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:[z 57 ]; [z 57 ]), 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 Tn 6777 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.