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Extraction and qPCR of Environmental Surveillance samples for the detection of Salmonella Typhi v2

Article scientifique 2025 Autre

Résumé

The following protocol is for use on environmental samples that have been collected by Moore swab or grab sampling methods and processed up to the stage of DNA extraction. The protocol includes DNA extraction and qPCR analysis of the samples to detect three gene targets for identifying Salmonella Typhi, a human faecal indicator (HF183), and a commercial spike-in control. The qPCR uses fluorescence of Taqman probes for measuring the product. Care must be taken to ensure that the fluorescent dyes chosen for the probes are suitable for the machine being used or can be calibrated for use on the machine. If the dyes selected are different from those described in the protocol, make sure that their excitation/emission spectra do not overlap to avoid crossover between targets. Generation of standard curves is mentioned in this protocol but is described in more detail in a separate protocol in the Typhoid ES workspace.

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Rigby, J., Troman, C., Abraham, D., Mahindroo, J., Uzzell, C., John, J., Mohan, V., Srinivasan, R., Zhou, N., Nair, S., Shaw, A., Elviss, N., Feasey, N., Meschke, J., Kang, G., Grassly, N. (2025). Extraction and qPCR of Environmental Surveillance samples for the detection of Salmonella Typhi v2. https://doi.org/10.17504/protocols.io.8epv5zrw4v1b/v4

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Auteur(s)

Jonathan Rigby Catherine Troman Dilip Abraham Jaspreet Mahindroo Christopher Uzzell Jacob John Venkata Raghava Mohan Rajan Srinivasan Nicolette Zhou Satheesh Nair Alex Shaw Nicola Elviss Nicholas Feasey John Scott Meschke Gagandeep Kang Nick Grassly

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