ObjectiveTo retrospectively analyze the correlation among serotypes, antimicrobial resistance phenotypes, and resistance genotypes of Salmonella isolates from diarrheal cases in Baoshan District of Shanghai from 2023 to 2024, and to provide a reference for the prevention and control of Salmonella infections and the rational use of antibiotics in clinical practice. MethodsSalmonella isolates collected from diarrheal cases under surveillance in Baoshan District from 2023 to 2024 were serotyped. Antimicrobial resistance phenotypes were determined using the broth microdilution method, and whole-genome sequencing was performed to identify resistance genes. Positive predictive value and Kappa were calculated to evaluate the agreement between phenotypic and genotypic resistance profiles of Salmonella. ResultsA total of 64 Salmonella isolates belonged to 17 serotypes, with the predominant ones being Salmonella Typhimurium (25.00%) and Salmonella Enteritidis (18.75%). The tested strains exhibited high resistance rates to ampicillin (60.94%), streptomycin (59.38%), and ampicillin/sulbactam (45.31%). All isolates remained susceptible to ceftiofur and ceftazidime/avibactam. Forty different resistance profiles were identified, and 39 isolates accounting for 60.94%, were multidrug-resistant. Overall, 80 resistance genes belonging to 13 categories were detected, with the most prevalent being bla_TEM-1 (57.81%), aac(6')⁃Iy (54.69%), and aph(6)⁃Id (46.88%). No carbapenem or polymyxin resistance genes were found. The types and numbers of resistance genes varied significantly across serotypes. A high concordance was observed between genotype and phenotype for penicillins (positive predictive value: 94.59%, Kappa: 0.81), cephalosporins (90.91%, 0.46), cephamycins (100.00%, 0.65), macrolides (77.78%, 0.86), tetracyclines (100.00%, 0.93), and chloramphenicol (95.83%, 0.93). ConclusionSalmonella isolates from diarrheal diseases in Baoshan District exhibit high antimicrobial resistance. Whole-genome sequencing provides valuable support for resistance surveillance, however, it still needs to be integrated with phenotypic susceptibility testing for comprehensive assessment. Further studies are warranted to elucidate the mechanisms and transmission patterns of resistance in Salmonella.