Research group

Analysis packages (R, Python, etc.), Genome Assembly, High-performance Computing, Mapping, Metagenomics, Microbial Communities, Phylogenetic Analysis, Sequence Alignment, Sequence analysis

Coll, F., Gouliouris, T., Blane, B., Yeats, C. A., Raven, K. E., Ludden, C., Khokhar, F. A., Wilson, H. J., Roberts, L. W., Harrison, E. M., Horner, C. S., Le, T. H., Nguyen, T. H., Nguyen, V. T., Brown, N. M., Holmes, M. A., Parkhill, J., Estee Török, M., & Peacock, S. J. (2024). Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data. The Lancet Microbe, 5(2), e151–e163. https://doi.org/10.1016/s2666-5247(23)00297-5

Coll, F., Gouliouris, T., Blane, B., Raven, K. E., Ludden, C., Khokhar, F. A., Wilson, H. J., Roberts, L. W., Harrison, E. M., Horner, C. S., Hoi, L. T., Hoa, N. T., Trung, N. V., Nguyen Van, K., Brown, N. M., Holmes, M., Parkhill, J., Török, M. E., & Peacock, S. (2023). Improved Accuracy of Antibiotic Resistance Determination from <i>Enterococcus faecium</i> Whole-Genome Sequences. https://doi.org/10.2139/ssrn.4345808

Blane, B., Coll, F., Raven, K., Allen, O., Kappeler, A. R. M., Pai, S., Floto, R. A., Peacock, S. J., & Gouliouris, T. (2023). Impact of a new hospital with close to 100% single-occupancy rooms on environmental contamination and incidence of vancomycin-resistant Enterococcus faecium colonization or infection: a genomic surveillance study. Journal of Hospital Infection, 139, 192–200. https://doi.org/10.1016/j.jhin.2023.06.025

Twohig, K. A., Nyberg, T., Zaidi, A., Thelwall, S., Sinnathamby, M. A., Aliabadi, S., Seaman, S. R., Harris, R. J., Hope, R., Lopez-Bernal, J., Gallagher, E., Charlett, A., De Angelis, D., Presanis, A. M., Dabrera, G., Koshy, C., Ash, A., Wise, E., Moore, N., … Gunson, R. (2022). Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. The Lancet Infectious Diseases, 22(1), 35–42. https://doi.org/10.1016/s1473-3099(21)00475-8

Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., Hill, V., Blane, B., Watkins, E., Wright, E., Hall, G., Ludden, C., Myers, R., Hosmillo, M., Chaudhry, Y., Pinckert, M. L., Georgana, I., Izuagbe, R., Leek, D., … Goodfellow, I. G. (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13(1). https://doi.org/10.1038/s41467-021-27942-w

Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., Ellaby, N., Platt, S., Groves, N., Gallagher, E., Tumelty, N. M., Le Viet, T., Hughes, G. J., Chen, C., Turner, C., Logan, S., Harrison, A., Koshy, C., … Harrison, E. M. (2022). Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-28371-z

Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., Machin, N., Shin, G. Y., Mahungu, T., Saeed, K., Saluja, T., Taha, Y., Mahida, N., Pope, C., Chawla, A., Cutino-Moguel, M.-T., Tamuri, A., Williams, R., Darby, A., … Breuer, J. (2022). Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study. https://doi.org/10.1101/2022.02.10.22270799

Coll, F., Gouliouris, T., Bruchmann, S., Phelan, J., Raven, K. E., Clark, T. G., Parkhill, J., & Peacock, S. J. (2022). PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03194-2

Walker, T. M., Miotto, P., Köser, C. U., Fowler, P. W., Knaggs, J., Iqbal, Z., Hunt, M., Chindelevitch, L., Farhat, M. R., Cirillo, D. M., Comas, I., Posey, J., Omar, S. V., Peto, T. E., Suresh, A., Uplekar, S., Laurent, S., Colman, R. E., Nathanson, C.-M., … Puyen, Z. M. (2022). The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis. The Lancet Microbe, 3(4), e265–e273. https://doi.org/10.1016/s2666-5247(21)00301-3

Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., Machin, N., Shin, G. Y., Mahungu, T., Saeed, K., Saluja, T., Taha, Y., Mahida, N., Pope, C., Chawla, A., Cutino-Moguel, M.-T., Tamuri, A., Williams, R., Darby, 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. CLOCKSS. https://doi.org/10.7554/elife.78427

Obanda, B. A., Gibbons, C. L., Fèvre, E. M., Bebora, L., Gitao, G., Ogara, W., Wang, S.-H., Gebreyes, W., Ngetich, R., Blane, B., Coll, F., Harrison, E. M., Kariuki, S., Peacock, S. J., & Cook, E. A. J. (2022). Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya. Antibiotics, 11(12), 1726. https://doi.org/10.3390/antibiotics11121726

Obanda, B. A., Cook, E. A. J., Fèvre, E. M., Bebora, L., Ogara, W., Wang, S.-H., Gebreyes, W., Ngetich, R., Wandede, D., Muyodi, J., Blane, B., Coll, F., Harrison, E. M., Peacock, S. J., & Gitao, G. C. (2022). Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya. Pathogens, 11(12), 1504. https://doi.org/10.3390/pathogens11121504

Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., … Ferguson, N. M. (2021). Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data. https://doi.org/10.1101/2020.12.30.20249034

Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., Kemp, S. A., Bassi, J., Pinto, D., Silacci-Fregni, C., Bianchi, S., Tortorici, M. A., Bowen, J., Culap, K., Jaconi, S., Cameroni, E., Snell, G., Pizzuto, M. S., Pellanda, A. F., … Gupta, R. K. (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature, 593(7857), 136–141. https://doi.org/10.1038/s41586-021-03412-7

Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., Roberts, D. J., Chandra, A., Temperton, N., Baker, S., Dougan, G., Hess, C., Kingston, N., … Gupta, R. K. (2021). SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592(7853), 277–282. https://doi.org/10.1038/s41586-021-03291-y

Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., Bianchi, S., Tortorici, M. A., Bowen, J., Culap, K., Jaconi, S., Cameroni, E., Snell, G., Pizzuto, M. S., Pellanda, A. F., … Gupta, R. K. (2021). SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. https://doi.org/10.1101/2021.01.19.21249840

Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., Thakur, N., Collier, D. A., Mlcochova, P., Robson, S. C., Loman, N. J., Connor, T. R., Golubchik, T., Martinez Nunez, R. T., Ludden, C., … Gupta, R. K. (2021). Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Reports, 35(13), 109292. https://doi.org/10.1016/j.celrep.2021.109292

Mashe, T., Takawira, F. T., Martins, L. de O., Gudza-Mugabe, M., Chirenda, J., Munyanyi, M., Chaibva, B. V., Tarupiwa, A., Gumbo, H., Juru, A., Nyagupe, C., Phiri, I., Manangazira, P., Goredema, A., Danda, S., Chabata, I., Jonga, J., Munharira, R., Masunda, K., … Mhlanga, G. (2021). Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread. https://doi.org/10.1101/2021.01.04.20232520

Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., Rey, S. M., Nicholls, S. M., Colquhoun, R. M., da Silva Filipe, A., Shepherd, J., Pascall, D. J., Shah, R., Jesudason, N., Li, K., … Neaverson, A. S. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184(1), 64-75.e11. https://doi.org/10.1016/j.cell.2020.11.020

Golubchik, T., Lythgoe, K. A., Hall, M., Ferretti, L., Fryer, H. R., MacIntyre-Cockett, G., de Cesare, M., Trebes, A., Piazza, P., Buck, D., Todd, J. A., Fraser, C., & Bonsall, D. (2021). Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein. https://doi.org/10.1101/2021.01.12.20249080

Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsavsky, T., Kläser, K., Canas, L. S., Molteni, E., Modat, M., Drew, D. A., Nguyen, L. H., Polidori, L., Selvachandran, S., Hu, C., Capdevila, J., Hammers, A., Chan, A. T., Wolf, J., … Gunson, R. N. (2021). Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. The Lancet Public Health, 6(5), e335–e345. https://doi.org/10.1016/s2468-2667(21)00055-4

Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsavsky, T., Kläser, K., Canas, L. S., Molteni, E., Modat, M., Drew, D. A., Nguyen, L. H., Polidori, L., Selvachandran, S., Hu, C., Capdevila, J., Hammers, A., Chan, A. T., … Ourselin, S. (2021). Changes in symptomatology, re-infection and transmissibility associated with SARS-CoV-2 variant B.1.1.7: an ecological study. https://doi.org/10.1101/2021.01.28.21250680

Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., … Ferguson, N. M. (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), 266–269. https://doi.org/10.1038/s41586-021-03470-x

Ludden, C., Coll, F., Gouliouris, T., Restif, O., Blane, B., Blackwell, G. A., Kumar, N., Naydenova, P., Crawley, C., Brown, N. M., Parkhill, J., & Peacock, S. J. (2021). Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study. The Lancet Microbe, 2(9), e472–e480. https://doi.org/10.1016/s2666-5247(21)00117-8

Coll, F. (2021). Key variables affecting genetic distance calculations in genomic epidemiology. The Lancet Microbe, 2(10), e486–e487. https://doi.org/10.1016/s2666-5247(21)00183-x

Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., Lytras, S., Czudnochowski, N., Shah, R., Meury, M., Jesudason, N., De Marco, A., Li, K., Bassi, J., O’Toole, A., … Snell, G. (2020). The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. https://doi.org/10.1101/2020.11.04.355842

Stirrup, O. T., Hughes, J., Parker, M., Partridge, D. G., Shepherd, J. G., Blackstone, J., Coll, F., Keeley, A. J., Lindsey, B. B., Marek, A., Peters, C., Singer, J. B., Tamuri, A., de Silva, T. I., Thomson, E. C., & Breuer, J. (2020). Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. https://doi.org/10.1101/2020.11.12.20230326

Nicholls, S. M., Poplawski, R., Bull, M. J., Underwood, A., Chapman, M., Abu-Dahab, K., Taylor, B., Jackson, B., Rey, S., Amato, R., Livett, R., Gonçalves, S., Harrison, E. M., Peacock, S. J., Aanensen, D. M., Rambaut, A., Connor, T. R., & Loman, N. J. (2020). MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. https://doi.org/10.1101/2020.10.06.328328

Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., Wenseleers, T., Gimma, A., Waites, W., Wong, K. L. M., van Zandvoort, K., Silverman, J. D., Diaz-Ordaz, K., … Edmunds, W. J. (2020). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. https://doi.org/10.1101/2020.12.24.20248822

Raven, K. E., Blane, B., Kumar, N., Leek, D., Bragin, E., Coll, F., Parkhill, J., & Peacock, S. J. (2020). Defining metrics for whole-genome sequence analysis of MRSA in clinical practice. Microbial Genomics, 6(4). https://doi.org/10.1099/mgen.0.000354

Passmore, I. J., Dow, J. M., Coll, F., Cuccui, J., Palmer, T., & Wren, B. W. (2020). Ferric Citrate Regulator FecR Is Translocated across the Bacterial Inner Membrane via a Unique Twin-Arginine Transport-Dependent Mechanism. Journal of Bacteriology, 202(9). https://doi.org/10.1128/jb.00541-19

Leclerc, Q. J., Naylor, N. R., Aiken, A. M., Coll, F., & Knight, G. M. (2020). Feasibility of informing syndrome-level empiric antibiotic recommendations using publicly available antibiotic resistance datasets. Wellcome Open Research, 4, 140. https://doi.org/10.12688/wellcomeopenres.15477.2

Gouliouris, T., Coll, F., Ludden, C., Blane, B., Raven, K. E., Naydenova, P., Crawley, C., Török, M. E., Enoch, D. A., Brown, N. M., Harrison, E. M., Parkhill, J., & Peacock, S. J. (2020). Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance. Nature Microbiology, 6(1), 103–111. https://doi.org/10.1038/s41564-020-00806-7

Coll, F., Raven, K. E., Knight, G. M., Blane, B., Harrison, E. M., Leek, D., Enoch, D. A., Brown, N. M., Parkhill, J., & Peacock, S. J. (2020). Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis. The Lancet Microbe, 1(8), e328–e335. https://doi.org/10.1016/s2666-5247(20)30149-x

