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Bengtsson, Rebecca J, Dallman, Timothy J, Allen, Hester, De Silva, P Malaka ORCID: 0000-0002-0579-0131, Stenhouse, George, Pulford, Caisey V, Bennett, Rebecca J, Jenkins, Claire and Baker, Kate S ORCID: 0000-0001-5850-1949 (2021) Accessory Genome Dynamics and Structural Variation of <i>Shigella</i> from Persistent Infections. mBio, 12 (2). e00254-e00221.

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Baker, Kate S ORCID: 0000-0001-5850-1949, Tachedjian, Mary, Barr, Jennifer, Marsh, Glenn A, Todd, Shawn, Crameri, Gary, Crameri, Sandra, Smith, Ina, Holmes, Clare EG, Suu-Ire, Richard et al (show 4 more authors) , Fernandez-Loras, Andres, Cunningham, Andrew A, Wood, James LN and Wang, Lin-Fa (2020) Achimota Pararubulavirus 3: A New Bat-Derived Paramyxovirus of the Genus Pararubulavirus. VIRUSES-BASEL, 12 (11). E1236-.

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Barr, Jennifer, Todd, Shawn, Crameri, Gary, Foord, Adam, Marsh, Glenn, Frazer, Leah, Payne, Jean, Harper, Jenni, Baker, Kate S ORCID: 0000-0001-5850-1949, Cunningham, Andrew A et al (show 3 more authors) , Wood, James LN, Middleton, Deborah and Wang, Lin-Fa (2018) Animal infection studies of two recently discovered African bat paramyxoviruses, Achimota 1 and Achimota 2. SCIENTIFIC REPORTS, 8 (1).

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Peel, Alison J, Baker, Kate S ORCID: 0000-0001-5850-1949, Hayman, David TS, Suu-Ire, Richard, Breed, Andrew C, Gembu, Guy-Crispin, Lembo, Tiziana, Fernandez-Loras, Andres, Sargan, David R, Fooks, Anthony R et al (show 2 more authors) , Cunningham, Andrew A and Wood, James LN (2016) Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum. SCIENTIFIC DATA, 3 (1). 160049-.

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Suarez-Esquivel, Marcela, Baker, Kate S ORCID: 0000-0001-5850-1949, Ruiz-Villalobos, Nazareth, Hernandez-Mora, Gabriela, Barquero-Calvo, Elias, Gonzalez-Barrientos, Rocio, Castillo-Zeledon, Amanda, Jimenez-Rojas, Cesar, Chacon-Diaz, Carlos, Cloeckaert, Axel et al (show 4 more authors) , Chaves-Olarte, Esteban, Thomson, Nicholas R, Moreno, Edgardo and Guzman-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.

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Suarez-Esquivel, Marcela, Ruiz-Villalobos, Nazareth, Castillo-Zeledon, Amanda, Jimenez-Rojas, Cesar, Roop, R Martin II, Comerci, Diego J, Barquero-Calvo, Elias, Chacon-Diaz, Carlos, Caswell, Clayton C, Baker, Kate S ORCID: 0000-0001-5850-1949 et al (show 6 more authors) , Chaves-Olarte, Esteban, Thomson, Nicholas R, Moreno, Edgardo, Letesson, Jean J, De Bolle, Xavier and Guzman-Verri, Caterina (2016) Brucella abortus Strain 2308 Wisconsin Genome: Importance of the Definition of Reference Strains. FRONTIERS IN MICROBIOLOGY, 7 (SEP). 1557-.

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Suarez-Esquivel, Marcela, Ruiz-Villalobos, Nazareth, Jimenez-Rojas, Cesar, Barquero-Calvo, Elias, Chacon-Diaz, Carlos, Viquez-Ruiz, Eunice, Rojas-Campos, Norman, Baker, Kate S ORCID: 0000-0001-5850-1949, Oviedo-Sanchez, Gerardo, Amuy, Ernesto et al (show 4 more authors) , Chaves-Olarte, Esteban, Thomson, Nicholas R, Moreno, Edgardo and Guzman-Verri, Caterina (2017) Brucella neotomae Infection in Humans, Costa Rica. EMERGING INFECTIOUS DISEASES, 23 (6). pp. 997-1000.

Bianco, Carlo, Baker, Kate S ORCID: 0000-0001-5850-1949, Pazzini, Luca, Cafiso, Alessandra, Suu-Ire, Richard D, Cunningham, Andrew A, Wood, James LN and Nunez, Alejandro (2019) Demodicosis in a captive African straw-coloured fruit bat (Eidolon helvum). EXPERIMENTAL AND APPLIED ACAROLOGY, 78 (4). pp. 547-554.

Thorley, Katie, Charles, Hannah, Greig, David R, Prochazka, Mateo, Mason, Lewis CE ORCID: 0000-0001-5049-1352, Baker, Kate S ORCID: 0000-0001-5850-1949, Godbole, Gauri, Sinka, Katy and Jenkins, Claire (2023) Emergence of extensively drug-resistant and multidrug-resistant Shigella flexneri serotype 2a associated with sexual transmission among gay, bisexual, and other men who have sex with men, in England: a descriptive epidemiological study. The Lancet. Infectious diseases. S1473-3099(22)00807-6-.

