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Portable molecular diagnostics for on-site microbial water quality

Workshop report

05 October 2021


Workshop participants, wearing high vis jackets, conducting field work on the river Ouseburn
Workshop participants, wearing high vis jackets, conducting field work on the river Ouseburn

Workshop participants conducting field work on the river Ouseburn

Dr Kishor Acharya, a molecular microbiologist, and Prof David Werner, both at Newcastle University, successfully delivered a hands-on Continuing Professional Development (CPD) training workshop on ‘Portable molecular diagnostic for on-site microbial water quality monitoring’. The workshop was funded as a personal impact project award to Dr Acharya by UK Research and Innovation (UKRI), via the Engineering and Physical Sciences Research Council (EPSRC). It built on the outcomes of a three year collaboration with researchers in Tanzania and Ethiopia supported by UKRI via the Global Challenges Research Fund (GCRF). 

The main objective of this CPD was to provide training in the use of portable tools for the characterization of microbial communities in water samples, and related hazards. The portable toolbox assembled by the Newcastle University researchers fits readily into the suitcases of two travellers and includes a field deployable qPCR machine and memory stick sized DNA sequencing device from Oxford Nanopore Technology. The sequencing device enables the screening of hundreds of thousands of bacteria in a single analysis, while portable qPCR assays help in validating the screening data.

The workshop was held at Newcastle University, from 13-16 September 2021. A total of 8 researchers, technicians and academics from Leeds University, Glasgow University, and Newcastle University participated in the workshop. On day 3 of the CPD course, fieldwork was conducted in the Ouseburn catchment using the toolbox and a “Lab in a Van” for the successful demonstration of the on-site detection of human host associated Bacteroides in river water.

The organisers believe that the workshop was a full success. Portable next generation sequencing and qPCR devices can revolutionise our ability to describe and manage biotechnological processes and microbial hazards anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond. CPD participants highly appreciated the skills they gained from the molecular microbiology training, fieldwork, and computer based bioinformatics sessions.

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