Whole-genome insights into a multidrug-resistant, biofilm-forming, and pathogenic Salmonella Umbilo isolate and molecular characterization of rare Salmonella serovars from poultry.

Abstract

Salmonellosis is one of the leading foodborne zoonoses worldwide, with contaminated poultry products representing a major source of human infection. This study characterized rare Salmonella serovars circulating in poultry flocks with respect to biofilm formation, virulence, antimicrobial resistance (AMR), CRISPR loci diversity, and genomic features. Salmonella isolates were conventionally isolated from drug swap samples and serotyped. Biofilm- (csgA, csgB, csgD, ompR, adrA, rpoS, and fimH) and virulence-associated genes (sipA, sipD, sopB, sopD, sopE, sopE2, sitC, sifA, ssaR, spvC, and pefA) were investigated. CRISPR loci and phenotypic AMR were examined. The Salmonella isolate, which exhibited the highest MAR index, was analyzed by whole-genome sequencing (WGS). Bioinformatic analyses were conducted to determine its plasmid, AMR, and virulence capacity. Thirty rare Salmonella serovars were identified including, Aba, Atento, Ball, Blegdam, Bonariensis, Bradford, Chandans, Fallowfield, Ferruch, Idikan, II (1,9,12:g,m,s,t:e,n,x), Inganda, Korbol, Leeuwarden, Menden, Naestved, Ohlstedt, Papuana, Petahtikve, Sandow, Schwarzengrund, Svedvi, Telaviv, Thompson, Tinda, Tsevie, Tumodi, Umbilo, Uppsala, and Vejle. CsgA-B-C (100.0%) and sipA (96.7%) were the most prevalent genes. S. Sandow harbored all examined genes. CRISPR2 locus (23.3%) was more prevalent than the CRISPR1 locus (3.3%). Resistance to streptomycin (56.7%) and sulfonamides (46.7%) was most common, whereas 40.0% of the isolates were MDR. WGS of the S. Umbilo isolate, which exhibited the highest MAR index (0.48), identified the IncHI2A plasmid (a key factor in horizontal transfer of AMR genes), 12 AMR genes (responsible for resistance to beta-lactams, aminoglycosides, phenicols, and lincosamides), and 181 virulence-associated genes (involved in adhesion, invasion, chemotaxis, intracellular survival, and environmental persistence). The detection of highly resistant and potentially pathogenic S. Umbilo, previously linked to a multinational foodborne outbreak in Europe, highlights its potential public health significance. MLST further proved useful for serovar prediction, with ST2014. Rare Salmonella serovars circulating in poultry flocks possess substantial virulence, biofilm-forming, and AMR potential. These findings highlight the importance of including rare serovars in surveillance and control programs to mitigate foodborne transmission and the spread of AMR.