Dyson, Zoe A; Ashton, Philip M; Khanam, Farhana; Chunga Chirambo, Angeziwa; Shakya, Mila; Meiring, James E; Tonks, Susan; Karkey, Abhilasha; Msefula, Chisomo; Clemens, John D; +11 more... Dunstan, Sarah J; Baker, Stephen; Dougan, Gordon; Pitzer, Virginia E; Basnyat, Buddha; Qadri, Firdausi; Heyderman, Robert S; Gordon, Melita A; Pollard, Andrew J; Holt, Kathryn E; STRATAA Study Group; (2024) Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. The Lancet microbe, 5 (8). 100841-. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(24)00047-8

Carey, Megan E; Dyson, Zoe A; Argimón, Silvia; Cerdeira, Louise; Yeats, Corin; Aanensen, David; Mboowa, Gerald; Baker, Stephen; Tessema, Sofonias K; Smith, Anthony M; +2 more... Okeke, Iruka N; Holt, Kathryn E; (2023) Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. Open forum infectious diseases, 10 (Suppl ). S38-S46. ISSN 2328-8957 DOI: https://doi.org/10.1093/ofid/ofad044

Carey, Megan E; Dyson, Zoe A; Ingle, Danielle J; Amir, Afreenish; Aworh, Mabel K; Chattaway, Marie Anne; Chew, Ka Lip; Crump, John A; Feasey, Nicholas A; Howden, Benjamin P; +105 more... Keddy, Karen H; Maes, Mailis; Parry, Christopher M; Van Puyvelde, Sandra; Webb, Hattie E; Afolayan, Ayorinde Oluwatobiloba; Alexander, Anna P; Anandan, Shalini; Andrews, Jason R; Ashton, Philip M; Basnyat, Buddha; Bavdekar, Ashish; Bogoch, Isaac I; Clemens, John D; da Silva, Kesia Esther; De, Anuradha; de Ligt, Joep; Diaz Guevara, Paula Lucia; Dolecek, Christiane; Dutta, Shanta; Ehlers, Marthie M; Francois Watkins, Louise; Garrett, Denise O; Godbole, Gauri; Gordon, Melita A; Greenhill, Andrew R; Griffin, Chelsey; Gupta, Madhu; Hendriksen, Rene S; Heyderman, Robert S; Hooda, Yogesh; Hormazabal, Juan Carlos; Ikhimiukor, Odion O; Iqbal, Junaid; Jacob, Jobin John; Jenkins, Claire; Jinka, Dasaratha Ramaiah; John, Jacob; Kang, Gagandeep; Kanteh, Abdoulie; Kapil, Arti; Karkey, Abhilasha; Kariuki, Samuel; Kingsley, Robert A; Koshy, Roshine Mary; Lauer, AC; Levine, Myron M; Lingegowda, Ravikumar Kadahalli; Luby, Stephen P; Mackenzie, Grant Austin; Mashe, Tapfumanei; Msefula, Chisomo; Mutreja, Ankur; Nagaraj, Geetha; Nagaraj, Savitha; Nair, Satheesh; Naseri, Take K; Nimarota-Brown, Susana; Njamkepo, Elisabeth; Okeke, Iruka N; Perumal, Sulochana Putli Bai; Pollard, Andrew J; Pragasam, Agila Kumari; Qadri, Firdausi; Qamar, Farah N; Rahman, Sadia Isfat Ara; Rambocus, Savitra Devi; Rasko, David A; Ray, Pallab; Robins-Browne, Roy; Rongsen-Chandola, Temsunaro; Rutanga, Jean Pierre; Saha, Samir K; Saha, Senjuti; Saigal, Karnika; Sajib, Mohammad Saiful Islam; Seidman, Jessica C; Shakya, Jivan; Shamanna, Varun; Shastri, Jayanthi; Shrestha, Rajeev; Sia, Sonia; Sikorski, Michael J; Singh, Ashita; Smith, Anthony M; Tagg, Kaitlin A; Tamrakar, Dipesh; Tanmoy, Arif Mohammed; Thomas, Maria; Thomas, Mathew S; Thomsen, Robert; Thomson, Nicholas R; Tupua, Siaosi; Vaidya, Krista; Valcanis, Mary; Veeraraghavan, Balaji; Weill, François-Xavier; Wright, Jackie; Dougan, Gordon; Argimón, Silvia; Keane, Jacqueline A; Aanensen, David M; Baker, Stephen; Holt, Kathryn E; Global Typhoid Genomics Consortium Group Authorship; (2023) Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife, 12. e85867-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.85867

