Coll, Francesc; Gouliouris, Theodore; Bruchmann, Sebastian; Phelan, Jody; Raven, Kathy E; Clark, Taane G; Parkhill, Julian; Peacock, Sharon J; (2022) PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies. Communications Biology, 5 (1). 266-. ISSN 2399-3642 DOI: https://doi.org/10.1038/s42003-022-03194-2

Obanda, Benear Apollo; Cook, Elizabeth AJ; Fèvre, Eric M; Bebora, Lilly; Ogara, William; Wang, Shu-Hua; Gebreyes, Wondwossen; Ngetich, Ronald; Wandede, Dolphine; Muyodi, Johnstone; +5 more... Blane, Beth; Coll, Francesc; Harrison, Ewan M; Peacock, Sharon J; Gitao, George C; (2022) Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya. Pathogens, 11 (12). p. 1504. DOI: https://doi.org/10.3390/pathogens11121504

Obanda, Benear Apollo; Gibbons, Cheryl L; Fèvre, Eric M; Bebora, Lilly; Gitao, George; Ogara, William; Wang, Shu-Hua; Gebreyes, Wondwossen; Ngetich, Ronald; Blane, Beth; +5 more... Coll, Francesc; Harrison, Ewan M; Kariuki, Samuel; Peacock, Sharon J; Cook, Elizabeth AJ; (2022) Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya. Antibiotics, 11 (12). p. 1726. ISSN 2079-6382 DOI: https://doi.org/10.3390/antibiotics11121726

Stirrup, Oliver; Blackstone, James; Mapp, Fiona; MacNeil, Alyson; Panca, Monica; Holmes, Alison; Machin, Nicholas; Shin, Gee Yen; Mahungu, Tabitha; Saeed, Kordo; +41 more... Saluja, Tranprit; Taha, Yusri; Mahida, Nikunj; Pope, Cassie; Chawla, Anu; Cutino-Moguel, Maria-Teresa; Tamuri, Asif; Williams, Rachel; Darby, Alistair; Robertson, David L; Flaviani, Flavia; Nastouli, Eleni; Robson, Samuel; Smith, Darren; Loose, Matthew; Laing, Kenneth; Monahan, Irene; Kele, Beatrix; Haldenby, Sam; George, Ryan; Bashton, Matthew; Witney, Adam A; Byott, Matthew; Coll, Francesc; Chapman, Michael; Peacock, Sharon J; COG-UK HOCI Investigators; COVID-19 Genomics UK (COG-UK) consortium; Hughes, Joseph; Nebbia, Gaia; Partridge, David G; Parker, Matthew; Price, James Richard; Peters, Christine; Roy, Sunando; Snell, Luke B; de Silva, Thushan I; Thomson, Emma; Flowers, Paul; Copas, Andrew; Breuer, Judith; (2022) Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study. eLife, 11. e78427-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.78427

Coll, Francesc; (2021) Key variables affecting genetic distance calculations in genomic epidemiology. The Lancet Microbe, 2 (10). e486-e487. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(21)00183-X

Ludden, Catherine; Coll, Francesc; Gouliouris, Theodore; Restif, Olivier; Blane, Beth; Blackwell, Grace A; Kumar, Narender; Naydenova, Plamena; Crawley, Charles; Brown, Nicholas M; +2 more... Parkhill, Julian; Peacock, Sharon J; (2021) Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study. The Lancet Microbe, 2 (9). e472-e480. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(21)00117-8

Stirrup, Oliver; Hughes, Joseph; Parker, Matthew; Partridge, David G; Shepherd, James G; Blackstone, James; Coll, Francesc; Keeley, Alexander; Lindsey, Benjamin B; Marek, Aleksandra; +7 more... Peters, Christine; Singer, Joshua B; COVID-19 Genomics UK (COG-UK) consortium; Tamuri, Asif; de Silva, Thushan I; Thomson, Emma C; Breuer, Judith; COVID-19 Genomics UK (COG-UK) consortium; (2021) Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.65828

Coll, Francesc; Raven, Kathy E; Knight, Gwenan M; Blane, Beth; Harrison, Ewan M; Leek, Danielle; Enoch, David A; Brown, Nicholas M; Parkhill, Julian; Peacock, Sharon 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. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(20)30149-X

Leclerc, Quentin J; Naylor, Nichola R; Aiken, Alexander M; Coll, Francesc; Knight, Gwenan M; (2020) Feasibility of informing syndrome-level empiric antibiotic recommendations using publicly available antibiotic resistance datasets. Wellcome Open Research, 4 (140). 140-. DOI: https://doi.org/10.12688/wellcomeopenres.15477.2

