Genomic characterization of multidrug-resistant monophasic Salmonella 4,[5],12:I:- ST34 circulating along the food chain of Central Italy

The monophasic variant 4,[5],12:i:- of Salmonella enterica serovar Typhimurium (MVST) has emerged as a significant global public health concern. This study employs whole-genome sequencing (WGS) to characterize MVST isolates from Central Italy, focusing on antimicrobial resistance (AMR) genes, plasmids, virulence factors, the variability in the former fljBA operon region, and the genetic diversity of isolates through hierarchical cluster analysis to assess potential transmission pathways of circulating MVST clones in the food chain. Multidrug-resistant (MDR) MVST isolates (n = 28) from multiple sources (2015–2021) were characterized by real-time PCR and WGS (Illumina and Oxford Nanopore Technologies). Phenotypic and genotypic resistance profiles revealed the presence of different ASSuT profile variants (ASSuT, ASSuT-plus -additional resistances beyond the classical ASSuT profile-, and incomplete-ASSuT). Twenty-nine resistance genes across eleven antimicrobial classes were identified. Genes responsible for the classical ASSuT phenotype were highly prevalent but often complemented by further, mainly plasmid-borne, resistance genes. Indepth analysis of the former fljBA operon region revealed an extensive genetic variability, including the presence of ASSuT resistance genes (blaTEM-1, strA/aph(3″)-Ib, strB/aph(6)-Id, sul2, and tet(B)), heavy metal resistance genes (HMRGs; arsR and mer operon genes), and transposon insertions (IS10L, IS26, and IS1R). cgMLST analysis revealed the presence of two main clusters and suggested a potential transmission of this pathogen along the food chain. Global cgMLST analysis revealed that cluster II isolates presented an Italian endemic sub-lineage, whereas cluster I isolates were aligned broadly with international isolates, indicating their characteristic dissemination and persistence in the global food chain. These results emphasize the need for integrated genomic surveillance along with One Health monitoring.