ROLE OF PCR IN DIAGNOSING FOODBORNE PATHOGENS IN PUBLIC HEALTH SETTINGS

Abstract

Background

Foodborne diseases remain a major public health concern in low- and middle-income countries, where delayed laboratory confirmation can hinder outbreak detection and response. Conventional stool culture is widely used for identifying bacterial pathogens such as Salmonella and pathogenic Escherichia coli, but it is time-consuming and may lose sensitivity when patients have prior antibiotic exposure. Polymerase chain reaction (PCR) offers rapid detection and improved sensitivity, yet its practical role in hospital-linked surveillance systems in Pakistan remains underexplored.

Objective

To evaluate the role of PCR in diagnosing key foodborne pathogens—particularly Salmonella spp. and pathogenic E. coli—in a public health surveillance context at a tertiary care hospital in Karachi, Pakistan, and to compare PCR performance with conventional culture in terms of detection yield, agreement, and turnaround time.

Study Type: Cross-sectional Study

Methods

A cross-sectional study was conducted over six months at a tertiary hospital in Karachi. Consecutive patients presenting with acute gastroenteritis suggestive of foodborne illness were enrolled. Stool specimens were processed using parallel diagnostic workflows: routine bacterial culture and PCR-based detection targeting Salmonella and pathogenic E. coli markers including shiga toxin genes (stx1/stx2). Demographic, clinical, and exposure data were recorded. Outcomes included pathogen detection rates, turnaround time, and agreement between PCR and culture using Cohen’s kappa. Subgroup analysis assessed the influence of prior antibiotic use on diagnostic yield.

Results

A total of 420 participants were included (median age 20 years, IQR 10–32; 55.0% male). Prior antibiotic exposure within 72 hours was reported by 29.0%, and 19.8% met cluster indicators suggestive of outbreak-related illness. PCR demonstrated consistently higher detection rates than culture for all targeted pathogens. For Salmonella, PCR detected 11.4% versus 7.6% by culture, with substantial agreement (kappa 0.725). For STEC, PCR detected 12.4% compared to 4.8% by culture, showing moderate agreement (kappa 0.463), reflecting culture limitations for toxin-positive E. coli. PCR produced results within hours (approximately 3–16 h), while culture required multiple days (approximately 30–96 h). Culture positivity dropped markedly among antibiotic-exposed patients, whereas PCR detection remained comparatively stable, indicating stronger reliability of PCR in real-world clinical settings where pre-treatment is common.

Conclusion

PCR significantly strengthened foodborne pathogen diagnosis and surveillance capacity in this tertiary hospital setting by increasing detection yield, shortening turnaround time, and maintaining performance despite prior antibiotic exposure. The findings support integrating PCR as a frontline diagnostic tool for outbreak-sensitive gastroenteritis surveillance in Karachi, paired with reflex culture to preserve isolate recovery for antimicrobial resistance monitoring and epidemiologic characterization.