Bote, Lia; Taylor-Brown, Alyce; Maes, Mailis; Ingle, Danielle J; Valcanis, Mary; Howden, Benjamin P; Thomson, Nicholas R; (2024) Surveillance of travel-associated isolates elucidates the diversity of non-pandemic Vibrio cholerae. Microbial genomics, 10 (10). 001307. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.001307

Handley, Becca L; Sokana, Oliver; Addo, Kennedy Kwasi; Wagner, Josef; Fookes, María; Harding-Esch, Emma; Marks, Michael; Thomson, Nicholas R; Doyle, Ronan M; (2024) Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment. Microbial genomics, 10 (5). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.001234

Cuypers, Wim L; Meysman, Pieter; Weill, François-Xavier; Hendriksen, Rene S; Beyene, Getenet; Wain, John; Nair, Satheesh; Chattaway, Marie A; Perez-Sepulveda, Blanca M; Ceyssens, Pieter-Jan; +19 more... de Block, Tessa; Lee, Winnie WY; Pardos de la Gandara, Maria; Kornschober, Christian; Moran-Gilad, Jacob; Veldman, Kees T; Cormican, Martin; Torpdahl, Mia; Fields, Patricia I; Černý, Tomáš; Hardy, Liselotte; Tack, Bieke; Mellor, Kate C; Thomson, Nicholas; Dougan, Gordon; Deborggraeve, Stijn; Jacobs, Jan; Laukens, Kris; Van Puyvelde, Sandra; (2023) A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia. Nature communications, 14 (1). 3517-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-023-38902-x

Monir, Md Mamun; Islam, Mohammad Tarequl; Mazumder, Razib; Mondal, Dinesh; Nahar, Kazi Sumaita; Sultana, Marzia; Morita, Masatomo; Ohnishi, Makoto; Huq, Anwar; Watanabe, Haruo; +7 more... Qadri, Firdausi; Rahman, Mustafizur; Thomson, Nicholas; Seed, Kimberley; Colwell, Rita R; Ahmed, Tahmeed; Alam, Munirul; (2023) Genomic attributes of Vibrio cholerae O1 responsible for 2022 massive cholera outbreak in Bangladesh. Nature communications, 14 (1). 1154-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-023-36687-7

Van Puyvelde, Sandra; de Block, Tessa; Sridhar, Sushmita; Bawn, Matt; Kingsley, Robert A; Ingelbeen, Brecht; Beale, Mathew A; Barbé, Barbara; Jeon, Hyon Jin; Mbuyi-Kalonji, Lisette; +38 more... Phoba, Marie-France; Falay, Dadi; Martiny, Delphine; Vandenberg, Olivier; Affolabi, Dissou; Rutanga, Jean Pierre; Ceyssens, Pieter-Jan; Mattheus, Wesley; Cuypers, Wim L; van der Sande, Marianne AB; Park, Se Eun; Kariuki, Simon; Otieno, Kephas; Lusingu, John PA; Mbwana, Joyce R; Adjei, Samuel; Sarfo, Anima; Agyei, Seth O; Asante, Kwaku P; Otieno, Walter; Otieno, Lucas; Tahita, Marc C; Lompo, Palpouguini; Hoffman, Irving F; Mvalo, Tisungane; Msefula, Chisomo; Hassan-Hanga, Fatimah; Obaro, Stephen; Mackenzie, Grant; Deborggraeve, Stijn; Feasey, Nicholas; Marks, Florian; MacLennan, Calman A; Thomson, Nicholas R; Jacobs, Jan; Dougan, Gordon; Kariuki, Samuel; Lunguya, Octavie; (2023) A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa. Nature communications, 14 (1). 6392-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-023-41152-6

Bloomfield, Samuel; Duong, Vu Thuy; Tuyen, Ha Thanh; Campbell, James I; Thomson, Nicholas R; Parkhill, Julian; Le Phuc, Hoang; Chau, Tran Thi Hong; Maskell, Duncan J; Perron, Gabriel G; +5 more... Ngoc, Nguyen Minh; Vi, Lu Lan; Adriaenssens, Evelien M; Baker, Stephen; Mather, Alison E; (2022) Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam. Microbial Genomics, 8 (5). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000798

Gorrie, Claire L; Mirčeta, Mirjana; Wick, Ryan R; Judd, Louise M; Lam, Margaret MC; Gomi, Ryota; Abbott, Iain J; Thomson, Nicholas R; Strugnell, Richard A; Pratt, Nigel F; +9 more... Garlick, Jill S; Watson, Kerrie M; Hunter, Peter C; Pilcher, David V; McGloughlin, Steve A; Spelman, Denis W; Wyres, Kelly L; Jenney, Adam WJ; Holt, Kathryn E; (2022) Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nature communications, 13 (1). 3017-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-022-30717-6

Kane, L; (2022) Investigation of Vibrio cholerae pathogenesis using a novel human intestinal model of infection. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670346

Lewis, Joseph M; Mphasa, Madalitso; Banda, Rachel; Beale, Mathew A; Heinz, Eva; Mallewa, Jane; Jewell, Christopher; Faragher, Brian; Thomson, Nicholas R; Feasey, Nicholas A; (2022) Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults. Nature Microbiology, 7 (10). pp. 1593-1604. ISSN 2058-5276 DOI: https://doi.org/10.1038/s41564-022-01216-7

Mellor, Kate C; Blackwell, Grace A; Cawthraw, Shaun A; Mensah, Nana E; Reid, Stuart WJ; Thomson, Nicholas R; Petrovska, Liljana; Mather, Alison E; (2022) Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals. Microbial genomics, 8 (8). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000826

Njoroge, Samuel M; Madé, Laure F; von Mentzer, Astrid; Kulohoma, Benard W; Kamanu, Timothy K; Ouko, Tom T; Kiiru, John; Ward, Melissa J; Thomson, Nicholas R; Fèvre, Eric M; +2 more... Woolhouse, Mark; Kariuki, Samuel; (2022) Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin. Microbiology resource announcements, 11 (10). e0041622-. ISSN 2576-098X DOI: https://doi.org/10.1128/mra.00416-22

Ramamurthy, Thandavarayan; Pragasam, Agila Kumari; Taylor-Brown, Alyce; Will, Robert C; Vasudevan, Karthick; Das, Bhabatosh; Srivastava, Sunil Kumar; Chowdhury, Goutam; Mukhopadhyay, Asish K; Dutta, Shanta; +8 more... Veeraraghavan, Balaji; Thomson, Nicholas R; Sharma, Naresh C; Nair, Gopinath Balakrish; Takeda, Yoshifumi; Ghosh, Amit; Dougan, Gordon; Mutreja, Ankur; (2022) Vibrio cholerae O139 genomes provide a clue to why it may have failed to usher in the eighth cholera pandemic. Nature Communications, 13 (1). 3864-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-022-31391-4

Williams, David J; Grimont, Patrick AD; Cazares, Adrián; Grimont, Francine; Ageron, Elisabeth; Pettigrew, Kerry A; Cazares, Daniel; Njamkepo, Elisabeth; Weill, François-Xavier; Heinz, Eva; +3 more... Holden, Matthew TG; Thomson, Nicholas R; Coulthurst, Sarah J; (2022) The genus Serratia revisited by genomics. Nature Communications, 13 (1). 5195-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-022-32929-2

Yassine, Iman; Lefèvre, Sophie; Hansen, Elisabeth E; Ruckly, Corinne; Carle, Isabelle; Lejay-Collin, Monique; Fabre, Laëtitia; Rafei, Rayane; Clermont, Dominique; de la Gandara, Maria Pardos; +3 more... Dabboussi, Fouad; Thomson, Nicholas R; Weill, François-Xavier; (2022) Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing. Nature communications, 13 (1). 551-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-022-28121-1

Beale, Mathew A; Marks, Michael; Cole, Michelle J; Lee, Min-Kuang; Pitt, Rachel; Ruis, Christopher; Balla, Eszter; Crucitti, Tania; Ewens, Michael; Fernández-Naval, Candela; +28 more... Grankvist, Anna; Guiver, Malcolm; Kenyon, Chris R; Khairullin, Rafil; Kularatne, Ranmini; Arando, Maider; Molini, Barbara J; Obukhov, Andrey; Page, Emma E; Petrovay, Fruzsina; Rietmeijer, Cornelis; Rowley, Dominic; Shokoples, Sandy; Smit, Erasmus; Sweeney, Emma L; Taiaroa, George; Vera, Jaime H; Wennerås, Christine; Whiley, David M; Williamson, Deborah A; Hughes, Gwenda; Naidu, Prenilla; Unemo, Magnus; Krajden, Mel; Lukehart, Sheila A; Morshed, Muhammad G; Fifer, Helen; Thomson, Nicholas R; (2021) Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis. Nature Microbiology, 6 (12). pp. 1549-1560. ISSN 2058-5276 DOI: https://doi.org/10.1038/s41564-021-01000-z

Chung The, Hao; Bodhidatta, Ladaporn; Pham, Duy Thanh; Mason, Carl J; Ha Thanh, Tuyen; Voong Vinh, Phat; Turner, Paul; Hem, Sopheak; Dance, David AB; Newton, Paul N; +6 more... Phetsouvanh, Rattanaphone; Davong, Viengmon; Thwaites, Guy E; Thomson, Nicholas R; Baker, Stephen; Rabaa, Maia A; (2021) Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia. Communications biology, 4 (1). 353-. ISSN 2399-3642 DOI: https://doi.org/10.1038/s42003-021-01905-9

Cowley, Lauren A; Afrad, Mokibul Hassan; Rahman, Sadia Isfat Ara; Mamun, Md Mahfuz Al; Chin, Taylor; Mahmud, Ayesha; Rahman, Mohammed Ziaur; Billah, Mallick Masum; Khan, Manjur Hossain; Sultana, Sharmin; +12 more... Khondaker, Tilovatul; Baker, Stephen; Banik, Nandita; Alam, Ahmed Nawsher; Mannoor, Kaiissar; Banu, Sayera; Chowdhury, Anir; Flora, Meerjady Sabrina; Thomson, Nicholas R; Buckee, Caroline O; Qadri, Firdausi; Shirin, Tahmina; (2021) Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh. Nature microbiology, 6 (10). pp. 1271-1278. ISSN 2058-5276 DOI: https://doi.org/10.1038/s41564-021-00955-3

Dorman, Matthew J; Thomson, Nicholas R; Campos, Josefina; (2021) Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection. Microbial genomics, 7 (6). 000580-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000580

Fennell, Thea G; Blackwell, Grace A; Thomson, Nicholas R; Dorman, Matthew J; (2021) gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae. Microbial genomics, 7 (6). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000594

Hawkey, Jane; Paranagama, Kalani; Baker, Kate S; Bengtsson, Rebecca J; Weill, François-Xavier; Thomson, Nicholas R; Baker, Stephen; Cerdeira, Louise; Iqbal, Zamin; Hunt, Martin; +5 more... Ingle, Danielle J; Dallman, Timothy J; Jenkins, Claire; Williamson, Deborah A; Holt, Kathryn E; (2021) Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nature communications, 12 (1). 2684-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-22700-4

Horesh, Gal; Blackwell, Grace A; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R; (2021) A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Microbial genomics, 7 (2). pp. 1-15. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000499

Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R; (2021) Different evolutionary trends form the twilight zone of the bacterial pan-genome. Microbial genomics, 7 (9). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000670

Mai, Si-Nguyen T; Bodhidatta, Ladaporn; Turner, Paul; Wangchuk, Sonam; Ha Thanh, Tuyen; Voong Vinh, Phat; Pham, Duy Thanh; Rabaa, Maia A; Thwaites, Guy E; Thomson, Nicholas R; +2 more... Baker, Stephen; Chung The, Hao; (2021) The evolutionary history of Shigella flexneri serotype 6 in Asia. Microbial genomics, 7 (12). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000736

Dorman, Matthew J; Domman, Daryl; Poklepovich, Tomás; Tolley, Charlotte; Zolezzi, Gisella; Kane, Leanne; Viñas, María Rosa; Panagópulo, Marcela; Moroni, Miriam; Binsztein, Norma; +7 more... Caffer, María Inés; Clare, Simon; Dougan, Gordon; Salmond, George PC; Parkhill, Julian; Campos, Josefina; Thomson, Nicholas R; (2020) Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae. NATURE COMMUNICATIONS, 11 (1). 4918-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-020-18647-7

Dorman, Matthew J; Thomson, Nicholas R; (2020) 'Community evolution' - laboratory strains and pedigrees in the age of genomics. MICROBIOLOGY-SGM, 166 (3). pp. 233-238. ISSN 1350-0872 DOI: https://doi.org/10.1099/mic.0.000869

Nair, Satheesh; Fookes, Maria; Corton, Craig; Thomson, Nicholas R; Wain, John; Langridge, Gemma C; (2020) Genetic Markers in S. Paratyphi C Reveal Primary Adaptation to Pigs. Microorganisms, 8 (5). p. 657. ISSN 2076-2607 DOI: https://doi.org/10.3390/microorganisms8050657

Beale, Mathew A; Marks, Michael; Sahi, Sharon K; Tantalo, Lauren C; Nori, Achyuta V; French, Patrick; Lukehart, Sheila A; Marra, Christina M; Thomson, Nicholas R; (2019) Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages. Nature communications, 10 (1). 3255-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-019-11216-7

Boinett, Christine J; Cain, Amy K; Hawkey, Jane; Do Hoang, Nhu Tran; Khanh, Nhu Nguyen Thi; Thanh, Duy Pham; Dordel, Janina; Campbell, James I; Lan, Nguyen Phu Huong; Mayho, Matthew; +8 more... Langridge, Gemma C; Hadfield, James; Chau, Nguyen Van Vinh; Thwaites, Guy E; Parkhill, Julian; Thomson, Nicholas R; Holt, Kathryn E; Baker, Stephen; (2019) Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microbial genomics, 5 (2). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000246