Toleman, M. S., Reuter, S., Jamrozy, D., Wilson, H. J., Blane, B., Harrison, E. M., Coll, F., Hope, R. J., Kearns, A., Parkhill, J., Peacock, S. J., & Török, M. E. (2019). Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013. Eurosurveillance, 24(4). https://doi.org/10.2807/1560-7917.es.2019.24.4.1800215

Gouliouris, T., Raven, K. E., Moradigaravand, D., Ludden, C., Coll, F., Blane, B., Naydenova, P., Horner, C., Brown, N. M., Corander, J., Limmathurotsakul, D., Parkhill, J., & Peacock, S. J. (2019). Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment. Genome Research, 29(4), 626–634. https://doi.org/10.1101/gr.232629.117

Loiseau, C., Brites, D., Moser, I., Coll, F., Pourcel, C., Robbe-Austerman, S., Escuyer, V., Musser, K. A., Peacock, S. J., Feuerriegel, S., Kohl, T. A., Niemann, S., Gagneux, S., & Köser, C. U. (2019). Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex. Antimicrobial Agents and Chemotherapy, 63(6). https://doi.org/10.1128/aac.00159-19

Harrison, E. M., Ba, X., Coll, F., Blane, B., Restif, O., Carvell, H., Köser, C. U., Jamrozy, D., Reuter, S., Lovering, A., Gleadall, N., Bellis, K. L., Uhlemann, A.-C., Lowy, F. D., Massey, R. C., Grilo, I. R., Sobral, R., Larsen, J., Rhod Larsen, A., … Holmes, M. A. (2019). Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus. Nature Microbiology, 4(10), 1680–1691. https://doi.org/10.1038/s41564-019-0471-0

Conceição, E. C., Refregier, G., Gomes, H. M., Olessa-Daragon, X., Coll, F., Ratovonirina, N. H., Rasolofo-Razanamparany, V., Lopes, M. L., van Soolingen, D., Rutaihwa, L., Gagneux, S., Bollela, V. R., Suffys, P. N., Duarte, R. S., Lima, K. V. B., & Sola, C. (2019). Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade. Infection, Genetics and Evolution, 73, 337–341. https://doi.org/10.1016/j.meegid.2019.06.001

Kime, L., Randall, C. P., Banda, F. I., Coll, F., Wright, J., Richardson, J., Empel, J., Parkhill, J., & O’Neill, A. J. (2019). Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure. MBio, 10(5). https://doi.org/10.1128/mbio.01755-19

Knight, G. M., Davies, N. G., Colijn, C., Coll, F., Donker, T., Gifford, D. R., Glover, R. E., Jit, M., Klemm, E., Lehtinen, S., Lindsay, J. A., Lipsitch, M., Llewelyn, M. J., Mateus, A. L. P., Robotham, J. V., Sharland, M., Stekel, D., Yakob, L., & Atkins, K. E. (2019). Mathematical modelling for antibiotic resistance control policy: do we know enough? BMC Infectious Diseases, 19(1). https://doi.org/10.1186/s12879-019-4630-y

Dymond, A., Davies, H., Mealing, S., Pollit, V., Coll, F., Brown, N. M., & Peacock, S. J. (2019). Genomic Surveillance of Methicillin-resistant Staphylococcus aureus: A Mathematical Early Modeling Study of Cost-effectiveness. Clinical Infectious Diseases, 70(8), 1613–1619. https://doi.org/10.1093/cid/ciz480

Wailan, A. M., Coll, F., Heinz, E., Tonkin-Hill, G., Corander, J., Feasey, N. A., & Thomson, N. R. (2018). rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. https://doi.org/10.1101/404624

Ludden, C., Raven, K. E., Jamrozy, D., Gouliouris, T., Blane, B., Coll, F., de Goffau, M., Naydenova, P., Horner, C., Hernandez-Garcia, J., Wood, P., Hadjirin, N., Radakovic, M., Brown, N. M., Holmes, M., Parkhill, J., & Peacock, S. J. (2018). One Health genomic surveillance ofEscherichia colidemonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock. https://doi.org/10.1101/434001

