Abstract
Shigellosis is still a serious public health issue in countries with middle and low incomes, particularly in South Asia, where it is spread by crowded cities and poor sanitation. Shigella species are major causes of bacillary dysentery and are associated with considerable morbidity and mortality, especially in children. Shigella species are linked to significant morbidity and mortality, particularly in children, and are primary causes of bacillary dysentery. Molecular epidemiology studies are crucial for directing treatment and control methods since the spread of virulence genes and the advent of MDR (multidrug-resistant) strains make clinical management even more difficult. Between March and August 2025, this study examined the molecular traits, virulence factors, and patterns of antibiotic resistance of Shigella species isolated from patients suffering from gastrointestinal tract infections in District Peshawar, Khyber Pakhtunkhwa, Pakistan. This study investigated the molecular characteristics, virulence determinants, and antimicrobial resistance patterns of Shigella species isolated from patients with gastrointestinal tract infections in District Peshawar, Khyber Pakhtunkhwa, Pakistan, between March and August 2025. Total 400 stool samples were collected from major tertiary hospitals, of which 120 isolates were confirmed as Shigella spp. through biochemical testing and serological analysis. The predominant species was S. sonnei (74%), followed by S. flexneri (24%) and S. boydii (2%). Molecular screening of virulence genes revealed that ipaH (95.4%) and ial (75.1%) were the most prevalent, while set1B was detected at lower frequency (7.8%). Notably, eight S. sonnei isolates carried the Shiga toxin (STX) gene, traditionally restricted to S. dysenteriae type 1, and were associated with severe clinical outcomes. Antimicrobial susceptibility testing showed alarming resistance to cotrimoxazole (90.4%) and tetracycline (79.5%), alongside moderate resistance to nalidixic acid (45.8%) and ampicillin (42.2%). Lower resistance rates were recorded for azithromycin (17.0%), ciprofloxacin (12.0%), and cefotaxime (6.0%), with gentamicin (3.0%) and cefixime (3.6%) remaining highly effective. Furthermore, PMQR genes were detected in 45.8% among Shigella species, with qnrA, qnrS, and qnrD being the most common, and multi-gene combinations frequently observed. The strong association between PMQR positivity and nalidixic acid resistance highlights a growing threat of fluoroquinolone resistance. Overall, these findings underscore the predominance of S. sonnei, the heterogeneity of virulence genes, and the emergence of multidrug resistance, emphasizing the urgent need for rational antibiotic stewardship and continuous molecular surveillance to guide effective treatment strategies against shigellosis in Pakistan.