Passmore, Ian J; Dow, Jennifer M; Coll, Francesc; Cuccui, Jon; Palmer, Tracy; Wren, Brendan 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). ISSN 0021-9193 DOI: https://doi.org/10.1128/JB.00541-19

Raven, Kathy E; Blane, Beth; Kumar, Narender; Leek, Danielle; Bragin, Eugene; Coll, Francesc; Parkhill, Julian; Peacock, Sharon J; (2020) Defining metrics for whole-genome sequence analysis of MRSA in clinical practice. MICROBIAL GENOMICS, 6 (4). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000354

Stirrup, Oliver T; Hughes, Joseph; Parker, Matthew; Partridge, David G; Shepherd, James G; Blackstone, James; Coll, Francesc; Keeley, Alexander J; Lindsey, Benjamin B; Marek, Aleksandra; +6 more... Peters, Christine; Singer, Joshua B; Tamuri, Asif; de Silva, Thushan I; Thomson, Emma C; Breuer, Judith; (2020) Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. medRxiv preprint - BMJ Yale. ISSN 1468-5833 DOI: https://doi.org/10.1101/2020.11.12.20230326

Dymond, Amy; Davies, Heather; Mealing, Stuart; Pollit, Vicki; Coll, Francesc; Brown, Nicholas M; Peacock, Sharon J; (2019) Genomic Surveillance of Methicillin-resistant Staphylococcus aureus: A Mathematical Early Modeling Study of Cost-effectiveness. Clinical infectious diseases, 70 (8). pp. 1613-1619. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciz480

Gouliouris, Theodore; Raven, Kathy E; Moradigaravand, Danesh; Ludden, Catherine; Coll, Francesc; Blane, Beth; Naydenova, Plamena; Horner, Carolyne; Brown, Nicholas M; Corander, Jukka; +3 more... Limmathurotsakul, Direk; Parkhill, Julian; Peacock, Sharon 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). pp. 626-634. ISSN 1088-9051 DOI: https://doi.org/10.1101/gr.232629.117

Kime, Louise; Randall, Christopher P; Banda, Frank I; Coll, Francesc; Wright, John; Richardson, Joseph; Empel, Joanna; Parkhill, Julian; O'Neill, Alex J; (2019) Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure. mBio, 10 (5). e01755-e01719. ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.01755-19

Knight, Gwenan M; Davies, Nicholas G; Colijn, Caroline; Coll, Francesc; Donker, Tjibbe; Gifford, Danna R; Glover, Rebecca E; Jit, Mark; Klemm, Elizabeth; Lehtinen, Sonja; +9 more... Lindsay, Jodi A; Lipsitch, Marc; Llewelyn, Martin J; Mateus, Ana LP; Robotham, Julie V; Sharland, Mike; Stekel, Dov; Yakob, Laith; Atkins, Katherine E; (2019) Mathematical modelling for antibiotic resistance control policy: do we know enough? BMC infectious diseases, 19 (1). 1011-. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-019-4630-y

Loiseau, Chloé; Brites, Daniela; Moser, Irmgard; Coll, Francesc; Pourcel, Christine; Robbe-Austerman, Suelee; Escuyer, Vincent; Musser, Kimberlee A; Peacock, Sharon J; Feuerriegel, Silke; +4 more... Kohl, Thomas A; Niemann, Stefan; Gagneux, Sebastien; Köser, Claudio 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). ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.00159-19

Ludden, Catherine; Raven, Kathy E; Jamrozy, Dorota; Gouliouris, Theodore; Blane, Beth; Coll, Francesc; de Goffau, Marcus; Naydenova, Plamena; Horner, Carolyne; Hernandez-Garcia, Juan; +7 more... Wood, Paul; Hadjirin, Nazreen; Radakovic, Milorad; Brown, Nicholas M; Holmes, Mark; Parkhill, Julian; Peacock, Sharon J; (2019) One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock. mBio, 10 (1). ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.02693-18

Toleman, Michelle S; Reuter, Sandra; Jamrozy, Dorota; Wilson, Hayley J; Blane, Beth; Harrison, Ewan M; Coll, Francesc; Hope, Russell J; Kearns, Angela; Parkhill, Julian; +2 more... Peacock, Sharon J; Török, M Estée; (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). pp. 42-53. ISSN 1560-7917 DOI: https://doi.org/10.2807/1560-7917.ES.2019.24.4.1800215

Wailan, Alexander M; Coll, Francesc; Heinz, Eva; Tonkin-Hill, Gerry; Corander, Jukka; Feasey, Nicholas A; Thomson, Nicholas R; (2019) rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. Microbial genomics, 5 (4). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000264

Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah M; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O; +41 more... Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R; Grandjean, Louis; Ha, Dang Minh; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L; Joloba, Moses; Jones-López, Edward C; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigão, João; Portugal, Isabel; Rchiad, Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A; Sola, Christophe; Sousa, Erivelton Oliveira; Streicher, Elizabeth M; Van Helden, Paul; Viveiros, Miguel; Warren, Robert M; McNerney, Ruth; Pain, Arnab; Clark, Taane G; (2018) Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics, 50 (5). 764-. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-018-0074-3 Full text not available from this repository.

Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah M; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O; +41 more... Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R; Grandjean, Louis; Minh Ha, Dang; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L; Joloba, Moses; Jones-López, Edward C; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigão, João; Portugal, Isabel; Rchiad, Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A; Sola, Christophe; Oliveira Sousa, Erivelton; Streicher, Elizabeth M; Helden, Paul Van; Viveiros, Miguel; Warren, Robert M; McNerney, Ruth; Pain, Arnab; Clark, Taane G; (2018) Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics, 50 (2). pp. 307-316. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-017-0029-0

Last, AR; Pickering, H; Roberts, CH; Coll, F; Phelan, J; Burr, SE; Cassama, E; Nabicassa, M; Seth-Smith, HMB; Hadfield, J; +7 more... Cutcliffe, LT; Clarke, IN; Mabey, DCW; Bailey, RL; Clark, TG; Thomson, NR; Holland, MJ; (2018) Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. Genome medicine, 10 (1). 15-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-018-0521-x

Ajileye, Adebisi; Alvarez, Nataly; Merker, Matthias; Walker, Timothy M; Akter, Suriya; Brown, Kerstin; Moradigaravand, Danesh; Schön, Thomas; Andres, Sönke; Schleusener, Viola; +14 more... Omar, Shaheed V; Coll, Francesc; Huang, Hairong; Diel, Roland; Ismail, Nazir; Parkhill, Julian; de Jong, Bouke C; Peto, Tim EA; Crook, Derrick W; Niemann, Stefan; Robledo, Jaime; Smith, E Grace; Peacock, Sharon J; Köser, Claudio U; (2017) Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays. Antimicrobial agents and chemotherapy, 61 (4). ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.02169-16

Coll, Francesc; Harrison, Ewan M; Toleman, Michelle S; Reuter, Sandra; Raven, Kathy E; Blane, Beth; Palmer, Beverley; Kappeler, A Ruth M; Brown, Nicholas M; Török, M Estée; +2 more... Parkhill, Julian; Peacock, Sharon J; (2017) Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Science translational medicine, 9 (413). eaak9745-eaak9745. ISSN 1946-6234 DOI: https://doi.org/10.1126/scitranslmed.aak9745

Harrison, Ewan M; Coll, Francesc; Toleman, Michelle S; Blane, Beth; Brown, Nicholas M; Török, M Estee; Parkhill, Julian; Peacock, Sharon J; (2017) Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England. Scientific reports, 7 (1). 7406-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-017-07662-2

Jamrozy, Dorota; Coll, Francesc; Mather, Alison E; Harris, Simon R; Harrison, Ewan M; MacGowan, Alasdair; Karas, Andreas; Elston, Tony; Estée Török, M; Parkhill, Julian; +1 more... Peacock, Sharon 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). 684-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-017-4065-z

Last, AR; Pickering, H; Roberts, Ch; Coll, F; Phelan, J; Burr, SE; Cassama, E; Nabicassa, M; Seth-Smith, HMB; Hadfield, J; +7 more... Cutcliffe, LT; Clarke, IN; Mabey, DCW; Bailey, RL; Clark, TG; Thomson, NR; Holland, MJ; (2017) Population-based analysis of ocular<i>Chlamydia trachomatis</i>in trachoma-endemic West African communities identifies genomic markers of disease severity. BioRxiv. DOI: https://doi.org/10.1101/205336

Ludden, Catherine; Reuter, Sandra; Judge, Kim; Gouliouris, Theodore; Blane, Beth; Coll, Francesc; Naydenova, Plamena; Hunt, Martin; Tracey, Alan; Hopkins, Katie L; +4 more... Brown, Nicholas M; Woodford, Neil; Parkhill, Julian; Peacock, Sharon J; (2017) Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. Microbial genomics, 3 (7). e000114-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000114