Coll, F., Phelan, J., Hill-Cawthorne, G. A., Nair, M. B., Mallard, K., Ali, S., Abdallah, A. M., Alghamdi, S., Alsomali, M., Ahmed, A. O., Portelli, S., Oppong, Y., Alves, A., Bessa, T. B., Campino, S., Caws, M., Chatterjee, A., Crampin, A. C., Dheda, K., … Clark, T. G. (2018). Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature Genetics, 50(2), 307–316. https://doi.org/10.1038/s41588-017-0029-0

Ajileye, A., Alvarez, N., Merker, M., Walker, T. M., Akter, S., Brown, K., Moradigaravand, D., Schön, T., Andres, S., Schleusener, V., Omar, S. V., Coll, F., Huang, H., Diel, R., Ismail, N., Parkhill, J., de Jong, B. C., Peto, T. E. A., Crook, D. W., … Köser, C. U. (2017). Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDR sl Assays. Antimicrobial Agents and Chemotherapy, 61(4). https://doi.org/10.1128/aac.02169-16

Ludden, C., Reuter, S., Judge, K., Gouliouris, T., Blane, B., Coll, F., Naydenova, P., Hunt, M., Tracey, A., Hopkins, K. L., Brown, N. M., Woodford, N., Parkhill, J., & Peacock, S. J. (2017). Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. Microbial Genomics, 3(7). https://doi.org/10.1099/mgen.0.000114

Nakatani, Y., Opel-Reading, H. K., Merker, M., Machado, D., Andres, S., Kumar, S. S., Moradigaravand, D., Coll, F., Perdigão, J., Portugal, I., Schön, T., Nair, D., Devi, K. R. U., Kohl, T. A., Beckert, P., Clark, T. G., Maphalala, G., Khumalo, D., Diel, R., … Köser, C. U. (2017). Role of Alanine Racemase Mutations in Mycobacterium tuberculosis <scp>d</scp> -Cycloserine Resistance. Antimicrobial Agents and Chemotherapy, 61(12). https://doi.org/10.1128/aac.01575-17

Last, A., Pickering, H., Roberts, C., Coll, F., Phelan, J., Burr, S., Cassama, E., Nabicassa, M., Seth-Smith, H., Hadfield, J., Cutcliffe, L., Clarke, I., Mabey, D., Bailey, R., Clark, T., Thomson, N., & Holland, M. (2017). Population-based analysis of ocularChlamydia trachomatisin trachoma-endemic West African communities identifies genomic markers of disease severity. https://doi.org/10.1101/205336

Coll, F., Harrison, E. M., Toleman, M. S., Reuter, S., Raven, K. E., Blane, B., Palmer, B., Kappeler, A. R. M., Brown, N. M., Török, M. E., Parkhill, J., & Peacock, S. J. (2017). Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Science Translational Medicine, 9(413). https://doi.org/10.1126/scitranslmed.aak9745

Toleman, M. S., Watkins, E. R., Williams, T., Blane, B., Sadler, B., Harrison, E. M., Coll, F., Parkhill, J., Nazareth, B., Brown, N. M., & Peacock, S. J. (2017). Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting. Clinical Infectious Diseases, 65(12), 2069–2077. https://doi.org/10.1093/cid/cix539

Harrison, E. M., Coll, F., Toleman, M. S., Blane, B., Brown, N. M., Török, M. E., Parkhill, J., & Peacock, S. J. (2017). Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-07662-2

Jamrozy, D., Coll, F., Mather, A. E., Harris, S. R., Harrison, E. M., MacGowan, A., Karas, A., Elston, T., Estée Török, M., Parkhill, J., & Peacock, S. J. (2017). Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events. BMC Genomics, 18(1). https://doi.org/10.1186/s12864-017-4065-z

Raven, K. E., Gouliouris, T., Brodrick, H., Coll, F., Brown, N. M., Reynolds, R., Reuter, S., Török, M. E., Parkhill, J., & Peacock, S. J. (2017). Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing. Clinical Infectious Diseases, 64(7), 886–893. https://doi.org/10.1093/cid/ciw872