Bénard, Angèle HM; Guenou, Etienne; Fookes, Maria; Ateudjieu, Jerome; Kasambara, Watipaso; Siever, Matthew; Rebaudet, Stanislas; Boncy, Jacques; Adrien, Paul; Piarroux, Renaud; +3 more... Sack, David A; Thomson, Nicholas; Debes, Amanda K; (2019) Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper. PLOS NEGLECTED TROPICAL DISEASES, 13 (5). e0007330-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0007330

Dorman, Matthew J; Domman, Daryl; Uddin, Muhammad Ikhtear; Sharmin, Salma; Afrad, Mokibul Hassan; Begum, Yasmin Ara; Qadri, Firdausi; Thomson, Nicholas R; (2019) High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139. SCIENTIFIC REPORTS, 9 (1). 5865-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-41883-x

Dorman, Matthew J; Kane, Leanne; Domman, Daryl; Turnbull, Jake D; Cormie, Claire; Fazal, Mohammed-Abbas; Goulding, David A; Russell, Julie E; Alexander, Sarah; Thomson, Nicholas R; (2019) The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One. Proceedings. Biological sciences, 286 (1900). 20182025-. ISSN 0962-8452 DOI: https://doi.org/10.1098/rspb.2018.2025

Heinz, Eva; Brindle, Richard; Morgan-McCalla, Andrina; Peters, Keisha; Thomson, Nicholas R; (2019) Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors. MICROBIAL GENOMICS, 5 (5). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000266

Mellor, Kate C; Petrovska, Liljana; Thomson, Nicholas R; Harris, Kate; Reid, Stuart WJ; Mather, Alison E; (2019) Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals. FRONTIERS IN MICROBIOLOGY, 10 (APR). 708-. ISSN 1664-302X DOI: https://doi.org/10.3389/fmicb.2019.00708

Mercer, Catherine H; Clifton, Soazig; Prior, Gillian; Aldridge, Robert W; Bonell, Chris; Copas, Andrew J; Field, Nigel; Gibbs, Jo; Macdowall, Wendy; Mitchell, Kirstin R; +4 more... Tanton, Clare; Thomson, Nick; Unemo, Magnus; Sonnenberg, Pam; (2019) Collecting and exploiting data to understand a nation's sexual health needs: Implications for the British National Surveys of Sexual Attitudes and Lifestyles (Natsal). Sexually Transmitted Infections, 95 (3). pp. 159-161. ISSN 1368-4973 DOI: https://doi.org/10.1136/sextrans-2018-053571

Mitchell, Holly D; Mikhail, Amy FW; Painset, Anaïs; Dallman, Timothy J; Jenkins, Claire; Thomson, Nicholas R; Field, Nigel; Hughes, Gwenda; (2019) Use of whole-genome sequencing to identify clusters of Shigella flexneri associated with sexual transmission in men who have sex with men in England: a validation study using linked behavioural data. Microbial genomics, 5 (11). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000311

Musicha, Patrick; Msefula, Chisomo L; Mather, Alison E; Chaguza, Chrispin; Cain, Amy K; Peno, Chikondi; Kallonen, Teemu; Khonga, Margaret; Denis, Brigitte; Gray, Katherine J; +4 more... Heyderman, Robert S; Thomson, Nicholas R; Everett, Dean B; Feasey, Nicholas A; (2019) Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. Journal of Antimicrobial Chemotherapy, 74 (5). pp. 1223-1232. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz032

Weill, François-Xavier; Domman, Daryl; Njamkepo, Elisabeth; Almesbahi, Abdullrahman A; Naji, Mona; Nasher, Samar Saeed; Rakesh, Ankur; Assiri, Abdullah M; Sharma, Naresh Chand; Kariuki, Samuel; +19 more... Pourshafie, Mohammad Reza; Rauzier, Jean; Abubakar, Abdinasir; Carter, Jane Y; Wamala, Joseph F; Seguin, Caroline; Bouchier, Christiane; Malliavin, Thérèse; Bakhshi, Bita; Abulmaali, Hayder HN; Kumar, Dhirendra; Njoroge, Samuel M; Malik, Mamunur Rahman; Kiiru, John; Luquero, Francisco J; Azman, Andrew S; Ramamurthy, Thandavarayan; Thomson, Nicholas R; Quilici, Marie-Laure; (2019) Genomic insights into the 2016-2017 cholera epidemic in Yemen. Nature, 565 (7738). pp. 230-233. ISSN 0028-0836 DOI: https://doi.org/10.1038/s41586-018-0818-3

Baker, Kate S; Dallman, Timothy J; Field, Nigel; Childs, Tristan; Mitchell, Holly; Day, Martin; Weill, François-Xavier; Lefèvre, Sophie; Tourdjman, Mathieu; Hughes, Gwenda; +2 more... Jenkins, Claire; Thomson, Nicholas; (2018) Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species. Nature communications, 9 (1). 1462-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-018-03949-8

Baker, Kate S; Dallman, Timothy J; Field, Nigel; Childs, Tristan; Mitchell, Holly; Day, Martin; Weill, François-Xavier; Lefèvre, Sophie; Tourdjman, Mathieu; Hughes, Gwenda; +2 more... Jenkins, Claire; Thomson, Nicholas; (2018) Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance. Scientific reports, 8 (1). 7389-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-25764-3

Baker, Kate S; Dallman, Timothy J; Thomson, Nicholas R; Jenkins, Claire; (2018) An outbreak of a rare Shiga-toxin-producing Escherichia coli serotype (O117:H7) among men who have sex with men. MICROBIAL GENOMICS, 4 (7). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000181

Baker, Stephen; Thomson, Nicholas; Weill, François-Xavier; Holt, Kathryn E; (2018) Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science, 360 (6390). pp. 733-738. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aar3777

Behar, Adi; Baker, Kate Susan; Bassal, Ravit; Ezernitchi, Analia; Valinsky, Lea; Thomson, Nicholas R; Cohen, Daniel; (2018) Microevolution and Patterns of Transmission of Shigella sonnei within Cyclic Outbreaks Shigellosis, Israel. EMERGING INFECTIOUS DISEASES, 24 (7). pp. 1335-1339. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2407.171313

Cain, Amy K; Boinett, Christine J; Barquist, Lars; Dordel, Janina; Fookes, Maria; Mayho, Matthew; Ellington, Matthew J; Goulding, David; Pickard, Derek; Wick, Ryan R; +3 more... Holt, Kathryn E; Parkhill, Julian; Thomson, Nicholas R; (2018) Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Scientific reports, 8 (1). 9868-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-28199-y

Domman, Daryl; Chowdhury, Fahima; Khan, Ashraful I; Dorman, Matthew J; Mutreja, Ankur; Uddin, Muhammad Ikhtear; Paul, Anik; Begum, Yasmin A; Charles, Richelle C; Calderwood, Stephen B; +6 more... Bhuiyan, Taufiqur R; Harris, Jason B; LaRocque, Regina C; Ryan, Edward T; Qadri, Firdausi; Thomson, Nicholas R; (2018) Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh. Nature genetics, 50 (7). pp. 951-955. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-018-0150-8

Gorrie, Claire L; Mirceta, Mirjana; Wick, Ryan R; Judd, Louise M; Wyres, Kelly L; Thomson, Nicholas R; Strugnell, Richard A; Pratt, Nigel F; Garlick, Jill S; Watson, Kerrie M; +5 more... Hunter, Peter C; McGloughlin, Steve A; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E; (2018) Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital. CLINICAL INFECTIOUS DISEASES, 67 (2). pp. 161-170. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciy027

Horesh, Gal; Harms, Alexander; Fino, Cinzia; Parts, Leopold; Gerdes, Kenn; Heinz, Eva; Thomson, Nicholas Robert; (2018) SLING: a tool to search for linked genes in bacterial datasets. Nucleic acids research, 46 (21). e128-. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gky738

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

Longbottom, David; Sait, Michelle; Livingstone, Morag; Laroucau, Karine; Sachse, Konrad; Harris, Simon R; Thomson, Nicholas R; Seth-Smith, Helena MB; (2018) Genomic evidence that the live Chlamydia abortus vaccine strain 1B is not attenuated and has the potential to cause disease. VACCINE, 36 (25). pp. 3593-3598. ISSN 0264-410X DOI: https://doi.org/10.1016/j.vaccine.2018.05.042

Loraine, Jessica; Heinz, Eva; De Sousa Almeida, Jessica; Milevskyy, Oleksandr; Voravuthikunchai, Supayang P; Srimanote, Potjanee; Kiratisin, Pattarachai; Thomson, Nicholas R; Taylor, Peter W; (2018) Complement Susceptibility in Relation to Genome Sequence of Recent Klebsiella pneumoniae Isolates from Thai Hospitals. mSphere, 3 (6). ISSN 2379-5042 DOI: https://doi.org/10.1128/mSphere.00537-18

Marks, Michael; Fookes, Maria; Wagner, Josef; Ghinai, Rosanna; Sokana, Oliver; Sarkodie, Yaw-Adu; Solomon, Anthony W; Mabey, David CW; Thomson, Nicholas R; (2018) Direct Whole-Genome Sequencing of Cutaneous Strains of Haemophilus ducreyi. Emerging infectious diseases, 24 (4). pp. 786-789. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2404.171726

Mather, Alison E; Phuong, Tu Le Thi; Gao, Yunfeng; Clare, Simon; Mukhopadhyay, Subhankar; Goulding, David A; Hoang, Nhu Tran Do; Tuyen, Ha Thanh; Lan, Nguyen Phu Huong; Thompson, Corinne N; +22 more... Trang, Nguyen Hoang Thu; Carrique-Mas, Juan; Tue, Ngo Tri; Campbell, James I; Rabaa, Maia A; Thanh, Duy Pham; Harcourt, Katherine; Hoa, Ngo Thi; Trung, Nguyen Vinh; Schultsz, Constance; Perron, Gabriel G; Coia, John E; Brown, Derek J; Okoro, Chinyere; Parkhill, Julian; Thomson, Nicholas R; Chau, Nguyen Van Vinh; Thwaites, Guy E; Maskell, Duncan J; Dougan, Gordon; Kenney, Linda J; Baker, Stephen; (2018) New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam. MBIO, 9 (5). ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.01056-18

Moore, Sandra; Dongdem, Anthony Zunuo; Opare, David; Cottavoz, Paul; Fookes, Maria; Sadji, Adodo Yao; Dzotsi, Emmanuel; Dogbe, Michael; Jeddi, Fakhri; Bidjada, Bawimodom; +12 more... Piarroux, Martine; Valentin, Ouyi Tante; Glèlè, Clément Kakaï; Rebaudet, Stanislas; Sow, Amy Gassama; Constantin de Magny, Guillaume; Koivogui, Lamine; Dunoyer, Jessica; Bellet, Francois; Garnotel, Eric; Thomson, Nicholas; Piarroux, Renaud; (2018) Dynamics of cholera epidemics from Benin to Mauritania. PLoS neglected tropical diseases, 12 (4). e0006379-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0006379

Page, Andrew J; Wailan, Alexander; Shao, Yan; Judge, Kim; Dougan, Gordon; Klemm, Elizabeth J; Thomson, Nicholas R; Keane, Jacqueline A; (2018) PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data. MICROBIAL GENOMICS, 4 (3). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000164

Rew, Vanessa; Mook, Piers; Trienekens, Suzan; Baker, Kate S; Dallman, Timothy J; Jenkins, Claire; Crook, Paul D; Thomson, Nicholas R; (2018) Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel. MICROBIAL GENOMICS, 4 (3). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000170

Skilton, Rachel J; Wang, Yibing; O'Neill, Colette; Filardo, Simone; Marsh, Peter; Bénard, Angèle; Thomson, Nicholas R; Ramsey, Kyle H; Clarke, Ian N; (2018) The Chlamydia muridarum plasmid revisited : new insights into growth kinetics. Wellcome open research, 3. 25-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.13905.1

Zhou, Zhemin; Lundstrøm, Inge; Tran-Dien, Alicia; Duchêne, Sebastián; Alikhan, Nabil-Fareed; Sergeant, Martin J; Langridge, Gemma; Fotakis, Anna K; Nair, Satheesh; Stenøien, Hans K; +9 more... Hamre, Stian S; Casjens, Sherwood; Christophersen, Axel; Quince, Christopher; Thomson, Nicholas R; Weill, François-Xavier; Ho, Simon YW; Gilbert, M Thomas P; Achtman, Mark; (2018) Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. CURRENT BIOLOGY, 28 (15). 2420-2428.e10. ISSN 0960-9822 DOI: https://doi.org/10.1016/j.cub.2018.05.058

Baker, KS; Campos, J; Pichel, M; Della Gaspera, A; Duarte-Martínez, F; Campos-Chacón, E; Bolaños-Acuña, HM; Guzmán-Verri, C; Mather, AE; Diaz Velasco, S; +19 more... Zamudio Rojas, ML; Forbester, JL; Connor, TR; Keddy, KH; Smith, AM; López de Delgado, EA; Angiolillo, G; Cuaical, N; Fernández, J; Aguayo, C; Morales Aguilar, M; Valenzuela, C; Morales Medrano, AJ; Sirok, A; Weiler Gustafson, N; Diaz Guevara, PL; Montaño, LA; Perez, E; Thomson, NR; (2017) Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses. Clinical microbiology and infection, 23 (11). pp. 845-853. ISSN 1198-743X DOI: https://doi.org/10.1016/j.cmi.2017.03.021

Bokhari, Habib; Ali, Amjad; Noreen, Zobia; Thomson, Nicholas; Wren, Brendan W; (2017) Galleria mellonella is low cost and suitable surrogate host for studying virulence of human pathogenic Vibrio cholerae. Gene, 628. pp. 1-7. ISSN 0378-1119 DOI: https://doi.org/10.1016/j.gene.2017.07.019

Domman, Daryl; Quilici, Marie-Laure; Dorman, Matthew J; Njamkepo, Elisabeth; Mutreja, Ankur; Mather, Alison E; Delgado, Gabriella; Morales-Espinosa, Rosario; Grimont, Patrick AD; Lizárraga-Partida, Marcial Leonardo; +10 more... Bouchier, Christiane; Aanensen, David M; Kuri-Morales, Pablo; Tarr, Cheryl L; Dougan, Gordon; Parkhill, Julian; Campos, Josefina; Cravioto, Alejandro; Weill, François-Xavier; Thomson, Nicholas R; (2017) Integrated view of Vibrio cholerae in the Americas. Science (New York, NY), 358 (6364). pp. 789-793. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aao2136 Full text not available from this repository.

