Dr Witney applies genomic and bioinformatic methods to understand drug resistance and transmission dynamics in infectious diseases. The proximity to clinical colleagues in St George's Trust enable close collaboration on clinically focused projects, in particular the prediction of drug resistance in Mycobacterium tuberculosis isolates, identification of resistance markers in various gram negatives e.g Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae

Projects also include the development of methods and pipelines to apply to pre and post treatment isolates of M. tuberculosis from clinical trials in order to differentiate relapse from reinfection as well as monitor the development of any new drug resistance markers.

We are also working with several collaborators, using long and short read shotgun metagenomic and microbiome approaches to understand several clinical conditions.

Recent publications

Vasiljevs S, Witney AA, Baines DL (2024) The presence of cystic fibrosis-related diabetes modifies the sputum microbiome in cystic fibrosis disease. Am J Physiol Lung Cell Mol Physiol. 2024 Feb 1;326(2):L125-L134. doi: 10.1152/ajplung.00219.2023.

Jindani A, Atwine D, Grint D, Bah B, Adams J, Ticona ER, Shrestha B, Agizew T, Hamid S, Jamil B, Byamukama A, Kananura K, Mugisha Taremwa I, Bonnet M, Camara LM, Bah-Sow OY, Bah KS, Bah NM, Sow M, Ticona Huaroto CE, Mugruza Pineda R, Tandukar B, Raya BB, Shrestha N, Mathoma A, Mathebula-Modongo UP, Basotli J, Irfan M, Begum D, Muzammil A, Ahmed I, Hasan R, Burgos MV, Sultan F, Hassan M, Masood I, Robb C, Decker J, Grubnic S, Butcher PD, Witney A, Dhillon J, Munshi T, Fielding K, Harrison TS (2023) Four-Month High-Dose Rifampicin Regimens for Pulmonary Tuberculosis.NEJM Evid. 2023 Sep;2(9):EVIDoa2300054. doi: 10.1056/EVIDoa2300054.

Timm, J., Bateson, A., Solanki, P., Paleckyte, A., Witney, A. A., Rofael, S. A. D., . . . Sun, E. (2023). Baseline and acquired resistance to bedaquiline, linezolid and pretomanid, and impact on treatment outcomes in four tuberculosis clinical trials containing pretomanid.. PLOS Glob Public Health, 3(10), e0002283. doi:10.1371/journal.pgph.0002283

Elton, L., Kasaragod, S., Donoghue, H., Safar, H. A., Amankwah, P., Zumla, A., . . . McHugh, T. D. (2023). Mapping the phylogeny and lineage history of geographically distinct BCG vaccine strains.. Microb Genom, 9(8). doi:10.1099/mgen.0.001077

Phillips, L. T., Witney, A. A., Furegato, M., Laing, K. G., Zhou, L., & Sadiq, S. T. (2023). Time Required for Nanopore Whole-Genome Sequencing of Neisseria gonorrhoeae for Identification of Phylogenetic Relationships.. J Infect Dis, 228(9), 1179-1188. doi:10.1093/infdis/jiad170

Baede, V. O., Gupta, A., Knight, G. M., Schouls, L. M., Laing, K., Tavakol, M., . . . Lindsay, J. A. (2023). Markers of epidemiological success of methicillin-resistant Staphylococcus aureus isolates in European populations.. Clin Microbiol Infect, 29(9), 1166-1173. doi:10.1016/j.cmi.2023.05.015

Lee, S. H., Ferran, E., Witney, A. A., Ryu, S., Kang, H., Storey, N., . . . Satta, G. (2023). A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea.. JAC Antimicrob Resist, 5(3), dlad056. doi:10.1093/jacamr/dlad056

Lista, M. J., Witney, A. A., Nichols, J., Davison, A. J., Wilson, H., Latham, K. A., . . . Strang, B. L. (2023). Strain-Dependent Restriction of Human Cytomegalovirus by Zinc Finger Antiviral Proteins.. J Virol, 97(3), e0184622. doi:10.1128/jvi.01846-22

Kloprogge, F., Ortiz Canseco, J., Phee, L., Sadouki, Z., Kipper, K., Witney, A. A., . . . McHugh, T. D. (2022). Emergence of phenotypic and genotypic antimicrobial resistance in Mycobacterium tuberculosis.. Sci Rep, 12(1), 21429. doi:10.1038/s41598-022-25827-6

Karampatsas, K., Faal, A., Jaiteh, M., Garcia-Perez, I., Aller, S., Shaw, A. G., . . . Le Doare, K. (2022). Gastrointestinal, vaginal, nasopharyngeal, and breast milk microbiota profiles and breast milk metabolomic changes in Gambian infants over the first two months of lactation: A prospective cohort study.. Medicine (Baltimore), 101(46), e31419. doi:10.1097/MD.0000000000031419

da Silva, G. C., Rossi, C. C., Rosa, J. N., Sanches, N. M., Cardoso, D. L., Li, Y., . . . Bazzolli, D. M. S. (2022). Identification of small RNAs associated with RNA chaperone Hfq reveals a new stress response regulator in Actinobacillus pleuropneumoniae.. Front Microbiol, 13, 1017278. doi:10.3389/fmicb.2022.1017278

Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., . . . Breuer, J. (2022). Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.. Elife, 11. doi:10.7554/eLife.78427

Conradie, F., Bagdasaryan, T. R., Borisov, S., Howell, P., Mikiashvili, L., Ngubane, N., . . . Spigelman, M. (2022). Bedaquiline–Pretomanid–Linezolid Regimens for Drug-Resistant Tuberculosis. New England Journal of Medicine, 387(9), 810-823. doi:10.1056/nejmoa2119430

Bateson, A., Ortiz Canseco, J., McHugh, T. D., Witney, A. A., Feuerriegel, S., Merker, M., . . . Timm, J. (2022). Ancient and recent differences in the intrinsic susceptibility of Mycobacterium tuberculosis complex to pretomanid.. J Antimicrob Chemother, 77(6), 1685-1693. doi:10.1093/jac/dkac070

Pallett, S. J. C., Wake, R., Youngs, J., Pope, C., Tan, N. K., Taylor, J., . . . Bicanic, T. (2022). Adjunctive viral cell culture supports treatment decision-making in patients with secondary humoral immunodeficiency and persistent SARS-CoV-2 infection.. Br J Haematol, 196(5), 1170-1174. doi:10.1111/bjh.17957

Griffiths, E. J., Timme, R. E., Mendes, C. I., Page, A. J., Alikhan, N. -F., Fornika, D., . . . MacCannell, D. R. (2022). Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.. Gigascience, 11. doi:10.1093/gigascience/giac003

Gray, B., Baruteau, A. -E., Antolin, A. A., Pittman, A., Sarganas, G., Molokhia, M., . . . Behr, E. R. (2022). Rare Variation in Drug Metabolism and Long QT Genes and the Genetic Susceptibility to Acquired Long QT Syndrome.. Circ Genom Precis Med, 15(1), e003391. doi:10.1161/CIRCGEN.121.003391

Kerry-Barnard, S., Zhou, L., Phillips, L., Furegato, M., Witney, A. A., Sadiq, S. T., & Oakeshott, P. (2022). Vaginal microbiota in ethnically diverse young women who did or did not develop pelvic inflammatory disease: community-based prospective study. Sexually Transmitted Infections, 98(7), 503-509. doi:10.1136/sextrans-2021-055260

Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England.. Nature, 600(7889), 506-511. doi:10.1038/s41586-021-04069-y

Boshier, F. A. T., Venturini, C., Stirrup, O., Guerra-Assunção, J. A., Alcolea-Medina, A., Becket, A. H., . . . COG-UK HOCI Variant Substudy consortium*, The COVID-19 Genomics UK (COG-UK) consortium. (2021). The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study.. J Infect, 83(6), 693-700. doi:10.1016/j.jinf.2021.09.022

Witney, A. A., Aller, S., & Strang, B. L. (2021). Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare.. J Gen Virol, 102(11). doi:10.1099/jgv.0.001677

Stirrup, O., Boshier, F., Venturini, C., Guerra-Assunção, J. A., Alcolea-Medina, A., Beckett, A., . . . Breuer, J. (2021). SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study.. BMJ Open Respir Res, 8(1). doi:10.1136/bmjresp-2021-001029

Folgori, L., Di Carlo, D., Comandatore, F., Piazza, A., Witney, A. A., Bresesti, I., . . . Sharland, M. (2021). Antibiotic Susceptibility, Virulome, and Clinical Outcomes in European Infants with Bloodstream Infections Caused by Enterobacterales.. Antibiotics (Basel), 10(6). doi:10.3390/antibiotics10060706

Marrs, T., Jo, J. -H., Perkin, M. R., Rivett, D. W., Witney, A. A., Bruce, K. D., . . . Flohr, C. (2021). Gut microbiota development during infancy: Impact of introducing allergenic foods.. J Allergy Clin Immunol, 147(2), 613-621.e9. doi:10.1016/j.jaci.2020.09.042

Satta, G., Witney, A. A., Begum, N., Ortiz Canseco, J., Boa, A. N., & McHugh, T. D. (2020). Role of Whole-Genome Sequencing in Characterizing the Mechanism of Action of para-Aminosalicylic Acid and Its Resistance.. Antimicrob Agents Chemother, 64(9). doi:10.1128/AAC.00675-20

Co-organiser MSc Genomic Medicine Infectious Diseases Module

Co-organiser MSc Translational Medicine Big Data in Biomedicine Module

Provide several lectures covering genomics and bioinformatics methods on several course modules on the BSc Biomedical Sciences course as well as MSc Genomic Medicine and MRes Infection and Immunity

Organise bioinformatics training workshops for staff and students