Miles, Sydney L; Torraca, Vincenzo; Dyson, Zoe A; López-Jiménez, Ana Teresa; Foster-Nyarko, Ebenezer; Lobato-Márquez, Damián; Jenkins, Claire; Holt, Kathryn E; Mostowy, Serge; (2023) Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive Escherichia coli. mBio, 14 (4). e0088223-. ISSN 2150-7511 DOI: https://doi.org/10.1128/mbio.00882-23

Pereira-Dias, Joana; Taneja, Neelam; Mahindroo, Jaspreet; Maheshwari, Geeti; Patel, Padma J; Thu, Trang Nguyen Hoang; Keane, Jacqui; Dyson, Zoe A; Baker, Stephen; Mylona, Elli; (2023) The genomic characterization of Salmonella Paratyphi A from an outbreak of enteric fever in Vadodara, India. Microbial genomics, 9 (1). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000914

Dyson, Zoe Anne; Malau, Elisheba; Horwood, Paul F; Ford, Rebecca; Siba, Valentine; Yoannes, Mition; Pomat, William; Passey, Megan; Judd, Louise M; Ingle, Danielle J; +4 more... Williamson, Deborah A; Dougan, Gordon; Greenhill, Andrew R; Holt, Kathryn E; (2022) Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials. PLoS Neglected Tropical Diseases, 16 (3). e0010306-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0010306

Khokhar, Fahad; Pickard, Derek; Dyson, Zoe; Iqbal, Junaid; Pragasam, Agila; John, Jobin Jacob; Veeraraghavan, Balaji; Qamar, Farah; Dougan, Gordon; MacQueen, Hilary; +3 more... Rigas, Sushila; Holmes, Mark; Mutreja, Ankur; (2022) Multiplex PCR assay to detect high risk lineages of Salmonella Typhi and Paratyphi A. PLoS One, 17 (7). e0267805-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0267805

Maes, Mailis; Sikorski, Michael J; Carey, Megan E; Higginson, Ellen E; Dyson, Zoe A; Fernandez, Alda; Araya, Pamela; Tennant, Sharon M; Baker, Stephen; Lagos, Rosanna; +3 more... Hormazábal, Juan Carlos; Levine, Myron M; Dougan, Gordon; (2022) Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016. PLoS neglected tropical diseases, 16 (6). e0010178-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0010178

Tanmoy, Arif M; Hooda, Yogesh; Sajib, Mohammad SI; da Silva, Kesia E; Iqbal, Junaid; Qamar, Farah N; Luby, Stephen P; Dougan, Gordon; Dyson, Zoe A; Baker, Stephen; +4 more... Garrett, Denise O; Andrews, Jason R; Saha, Samir K; Saha, Senjuti; (2022) Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity. Nature communications, 13 (1). 7912-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-022-35587-6

da Silva, Kesia Esther; Tanmoy, Arif Mohammad; Pragasam, Agila Kumari; Iqbal, Junaid; Sajib, Mohammad Saiful Islam; Mutreja, Ankur; Veeraraghavan, Balaji; Tamrakar, Dipesh; Qamar, Farah Naz; Dougan, Gordon; +18 more... Bogoch, Isaac; Seidman, Jessica C; Shakya, Jivan; Vaidya, Krista; Carey, Megan E; Shrestha, Rajeev; Irfan, Seema; Baker, Stephen; Luby, Steve P; Cao, Yanjia; Dyson, Zoe Anne; Garrett, Denise O; John, Jacob; Kang, Gagandeep; Hooda, Yogesh; Saha, Samir K; Saha, Senjuti; Andrews, Jason R; (2022) The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study. The Lancet Microbe, 3 (8). e567-e577. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(22)00093-3