Esson, Diane; Gupta, Srishti; Bailey, David; Wigley, Paul; Wedley, Amy; Mather, Alison E; Méric, Guillaume; Mastroeni, Pietro; Sheppard, Samuel K; Thomson, Nicholas R; +4 more... Parkhill, Julian; Maskell, Duncan J; Christie, Graham; Grant, Andrew J; (2017) Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape. Microbial pathogenesis, 104. pp. 202-211. ISSN 0882-4010 DOI: https://doi.org/10.1016/j.micpath.2017.01.042

Fookes, Maria C; Hadfield, James; Harris, Simon; Parmar, Surendra; Unemo, Magnus; Jensen, Jørgen S; Thomson, Nicholas R; (2017) Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure. BMC genomics, 18 (1). 993-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-017-4399-6

Garrine, Marcelino; Mandomando, Inácio; Vubil, Delfino; Nhampossa, Tacilta; Acacio, Sozinho; Li, Shan; Paulson, Joseph N; Almeida, Mathieu; Domman, Daryl; Thomson, Nicholas R; +2 more... Alonso, Pedro; Stine, Oscar Colin; (2017) Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing. PLOS NEGLECTED TROPICAL DISEASES, 11 (6). e0005671-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0005671

Gorrie, Claire L; Mirceta, Mirjana; Wick, Ryan R; Edwards, David J; Thomson, Nicholas R; Strugnell, Richard A; Pratt, Nigel F; Garlick, Jill S; Watson, Kerri M; Pilcher, David V; +4 more... McGloughlin, Steve A; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E; (2017) Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients. CLINICAL INFECTIOUS DISEASES, 65 (2). pp. 208-215. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cix270

Gorrie, Claire L; Mirceta, Mirjana; Wick, Ryan R; Judd, Louise M; Wyres, Kelly L; Thomson, Nicholas R; Strugnell, Richard A; Pratt, Nigel F; Garlick, Jill S; Watson, Kerrie M; +5 more... Hunter, Peter C; McGloughlin, Steve A; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E; (2017) Antimicrobial resistant <i>Klebsiella pneumoniae</i> carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital. BiorXiv. DOI: https://doi.org/10.1101/218461

Hadfield, James; Bénard, Angèle; Domman, Daryl; Thomson, Nicholas; (2017) The Hidden Genomics of Chlamydia trachomatis. Current topics in microbiology and immunology, 412. pp. 107-131. ISSN 0070-217X DOI: https://doi.org/10.1007/82_2017_39 Full text not available from this repository.

Hadfield, James; Harris, Simon R; Seth-Smith, Helena MB; Parmar, Surendra; Andersson, Patiyan; Giffard, Philip M; Schachter, Julius; Moncada, Jeanne; Ellison, Louise; Vaulet, María Lucía Gallo; +28 more... Fermepin, Marcelo Rodríguez; Radebe, Frans; Mendoza, Suyapa; Ouburg, Sander; Morré, Servaas A; Sachse, Konrad; Puolakkainen, Mirja; Korhonen, Suvi J; Sonnex, Chris; Wiggins, Rebecca; Jalal, Hamid; Brunelli, Tamara; Casprini, Patrizia; Pitt, Rachel; Ison, Cathy; Savicheva, Alevtina; Shipitsyna, Elena; Hadad, Ronza; Kari, Laszlo; Burton, Matthew J; Mabey, David; Solomon, Anthony W; Lewis, David; Marsh, Peter; Unemo, Magnus; Clarke, Ian N; Parkhill, Julian; Thomson, Nicholas R; (2017) Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion. Genome research, 27 (7). pp. 1220-1229. ISSN 1088-9051 DOI: https://doi.org/10.1101/gr.212647.116

Henson, Sonal P; Boinett, Christine J; Ellington, Matthew J; Kagia, Ngure; Mwarumba, Salim; Nyongesa, Sammy; Mturi, Neema; Kariuki, Samuel; Scott, J Anthony G; Thomson, Nicholas R; +1 more... Morpeth, Susan C; (2017) Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya. International journal of medical microbiology, 307 (7). pp. 422-429. ISSN 1438-4221 DOI: https://doi.org/10.1016/j.ijmm.2017.07.006

Iguchi, Atsushi; von Mentzer, Astrid; Kikuchi, Taisei; Thomson, Nicholas R; (2017) An untypeable enterotoxigenic Escherichia coli represents one of the dominant types causing human disease. MICROBIAL GENOMICS, 3 (9). e000121-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000121

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

Marks, Michael; Fookes, Maria; Wagner, Josef; Butcher, Robert; Ghinai, Rosanna; Sokana, Oliver; Sarkodie, Yaw-Adu; Lukehart, Sheila A; Solomon, Anthony W; Mabey, David CW; +1 more... Thomson, Nicholas; (2017) Diagnostics for Yaws Eradication: Insights From Direct Next-Generation Sequencing of Cutaneous Strains of Treponema pallidum. Clinical infectious diseases, 66 (6). pp. 818-824. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cix892

Musicha, Patrick; Feasey, Nicholas A; Cain, Amy K; Kallonen, Teemu; Chaguza, Chrispin; Peno, Chikondi; Khonga, Margaret; Thompson, Sarah; Gray, Katherine J; Mather, Alison E; +4 more... Heyderman, Robert S; Everett, Dean B; Thomson, Nicholas R; Msefula, Chisomo L; (2017) Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. The Journal of antimicrobial chemotherapy, 72 (6). pp. 1602-1609. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkx058

Oshota, Olusegun; Conway, Max; Fookes, Maria; Schreiber, Fernanda; Chaudhuri, Roy R; Yu, Lu; Morgan, Fiona JE; Clare, Simon; Choudhary, Jyoti; Thomson, Nicholas R; +4 more... Lio, Pietro; Maskell, Duncan J; Mastroeni, Pietro; Grant, Andrew J; (2017) Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice. PloS one, 12 (8). e0181365-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0181365

Page, Andrew J; Wailan, Alexander; Shao, Yan; Judge, Kim; Dougan, Gordon; Klemm, Elizabeth J; Thomson, Nicholas R; Keane, Jacqueline A; (2017) PlasmidTron: assembling the cause of phenotypes from NGS data. BiorXiv. DOI: https://doi.org/10.1101/188920

Pickering, Harry; Teng, Andy; Faal, Nkoyo; Joof, Hassan; Makalo, Pateh; Cassama, Eunice; Nabicassa, Meno; Last, Anna R; Burr, Sarah E; Rowland-Jones, Sarah L; +7 more... Thomson, Nicholas R; Roberts, Chrissy H; Mabey, David CW; Bailey, Robin L; Hayward, Richard D; de la Maza, Luis M; Holland, Martin J; (2017) Genome-wide profiling of humoral immunity and pathogen genes under selection identifies immune evasion tactics of Chlamydia trachomatis during ocular infection. Scientific reports, 7 (1). 9634-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-017-09193-2

Ramírez-Vargas, Gabriel; Quesada-Gómez, Carlos; Acuña-Amador, Luis; López-Ureña, Diana; Murillo, Tatiana; Del Mar Gamboa-Coronado, María; Chaves-Olarte, Esteban; Thomson, Nicholas; Rodríguez-Cavallini, Evelyn; Rodríguez, César; (2017) A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements. Antimicrobial agents and chemotherapy, 61 (4). ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.02054-16

Seth-Smith, HMB; Busó, Leonor Sánchez; Livingstone, M; Sait, M; Harris, SR; Aitchison, KD; Vretou, Evangelia; Siarkou, VI; Laroucau, K; Sachse, K; +2 more... Longbottom, D; Thomson, NR; (2017) European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures. BMC GENOMICS, 18 (1). 344-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-017-3657-y

Seth-Smith, Helena Mb; Galán, Juan C; Goldenberger, Daniel; Lewis, David A; Peuchant, Olivia; Bébéar, Cecile; de Barbeyrac, Bertille; Bénard, Angele; Carter, Ian; Kok, Jen; +6 more... Bruisten, Sylvia M; Versteeg, Bart; Morré, Servaas A; Thomson, Nicholas R; Egli, Adrian; de Vries, Henry Jc; (2017) Concern regarding the alleged spread of hypervirulent lymphogranuloma venereum Chlamydia trachomatis strain in Europe. Euro surveillance, 22 (15). pp. 16-17. ISSN 1025-496X DOI: https://doi.org/10.2807/1560-7917.ES.2017.22.15.30511

Suárez-Esquivel, Marcela; Baker, Kate S; Ruiz-Villalobos, Nazareth; Hernández-Mora, Gabriela; Barquero-Calvo, Elías; González-Barrientos, Rocío; Castillo-Zeledón, Amanda; Jiménez-Rojas, César; Chacón-Díaz, Carlos; Cloeckaert, Axel; +4 more... Chaves-Olarte, Esteban; Thomson, Nicholas R; Moreno, Edgardo; Guzmán-Verri, Caterina; (2017) Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution. GENOME BIOLOGY AND EVOLUTION, 9 (7). pp. 1901-1912. ISSN 1759-6653 DOI: https://doi.org/10.1093/gbe/evx137

Suárez-Esquivel, Marcela; Ruiz-Villalobos, Nazareth; Jiménez-Rojas, César; Barquero-Calvo, Elías; Chacón-Díaz, Carlos; Víquez-Ruiz, Eunice; Rojas-Campos, Norman; Baker, Kate S; Oviedo-Sánchez, Gerardo; Amuy, Ernesto; +4 more... Chaves-Olarte, Esteban; Thomson, Nicholas R; Moreno, Edgardo; Guzmán-Verri, Caterina; (2017) Brucella neotomae Infection in Humans, Costa Rica. EMERGING INFECTIOUS DISEASES, 23 (6). pp. 997-1000. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2306.162018

The, Hao Chung; Florez de Sessions, Paola; Jie, Song; Pham Thanh, Duy; Thompson, Corinne N; Nguyen Ngoc Minh, Chau; Chu, Collins Wenhan; Tran, Tuan-Anh; Thomson, Nicholas R; Thwaites, Guy E; +3 more... Rabaa, Maia A; Hibberd, Martin; Baker, Stephen; (2017) Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. Gut microbes, 9 (1). pp. 38-54. ISSN 1949-0976 DOI: https://doi.org/10.1080/19490976.2017.1361093

Thomas, Christopher M; Thomson, Nicholas R; Cerdeño-Tárraga, Ana M; Brown, Celeste J; Top, Eva M; Frost, Laura S; (2017) Annotation of plasmid genes. PLASMID, 91. pp. 61-67. ISSN 0147-619X DOI: https://doi.org/10.1016/j.plasmid.2017.03.006

Torok, Estee; Brodrick, Hayley; Khokhar, Fahad; Blane, Beth; Polgarova, Petra; Brown, Joanne; Enoch, David; Brown, Nicholas; Summers, Charlotte; Preller, Jacobus; +4 more... Thomson, Nick; Dougan, Gordon; Parkhill, Julian; Peacock, Sharon; (2017) Prospective Surveillance and Rapid Whole-Genome Sequencing Detects Two Unsuspected Outbreaks of Carbapenemase-Producing Klebsiella pneumoniae in a UK Teaching Hospital. Open Forum Infectious Diseases, 4 (suppl_). S43-S44. ISSN 2328-8957 DOI: https://doi.org/10.1093/ofid/ofx162.104

Weill, François-Xavier; Domman, Daryl; Njamkepo, Elisabeth; Tarr, Cheryl; Rauzier, Jean; Fawal, Nizar; Keddy, Karen H; Salje, Henrik; Moore, Sandra; Mukhopadhyay, Asish K; +31 more... Bercion, Raymond; Luquero, Francisco J; Ngandjio, Antoinette; Dosso, Mireille; Monakhova, Elena; Garin, Benoit; Bouchier, Christiane; Pazzani, Carlo; Mutreja, Ankur; Grunow, Roland; Sidikou, Fati; Bonte, Laurence; Breurec, Sébastien; Damian, Maria; Njanpop-Lafourcade, Berthe-Marie; Sapriel, Guillaume; Page, Anne-Laure; Hamze, Monzer; Henkens, Myriam; Chowdhury, Goutam; Mengel, Martin; Koeck, Jean-Louis; Fournier, Jean-Michel; Dougan, Gordon; Grimont, Patrick AD; Parkhill, Julian; Holt, Kathryn E; Piarroux, Renaud; Ramamurthy, Thandavarayan; Quilici, Marie-Laure; Thomson, Nicholas R; (2017) Genomic history of the seventh pandemic of cholera in Africa. Science (New York, NY), 358 (6364). pp. 785-789. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aad5901 Full text not available from this repository.