Nakatani, Yoshio; Opel-Reading, Helen K; Merker, Matthias; Machado, Diana; Andres, Sönke; Kumar, S Siva; Moradigaravand, Danesh; Coll, Francesc; Perdigão, João; Portugal, Isabel; +19 more... Schön, Thomas; Nair, Dina; Devi, KR Uma; Kohl, Thomas A; Beckert, Patrick; Clark, Taane G; Maphalala, Gugu; Khumalo, Derrick; Diel, Roland; Klaos, Kadri; Aung, Htin Lin; Cook, Gregory M; Parkhill, Julian; Peacock, Sharon J; Swaminathan, Soumya; Viveiros, Miguel; Niemann, Stefan; Krause, Kurt L; Köser, Claudio U; (2017) Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance. Antimicrobial agents and chemotherapy, 61 (12). ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.01575-17

Raven, Kathy E; Gouliouris, Theodore; Brodrick, Hayley; Coll, Francesc; Brown, Nicholas M; Reynolds, Rosy; Reuter, Sandra; Török, M Estée; Parkhill, Julian; Peacock, Sharon J; (2017) Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing. Clinical infectious diseases, 64 (7). pp. 886-893. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciw872

Toleman, Michelle S; Watkins, Emmeline R; Williams, Tom; Blane, Beth; Sadler, Belinda; Harrison, Ewan M; Coll, Francesc; Parkhill, Julian; Nazareth, Bernadette; Brown, Nicholas M; +1 more... Peacock, Sharon J; (2017) Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting. Clinical infectious diseases, 65 (12). pp. 2069-2077. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cix539

Harrison, Ewan M; Ludden, Catherine; Brodrick, Hayley J; Blane, Beth; Brennan, Gráinne; Morris, Dearbháile; Coll, Francesc; Reuter, Sandra; Brown, Nicholas M; Holmes, Mark A; +5 more... O'Connell, Brian; Parkhill, Julian; Török, M Estee; Cormican, Martin; Peacock, Sharon J; (2016) Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. Genome medicine, 8 (1). 102-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-016-0353-5

Phelan, Jody E; Coll, Francesc; Bergval, Indra; Anthony, Richard M; Warren, Rob; Sampson, Samantha L; Gey van Pittius, Nicolaas C; Glynn, Judith R; Crampin, Amelia C; Alves, Adriana; +20 more... Bessa, Theolis Barbosa; Campino, Susana; Dheda, Keertan; Grandjean, Louis; Hasan, Rumina; Hasan, Zahra; Miranda, Anabela; Moore, David; Panaiotov, Stefan; Perdigao, Joao; Portugal, Isabel; Sheen, Patricia; de Oliveira Sousa, Erivelton; Streicher, Elizabeth M; van Helden, Paul D; Viveiros, Miguel; Hibberd, Martin L; Pain, Arnab; McNerney, Ruth; Clark, Taane G; (2016) Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC genomics, 17 (1). 151-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-016-2467-y

Phelan, Jody; Coll, Francesc; McNerney, Ruth; Ascher, David B; Pires, Douglas EV; Furnham, Nick; Coeck, Nele; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; +6 more... Ramsay, Andrew; Campino, Susana; Hibberd, Martin L; Pain, Arnab; Rigouts, Leen; Clark, Taane G; (2016) Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC medicine, 14 (1). 31-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-016-0575-9

Refrégier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cömert, Füsun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; +6 more... Phelan, Jody; Coll, Francesc; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Sola, Christophe; (2016) Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. Infection, genetics and evolution, 45. pp. 461-473. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2016.10.009

Toleman, Michelle S; Reuter, Sandra; Coll, Francesc; Harrison, Ewan M; Blane, Beth; Brown, Nicholas M; Török, M Estée; Parkhill, Julian; Peacock, Sharon J; (2016) Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England. The Journal of infectious diseases, 214 (3). pp. 447-453. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiw166

Toleman, Michelle S; Reuter, Sandra; Coll, Francesc; Harrison, Ewan M; Peacock, Sharon J; (2016) Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011-2013. Emerging infectious diseases, 22 (9). pp. 1658-1659. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2209.151100

Abdallah, Abdallah M; Hill-Cawthorne, Grant A; Otto, Thomas D; Coll, Francesc; Guerra-Assunção, José Afonso; Gao, Ge; Naeem, Raeece; Ansari, Hifzur; Malas, Tareq B; Adroub, Sabir A; +10 more... Verboom, Theo; Ummels, Roy; Zhang, Huoming; Panigrahi, Aswini Kumar; McNerney, Ruth; Brosch, Roland; Clark, Taane G; Behr, Marcel A; Bitter, Wilbert; Pain, Arnab; (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). 15443-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep15443