Argimón, Silvia; Yeats, Corin A; Goater, Richard J; Abudahab, Khalil; Taylor, Benjamin; Underwood, Anthony; Sánchez-Busó, Leonor; Wong, Vanessa K; Dyson, Zoe A; Nair, Satheesh; +8 more... Park, Se Eun; Marks, Florian; Page, Andrew J; Keane, Jacqueline A; Baker, Stephen; Holt, Kathryn E; Dougan, Gordon; Aanensen, David M; (2021) A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. Nature communications, 12 (1). 2879-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-23091-2

Carey, Megan E; Jain, Ruby; Yousuf, Mohammad; Maes, Mailis; Dyson, Zoe A; Thu, Trang Nguyen Hoang; Nguyen Thi Nguyen, To; Ho Ngoc Dan, Thanh; Nhu Pham Nguyen, Quynh; Mahindroo, Jaspreet; +4 more... Thanh Pham, Duy; Sandha, Kawaljeet Singh; Baker, Stephen; Taneja, Neelam; (2021) Spontaneous Emergence of Azithromycin Resistance in Independent Lineages of Salmonella Typhi in Northern India. Clinical Infectious Diseases, 72 (5). e120-e127. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciaa1773

Dyson, Zoe A; Holt, Kathryn E; (2021) Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework. JOURNAL OF INFECTIOUS DISEASES, 224 (12 Sup). S775-S780. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiab414

Kariuki, Samuel; Dyson, Zoe A; Mbae, Cecilia; Ngetich, Ronald; Kavai, Susan M; Wairimu, Celestine; Anyona, Stephen; Gitau, Naomi; Onsare, Robert Sanaya; Ongandi, Beatrice; +5 more... Duchene, Sebastian; Ali, Mohamed; Clemens, John David; Holt, Kathryn E; Dougan, Gordon; (2021) Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya. eLife, 10. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.67852

Rahman, Sadia Isfat Ara; Nguyen, To Nguyen Thi; Khanam, Farhana; Thomson, Nicholas R; Dyson, Zoe A; Taylor-Brown, Alyce; Chowdhury, Emran Kabir; Dougan, Gordon; Baker, Stephen; Qadri, Firdausi; (2021) Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018. PLoS Neglected Tropical Diseases, 15 (10). e0009748-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0009748

Rahman, Sadia Isfat Ara; Taylor-Brown, Alyce; Khanam, Farhana; Khan, Ashraful Islam; Horesh, Gal; Dyson, Zoe A; Begum, Yasmin Ara; Chowdhury, Emran Kabir; Qadri, Firdausi; Dougan, Gordon; +1 more... Thomson, Nicholas R; (2021) Genome-wide analysis provides a deeper understanding of the population structure of the Salmonella enterica serotype Paratyphi B complex in Bangladesh. Microbial Genomics, 7 (9). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000617

Britto, Carl D; Dyson, Zoe A; Mathias, Sitarah; Bosco, Ashish; Dougan, Gordon; Jose, Sanju; Nagaraj, Savitha; Holt, Kathryn E; Pollard, Andrew J; (2020) Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 75 (2). pp. 337-341. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz435

Rahman, Sadia Isfat Ara; Dyson, Zoe A; Klemm, Elizabeth J; Khanam, Farhana; Holt, Kathryn E; Chowdhury, Emran Kabir; Dougan, Gordon; Qadri, Firdausi; (2020) Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. PLOS NEGLECTED TROPICAL DISEASES, 14 (2). e0008036-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0008036

Ingle, Danielle J; Nair, Satheesh; Hartman, Hassan; Ashton, Philip M; Dyson, Zoe A; Day, Martin; Freedman, Joanne; Chattaway, Marie A; Holt, Kathryn E; Dallman, Timothy J; (2019) Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLoS neglected tropical diseases, 13 (9). e0007620-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0007620