Yeung, Amy TY; Hale, Christine; Lee, Amy H; Gill, Erin E; Bushell, Wendy; Parry-Smith, David; Goulding, David; Pickard, Derek; Roumeliotis, Theodoros; Choudhary, Jyoti; +4 more... Thomson, Nick; Skarnes, William C; Dougan, Gordon; Hancock, Robert EW; (2017) Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis. NATURE COMMUNICATIONS, 8 (1). 15013-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms15013

Yeung, Amy TY; Hale, Christine; Lee, Amy H; Gill, Erin E; Bushell, Wendy; Parry-Smith, David; Goulding, David; Pickard, Derek; Roumeliotis, Theodoros; Choudhary, Jyoti; +4 more... Thomson, Nick; Skarnes, William C; Dougan, Gordon; Hancock, Robert EW; (2017) Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis. NATURE COMMUNICATIONS, 8. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms15013

Andersson, Patiyan; Harris, Simon R; Smith, Helena MB Seth; Hadfield, James; O'Neill, Colette; Cutcliffe, Lesley T; Douglas, Fiona P; Asche, L Valerie; Mathews, John D; Hutton, Susan I; +5 more... Sarovich, Derek S; Tong, Steven YC; Clarke, Ian N; Thomson, Nicholas R; Giffard, Philip M; (2016) Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages. Nature communications, 7 (1). 10688-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms10688

Baker, Kate S; Dallman, Timothy J; Behar, Adi; Weill, François-Xavier; Gouali, Malika; Sobel, Jeremy; Fookes, Maria; Valinsky, Lea; Gal-Mor, Ohad; Connor, Thomas R; +6 more... Nissan, Israel; Bertrand, Sophie; Parkhill, Julian; Jenkins, Claire; Cohen, Dani; Thomson, Nicholas R; (2016) Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities. EMERGING INFECTIOUS DISEASES, 22 (9). pp. 1545-1553. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2209.151953

Chinen, Isabel; Galas, Marcelo; Tuduri, Ezequiel; Viñas, Maria Rosa; Carbonari, Carolina; Della Gaspera, Anabella; Nápoli, Daniela; Aanensen, David M; Argimón, Silvia; Thomson, Nicholas R; +25 more... Hughes, Darren; Baker, Stephen; Guzmán-Verri, Caterina; Holden, Matthew TG; Abdala, Alejandra M; Alvarez, Lucia P; Alvez, Beatriz; Barros, Rosana; Budall, Shirley; Campano, Constanza; Chamosa, Luciana S; Cheddie, Paul; Cisterna, Daniel; De Belder, Denise; Dropa, Milena; Durand, David; Elena, Alan; Fontecha, Gustavo; Huber, Claudia; Lemos, Ana Paula; Melli, Luciano; Paul, Roxana Elizabeth; Suarez, Lesly; Torres Flores, Julian; Campos, Josefina; (2016) Whole genome sequencing identifies independent outbreaks of Shigellosis in 2010 and 2011 in La Pampa Province, Argentina. BiorXiv. DOI: https://doi.org/10.1101/049940

Chung The, Hao; Rabaa, Maia A; Pham Thanh, Duy; De Lappe, Niall; Cormican, Martin; Valcanis, Mary; Howden, Benjamin P; Wangchuk, Sonam; Bodhidatta, Ladaporn; Mason, Carl J; +12 more... Nguyen Thi Nguyen, To; Vu Thuy, Duong; Thompson, Corinne N; Phu Huong Lan, Nguyen; Voong Vinh, Phat; Ha Thanh, Tuyen; Turner, Paul; Sar, Poda; Thwaites, Guy; Thomson, Nicholas R; Holt, Kathryn E; Baker, Stephen; (2016) South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study. PLoS medicine, 13 (8). e1002055-. ISSN 1549-1277 DOI: https://doi.org/10.1371/journal.pmed.1002055

Connor, Thomas R; Owen, Sian V; Langridge, Gemma; Connell, Steve; Nair, Satheesh; Reuter, Sandra; Dallman, Timothy J; Corander, Jukka; Tabing, Kristine C; Le Hello, Simon; +15 more... Fookes, Maria; Doublet, Benoît; Zhou, Zhemin; Feltwell, Theresa; Ellington, Matthew J; Herrera, Silvia; Gilmour, Matthew; Cloeckaert, Axel; Achtman, Mark; Parkhill, Julian; Wain, John; De Pinna, Elizabeth; Weill, François-Xavier; Peters, Tansy; Thomson, Nick; (2016) What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B. mBio, 7 (4). ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00527-16

Di Pilato, Vincenzo; Chiarelli, Adriana; Boinett, Christine J; Riccobono, Eleonora; Harris, Simon R; D'Andrea, Marco Maria; Thomson, Nicholas R; Rossolini, Gian Maria; Giani, Tommaso; (2016) Complete Genome Sequence of the First KPC-Type Carbapenemase-Positive Proteus mirabilis Strain from a Bloodstream Infection. Genome announcements, 4 (3). ISSN 2169-8287 DOI: https://doi.org/10.1128/genomeA.00607-16

Esson, Diane; Mather, Alison E; Scanlan, Eoin; Gupta, Srishti; de Vries, Stefan PW; Bailey, David; Harris, Simon R; McKinley, Trevelyan J; Méric, Guillaume; Berry, Sophia K; +7 more... Mastroeni, Pietro; Sheppard, Samuel K; Christie, Graham; Thomson, Nicholas R; Parkhill, Julian; Maskell, Duncan J; Grant, Andrew J; (2016) Genomic variations leading to alterations in cell morphology of Campylobacter spp. Scientific reports, 6 (1). 38303-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep38303

Feasey, Nicholas A; Hadfield, James; Keddy, Karen H; Dallman, Timothy J; Jacobs, Jan; Deng, Xiangyu; Wigley, Paul; Barquist, Lars; Langridge, Gemma C; Feltwell, Theresa; +37 more... Harris, Simon R; Mather, Alison E; Fookes, Maria; Aslett, Martin; Msefula, Chisomo; Kariuki, Samuel; Maclennan, Calman A; Onsare, Robert S; Weill, François-Xavier; Le Hello, Simon; Smith, Anthony M; McClelland, Michael; Desai, Prerak; Parry, Christopher M; Cheesbrough, John; French, Neil; Campos, Josefina; Chabalgoity, Jose A; Betancor, Laura; Hopkins, Katie L; Nair, Satheesh; Humphrey, Tom J; Lunguya, Octavie; Cogan, Tristan A; Tapia, Milagritos D; Sow, Samba O; Tennant, Sharon M; Bornstein, Kristin; Levine, Myron M; Lacharme-Lora, Lizeth; Everett, Dean B; Kingsley, Robert A; Parkhill, Julian; Heyderman, Robert S; Dougan, Gordon; Gordon, Melita A; Thomson, Nicholas R; (2016) Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. Nature genetics, 48 (10). pp. 1211-1217. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.3644

Follador, Rainer; Heinz, Eva; Wyres, Kelly L; Ellington, Matthew J; Kowarik, Michael; Holt, Kathryn E; Thomson, Nicholas R; (2016) The diversity of Klebsiella pneumoniae surface polysaccharides. Microbial genomics, 2 (8). e000073-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000073

Jones-Dias, Daniela; Clemente, Lurdes; Egas, Conceição; Froufe, Hugo; Sampaio, Daniel A; Vieira, Luís; Fookes, Maria; Thomson, Nicholas R; Manageiro, Vera; Caniça, Manuela; (2016) Salmonella Enteritidis Isolate Harboring Multiple Efflux Pumps and Pathogenicity Factors, Shows Absence of O Antigen Polymerase Gene. FRONTIERS IN MICROBIOLOGY, 7 (AUG). 1130-. ISSN 1664-302X DOI: https://doi.org/10.3389/fmicb.2016.01130

Karlsson, Stefan L; Thomson, Nicholas; Mutreja, Ankur; Connor, Thomas; Sur, Dipika; Ali, Mohammad; Clemens, John; Dougan, Gordon; Holmgren, Jan; Lebens, Michael; (2016) Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process. PLoS neglected tropical diseases, 10 (10). e0005044-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0005044

Labbate, Maurizio; Orata, Fabini D; Petty, Nicola K; Jayatilleke, Nathasha D; King, William L; Kirchberger, Paul C; Allen, Chris; Mann, Gulay; Mutreja, Ankur; Thomson, Nicholas R; +2 more... Boucher, Yan; Charles, Ian G; (2016) A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules. SCIENTIFIC REPORTS, 6 (1). 36891-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep36891

Mather, Alison E; Lawson, Becki; de Pinna, Elizabeth; Wigley, Paul; Parkhill, Julian; Thomson, Nicholas R; Page, Andrew J; Holmes, Mark A; Paterson, Gavin K; (2016) Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 82 (22). pp. 6728-6735. ISSN 0099-2240 DOI: https://doi.org/10.1128/AEM.01660-16

McNally, Alan; Thomson, Nicholas R; Reuter, Sandra; Wren, Brendan W; (2016) 'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution. Nature reviews Microbiology, 14 (3). pp. 177-190. ISSN 1740-1526 DOI: https://doi.org/10.1038/nrmicro.2015.29 Full text not available from this repository.

Njamkepo, Elisabeth; Fawal, Nizar; Tran-Dien, Alicia; Hawkey, Jane; Strockbine, Nancy; Jenkins, Claire; Talukder, Kaisar A; Bercion, Raymond; Kuleshov, Konstantin; Kolínská, Renáta; +62 more... Russell, Julie E; Kaftyreva, Lidia; Accou-Demartin, Marie; Karas, Andreas; Vandenberg, Olivier; Mather, Alison E; Mason, Carl J; Page, Andrew J; Ramamurthy, Thandavarayan; Bizet, Chantal; Gamian, Andrzej; Carle, Isabelle; Sow, Amy Gassama; Bouchier, Christiane; Wester, Astrid Louise; Lejay-Collin, Monique; Fonkoua, Marie-Christine; Le Hello, Simon; Blaser, Martin J; Jernberg, Cecilia; Ruckly, Corinne; Mérens, Audrey; Page, Anne-Laure; Aslett, Martin; Roggentin, Peter; Fruth, Angelika; Denamur, Erick; Venkatesan, Malabi; Bercovier, Hervé; Bodhidatta, Ladaporn; Chiou, Chien-Shun; Clermont, Dominique; Colonna, Bianca; Egorova, Svetlana; Pazhani, Gururaja P; Ezernitchi, Analia V; Guigon, Ghislaine; Harris, Simon R; Izumiya, Hidemasa; Korzeniowska-Kowal, Agnieszka; Lutyńska, Anna; Gouali, Malika; Grimont, Francine; Langendorf, Céline; Marejková, Monika; Peterson, Lorea AM; Perez-Perez, Guillermo; Ngandjio, Antoinette; Podkolzin, Alexander; Souche, Erika; Makarova, Mariia; Shipulin, German A; Ye, Changyun; Žemličková, Helena; Herpay, Mária; Grimont, Patrick AD; Parkhill, Julian; Sansonetti, Philippe; Holt, Kathryn E; Brisse, Sylvain; Thomson, Nicholas R; Weill, François-Xavier; (2016) Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nature microbiology, 1 (4). 16027-. ISSN 2058-5276 DOI: https://doi.org/10.1038/nmicrobiol.2016.27 Full text not available from this repository.

Pollard, Dominic J; Young, Joanna C; Covarelli, Valentina; Herrera-León, Silvia; Connor, Thomas R; Fookes, Maria; Walker, Danielle; Echeita, Aurora; Thomson, Nicholas R; Berger, Cedric N; +1 more... Frankel, Gad; (2016) The Type III Secretion System Effector SeoC of Salmonella enterica subsp. salamae and S. enterica subsp. arizonae ADP-Ribosylates Src and Inhibits Opsonophagocytosis. Infection and immunity, 84 (12). pp. 3618-3628. ISSN 0019-9567 DOI: https://doi.org/10.1128/IAI.00704-16

Skipp, Paul JS; Hughes, Chris; McKenna, Thérèse; Edwards, Richard; Langridge, James; Thomson, Nicholas R; Clarke, Ian N; (2016) Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis. PLOS ONE, 11 (2). e0149011-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0149011

Suárez-Esquivel, Marcela; Ruiz-Villalobos, Nazareth; Castillo-Zeledón, Amanda; Jiménez-Rojas, César; Roop Ii, R Martin; Comerci, Diego J; Barquero-Calvo, Elías; Chacón-Díaz, Carlos; Caswell, Clayton C; Baker, Kate S; +6 more... Chaves-Olarte, Esteban; Thomson, Nicholas R; Moreno, Edgardo; Letesson, Jean J; De Bolle, Xavier; Guzmán-Verri, Caterina; (2016) Brucella abortus Strain 2308 Wisconsin Genome: Importance of the Definition of Reference Strains. Frontiers in microbiology, 7 (SEP). 1557-. ISSN 1664-302X DOI: https://doi.org/10.3389/fmicb.2016.01557

The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen; (2016) The genomic signatures of Shigella evolution, adaptation and geographical spread. Nature reviews Microbiology, 14 (4). pp. 235-250. ISSN 1740-1526 DOI: https://doi.org/10.1038/nrmicro.2016.10 Full text not available from this repository.