Ali, Asho; Hasan, Zahra; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G; Hasan, Rumina; (2015) Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan. PloS one, 10 (2). e0117771-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0117771

Benavente, Ernest D; Coll, Francesc; Furnham, Nick; McNerney, Ruth; Glynn, Judith R; Campino, Susana; Pain, Arnab; Mohareb, Fady R; Clark, Taane G; (2015) PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics, 16 (1). 155-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-015-0603-3

Coll, Francesc; McNerney, Ruth; Preston, Mark D; Guerra-Assunção, José Afonso; Warry, Andrew; Hill-Cawthorne, Grant; Mallard, Kim; Nair, Mridul; Miranda, Anabela; Alves, Adriana; +9 more... Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Hasan, Zahra; Hasan, Rumina; Glynn, Judith R; Martin, Nigel; Pain, Arnab; Clark, Taane G; (2015) Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome medicine, 7 (1). 51-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-015-0164-0

Guerra-Assunção, JA; Crampin, AC; Houben, RMGJ; Mzembe, T; Mallard, K; Coll, F; Khan, P; Banda, L; Chiwaya, A; Pereira, RPA; +5 more... McNerney, R; Fine, PEM; Parkhill, J; Clark, TG; Glynn, JR; (2015) Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife, 4 (4). ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.05166

Kanji, Akbar; Hasan, Zahra; Ali, Asho; McNerney, Ruth; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant; Nair, Mridul; Clark, Taane G; Zaver, Ambreen; +2 more... Jafri, Sana; Hasan, Rumina; (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). pp. 73-79. ISSN 2212-5531 DOI: https://doi.org/10.1016/j.ijmyco.2014.11.049

Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane 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). pp. 207-216. ISSN 2212-5531 DOI: https://doi.org/10.1016/j.ijmyco.2015.05.001

Samad, Hanif; Coll, Francesc; Preston, Mark D; Ocholla, Harold; Fairhurst, Rick M; Clark, Taane G; (2015) Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites. PLoS genetics, 11 (4). e1005131-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1005131

Bergval, Indra; Coll, Francesc; Schuitema, Anja; de Ronde, Hans; Mallard, Kim; Pain, Arnab; McNerney, Ruth; Clark, Taane G; Anthony, Richard 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). pp. 1-7. ISSN 0378-1097 DOI: https://doi.org/10.1093/femsle/fnu037

Coll, Francesc; McNerney, Ruth; Guerra-Assunção, José Afonso; Glynn, Judith R; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Pain, Arnab; Martin, Nigel; Clark, Taane G; (2014) A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature communications, 5 (1). 4812-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms5812

Coll, Francesc; Preston, Mark; Guerra-Assunção, José Afonso; Hill-Cawthorn, Grant; Harris, David; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Drobniewski, Francis; Gagneux, Sebastien; +6 more... Glynn, Judith R; Pain, Arnab; Parkhill, Julian; McNerney, Ruth; Martin, Nigel; Clark, Taane G; (2014) PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland), 94 (3). pp. 346-354. ISSN 1472-9792 DOI: https://doi.org/10.1016/j.tube.2014.02.005

Guerra-Assunção, José Afonso; Houben, Rein MGJ; Crampin, Amelia C; Mzembe, Themba; Mallard, Kim; Coll, Francesc; Khan, Palwasha; Banda, Louis; Chiwaya, Arthur; Pereira, Rui PA; +5 more... McNerney, Ruth; Harris, David; Parkhill, Julian; Clark, Taane G; Glynn, Judith R; (2014) Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. The Journal of infectious diseases, 211 (7). pp. 1154-1163. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiu574

Perdigão, João; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; +6 more... Hill-Cawthorne, Grant A; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Viveiros, Miguel; Portugal, Isabel; (2014) Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC genomics, 15 (1). 991-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-15-991

Clark, Taane G; Mallard, Kim; Coll, Francesc; Preston, Mark; Assefa, Samuel; Harris, David; Ogwang, Sam; Mumbowa, Francis; Kirenga, Bruce; O'Sullivan, Denise M; +8 more... Okwera, Alphonse; Eisenach, Kathleen D; Joloba, Moses; Bentley, Stephen D; Ellner, Jerrold J; Parkhill, Julian; Jones-López, Edward C; McNerney, Ruth; (2013) Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PloS one, 8 (12). e83012-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0083012

Coll, Francesc; Mallard, Kim; Preston, Mark D; Bentley, Stephen; Parkhill, Julian; McNerney, Ruth; Martin, Nigel; Clark, Taane G; (2012) SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics (Oxford, England), 28 (22). pp. 2991-2993. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bts544