Refrégier, G., Abadia, E., Matsumoto, T., Ano, H., Takashima, T., Tsuyuguchi, I., Aktas, E., Cömert, F., Gomgnimbou, M. K., Panaiotov, S., Phelan, J., Coll, F., McNerney, R., Pain, A., Clark, T. G., & Sola, C. (2016). Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. Infection, Genetics and Evolution, 45, 461–473. https://doi.org/10.1016/j.meegid.2016.10.009

Harrison, E. M., Ludden, C., Brodrick, H. J., Blane, B., Brennan, G., Morris, D., Coll, F., Reuter, S., Brown, N. M., Holmes, M. A., O’Connell, B., Parkhill, J., Török, M. E., Cormican, M., & Peacock, S. J. (2016). Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. Genome Medicine, 8(1). https://doi.org/10.1186/s13073-016-0353-5

Toleman, M. S., Reuter, S., Coll, F., Harrison, E. M., Blane, B., Brown, N. M., Török, M. E., Parkhill, J., & Peacock, S. J. (2016). Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-ResistantStaphylococcus aureusUSA300 in the East of England. Journal of Infectious Diseases, 214(3), 447–453. https://doi.org/10.1093/infdis/jiw166

Phelan, J. E., Coll, F., Bergval, I., Anthony, R. M., Warren, R., Sampson, S. L., Gey van Pittius, N. C., Glynn, J. R., Crampin, A. C., Alves, A., Bessa, T. B., Campino, S., Dheda, K., Grandjean, L., Hasan, R., Hasan, Z., Miranda, A., Moore, D., Panaiotov, S., … Clark, T. G. (2016). Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-2467-y

Last, A., Roberts, C., Coll, F., Burr, S., Clarke, I., Mabey, D., Bailey, R., Clark, T., Thomson, N., & Holland, M. (2016). Ocular chlamydial genomic variants and disease severity in trachoma: a cross-sectional population-based genome-wide association study. The Lancet, 387, S63. https://doi.org/10.1016/s0140-6736(16)00450-5

Phelan, J., Coll, F., McNerney, R., Ascher, D. B., Pires, D. E. V., Furnham, N., Coeck, N., Hill-Cawthorne, G. A., Nair, M. B., Mallard, K., Ramsay, A., Campino, S., Hibberd, M. L., Pain, A., Rigouts, L., & Clark, T. G. (2016). Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Medicine, 14(1). https://doi.org/10.1186/s12916-016-0575-9

Toleman, M. S., Reuter, S., Coll, F., Harrison, E. M., & Peacock, S. J. (2016). Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011–2013. Emerging Infectious Diseases, 22(9), 1658–1659. https://doi.org/10.3201/eid2209.151100

(2016). Correction: Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites. PLOS Genetics, 12(8), e1006300. https://doi.org/10.1371/journal.pgen.1006300

Ali, A., Hasan, Z., McNerney, R., Mallard, K., Hill-Cawthorne, G., Coll, F., Nair, M., Pain, A., Clark, T. G., & Hasan, R. (2015). Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan. PLOS ONE, 10(2), e0117771. https://doi.org/10.1371/journal.pone.0117771

Phelan, J., Maitra, A., McNerney, R., Nair, M., Gupta, A., Coll, F., Pain, A., Bhakta, S., & Clark, T. G. (2015). The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae. International Journal of Mycobacteriology, 4(3), 207–216. https://doi.org/10.1016/j.ijmyco.2015.05.001

Coll, F., McNerney, R., Preston, M. D., Guerra-Assunção, J. A., Warry, A., Hill-Cawthorne, G., Mallard, K., Nair, M., Miranda, A., Alves, A., Perdigão, J., Viveiros, M., Portugal, I., Hasan, Z., Hasan, R., Glynn, J. R., Martin, N., Pain, A., & Clark, T. G. (2015). Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Medicine, 7(1). https://doi.org/10.1186/s13073-015-0164-0

Benavente, E. D., Coll, F., Furnham, N., McNerney, R., Glynn, J. R., Campino, S., Pain, A., Mohareb, F. R., & Clark, T. G. (2015). PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics, 16(1). https://doi.org/10.1186/s12859-015-0603-3