Wyres, Kelly L; Wick, Ryan R; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R; Holt, Kathryn E; (2016) Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial genomics, 2 (12). e000102-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000102

Wyres, Kelly L; Wick, Ryan R; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R; Holt, Kathryn E; (2016) Identification of<i>Klebsiella</i>capsule synthesis loci from whole genome data. BioRxiv. DOI: https://doi.org/10.1101/071415

Baker, Kate S; Burnett, Edward; McGregor, Hannah; Deheer-Graham, Ana; Boinett, Christine; Langridge, Gemma C; Wailan, Alexander M; Cain, Amy K; Thomson, Nicholas R; Russell, Julie E; +1 more... Parkhill, Julian; (2015) The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource. Genome medicine, 7 (1). 97-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-015-0222-7

Baker, Kate S; Dallman, Timothy J; Ashton, Philip M; Day, Martin; Hughes, Gwenda; Crook, Paul D; Gilbart, Victoria L; Zittermann, Sandra; Allen, Vanessa G; Howden, Benjamin P; +19 more... Tomita, Takehiro; Valcanis, Mary; Harris, Simon R; Connor, Thomas R; Sintchenko, Vitali; Howard, Peter; Brown, Jeremy D; Petty, Nicola K; Gouali, Malika; Thanh, Duy Pham; Keddy, Karen H; Smith, Anthony M; Talukder, Kaisar A; Faruque, Shah M; Parkhill, Julian; Baker, Stephen; Weill, François-Xavier; Jenkins, Claire; Thomson, Nicholas R; (2015) Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. The Lancet infectious diseases, 15 (8). pp. 913-921. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(15)00002-X Full text not available from this repository.

Bentley, Stephen; Thomson, Nicholas; (2015) 70th Anniversary Collection for the Microbiology Society: Microbial Genomics. MICROBIAL GENOMICS, 1 (6). e000040-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000040

Chowdhury, Fahima; Mather, Alison E; Begum, Yasmin Ara; Asaduzzaman, Muhammad; Baby, Nabilah; Sharmin, Salma; Biswas, Rajib; Uddin, Muhammad Ikhtear; LaRocque, Regina C; Harris, Jason B; +5 more... Calderwood, Stephen B; Ryan, Edward T; Clemens, John D; Thomson, Nicholas R; Qadri, Firdausi; (2015) Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014. PLoS neglected tropical diseases, 9 (11). e0004183-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0004183

Chung The, Hao; Karkey, Abhilasha; Pham Thanh, Duy; Boinett, Christine J; Cain, Amy K; Ellington, Matthew; Baker, Kate S; Dongol, Sabina; Thompson, Corinne; Harris, Simon R; +11 more... Jombart, Thibaut; Le Thi Phuong, Tu; Tran Do Hoang, Nhu; Ha Thanh, Tuyen; Shretha, Shrijana; Joshi, Suchita; Basnyat, Buddha; Thwaites, Guy; Thomson, Nicholas R; Rabaa, Maia A; Baker, Stephen; (2015) A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO molecular medicine, 7 (3). pp. 227-239. ISSN 1757-4676 DOI: https://doi.org/10.15252/emmm.201404767

Chung The, Hao; Rabaa, Maia A; Thanh, Duy Pham; Ruekit, Sirigade; Wangchuk, Sonam; Dorji, Tshering; Tshering, Kinzang Pem; Nguyen, To Nguyen Thi; Vinh, Phat Voong; Thanh, Tuyen Ha; +9 more... Minh, Chau Nguyen Ngoc; Turner, Paul; Sar, Poda; Thwaites, Guy; Holt, Kathryn E; Thomson, Nicholas R; Bodhidatta, Ladaporn; Jeffries Mason, Carl; Baker, Stephen; (2015) Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan. Microbial genomics, 1 (6). e000042-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000042

Connor, Thomas R; Barker, Clare R; Baker, Kate S; Weill, François-Xavier; Talukder, Kaisar Ali; Smith, Anthony M; Baker, Stephen; Gouali, Malika; Pham Thanh, Duy; Jahan Azmi, Ishrat; +10 more... Dias da Silveira, Wanderley; Semmler, Torsten; Wieler, Lothar H; Jenkins, Claire; Cravioto, Alejandro; Faruque, Shah M; Parkhill, Julian; Wook Kim, Dong; Keddy, Karen H; Thomson, Nicholas R; (2015) Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife, 4 (AUGUST). e07335-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.07335

Hjerde, Erik; Karlsen, Christian; Sørum, Henning; Parkhill, Julian; Willassen, Nils Peder; Thomson, Nicholas R; (2015) Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis. BMC GENOMICS, 16 (1). 447-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-015-1669-z

Holt, Kathryn E; Wertheim, Heiman; Zadoks, Ruth N; Baker, Stephen; Whitehouse, Chris A; Dance, David; Jenney, Adam; Connor, Thomas R; Hsu, Li Yang; Severin, Juliëtte; +18 more... Brisse, Sylvain; Cao, Hanwei; Wilksch, Jonathan; Gorrie, Claire; Schultz, Mark B; Edwards, David J; Nguyen, Kinh Van; Nguyen, Trung Vu; Dao, Trinh Tuyet; Mensink, Martijn; Minh, Vien Le; Nhu, Nguyen Thi Khanh; Schultsz, Constance; Kuntaman, Kuntaman; Newton, Paul N; Moore, Catrin E; Strugnell, Richard A; Thomson, Nicholas R; (2015) Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proceedings of the National Academy of Sciences of the United States of America, 112 (27). E3574-E3581. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1501049112 Full text not available from this repository.

Le, Vien; Nhu, Nguyen Thi Khanh; Cerdeno-Tarraga, Ana; Campbell, James I; Tuyen, Ha Thanh; Nhu, Tran Do Hoang; Tam, Pham Thi Thanh; Schultsz, Constance; Thwaites, Guy; Thomson, Nicholas R; +1 more... Baker, Stephen; (2015) Genetic characterization of three qnrS1-harbouring multidrug-resistance plasmids and qnrS1-containing transposons circulating in Ho Chi Minh City, Vietnam. Journal of medical microbiology, 64 (8). pp. 869-878. ISSN 0022-2615 DOI: https://doi.org/10.1099/jmm.0.000100

Miwanda, Berthe; Moore, Sandra; Muyembe, Jean-Jacques; Nguefack-Tsague, Georges; Kabangwa, Ickel Kakongo; Ndjakani, Daniel Yassa; Mutreja, Ankur; Thomson, Nicholas; Thefenne, Helene; Garnotel, Eric; +4 more... Tshapenda, Gaston; Kakongo, Denis Kandolo; Kalambayi, Guy; Piarroux, Renaud; (2015) Antimicrobial Drug Resistance of Vibrio cholerae, Democratic Republic of the Congo. Emerging infectious diseases, 21 (5). pp. 847-851. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2105.141233

Moore, Sandra; Miwanda, Berthe; Sadji, Adodo Yao; Thefenne, Hélène; Jeddi, Fakhri; Rebaudet, Stanislas; de Boeck, Hilde; Bidjada, Bawimodom; Depina, Jean-Jacques; Bompangue, Didier; +9 more... Abedi, Aaron Aruna; Koivogui, Lamine; Keita, Sakoba; Garnotel, Eric; Plisnier, Pierre-Denis; Ruimy, Raymond; Thomson, Nicholas; Muyembe, Jean-Jacques; Piarroux, Renaud; (2015) Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates. PLoS neglected tropical diseases, 9 (6). e0003817-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0003817

Njoroge, Samuel M; Boinett, Christine J; Madé, Laure F; Ouko, Tom T; Fèvre, Eric M; Thomson, Nicholas R; Kariuki, Samuel; (2015) A putative, novel coli surface antigen 8B (CS8B) of enterotoxigenic Escherichia coli. PATHOGENS AND DISEASE, 73 (7). ftv047-ftv047. ISSN 2049-632X DOI: https://doi.org/10.1093/femspd/ftv047

Olasz, Ferenc; Nagy, Tibor; Szabó, Móni; Kiss, János; Szmolka, Ama; Barta, Endre; van Tonder, Andries; Thomson, Nicholas; Barrow, Paul; Nagy, Béla; (2015) Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Infantis Strains from Healthy Broiler Chicks in Hungary and in the United Kingdom. Genome announcements, 3 (1). ISSN 2169-8287 DOI: https://doi.org/10.1128/genomeA.01468-14

Rapa, Rita A; Islam, Atiqul; Monahan, Leigh G; Mutreja, Ankur; Thomson, Nicholas; Charles, Ian G; Stokes, Harold W; Labbate, Maurizio; (2015) A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage. ENVIRONMENTAL MICROBIOLOGY, 17 (4). pp. 1090-1102. ISSN 1462-2912 DOI: https://doi.org/10.1111/1462-2920.12512

Reuter, Sandra; Corander, Jukka; de Been, Mark; Harris, Simon; Cheng, Lu; Hall, Miquette; Thomson, Nicholas R; McNally, Alan; (2015) Directional gene flow and ecological separation in Yersinia enterocolitica. Microbial genomics, 1 (3). e000030-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000030

Vehkala, Minna; Shubin, Mikhail; Connor, Thomas R; Thomson, Nicholas R; Corander, Jukka; (2015) Novel R pipeline for analyzing Biolog Phenotypic MicroArray data. PloS one, 10 (3). e0118392-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0118392

Wong, Vanessa K; Baker, Stephen; Pickard, Derek J; Parkhill, Julian; Page, Andrew J; Feasey, Nicholas A; Kingsley, Robert A; Thomson, Nicholas R; Keane, Jacqueline A; Weill, François-Xavier; +64 more... Edwards, David J; Hawkey, Jane; Harris, Simon R; Mather, Alison E; Cain, Amy K; Hadfield, James; Hart, Peter J; Thieu, Nga Tran Vu; Klemm, Elizabeth J; Glinos, Dafni A; Breiman, Robert F; Watson, Conall H; Kariuki, Samuel; Gordon, Melita A; Heyderman, Robert S; Okoro, Chinyere; Jacobs, Jan; Lunguya, Octavie; Edmunds, W John; Msefula, Chisomo; Chabalgoity, Jose A; Kama, Mike; Jenkins, Kylie; Dutta, Shanta; Marks, Florian; Campos, Josefina; Thompson, Corinne; Obaro, Stephen; MacLennan, Calman A; Dolecek, Christiane; Keddy, Karen H; Smith, Anthony M; Parry, Christopher M; Karkey, Abhilasha; Mulholland, E Kim; Campbell, James I; Dongol, Sabina; Basnyat, Buddha; Dufour, Muriel; Bandaranayake, Don; Naseri, Take Toleafoa; Singh, Shalini Pravin; Hatta, Mochammad; Newton, Paul; Onsare, Robert S; Isaia, Lupeoletalalei; Dance, David; Davong, Viengmon; Thwaites, Guy; Wijedoru, Lalith; Crump, John A; De Pinna, Elizabeth; Nair, Satheesh; Nilles, Eric J; Thanh, Duy Pham; Turner, Paul; Soeng, Sona; Valcanis, Mary; Powling, Joan; Dimovski, Karolina; Hogg, Geoff; Farrar, Jeremy; Holt, Kathryn E; Dougan, Gordon; (2015) Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nature genetics, 47 (6). pp. 632-639. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.3281 Full text not available from this repository.

Abd El Ghany, Moataz; Chander, Jagadish; Mutreja, Ankur; Rashid, Mamoon; Hill-Cawthorne, Grant A; Ali, Shahjahan; Naeem, Raeece; Thomson, Nicholas R; Dougan, Gordon; Pain, Arnab; (2014) The population structure of Vibrio cholerae from the Chandigarh Region of Northern India. PLOS NEGLECTED TROPICAL DISEASES, 8 (7). e2981-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0002981

Ashton, Philip M; Baker, Kate S; Gentle, Amy; Wooldridge, David J; Thomson, Nicholas R; Dallman, Timothy J; Jenkins, Claire; (2014) Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence. GUT PATHOGENS, 6 (1). 7-. ISSN 1757-4749 DOI: https://doi.org/10.1186/1757-4749-6-7

Baker, Kate S; Mather, Alison E; McGregor, Hannah; Coupland, Paul; Langridge, Gemma C; Day, Martin; Deheer-Graham, Ana; Parkhill, Julian; Russell, Julie E; Thomson, Nicholas R; (2014) The extant World War 1 dysentery bacillus NCTC1: a genomic analysis. Lancet, 384 (9955). pp. 1691-1697. ISSN 0140-6736 DOI: https://doi.org/10.1016/S0140-6736(14)61789-X

Iguchi, Atsushi; Iyoda, Sunao; Kikuchi, Taisei; Ogura, Yoshitoshi; Katsura, Keisuke; Ohnishi, Makoto; Hayashi, Tetsuya; Thomson, Nicholas R; (2014) A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster. DNA research, 22 (1). pp. 101-107. ISSN 1340-2838 DOI: https://doi.org/10.1093/dnares/dsu043

Iguchi, Atsushi; Nagaya, Yutaka; Pradel, Elizabeth; Ooka, Tadasuke; Ogura, Yoshitoshi; Katsura, Keisuke; Kurokawa, Ken; Oshima, Kenshiro; Hattori, Masahira; Parkhill, Julian; +6 more... Sebaihia, Mohamed; Coulthurst, Sarah J; Gotoh, Naomasa; Thomson, Nicholas R; Ewbank, Jonathan J; Hayashi, Tetsuya; (2014) Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen. Genome biology and evolution, 6 (8). pp. 2096-2110. ISSN 1759-6653 DOI: https://doi.org/10.1093/gbe/evu160

Lindgreen, Stinus; Umu, Sinan Uğur; Lai, Alicia Sook-Wei; Eldai, Hisham; Liu, Wenting; McGimpsey, Stephanie; Wheeler, Nicole E; Biggs, Patrick J; Thomson, Nick R; Barquist, Lars; +2 more... Poole, Anthony M; Gardner, Paul P; (2014) Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLOS COMPUTATIONAL BIOLOGY, 10 (10). e1003907-. ISSN 1553-7358 DOI: https://doi.org/10.1371/journal.pcbi.1003907

Mather, Alison E; Baker, Kate S; McGregor, Hannah; Coupland, Paul; Mather, Pamela L; Deheer-Graham, Ana; Parkhill, Julian; Bracegirdle, Philippa; Russell, Julie E; Thomson, Nicholas R; (2014) Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection. Lancet, 384 (9955). 1720-. ISSN 0140-6736 DOI: https://doi.org/10.1016/S0140-6736(14)61790-6 Full text not available from this repository.

