Isolation, Identification, and Whole Genome Sequencing Analysis of Common Foodborne Bacteria from Fresh Fruits, Vegetables, and Their Ready-to-Eat Products in Shijiazhuang, China

With evolving lifestyles, consumer demand for fresh fruits and vegetables has increased. However, these products are susceptible to contamination by foodborne bacteria from farm to table. To investigate the contamination status of foodborne bacteria in commercially available fresh fruits, vegetables, and their ready-to-eat (RTE) products in Shijiazhuang City, a total of 406 samples were collected from 2024 to 2025. Staphylococcus aureus ( S. aureus ), Clostridium perfringens ( C. perfringens ), diarrheagenic Escherichia coli (diarrheagenic E. coli ), and Salmonella were identified and analyzed for genomic characteristics using traditional biochemical tests and whole genome sequencing (WGS). The results showed that the detection rate of S. aureus was 4.68% (19/406), of which 5 isolates were identified as methicillin-resistant S. aureus (MRSA), accounting for 1.23% (5/406). The detection rate of C. perfringens was 8.37% (34/406), and the detection rate of diarrheagenic E. coli was 0.25% (1/406). No Salmonella was detected. Genomic characterization revealed that S. aureus strains were predominantly ST59 and ST22, with the MRSA strains primarily identified as ST59-SCCmec-IVa (2B)-t437. A total of 20 enterotoxin genes were detected, with 94.74% (18/19) of the strains carrying at least one enterotoxin gene. The sea gene was the most prevalent (52.63%, 10/19), and the tsst-1 gene, which can cause toxic shock syndrome, was detected in 2 strains. C. perfringens isolates were divided into 30 STs, exhibiting high genetic diversity. All toxin types were classified as type A. The mprF gene showed the highest carriage rate of resistance genes (94.12%, 32/34), and the main resistance profile was mprF + cplR (55.88%, 19/34). The diarrheagenic E. coli isolate was identified as enterotoxigenic E. coli (ETEC) and carried multiple antimicrobial resistance genes. This study systematically reveals the contamination levels and molecular characteristics of common foodborne bacteria in fresh fruits, vegetables, and their RTE products sold in Shijiazhuang for the first time.