Guerra-Assunção, J., Crampin, A., Houben, R., Mzembe, T., Mallard, K., Coll, F., Khan, P., Banda, L., Chiwaya, A., Pereira, R., McNerney, R., Fine, P., Parkhill, J., Clark, T., & Glynn, J. (2015). Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. ELife, 4. CLOCKSS. https://doi.org/10.7554/elife.05166

Samad, H., Coll, F., Preston, M. D., Ocholla, H., Fairhurst, R. M., & Clark, T. G. (2015). Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites. PLOS Genetics, 11(4), e1005131. https://doi.org/10.1371/journal.pgen.1005131

Abdallah, A. M., Hill-Cawthorne, G. A., Otto, T. D., Coll, F., Guerra-Assunção, J. A., Gao, G., Naeem, R., Ansari, H., Malas, T. B., Adroub, S. A., Verboom, T., Ummels, R., Zhang, H., Panigrahi, A. K., McNerney, R., Brosch, R., Clark, T. G., Behr, M. A., Bitter, W., & Pain, A. (2015). Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports, 5(1). https://doi.org/10.1038/srep15443

Kanji, A., Hasan, Z., Ali, A., McNerney, R., Mallard, K., Coll, F., Hill-Cawthorne, G., Nair, M., Clark, T. G., Zaver, A., Jafri, S., & Hasan, R. (2015). Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan. International Journal of Mycobacteriology, 4(1), 73–79. https://doi.org/10.1016/j.ijmyco.2014.11.049

Perdigão, J., Silva, H., Machado, D., Macedo, R., Maltez, F., Silva, C., Jordao, L., Couto, I., Mallard, K., Coll, F., Hill-Cawthorne, G. A., McNerney, R., Pain, A., Clark, T. G., Viveiros, M., & Portugal, I. (2014). Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-991

Coll, F., Preston, M., Guerra-Assunção, J. A., Hill-Cawthorn, G., Harris, D., Perdigão, J., Viveiros, M., Portugal, I., Drobniewski, F., Gagneux, S., Glynn, J. R., Pain, A., Parkhill, J., McNerney, R., Martin, N., & Clark, T. G. (2014). PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis, 94(3), 346–354. https://doi.org/10.1016/j.tube.2014.02.005

Coll, F., McNerney, R., Guerra-Assunção, J. A., Glynn, J. R., Perdigão, J., Viveiros, M., Portugal, I., Pain, A., Martin, N., & Clark, T. G. (2014). A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications, 5(1). https://doi.org/10.1038/ncomms5812

Guerra-Assunção, J. A., Houben, R. M. G. J., Crampin, A. C., Mzembe, T., Mallard, K., Coll, F., Khan, P., Banda, L., Chiwaya, A., Pereira, R. P. A., McNerney, R., Harris, D., Parkhill, J., Clark, T. G., & Glynn, J. R. (2014). Recurrence due to Relapse or Reinfection WithMycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up. Journal of Infectious Diseases, 211(7), 1154–1163. https://doi.org/10.1093/infdis/jiu574

Bergval, I., Coll, F., Schuitema, A., de Ronde, H., Mallard, K., Pain, A., McNerney, R., Clark, T. G., & Anthony, R. M. (2014). A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture. FEMS Microbiology Letters, 362(2), 1–7. https://doi.org/10.1093/femsle/fnu037

Clark, T. G., Mallard, K., Coll, F., Preston, M., Assefa, S., Harris, D., Ogwang, S., Mumbowa, F., Kirenga, B., O’Sullivan, D. M., Okwera, A., Eisenach, K. D., Joloba, M., Bentley, S. D., Ellner, J. J., Parkhill, J., Jones-López, E. C., & McNerney, R. (2013). Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing. PLoS ONE, 8(12), e83012. https://doi.org/10.1371/journal.pone.0083012

Coll, F., Mallard, K., Preston, M. D., Bentley, S., Parkhill, J., McNerney, R., Martin, N., & Clark, T. G. (2012). SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics, 28(22), 2991–2993. https://doi.org/10.1093/bioinformatics/bts544