Reuter, Sandra; Connor, Thomas R; Barquist, Lars; Walker, Danielle; Feltwell, Theresa; Harris, Simon R; Fookes, Maria; Hall, Miquette E; Petty, Nicola K; Fuchs, Thilo M; +23 more... Corander, Jukka; Dufour, Muriel; Ringwood, Tamara; Savin, Cyril; Bouchier, Christiane; Martin, Liliane; Miettinen, Minna; Shubin, Mikhail; Riehm, Julia M; Laukkanen-Ninios, Riikka; Sihvonen, Leila M; Siitonen, Anja; Skurnik, Mikael; Falcão, Juliana Pfrimer; Fukushima, Hiroshi; Scholz, Holger C; Prentice, Michael B; Wren, Brendan W; Parkhill, Julian; Carniel, Elisabeth; Achtman, Mark; McNally, Alan; Thomson, Nicholas R; (2014) Parallel independent evolution of pathogenicity within the genus Yersinia. Proceedings of the National Academy of Sciences of the United States of America, 111 (18). pp. 6768-6773. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1317161111 Full text not available from this repository.

Sigar, Ira M; Schripsema, Justin H; Wang, Yibing; Clarke, Ian N; Cutcliffe, Lesley T; Seth-Smith, Helena MB; Thomson, Nicholas R; Bjartling, Carina; Unemo, Magnus; Persson, Kenneth; +1 more... Ramsey, Kyle H; (2014) Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model. PATHOGENS AND DISEASE, 70 (1). pp. 61-69. ISSN 2049-632X DOI: https://doi.org/10.1111/2049-632X.12086

Vergara-Irigaray, Marta; Fookes, Maria C; Thomson, Nicholas R; Tang, Christoph M; (2014) RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. BMC GENOMICS, 15 (1). 438-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-15-438

Bronowski, Christina; Fookes, Maria C; Gilderthorp, Ruth; Ashelford, Kevin E; Harris, Simon R; Phiri, Amos; Hall, Neil; Gordon, Melita A; Wain, John; Hart, Charles A; +3 more... Wigley, Paul; Thomson, Nicholas R; Winstanley, Craig; (2013) Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi. PLOS NEGLECTED TROPICAL DISEASES, 7 (11). e2557-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0002557

Davies, Mark R; Broadbent, Sarah E; Harris, Simon R; Thomson, Nicholas R; van der Woude, Marjan W; (2013) Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity. PLoS genetics, 9 (6). e1003568-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1003568

Holt, Kathryn E; Thieu Nga, Tran Vu; Thanh, Duy Pham; Vinh, Ha; Kim, Dong Wook; Vu Tra, My Phan; Campbell, James I; Hoang, Nguyen Van Minh; Vinh, Nguyen Thanh; Minh, Pham Van; +20 more... Thuy, Cao Thu; Nga, Tran Thi Thu; Thompson, Corinne; Dung, Tran Thi Ngoc; Nhu, Nguyen Thi Khanh; Vinh, Phat Voong; Tuyet, Pham Thi Ngoc; Phuc, Hoang Le; Lien, Nguyen Thi Nam; Phu, Bui Duc; Ai, Nguyen Thi Thuy; Tien, Nguyen Manh; Dong, Nguyen; Parry, Christopher M; Hien, Tran Tinh; Farrar, Jeremy J; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R; Baker, Stephen; (2013) Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proceedings of the National Academy of Sciences of the United States of America, 110 (43). pp. 17522-17527. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1308632110 Full text not available from this repository.

Hopkinson, Nicholas; Wallis, Colin; Higgins, Bernard; Gaduzo, Stephen; Sherrington, Rebecca; Keilty, Sarah; Stern, Myra; Britton, John; Bush, Andrew; Moxham, John; +438 more... Sylvester, Karl; Griffiths, Valerie; Sutherland, Tim; Crossingham, Iain; Raju, Raghu; Spencer, Charlotte; Safavi, Shahideh; Deegan, Paul; Seymour, John; Hickman, Katherine; Hughes, John; Wieboldt, Jason; Shaheen, Fizah; Peedell, Clive; Mackenzie, Nesta; Nicholl, David; Jolley, Caroline; Crooks, Gillian; Crooks, Gillian; Dow, Claire; Deveson, Pete; Bintcliffe, Oliver; Gray, Barry; Kumar, Sanjay; Haney, Sarah; Docherty, Marianne; Thomas, Angela; Chua, Felix; Dwarakanath, Akshay; Summers, Geoffrey; Prowse, Keith; Lytton, Stephen; Ong, Yee Ean; Graves, Jennifer; Banerjee, Tushar; English, Peter; Leonard, Andrew; Brunet, Martin; Chaudhry, Nauman; Ketchell, Robert Ian; Cummings, Natalie; Lebus, Jenny; Sharp, Charles; Meadows, Chris; Harle, Amelie; Stewart, Tara; Parry, Diane; Templeton-Wright, Suzanne; Moore-Gillon, John; Stratford- Martin, James; Saini, Sarvesh; Matusiewicz, Simon; Merritt, Simon; Dowson, Lee; Satkunam, Karnan; Hodgson, Luke; Suh, Eui-Sik; Durrington, Hannah; Browne, Emma; Walters, Nicola; Steier, Joerg; Barry, Simon; Griffiths, Mark; Hart, Nicholas; Nikolic, Marko; Berry, Matthew; Thomas, Ajit; Miller, Joy; McNicholl, Diarmuid; Marsden, Paul; Warwick, Geoffrey; Barr, Laura; Adeboyeku, David; Mohd Noh, Mohd Shahrin; Griffiths, Paul; Davies, Lisa; Quint, Jennifer; Lyall, Rebecca; Shribman, Jonathan; Collins, Andrea; Goldman, Jon; Bloch, Susannah; Gill, Alison; Man, William; Christopher, Anne; Yasso, Razouqi; Rajhan, Ashwin; Shrikrishna, Dinesh; Moore, Caroline; Absalom, Gareth; Booton, Richard; Fowler, Robert William; Mackinlay, Carolyn; Sapey, Elizabeth; Lock, Sara; Walker, Paul; Jha, Akhilesh; Satia, Imran; Bradley, Bethia; Mustfa, Naveed; Haqqee, Raana; Thomas, Matt; Patel, Anant; Redington, Anthony; Pillai, Anilkumar; Keaney, Niall; Fowler, Stephen; Lowe, Lesley; Brennan, Amanda; Morrison, Douglas; Murray, Clare; Hankinson, Jenny; Dutta, P; Maddocks, Matthew; Pengo, Martino; Curtis, Katrina; Rafferty, Gerrard; Hutchinson, John; Whitfield, Ruth; Turner, Steve; Breen, Ronan; Naveed, Shams-un-nisa; Goode, Chris; Esterbrook, Georgina; Ahmed, Liju; Walker, Woolf; Ford, David; Connett, Gary; Davidson, Philip; Elston, Will; Stanton, Andrew; Morgan, David; Myerson, James; Maxwell, David; Harrris, Ann; Parmar, Sonia; Houghton, Catherine; Winter, Robert; Puthucheary, Zudin; Thomson, Fiona; Sturney, Sharon; Harvey, John; Haslam, Patricia L; Patel, Irem; Jennings, David; Range, Simon; Mallia-Milanes, Brendan; Collett, Anne; Tate, Paul; Russell, Richard; Feary, Johanna; O'Driscoll, Ronan; Eaden, James; Round, Jonathan; Sharkey, Emma; Montgomery, Mary; Vaughan, Sophie; Scheele, Kate; Lithgow, Anna; Partridge, Samuel; Chavasse, Richard; Restrick, Louise; Agrawal, Sanjay; Abdallah, Said; Lacy-Colson, Amruta; Adams, Nick; Mitchell, Sally; Haja Mydin, Helmy; Ward, Ann; Denniston, Sarah; Steel, Mark; Ghosh, Dipansu; Connellan, Stephen; Rigge, Lucy; Williams, Ruth; Grove, Alison; Anwar, Sadia; Dobson, Lee; Hosker, Harold; Stableforth, David; Greening, Neil; Howell, Tim; Casswell, Georgina; Davies, Sarah; Tunnicliffe, Georgia; Mitchelmore, Philip; Phitidis, Elpida; Robinson, Louise; Prowse, Keith; Bafadhel, Mona; Robinson, Grace; Boland, Alison; Lipman, Marc; Bourke, Stephen; Kaul, Sundeep; Cowie, Calvin; Forrest, Ian; Starren, Elizabeth; Burke, Hannah; Furness, John; Bhowmik, Angshu; Everett, Caroline; Seaton, Douglas; Holmes, Steve; Doe, Simon; Parker, Samuel; Graham, Annika; Paterson, Ian; Maqsood, Usman; Ohri, Chandra; Iles, Peter; Kemp, Samuel; Iftikhar, Ahsan; Carlin, Chris; Fletcher, Tim; Emerson, Peter; Beasley, Victoria; Ramsay, Michelle; Buttery, Robert; Mungall, Sarah; Crooks, Stephen; Ridyard, John; Ross, David; Guadagno, Alison; Holden, Emma; Coutts, Ian; Cullen, Kathy; O'Connor, Sally; Barker, Jack; Sloper, Katherine; Watson, John; Smith, Peter; Anderson, Paul; Brown, Louise; Nyman, Cyril; Milburn, Heather; Clive, Amelia; Serlin, Matthew; Bolton, Charlotte; Fuld, Jonathan; Powell, Helen; Dayer, Mark; Woolhouse, Ian; Georgiadi, Adamantia; Leonard, Helen; Dodd, James; Campbell, Ian; Ruiz, Gary; Zurek, Andrew; Paton, James Y; Malin, Adam; Wood, Fraser; Hynes, Gareth; Connell, David; Spencer, David; Brown, Sarah; Smith, David; Cooper, David; O'Kane, Cecilia; Hicks, Alex; Creagh-Brown, Ben; Lordan, James; Nickol, Annabel; Primhak, Robert; Fleming, Louise; Powrie, Duncan; Brown, Joanna; Zoumot, Zaid; Elkin, Sarah; Szram, Joanna; Scaffardi, Anthony; Marshall, Robert; Macdonald, Ian; Lightbody, Darren; Farmer, Ray; Wheatley, Iain; Radnan, Paul; Lane, Ian; Booth, Andrew; Tilbrook, Sean; Capstick, Toby; Hewitt, Lee; McHugh, Martin; Nelson, Christopher; Wilson, Patrick; Padmanaban, Vijay; White, John; Davison, John; O'Callaghan, Una; Hodson, Matthew; Edwards, John; Campbell, Colin; Ward, Simon; Wooler, Edwina; Ringrose, Elizabeth; Bridges, Diana; Matthew Hodson; John Edwards; Colin Campbell; Simon Ward; Edwina Wooler; Elizabeth Ringrose; Diana Bridges; Rosalind Backham; Kim Randall; Tracey Mathieson; Long, Alex; Parkes, Marilyn; Clarke, Sarah; Allen, Bev; Connelly, Carol; Forster, Georgia; Hoadley, Jacky; Martin, Katharine; Barnham, Kate; Khan, Katie; Munday, Maureen; Edwards, Catherine; O'Hara, Doreen; Turner, Sally; Pieri-Davies, Sue; Ford, Kate; Daniels, Tracey; Wright, Joanne; Towns, Rebecca; Fern, Karen; Butcher, Jane; Burgin, Karen; Winter, Barbara; Freeman, Debbie; Olive, Sandra; Gray, Linda; Pye, Kathy; Roots, Debbie; Cox, Nicola; Davies, Carol-Anne; Wicker, Jacquelyne; Hilton, Kay; Lloyd, Jananee; MacBean, Vicky; Wood, Marion; Kowal, Julia; Downs, Janis; Ryan, Helen; Guyatt, Fran; Nicoll, Debby; Lyons, Elizabeth; Narasimhan, Divya; Rodman, Anne; Walmsley, Sandy; Newey, Alison; Buxton, Maria; Dewar, Maria; Cooper, Angela; Reilly, Jacqui; Lloyd, Julie; Macmillan, Alison Bennett; Roots, Debbie; Olley, Amy; Voase, Nia; Martin, Sarah; McCarvill, Iona; Christensen, Anne; Agate, Rowan; Heslop, Karen; Timlett, Amber; Hailes, Karen; Davey, Claire; Pawulska, Barbara; Lane, Amber; Ioakim, Shona; Hough, Alexandra; Treharne, Jo; Jones, Helen; Winter-Burke, Alice; Miller, Lauren; Connolly, Bronwen; Bingham, Lyn; Fraser, Una; Bott, Julia; Johnston, Carol; Graham, Alison; Curry, Denise; Sumner, Helen; Costello, Carol Ann; Bartoszewicz, Charlotte; Badman, Ros; Williamson, Kathryn; Taylor, Amy; Purcell, Helen; Barnett, Emma; Molloy, Alanna; Crawfurd, Laura; Collins, Nicola; Monaghan, Valerie; Mir, Misbah; Lord, Victoria; Stocks, Janet; Edwards, Adrian; Greenhalgh, Trish; Lenney, Warren; McKee, Martin; McAuley, Danny; Majeed, Azeem; Cookson, John; Baker, Emma; Janes, Sam; Wedzicha, Wisia; Lomas Dean, David; Harrison, Brian; Davison, Tony; Calverley, Peter; Wilson, Robert; Stockley, Robert; Ayres, Jon; Gibson, John; Simpson, John; Burge, Sherwood; Warner, John; Lenney, Warren; Thomson, Neil; Davies, Peter; Woodcock, Ashley; Woodhead, Mark; Spiro, Stephen; Ormerod, Lawrence; Bothamley, Graham; Partridge, Martyn; Shields, Michael; Montgomery, Hugh; Simonds, Anita; Barnes, Peter; Durham, Stephen; Malone, Sarah; Arabnia, Gilda; Olivier, Sharon; Gardiner, Karen; Edwards, Sheila; (2013) Children must be protected from the tobacco industry's marketing tactics. BMJ (Clinical research ed), 347 (dec09 ). f7358-. ISSN 0959-8138 DOI: https://doi.org/10.1136/bmj.f7358

