Identification and characterization of gastroenteritis causing pathogens in households of peri-urban area of Islamabad

Abstract

Gastroenteritis remains a significant public health issue in peri-urban Pakistan, where waterborne pathogens like Escherichia coli, Salmonella spp., Campylobacter jejuni and Shigella spp. contribute to widespread disease, exacerbated by inadequate sanitation and contaminated water sources. This study investigates pathogen prevalence and microbial diversity along the Shahdara Stream, comparing contamination across upstream, midstream, and downstream segments, and includes analysis of both drinking water and stool samples. Using a One Health approach, culture-based methods, TaqMan-based quantitative PCR, and metagenomic sequencing were employed to detect bacterial pathogens, quantify loads, and examine microbial community diversity gradients. Metagenomic findings reveal distinct diversity patterns influenced by location, with upstream areas showing higher microbial diversity that progressively declines downstream, likely due to pollution and environmental stressors. Additionally, clinical samples from symptomatic individuals were analyzed, showing markedly higher pathogen loads, particularly for Salmonella spp. and Shigella spp., compared to asymptomatic household stool samples, underscoring asymptomatic carriage and transmission risks within households. These findings point to an urgent need for targeted interventions, such as water treatment, sanitation improvements, and hygiene education, to reduce gastroenteritis risks in communities across Shahdara stream. This research provides critical data to inform public health strategies aimed at mitigating waterborne diseases in similar settings.