Detection of antibiotic resistance and virulence genes in Salmonella strains isolated from refrigerated raw retail chicken in two regions of Chile

Salmonella enterica is a major cause of foodborne illness, resulting in over 90 million cases and 150,000 deaths annually worldwide. Found in water and foods like meat and milk, it generally causes gastroenteritis, requiring antibiotic treatment only in severe cases. However, increasing antibiotic resistance in this species presents a significant public health challenge globally. Objective: To genetically characterize Salmonella strains isolated from raw retail chicken in the Ñuble and Maule regions of Chile. Methodology: A total of 225 raw chicken meat samples (175 from Maule and 50 from Ñuble) were analyzed under the Salmonella surveillance program using sampling criteria n=5, c=0. Isolates were identified by the VIDAS system, confirmed by MALDI‑TOF, and sequenced on the MiSeq. Classic MLST, core genome MLST, and Salmonella In Silico Typing Resource (SISTR v1.1.3) were performed. Antibiotic resistance genes (ARG) were detected using AMRFinderPlus and virulence genes (VG) by AMRfinderPlus templates (MBioSEQ Rido Typer v11.1). Nine Salmonella strains were isolated from independent samples, of which eight were S. Infantis ST32 (CC31; 6,7,14: r:1,5) and one was S. Bredeney ST897 (CC33; 1,4,12,27: l, v:1,7). Three clusters of closely related strains were observed with 0-2 allele differences, and three unrelated strains were identified. IncFIB plasmids were common in S. Infantis and Col_rep_cluster in S. Bredeney. S. Infantis strains presented the ARGs aac(3)-IVa, aph(3')-Ia, aph(4)-Ia, aadA1, mdsA/mdsB, fosA3, floR, qacEdelta1, gyrA_D87Y, sul1, tet(A) and dfrA14. bla_CTX-M-65 (ESBL) was detected only in IncFIB plasmids . In S. Bredeney, the ARGs detected were aac(3)-IId, aph(3')-Ia, aadA2/aph(3'')-Ib/aph(6)-Id, blaTEM-1, mdsA/mdsB, lnu(G), floR, qnrB19, sul2, tet(A)/tet(B), and dfrA12. A total 147 VG were detected, highlighting exotoxin, adherence, and effector delivery systems. Conclusion: The analyzed Salmonella strains exhibited various ARG and VG, underscoring the need for continuous genomic surveillance to mitigate public health risks in Chile.