Kiiru, John; Mutreja, Ankur; Mohamed, Ahmed Abade; Kimani, Racheal W; Mwituria, Joyce; Sanaya, Robert Onsare; Muyodi, Jane; Revathi, Gunturu; Parkhill, Julian; Thomson, Nicholas; +2 more... Dougan, Gordon; Kariuki, Samuel; (2013) A study on the geophylogeny of clinical and environmental Vibrio cholerae in Kenya. PLOS ONE, 8 (9). e74829-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0074829

Kingsley, Robert A; Kay, Sally; Connor, Thomas; Barquist, Lars; Sait, Leanne; Holt, Kathryn E; Sivaraman, Karthi; Wileman, Thomas; Goulding, David; Clare, Simon; +10 more... Hale, Christine; Seshasayee, Aswin; Harris, Simon; Thomson, Nicholas R; Gardner, Paul; Rabsch, Wolfgang; Wigley, Paul; Humphrey, Tom; Parkhill, Julian; Dougan, Gordon; (2013) Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. MBIO, 4 (5). e00565-e00513. ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00565-13

Mather, AE; Reid, SWJ; Maskell, DJ; Parkhill, J; Fookes, MC; Harris, SR; Brown, DJ; Coia, JE; Mulvey, MR; Gilmour, MW; +11 more... Petrovska, L; de Pinna, E; Kuroda, M; Akiba, M; Izumiya, H; Connor, TR; Suchard, MA; Lemey, P; Mellor, DJ; Haydon, DT; Thomson, NR; (2013) Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science (New York, NY), 341 (6153). pp. 1514-1517. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.1240578 Full text not available from this repository.

Seth-Smith, Helena MB; Harris, Simon R; Skilton, Rachel J; Radebe, Frans M; Golparian, Daniel; Shipitsyna, Elena; Duy, Pham Thanh; Scott, Paul; Cutcliffe, Lesley T; O'Neill, Colette; +11 more... Parmar, Surendra; Pitt, Rachel; Baker, Stephen; Ison, Catherine A; Marsh, Peter; Jalal, Hamid; Lewis, David A; Unemo, Magnus; Clarke, Ian N; Parkhill, Julian; Thomson, Nicholas R; (2013) Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture. Genome research, 23 (5). pp. 855-866. ISSN 1088-9051 DOI: https://doi.org/10.1101/gr.150037.112 Full text not available from this repository.

Harris, Simon R; Clarke, Ian N; Seth-Smith, Helena MB; Solomon, Anthony W; Cutcliffe, Lesley T; Marsh, Peter; Skilton, Rachel J; Holland, Martin J; Mabey, David; Peeling, Rosanna W; +14 more... Lewis, David A; Spratt, Brian G; Unemo, Magnus; Persson, Kenneth; Bjartling, Carina; Brunham, Robert; de Vries, Henry JC; Morré, Servaas A; Speksnijder, Arjen; Bébéar, Cécile M; Clerc, Maïté; de Barbeyrac, Bertille; Parkhill, Julian; Thomson, Nicholas R; (2012) Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nature genetics, 44 (4). 413-S1. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.2214

Holt, Kathryn E; Baker, Stephen; Weill, François-Xavier; Holmes, Edward C; Kitchen, Andrew; Yu, Jun; Sangal, Vartul; Brown, Derek J; Coia, John E; Kim, Dong Wook; +8 more... Choi, Seon Young; Kim, Su Hee; da Silveira, Wanderley D; Pickard, Derek J; Farrar, Jeremy J; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R; (2012) Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature genetics, 44 (9). pp. 1056-1059. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.2369

Humphrey, Bruce; Thomson, Nicholas R; Thomas, Christopher M; Brooks, Karen; Sanders, Mandy; Delsol, Anne A; Roe, John M; Bennett, Peter M; Enne, Virve I; (2012) Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids. BMC MICROBIOLOGY, 12 (1). 53-. ISSN 1471-2180 DOI: https://doi.org/10.1186/1471-2180-12-53

Kröger, Carsten; Dillon, Shane C; Cameron, Andrew DS; Papenfort, Kai; Sivasankaran, Sathesh K; Hokamp, Karsten; Chao, Yanjie; Sittka, Alexandra; Hébrard, Magali; Händler, Kristian; +11 more... Colgan, Aoife; Leekitcharoenphon, Pimlapas; Langridge, Gemma C; Lohan, Amanda J; Loftus, Brendan; Lucchini, Sacha; Ussery, David W; Dorman, Charles J; Thomson, Nicholas R; Vogel, Jörg; Hinton, Jay CD; (2012) The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proceedings of the National Academy of Sciences of the United States of America, 109 (20). E1277-E1286. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1201061109 Full text not available from this repository.

Mellata, Melha; Maddux, Jacob T; Nam, Timothy; Thomson, Nicholas; Hauser, Heidi; Stevens, Mark P; Mukhopadhyay, Suman; Sarker, Shameema; Crabbé, Aurélie; Nickerson, Cheryl A; +2 more... Santander, Javier; Curtiss, Roy; (2012) New insights into the bacterial fitness-associated mechanisms revealed by the characterization of large plasmids of an avian pathogenic E. coli. PLOS ONE, 7 (1). e29481-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0029481

Arnvig, Kristine B; Comas, Iñaki; Thomson, Nicholas R; Houghton, Joanna; Boshoff, Helena I; Croucher, Nicholas J; Rose, Graham; Perkins, Timothy T; Parkhill, Julian; Dougan, Gordon; +1 more... Young, Douglas B; (2011) Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLOS PATHOGENS, 7 (11). e1002342-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1002342

Fookes, Maria; Schroeder, Gunnar N; Langridge, Gemma C; Blondel, Carlos J; Mammina, Caterina; Connor, Thomas R; Seth-Smith, Helena; Vernikos, Georgios S; Robinson, Keith S; Sanders, Mandy; +15 more... Petty, Nicola K; Kingsley, Robert A; Bäumler, Andreas J; Nuccio, Sean-Paul; Contreras, Inés; Santiviago, Carlos A; Maskell, Duncan; Barrow, Paul; Humphrey, Tom; Nastasi, Antonino; Roberts, Mark; Frankel, Gad; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R; (2011) Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS pathogens, 7 (8). e1002191-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1002191

Mutreja, Ankur; Kim, Dong Wook; Thomson, Nicholas R; Connor, Thomas R; Lee, Je Hee; Kariuki, Samuel; Croucher, Nicholas J; Choi, Seon Young; Harris, Simon R; Lebens, Michael; +11 more... Niyogi, Swapan Kumar; Kim, Eun Jin; Ramamurthy, T; Chun, Jongsik; Wood, James LN; Clemens, John D; Czerkinsky, Cecil; Nair, G Balakrish; Holmgren, Jan; Parkhill, Julian; Dougan, Gordon; (2011) Evidence for several waves of global transmission in the seventh cholera pandemic. Nature, 477 (7365). pp. 462-465. ISSN 0028-0836 DOI: https://doi.org/10.1038/nature10392 Full text not available from this repository.

Petty, Nicola K; Feltwell, Theresa; Pickard, Derek; Clare, Simon; Toribio, Ana L; Fookes, Maria; Roberts, Kevin; Monson, Rita; Nair, Satheesh; Kingsley, Robert A; +18 more... Bulgin, Richard; Wiles, Siouxsie; Goulding, David; Keane, Thomas; Corton, Craig; Lennard, Nicola; Harris, David; Willey, David; Rance, Richard; Yu, Lu; Choudhary, Jyoti S; Churcher, Carol; Quail, Michael A; Parkhill, Julian; Frankel, Gad; Dougan, Gordon; Salmond, George PC; Thomson, Nicholas R; (2011) Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux. PLoS pathogens, 7 (4). e1002018-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1002018

Chaudhuri, Roy R; Sebaihia, Mohammed; Hobman, Jon L; Webber, Mark A; Leyton, Denisse L; Goldberg, Martin D; Cunningham, Adam F; Scott-Tucker, Anthony; Ferguson, Paul R; Thomas, Christopher M; +10 more... Frankel, Gad; Tang, Christoph M; Dudley, Edward G; Roberts, Ian S; Rasko, David A; Pallen, Mark J; Parkhill, Julian; Nataro, James P; Thomson, Nicholas R; Henderson, Ian R; (2010) Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. PLOS ONE, 5 (1). e8801-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0008801

Morelli, Giovanna; Song, Yajun; Mazzoni, Camila J; Eppinger, Mark; Roumagnac, Philippe; Wagner, David M; Feldkamp, Mirjam; Kusecek, Barica; Vogler, Amy J; Li, Yanjun; +14 more... Cui, Yujun; Thomson, Nicholas R; Jombart, Thibaut; Leblois, Raphael; Lichtner, Peter; Rahalison, Lila; Petersen, Jeannine M; Balloux, Francois; Keim, Paul; Wirth, Thierry; Ravel, Jacques; Yang, Ruifu; Carniel, Elisabeth; Achtman, Mark; (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature genetics, 42 (12). pp. 1140-1143. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.705

Nguyen, Nhu Thi Khanh; Ha, Vinh; Tran, Nga Vu Thieu; Stabler, Richard; Pham, Duy Thanh; Le, Thi Minh Vien; van Doorn, H Rogier; Cerdeño-Tárraga, Ana; Thomson, Nicholas; Campbell, James; +7 more... Nguyen, Van Minh Hoang; Tran, Thi Thu Nga; Pham, Minh Van; Cao, Thuy Thu; Wren, Brendan; Farrar, Jeremy; Baker, Stephen; (2010) The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam. PLoS neglected tropical diseases, 4 (6). e702-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0000702

Timms, Andrew R; Cambray-Young, Joanna; Scott, Andrew E; Petty, Nicola K; Connerton, Phillippa L; Clarke, Louise; Seeger, Kathy; Quail, Mike; Cummings, Nicola; Maskell, Duncan J; +2 more... Thomson, Nicholas R; Connerton, Ian F; (2010) Evidence for a lineage of virulent bacteriophages that target Campylobacter. BMC GENOMICS, 11 (1). 214-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-11-214

Betancor, Laura; Yim, Lucia; Fookes, Maria; Martinez, Araci; Thomson, Nicholas R; Ivens, Alasdair; Peters, Sarah; Bryant, Clare; Algorta, Gabriela; Kariuki, Samuel; +4 more... Schelotto, Felipe; Maskell, Duncan; Dougan, Gordon; Chabalgoity, Jose A; (2009) Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates. BMC MICROBIOLOGY, 9 (1). 237-. ISSN 1471-2180 DOI: https://doi.org/10.1186/1471-2180-9-237

Carver, Tim; Thomson, Nick; Bleasby, Alan; Berriman, Matthew; Parkhill, Julian; (2009) DNAPlotter: circular and linear interactive genome visualization. BIOINFORMATICS, 25 (1). pp. 119-120. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btn578

Croucher, Nicholas J; Fookes, Maria C; Perkins, Timothy T; Turner, Daniel J; Marguerat, Samuel B; Keane, Thomas; Quail, Michael A; He, Miao; Assefa, Sammey; Bähler, Jürg; +5 more... Kingsley, Robert A; Parkhill, Julian; Bentley, Stephen D; Dougan, Gordon; Thomson, Nicholas R; (2009) A simple method for directional transcriptome sequencing using Illumina technology. NUCLEIC ACIDS RESEARCH, 37 (22). e148-. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkp811

Holt, Kathryn E; Thomson, Nicholas R; Wain, John; Langridge, Gemma C; Hasan, Rumina; Bhutta, Zulfiqar A; Quail, Michael A; Norbertczak, Halina; Walker, Danielle; Simmonds, Mark; +5 more... White, Brian; Bason, Nathalie; Mungall, Karen; Dougan, Gordon; Parkhill, Julian; (2009) Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. BMC GENOMICS, 10 (1). 36-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-10-36

Jackson, Andrew P; Thomas, Gavin H; Parkhill, Julian; Thomson, Nicholas R; (2009) Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC GENOMICS, 10 (1). 584-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-10-584

Perkins, Timothy T; Kingsley, Robert A; Fookes, Maria C; Gardner, Paul P; James, Keith D; Yu, Lu; Assefa, Samuel A; He, Miao; Croucher, Nicholas J; Pickard, Derek J; +5 more... Maskell, Duncan J; Parkhill, Julian; Choudhary, Jyoti; Thomson, Nicholas R; Dougan, Gordon; (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLOS GENETICS, 5 (7). e1000569-. ISSN 1553-7404 DOI: https://doi.org/10.1371/journal.pgen.1000569

Petty, Nicola K; Bulgin, Richard; Crepin, Valerie F; Cerdeño-Tárraga, Ana M; Schroeder, Gunnar N; Quail, Michael A; Lennard, Nicola; Corton, Craig; Barron, Andrew; Clark, Louise; +5 more... Toribio, Ana L; Parkhill, Julian; Dougan, Gordon; Frankel, Gad; Thomson, Nicholas R; (2009) The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli. Journal of bacteriology, 192 (2). pp. 525-538. ISSN 0021-9193 DOI: https://doi.org/10.1128/JB.01144-09

