My current research focuses on the application of host DNA depletion methods and next generation sequencing of 16S rRNA gene fragments, whole bacterial genomes and metagenomics to answer a multitude of clinical and evolutionary questions. This also involves working closely with industrial partners for the translation of this technology into clinical diagnostic applications.
I handle the running of the Norwich Medical School sequencing facility on a day-to-day basis, which includes training new users (students and staff) and providing guidance on experimental design (DNA and RNA sequencing) for both short and long read sequencing (Illumina and Oxford Nanopore Technologies platforms). Coupled with this, I have developed extensive bioinformatics skills in order to analyse a variety of sequencing data. This has included genome assembly and annotation, identification of pathogenic bacteria/fungi/viruses within metagenomic data sets, statistical analysis of differences in microbiomes (particularly gut microbiomes) and phylogenetic analysis of relevant species.
Djeghout, B., Saha, S., Sajib, M. S. I., Tanmoy, A. M., Islam, M., Kay, G. L., Langridge, G. C., Endtz, H. P., Wain, J. and Saha, S. K. (2018). Ceftriaxone-resistant Salmonella Typhi carries Incl1-ST31 plasmid encoding CTX-M-15. Journal of Medical Microbiology 67, 620-627. https://doi.org/10.1099/jmm.0.000727
Card, R. M., Cawthraw, S, A., Nunez-Garcia, J., Ellis, R. J., Kay, G. L., Pallen, M. J., Woodword, M. J., Anjum, M. F. (2016). An in vitro chicken gut model demonstrates transfer of a multidrug resistance plasmid from Salmonella to commensal Escherichia coli. mBio 8(4), e00777-17. https://doi.org/10.1128/mBio.00777-17
Kay, G. L., Sergeant, M. J., Zhou, Z., Chan, J. Z-M., Millard, A., Quick, J., Szikossy, I., Pap. I., Spigelman, M., Loman, N. J., Achtman, M., Donoghue, H. D. and Pallen, M. J. (2015). Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nature Communications, 6. https://doi.org/10.1038/ncomms7717
Kay, G. L., Millard, A., Sergeant, M. J., Midzi, N., Gwisai, R., Mduluza, T., Ivens, A., Nausch, N., Mutapi, F. and Pallen, M. (2015). Differences in the facecal microbiome in Schistosoma haematobium infected children vs. uninfected children. PLoS Neglected Tropical Diseases, 9 (6). https://doi.org/10.1371/journal.pntd.0003861
Kay, G. L., Sergeant, M. J., Giuffra, V., Bandiera, P., Milanese, M., Bramanti, B., Bianucci, R. and Pallen, M. J. (2014). Recovery of a medieval Brucella melitensis genome using shotgun metagenomics. mBio, 5 (4). https://doi.org/10.1128/mBio.01337-14