Britto, Carl D; Dyson, Zoe A; Duchene, Sebastian; Carter, Michael J; Gurung, Meeru; Kelly, Dominic F; Murdoch, David R; Ansari, Imran; Thorson, Stephen; Shrestha, Shrijana; +4 more... Adhikari, Neelam; Dougan, Gordon; Holt, Kathryn E; Pollard, Andrew J; (2018) Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy. PLOS NEGLECTED TROPICAL DISEASES, 12 (4). e0006408-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0006408

Duchene, Sebastian; Duchene, David A; Geoghegan, Jemma L; Dyson, Zoe A; Hawkey, Jane; Holt, Kathryn E; (2018) Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. BMC EVOLUTIONARY BIOLOGY, 18 (1). 95-. ISSN 1471-2148 DOI: https://doi.org/10.1186/s12862-018-1210-5

Park, Se Eun; Pham, Duy Thanh; Boinett, Christine; Wong, Vanessa K; Pak, Gi Deok; Panzner, Ursula; Espinoza, Ligia Maria Cruz; von Kalckreuth, Vera; Im, Justin; Schütt-Gerowitt, Heidi; +60 more... Crump, John A; Breiman, Robert F; Adu-Sarkodie, Yaw; Owusu-Dabo, Ellis; Rakotozandrindrainy, Raphaël; Soura, Abdramane Bassiahi; Aseffa, Abraham; Gasmelseed, Nagla; Keddy, Karen H; May, Jürgen; Sow, Amy Gassama; Aaby, Peter; Biggs, Holly M; Hertz, Julian T; Montgomery, Joel M; Cosmas, Leonard; Olack, Beatrice; Fields, Barry; Sarpong, Nimako; Razafindrabe, Tsiriniaina Jean Luco; Raminosoa, Tiana Mirana; Kabore, Leon Parfait; Sampo, Emmanuel; Teferi, Mekonnen; Yeshitela, Biruk; El Tayeb, Muna Ahmed; Sooka, Arvinda; Meyer, Christian G; Krumkamp, Ralf; Dekker, Denise Myriam; Jaeger, Anna; Poppert, Sven; Tall, Adama; Niang, Aissatou; Bjerregaard-Andersen, Morten; Løfberg, Sandra Valborg; Seo, Hye Jin; Jeon, Hyon Jin; Deerin, Jessica Fung; Park, Jinkyung; Konings, Frank; Ali, Mohammad; Clemens, John D; Hughes, Peter; Sendagala, Juliet Nsimire; Vudriko, Tobias; Downing, Robert; Ikumapayi, Usman N; Mackenzie, Grant A; Obaro, Stephen; Argimon, Silvia; Aanensen, David M; Page, Andrew; Keane, Jacqueline A; Duchene, Sebastian; Dyson, Zoe; Holt, Kathryn E; Dougan, Gordon; Marks, Florian; Baker, Stephen; (2018) The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nature communications, 9 (1). 5094-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-018-07370-z

Dyson, Zoe A; Thanh, Duy Pham; Bodhidatta, Ladaporn; Mason, Carl Jeffries; Srijan, Apichai; Rabaa, Maia A; Vinh, Phat Voong; Thanh, Tuyen Ha; Thwaites, Guy E; Baker, Stephen; +1 more... Holt, Kathryn E; (2017) Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program. PLoS neglected tropical diseases, 11 (1). e0005274-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0005274

Wong, Vanessa K; Baker, Stephen; Connor, Thomas R; Pickard, Derek; Page, Andrew J; Dave, Jayshree; Murphy, Niamh; Holliman, Richard; Sefton, Armine; Millar, Michael; +4 more... Dyson, Zoe A; Dougan, Gordon; Holt, Kathryn E; International Typhoid Consortium; (2016) An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature communications, 7 (1). 12827-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms12827