Detection of fliC gene by nested PCR in urine of suspected typhoid fever patients in Egypt

Background: This study aims to assess the diagnostic accuracy of nPCR targeting the fliC gene of S. Typhi in urine samples as a rapid tool to confirm diagnosis and support timely antimicrobial treatment in suspected typhoid fever patients. Methods: The study included 50 participants; 25 typhoid fever patients (confirmed or probable) and 25 age- and sex-matched healthy controls. Microbiologic testing for the patient group included blood, urine and stool cultures, nPCR targeting the fliC gene in urine, and the Widal test. For the control group, urine cultures, nPCR for the fliC gene, and the Widal test were performed. Results: nPCR targeting the fliC gene demonstrated the highest positivity rate with 92% (23 patients) testing positive, compared to 84% for the Widal test, 12% for blood culture, 4% for urine culture and 0% for stool culture. A highly significant difference in nPCR results was observed between patients and controls (χ² = 28.1, p < 0.001). The performance of the test in detecting confirmed and probable cases showed a sensitivity of 92%, specificity of 88%, a positive predictive value of 88.46%, and a negative predictive value of 91.6%. The positive likelihood ratio was 7.66 and a negative likelihood ratio of 0.09. Conclusion: The fliC-gene specific nPCR test in urine shows promising performance, particularly for excluding typhoid fever. It offers superior sensitivity compared to bacterial cultures, effectively detecting S. Typhi even in patients with prior antimicrobial treatment and during both the first and second weeks after symptom onset.