genes in S. Rissen were detected within the tnsD-silE region in the chromosome, suggesting an alternative AMR hotspot in S. Rissen. This tnsD-silE region was reported as a part of the Tn6777 transposon that can translocate from the S. Rissen chromosome to a plasmid, suggesting mobility of AMR genes in S. Rissen genomes. This study highlights the single emergence and clonal expansion of Thai MDR S. Rissen isolates and the plasticity of S. Rissen genomes.