Objective To analyze the phenotypic and genomic characteristics of clinical isolates of Salmonella typhimurium monophasic variants in Shaoxing, Zhejiang province, from 2021 to 2024.

Methods A total of 102 clinical strains of S. typhimurium monophasic variants isolated in Shaoxing were used for drug susceptibility testing and whole-genome sequencing. Bioinformatics analysis was performed by using genomic sequence data.

Results Most of the 102 strains of monophasic variants of S. typhimurium belonged to sequence type 34 (ST34). The 102 isolates were subdivided into 100 types by using core genome multilocus sequence typing (cgMLST). The absences of fljA, fljB and hin genes resulted in the inability to express the second-phase flagellar antigen. The core types of pathogenicity islands were SPI1-SPI2-SPI3-SPI4-SPI5-SPI9-SPI13-SPI14-C63PI-CS54. The resistance rate to tetracycline was 93.13%, while the sensitive rate to cefoxitin was 99.02%. The multidrug resistance rate reached 56.86%. Some strains exhibited resistance to eleven drugs categories simultaneously, and the most common drug resistance spectrum was ampicillin-tetracycline. The detection rates of the drug resistant genes associated with aminoglycosides, folic acid pathway antagonists, β-lactams, sulfonamides and tetracyclines exceeded 70%. For cephalosporins, the resistance phenotypes exhibited strong consistency with their drug resistance genotypes, and quinolone resistance demonstrated high phenotype-genotype consistency.

Conclusion Most strains of Salmonella typhimurium monophasic variants isolated in Shaoxing exhibited complete loss of the second-phase flagellar antigen due to deletions in fljA, fljB, and hin genes. Sequence analysis revealed low homology among the strains, indicating polymorphism in inheritance. All the strains showed genetic polymorphism: complex drug resistance patterns, high multidrug resistance and carriage of pathogenicity islands.