Genomic and transcriptomic analyses reveal a Gifsy-1 prophage-encoded virulence module associated with enhanced epithelial adhesion of Salmonella ST34 in Huzhou, China

Introduction Non-typhoidal Salmonella (NTS) is a leading cause of bacterial gastroenteritis worldwide, yet the pathogenic differences among co-circulating dominant clones remain poorly understood. Methods A 7.5-year surveillance study (2017–2024) was conducted using NTS isolates from patients with acute diarrheal illness in Huzhou, China. Quantitative IEC-6 cell-based adhesion and invasion assays, comparative genomics, transcriptomic profiling, and protein-protein interaction network analysis were integrated to compare the dominant sequence types (STs). Results Among 188 NTS isolates, 35 serotypes and 36 STs were identified. Three STs predominated: ST34 (26.1%, mainly monophasic S. Typhimurium ), ST11 (15.4%, exclusively S. Enteritidis ), and ST19 (13.3%, classical S. Typhimurium ). ST34 showed significantly enhanced epithelial adhesion in IEC-6 cells, whereas increased invasion was observed only in comparison with ST11 and not with ST19. Comparative genomics and transcriptomics identified an intact Gifsy-1 prophage as an ST34-specific genetic element encoding the T3SS effectors GogB and SteE/SarA, with gogB and steE/sarA being the only virulence genes consistently upregulated in ST34 versus both ST11 and ST19. Protein-protein interaction network analysis positioned these effectors as peripheral components of a 14-member prophage-associated module. All 49 ST34 isolates carried the intact Gifsy-1 prophage, whereas ST19 isolates harbored only truncated versions and ST11 completely lacked this element. ST34 also carried a broad antimicrobial resistance gene repertoire, including frequent tetracycline and sulfonamide resistance determinants and sporadic detection of clinically important beta-lactamase genes. Discussion These findings identify an intact Gifsy-1 prophage encoding GogB and SteE/SarA as a candidate module associated with enhanced epithelial adhesion in ST34, a dominant NTS lineage with an extensive antimicrobial resistance repertoire.