Selected publications
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Open access
Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium
McHugh, M. P., Pettigrew, K. A., Taori, S., Evans, T. J., Leanord, A., Gillespie, S. H., Templeton, K. E. & Holden, M. T. G., Mar 2024, In: Journal of Antimicrobial Chemotherapy. 79, 3, p. 656-668 13 p., dkae023.Research output: Contribution to journal › Article › peer-review
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Open access
Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations
Ulhuq, F. R., Barge, M., Falconer, K., Wild, J., Fernandes, G., Gallagher, A., McGinley, S., Sugadol, A., Tariq, M., Maloney, D., Kenicer, J., Dewar, R., Templeton, K. & McHugh, M. P., 21 Apr 2023, In: Microbial Genomics. 9, 4, 9 p., 000991.Research output: Contribution to journal › Article › peer-review
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Open access
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes
Cotton, S., McHugh, M. P., Dewar, R., Haas, J. G., Templeton, K. & COVID-19 Genomics UK (COG-UK) consortium, 1 May 2023, In: Journal of Hospital Infection. 135, p. 28-36 9 p.Research output: Contribution to journal › Article › peer-review
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Open access
The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis
Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N., Fjodorova, L., Forrest, R., Goldstein, E., Gunson, R., Haughney, J., Holden, M. T. G., Honour, P., Hughes, J., James, E. & Lewis, T. & 17 others, , 13 Apr 2023, In: PLoS ONE. 18, 4, 19 p., e0284187.Research output: Contribution to journal › Article › peer-review
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Open access
Whole genome sequencing and molecular epidemiology of clinical isolates of Staphylococcus aureus from Algeria
Namoune, R., Djebbar, A., Mekler, R., McHugh, M. P., El Amine Bekara, M., Decano, A., Holden, M. & Sebaihia, M., 9 Aug 2023, In: Microorganisms. 11, 8, 11 p., 2047.Research output: Contribution to journal › Article › peer-review
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Open access
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
Nickbakhsh, S., Hughes, J., Christofidis, N., Griffiths, E., Shaaban, S., Enright, J., Smollett, K., Nomikou, K., Palmalux, N., Tong, L., Carmichael, S., Sreenu, V. B., Orton, R., Goldstein, E. J., Tomb, R. M., The COVID-19 Genomics UK (COG-UK) Consortium, Templeton, K., Gunson, R. N., da Silva Filipe, A. & Milosevic, C. & 5 others, , 19 Jul 2022, In: Scientific Reports. 12, 17 p., 11735.Research output: Contribution to journal › Article › peer-review
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Open access
Genomics-informed outbreak investigations of SARS-CoV-2 using civet
O’Toole, Á., Hill, V., Jackson, B., Dewar, R., Sahadeo, N., Colquhoun, R., Rooke, S., McCrone, J. T., Duggan, K., McHugh, M. P., Nicholls, S. M., Poplawski, R., Consortium, T.C.-1. G. U., Group), C.-1. I. P., Aanensen, D., Holden, M., Connor, T., Loman, N., Goodfellow, I. & Carrington, C. V. F. & 2 others, , 9 Dec 2022, In: PLOS Global Public Health. 2, 12, 15 p., e0000704.Research output: Contribution to journal › Article › peer-review
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Open access
Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing
McHugh, M. P., Parcell, B. J., Pettigrew, K. A., Toner, G., Khatamzas, E., el Sakka, N., Karcher, A. M., Walker, J., Weir, R., Meunier, D., Hopkins, K. L., Woodford, N., Templeton, K. E., Gillespie, S. H. & Holden, M. T. G., 7 Feb 2022, In: Microbiology. 168, 2, 7 p., 001137.Research output: Contribution to journal › Article › peer-review
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Evaluation of the molecular detection of ciprofloxacin resistance in Neisseria gonorrhoeae by the ResistancePlus GC assay (SpeeDx)
Cotton, S., McHugh, M. P., Etherson, M., Shepherd, J. & Templeton, K. E., 1 Apr 2021, In: Diagnostic microbiology and infectious disease. 99, 4, 5 p., 115262.Research output: Contribution to journal › Article › peer-review
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Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland
The COVID-19 Genomics UK (COG-UK) Consortium, da Silva Filipe, A., Shepherd, J. G., Williams, T., Hughes, J., Aranday-Cortes, E., Asamaphan, P., Ashraf, S., Balcazar, C., Brunker, K., Campbell, A., Carmichael, S., Davis, C., Dewar, R., Gallagher, M. D., Gunson, R., Hill, V., Ho, A., Jackson, B. & James, E. & 33 others, , 1 Jan 2021, In: Nature Microbiology. 6, p. 112-122 11 p.Research output: Contribution to journal › Article › peer-review