Prevalence of Salmonella typhi among Patients with Febrile Illness in Rural and Peri-Urban Populations of Vellore District, as Determined by Nested PCR Targeting the Flagellin Gene

Background and Objective: Fever is one of the most common illnesses in all age groups in India. Typhoid fever is a continuing problem in developing countries such as India, which has poor sanitation facilities. The diagnosis of typhoid fever is still made by conventional culture-based isolation and identification. Serologic diagnostic tests, though widely used, have many deficiencies. Our objective was to investigate a molecular nested polymerase chain reaction (nPCR) technique to detect Salmonella typhi among patients with febrile illness in rural and peri-urban communities in Vellore district (Tamil Nadu, India). Methods: nPCR targeting the flagellin gene ( fliC ) was carried out using HotStar Taq DNA polymerase on DNA extracted from the buffy coat fraction of blood samples. Blood culture was done in a completely automated blood culture system, BacT/Alert®, on prospectively collected blood samples. Relevant clinicopathologic data were obtained. Results: nPCR was found to have a lower limit of detection of 0.01 colony-forming units per milliliter. The prevalence of typhoid fever as estimated by nPCR was 4.7% in pyrexia of unknown origin (PUO) in the rural/peri-urban communities of Vellore district. The prevalence of S. typhi as estimated by blood culture was 2.0%, which was lower than the nPCR estimation. nPCR had sensitivity and specificity of 100% and 97.3%, respectively. The observed agreement between blood culture and nPCR was 0.973 and the Kappa coefficient was 0.59 (p < 0.0001). The frequency of typhoid fever as detected by nPCR was 4.35% among rural patients and 5.32% among peri-urban individuals. Conclusion: nPCR on DNA extracts of buffy-coat samples using HotStar Taq was found to be a valuable and specific technique for diagnosis of typhoid fever.