Whole Genome Sequencing Reveals High Prevalence of Antimicrobial Resistance Genes in Salmonella Isolates From Diarrheal Patients in Jinan, China

Background The global emergence of multidrug‐resistant (MDR) Salmonella enterica poses a significant public health threat, particularly in developing countries where antibiotic consumption remains high. However, genomic data on circulating Salmonella strains in Eastern China remain limited. Objective To characterize the genomic profiles of antimicrobial resistance (AMR) and molecular epidemiology of Salmonella isolates from diarrheal patients in Jinan, China (2017–2020). Methods A total of 185 Salmonella strains isolated from secondary/tertiary hospital outpatients were subjected to whole genome sequencing (WGS) on the Illumina platform. Bioinformatic analyses included antimicrobial resistance gene (ARG) screening (ResFinder and CARD), multilocus sequence typing (MLST), in silico serotyping (SISTR), and pan‐genome analysis. Results All isolates exhibited multidrug resistance, with highest rates to fluoroquinolones (100%), aminoglycosides (99.46%), and nitroimidazoles (99.46%). ARG profiling revealed aac(6′)‐Iaa as the predominant gene (98.9%). MLST identified 33 sequence types (STs), dominated by ST34 (28.65%) and ST11 (24.86%). In silico serotyping further confirmed the predominance of the monophasic Salmonella Typhimurium (I 1,4, 5,12:i:‐; ST34) and Salmonella Enteritidis (ST11). Pan‐genome analysis defined a core genome of 3376 genes (23.35%) and an accessory genome of 9201 cloud genes (63.64%). Conclusion This first WGS‐based surveillance in Jinan highlights the predominance of MDR ST34/ST11 Salmonella with an extremely high prevalence (100%) of fluoroquinolone resistance. The integration of genomic and historical phenotypic data underscores the urgent need to revise empirical therapy for diarrheal diseases and implement genomic surveillance in public health practice.