Genomic Insights into the Population Structure and Antimicrobial Resistance of the Most Prevalent Human-Associated Non-Typhoidal Salmonella Serotypes in Romania

Abstract

This study aimed to identify circulating lineages of the most prevalent human-associated Salmonella serotypes identified through routine surveillance in Romania between 2023 and 2025 and assess their role in the spread of antimicrobial resistance (AMR). A total of 271 isolates (217 S. Enteritidis, 28 monophasic S. Typhimurium, and 26 S. Typhimurium) were investigated using Illumina short-read sequencing. The isolates were assigned to 9 MLST sequence types (STs) and 109 core genome MLST complex types. The predominant STs were ST11 (96% in S. Enteritidis), ST19 (77% in S. Typhimurium), and ST34 (79% in monophasic S. Typhimurium). Overall, 148 isolates carried at least one AMR determinant, including 28 acquired genes and 6 gene mutations, conferring resistance to ten antimicrobial classes. Four percent of all isolates were predicted to be multidrug-resistant, often associated with determinants conferring tolerances to biocides and/or heavy metals. The most prevalent resistance markers were GyrA_D87Y in S. Enteritidis ST11 (94/217) and blaTEM-1 in S. Typhimurium ST19 (7/26). Among monophasic S. Typhimurium ST34 isolates, the co-occurrence of blaTEM-1, aph(3”)-Ib, aph(6)-Id, sul2, and tet(B) genes was common (17/28). The 43 predicted AMR plasmids were not shared across serotypes, except among those carrying the qnrB19 gene. These results provide a genomic baseline for AMR surveillance in Romania and strengthen the human surveillance component of national One Health efforts to control resistant Salmonella.