Seth-Smith, Helena MB; Harris, Simon R; Persson, Kenneth; Marsh, Pete; Barron, Andrew; Bignell, Alexandra; Bjartling, Carina; Clark, Louise; Cutcliffe, Lesley T; Lambden, Paul R; +10 more... Lennard, Nicola; Lockey, Sarah J; Quail, Michael A; Salim, Omar; Skilton, Rachel J; Wang, Yibing; Holland, Martin J; Parkhill, Julian; Thomson, Nicholas R; Clarke, Ian N; (2009) Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain. BMC genomics, 10 (1). 239-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-10-239

Silby, Mark W; Cerdeño-Tárraga, Ana M; Vernikos, Georgios S; Giddens, Stephen R; Jackson, Robert W; Preston, Gail M; Zhang, Xue-Xian; Moon, Christina D; Gehrig, Stefanie M; Godfrey, Scott AC; +24 more... Knight, Christopher G; Malone, Jacob G; Robinson, Zena; Spiers, Andrew J; Harris, Simon; Challis, Gregory L; Yaxley, Alice M; Harris, David; Seeger, Kathy; Murphy, Lee; Rutter, Simon; Squares, Rob; Quail, Michael A; Saunders, Elizabeth; Mavromatis, Konstantinos; Brettin, Thomas S; Bentley, Stephen D; Hothersall, Joanne; Stephens, Elton; Thomas, Christopher M; Parkhill, Julian; Levy, Stuart B; Rainey, Paul B; Thomson, Nicholas R; (2009) Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome biology, 10 (5). R51-. ISSN 1465-6906 DOI: https://doi.org/10.1186/gb-2009-10-5-r51

Clayton, Debra J; Bowen, Alison J; Hulme, Scott D; Buckley, Anthony M; Deacon, Victoria L; Thomson, Nicholas R; Barrow, Paul A; Morgan, Eirwen; Jones, Michael A; Watson, Michael; +1 more... Stevens, Mark P; (2008) Analysis of the role of 13 major fimbrial subunits in colonisation of the chicken intestines by Salmonella enterica serovar Enteritidis reveals a role for a novel locus. BMC MICROBIOLOGY, 8 (1). 228-. ISSN 1471-2180 DOI: https://doi.org/10.1186/1471-2180-8-228

Crossman, Lisa C; Gould, Virginia C; Dow, J Maxwell; Vernikos, Georgios S; Okazaki, Aki; Sebaihia, Mohammed; Saunders, David; Arrowsmith, Claire; Carver, Tim; Peters, Nicholas; +15 more... Adlem, Ellen; Kerhornou, Arnaud; Lord, Angela; Murphy, Lee; Seeger, Katharine; Squares, Robert; Rutter, Simon; Quail, Michael A; Rajandream, Mari-Adele; Harris, David; Churcher, Carol; Bentley, Stephen D; Parkhill, Julian; Thomson, Nicholas R; Avison, Matthew B; (2008) The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. GENOME BIOLOGY, 9 (4). R74-. ISSN 1474-760X DOI: https://doi.org/10.1186/gb-2008-9-4-r74

Hjerde, Erik; Lorentzen, Marit Sjo; Holden, Matthew Tg; Seeger, Kathy; Paulsen, Steinar; Bason, Nathalie; Churcher, Carol; Harris, David; Norbertczak, Halina; Quail, Michael A; +5 more... Sanders, Suzanne; Thurston, Scott; Parkhill, Julian; Willassen, Nils Peder; Thomson, Nicholas R; (2008) The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay. BMC GENOMICS, 9 (1). 616-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-9-616

Klasson, Lisa; Walker, Thomas; Sebaihia, Mohammed; Sanders, Mandy J; Quail, Michael A; Lord, Angela; Sanders, Susanne; Earl, Julie; O'Neill, Scott L; Thomson, Nicholas; +2 more... Sinkins, Steven P; Parkhill, Julian; (2008) Genome evolution of Wolbachia strain wPip from the Culex pipiens group. Molecular biology and evolution, 25 (9). pp. 1877-1887. ISSN 0737-4038 DOI: https://doi.org/10.1093/molbev/msn133

Sebaihia, Mohammed; Peck, Michael W; Minton, Nigel P; Thomson, Nicholas R; Holden, Matthew TG; Mitchell, Wilfrid J; Carter, Andrew T; Bentley, Stephen D; Mason, David R; Crossman, Lisa; +24 more... Paul, Catherine J; Ivens, Alasdair; Wells-Bennik, Marjon HJ; Davis, Ian J; Cerdeño-Tárraga, Ana M; Churcher, Carol; Quail, Michael A; Chillingworth, Tracey; Feltwell, Theresa; Fraser, Audrey; Goodhead, Ian; Hance, Zahra; Jagels, Kay; Larke, Natasha; Maddison, Mark; Moule, Sharon; Mungall, Karen; Norbertczak, Halina; Rabbinowitsch, Ester; Sanders, Mandy; Simmonds, Mark; White, Brian; Whithead, Sally; Parkhill, Julian; (2007) Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome research, 17 (7). pp. 1082-1092. ISSN 1088-9051 DOI: https://doi.org/10.1101/gr.6282807 Full text not available from this repository.

Thomson, Nicholas R; Howard, Sarah; Wren, Brendan W; Prentice, Michael B; (2007) Comparative genome analyses of the pathogenic Yersiniae based on the genome sequence of Yersinia enterocolitica strain 8081. Advances in experimental medicine and biology, 603. pp. 2-16. ISSN 0065-2598 DOI: https://doi.org/10.1007/978-0-387-72124-8_1 Full text not available from this repository.

Vernikos, Georgios S; Thomson, Nicholas R; Parkhill, Julian; (2007) Genetic flux over time in the Salmonella lineage. GENOME BIOLOGY, 8 (6). R100-. ISSN 1465-6906 DOI: https://doi.org/10.1186/gb-2007-8-6-r100

Walker, Thomas; Klasson, Lisa; Sebaihia, Mohammed; Sanders, Mandy J; Thomson, Nicholas R; Parkhill, Julian; Sinkins, Steven P; (2007) Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group. BMC biology, 5 (1). 39-. ISSN 1741-7007 DOI: https://doi.org/10.1186/1741-7007-5-39

Riley, Monica; Abe, Takashi; Arnaud, Martha B; Berlyn, Mary KB; Blattner, Frederick R; Chaudhuri, Roy R; Glasner, Jeremy D; Horiuchi, Takashi; Keseler, Ingrid M; Kosuge, Takehide; +9 more... Mori, Hirotada; Perna, Nicole T; Plunkett, Guy; Rudd, Kenneth E; Serres, Margrethe H; Thomas, Gavin H; Thomson, Nicholas R; Wishart, David; Wanner, Barry L; (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. NUCLEIC ACIDS RESEARCH, 34 (1). pp. 1-9. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkj405

Sebaihia, Mohammed; Wren, Brendan W; Mullany, Peter; Fairweather, Neil F; Minton, Nigel; Stabler, Richard; Thomson, Nicholas R; Roberts, Adam P; Cerdeño-Tárraga, Ana M; Wang, Hongmei; +29 more... Holden, Matthew TG; Wright, Anne; Churcher, Carol; Quail, Michael A; Baker, Stephen; Bason, Nathalie; Brooks, Karen; Chillingworth, Tracey; Cronin, Ann; Davis, Paul; Dowd, Linda; Fraser, Audrey; Feltwell, Theresa; Hance, Zahra; Holroyd, Simon; Jagels, Kay; Moule, Sharon; Mungall, Karen; Price, Claire; Rabbinowitsch, Ester; Sharp, Sarah; Simmonds, Mark; Stevens, Kim; Unwin, Louise; Whithead, Sally; Dupuy, Bruno; Dougan, Gordon; Barrell, Bart; Parkhill, Julian; (2006) The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nature genetics, 38 (7). pp. 779-786. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng1830 Full text not available from this repository.

Thomson, Nicholas R; Howard, Sarah; Wren, Brendan W; Holden, Matthew TG; Crossman, Lisa; Challis, Gregory L; Churcher, Carol; Mungall, Karen; Brooks, Karen; Chillingworth, Tracey; +12 more... Feltwell, Theresa; Abdellah, Zahra; Hauser, Heidi; Jagels, Kay; Maddison, Mark; Moule, Sharon; Sanders, Mandy; Whitehead, Sally; Quail, Michael A; Dougan, Gordon; Parkhill, Julian; Prentice, Michael B; (2006) The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS genetics, 2 (12). e206-. ISSN 1553-7404 https://researchonline.lshtm.ac.uk/id/eprint/19591

Thomson, Nicholas R; Howard, Sarah; Wren, Brendan W; Holden, Matthew TG; Crossman, Lisa; Challis, Gregory L; Churcher, Carol; Mungall, Karen; Brooks, Karen; Chillingworth, Tracey; +12 more... Feltwell, Theresa; Abdellah, Zahra; Hauser, Heidi; Jagels, Kay; Maddison, Mark; Moule, Sharon; Sanders, Mandy; Whitehead, Sally; Quail, Michael A; Dougan, Gordon; Parkhill, Julian; Prentice, Michael B; (2006) The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS genetics, 2 (12). e206-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.0020206

Young, J Peter W; Crossman, Lisa C; Johnston, Andrew WB; Thomson, Nicholas R; Ghazoui, Zara F; Hull, Katherine H; Wexler, Margaret; Curson, Andrew RJ; Todd, Jonathan D; Poole, Philip S; +22 more... Mauchline, Tim H; East, Alison K; Quail, Michael A; Churcher, Carol; Arrowsmith, Claire; Cherevach, Inna; Chillingworth, Tracey; Clarke, Kay; Cronin, Ann; Davis, Paul; Fraser, Audrey; Hance, Zahra; Hauser, Heidi; Jagels, Kay; Moule, Sharon; Mungall, Karen; Norbertczak, Halina; Rabbinowitsch, Ester; Sanders, Mandy; Simmonds, Mark; Whitehead, Sally; Parkhill, Julian; (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. GENOME BIOLOGY, 7 (4). R34-. ISSN 1474-760X DOI: https://doi.org/10.1186/gb-2006-7-4-r34

Holden, Matthew TG; Titball, Richard W; Peacock, Sharon J; Cerdeño-Tárraga, Ana M; Atkins, Timothy; Crossman, Lisa C; Pitt, Tyrone; Churcher, Carol; Mungall, Karen; Bentley, Stephen D; +38 more... Sebaihia, Mohammed; Thomson, Nicholas R; Bason, Nathalie; Beacham, Ifor R; Brooks, Karen; Brown, Katherine A; Brown, Nat F; Challis, Greg L; Cherevach, Inna; Chillingworth, Tracy; Cronin, Ann; Crossett, Ben; Davis, Paul; DeShazer, David; Feltwell, Theresa; Fraser, Audrey; Hance, Zahra; Hauser, Heidi; Holroyd, Simon; Jagels, Kay; Keith, Karen E; Maddison, Mark; Moule, Sharon; Price, Claire; Quail, Michael A; Rabbinowitsch, Ester; Rutherford, Kim; Sanders, Mandy; Simmonds, Mark; Songsivilai, Sirirurg; Stevens, Kim; Tumapa, Sarinna; Vesaratchavest, Monkgol; Whitehead, Sally; Yeats, Corin; Barrell, Bart G; Oyston, Petra CF; Parkhill, Julian; (2004) Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proceedings of the National Academy of Sciences of the United States of America, 101 (39). pp. 14240-14245. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.0403302101 Full text not available from this repository.

Prentice, Michael B; Cuccui, Jon; Thomson, Nick; Parkhill, Julian; Deery, Evelyn; Warren, Martin J; (2003) Cobalamin synthesis in Yersinia enterocolitica 8081. Functional aspects of a putative metabolic island. Advances in experimental medicine and biology, 529. pp. 43-46. ISSN 0065-2598 DOI: https://doi.org/10.1007/0-306-48416-1_8 Full text not available from this repository.

Bentley, SD; Chater, KF; Cerdeño-Tárraga, A-M; Challis, GL; Thomson, NR; James, KD; Harris, DE; Quail, MA; Kieser, H; Harper, D; +33 more... Bateman, A; Brown, S; Chandra, G; Chen, CW; Collins, M; Cronin, A; Fraser, A; Goble, A; Hidalgo, J; Hornsby, T; Howarth, S; Huang, C-H; Kieser, T; Larke, L; Murphy, L; Oliver, K; O'Neil, S; Rabbinowitsch, E; Rajandream, M-A; Rutherford, K; Rutter, S; Seeger, K; Saunders, D; Sharp, S; Squares, R; Squares, S; Taylor, K; Warren, T; Wietzorrek, A; Woodward, J; Barrell, BG; Parkhill, J; Hopwood, DA; (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature, 417 (6885). pp. 141-147. ISSN 0028-0836 DOI: https://doi.org/10.1038/417141a Full text not available from this repository.

Parkhill, J; Wren, BW; Thomson, NR; Titball, RW; Holden, MT; Prentice, MB; Sebaihia, M; James, KD; Churcher, C; Mungall, KL; +25 more... Baker, S; Basham, D; Bentley, SD; Brooks, K; Cerdeño-Tárraga, AM; Chillingworth, T; Cronin, A; Davies, RM; Davis, P; Dougan, G; Feltwell, T; Hamlin, N; Holroyd, S; Jagels, K; Karlyshev, AV; Leather, S; Moule, S; Oyston, PC; Quail, M; Rutherford, K; Simmonds, M; Skelton, J; Stevens, K; Whitehead, S; Barrell, BG; (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature, 413 (6855). pp. 523-527. ISSN 0028-0836 DOI: https://doi.org/10.1038/35097083