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Guzman-Verri, Caterina, Suarez-Esquivel, Marcela, Ruiz-Villalobos, Nazareth, Zygmunt, Michel S, Gonnet, Mathieu, Campos, Elena, Viquez-Ruiz, Eunice, Chacon-Diaz, Carlos, Aragon-Aranda, Beatriz, Conde-Alvarez, Raquel et al (show 7 more authors) , Moriyon, Ignacio, Maria Blasco, Jose, Munoz, Pilar M, Baker, Kate S ORCID: 0000-0001-5850-1949, Thomson, Nicholas R, Cloeckaert, Axel and Moreno, Edgardo (2019) Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3. FRONTIERS IN VETERINARY SCIENCE, 6 (JUN). 175-.

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Baker, Kate S ORCID: 0000-0001-5850-1949, Dallman, Timothy J, Field, Nigel, Childs, Tristan, Mitchell, Holly, Day, Martin, Weill, Francois-Xavier, Lefevre, Sophie, Tourdjman, Mathieu, Hughes, Gwenda et al (show 2 more authors) , Jenkins, Claire and 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).

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Hawkey, Jane, Paranagama, Kalani, Baker, Kate S ORCID: 0000-0001-5850-1949, Bengtsson, Rebecca J, Weill, Francois-Xavier, Thomson, Nicholas R, Baker, Stephen, Cerdeira, Louise, Iqbal, Zamin, Hunt, Martin et al (show 5 more authors) , Ingle, Danielle J, Dallman, Timothy J, Jenkins, Claire, Williamson, Deborah A and 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-.

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Hayman, David TS, Luis, Angela D, Restif, Olivier, Baker, Kate S ORCID: 0000-0001-5850-1949, Fooks, Anthony R, Leach, Clint, Horton, Daniel L, Suu-Ire, Richard, Cunningham, Andrew A, Wood, James LN et al (show 1 more authors) and Webb, Colleen T (2018) Maternal antibody and the maintenance of a lyssavirus in populations of seasonally breeding African bats. PLoS One, 13 (6). e0198563-.

Bengtsson, Rebecca J, Simpkin, Adam J, Pulford, Caisey V, Low, Ross, Rasko, David A, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Hall, Neil, Barry, Eileen M, Tennant, Sharon M and Baker, Kate S ORCID: 0000-0001-5850-1949 (2022) Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. NATURE MICROBIOLOGY, 7 (2). 251-+.

Bardsley, Megan, Jenkins, Claire, Mitchell, Holly D, Mikhail, Amy FW, Baker, Kate S ORCID: 0000-0001-5850-1949, Foster, Kirsty, Hughes, Gwenda and Dallman, Timothy J (2020) Persistent Transmission of Shigellosis in England Is Associated with a Recently Emerged Multidrug-Resistant Strain of Shigella sonnei. JOURNAL OF CLINICAL MICROBIOLOGY, 58 (4). e01692-e01619.

Pulford, Caisey V, Perez-Sepulveda, Blanca M, Rodwell, Ella V, Weill, Franois-Xavier, Baker, Kate S ORCID: 0000-0001-5850-1949 and Hinton, Jay CD ORCID: 0000-0003-2671-6026 (2019) Salmonella enterica Serovar Panama, an Understudied Serovar Responsible for Extraintestinal Salmonellosis Worldwide. INFECTION AND IMMUNITY, 87 (9). e00273-e00219.

Rowe, Will ORCID: 0000-0003-0384-4463, Baker, Kate S ORCID: 0000-0001-5850-1949, Verner-Jeffreys, David, Baker-Austin, Craig, Ryan, Jim J, Maskell, Duncan and Pearce, Gareth (2015) Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data. PLOS ONE, 10 (7). e0133492-.

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Pulford, Caisey, Perez-Sepulveda, Blanca M, Canals, Rocio, Bevington, Jessica A, Bengtsson, Rebecca J, Wenner, Nicolas, Rodwell, Ella V, Kumwenda, Benjamin, Zhu, Xioajun, Bennett, Rebecca J ORCID: 0000-0001-5290-5109 et al (show 21 more authors) , Stenhouse, George E, De Silva, Malaka ORCID: 0000-0002-0579-0131, Webster, Hermione J ORCID: 0000-0001-8655-911X, Bengoechea, Jose A, Dumigan, Amy, Tran-Dien, ALicia, Prakash, Reenesh, Banda, Happy C, Alufandika, Lovemore, Mautanga, Mike P, Bowers-Barnard, Arthuer, Beliavskaia, Alexendra Y ORCID: 0000-0002-1194-5689, Predeus, Alexander V ORCID: 0000-0002-2750-1599, Rowe, Will PM, Darby, Alister C ORCID: 0000-0002-3786-6209, Nall, Neil, Weill, Francois-Xavier, Gordon, Melita A ORCID: 0000-0002-0629-0884, Feasey, Nicholas A, Baker, Kate S ORCID: 0000-0001-5850-1949 and Hinton, Jay ORCID: 0000-0003-2671-6026 (2020) Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology, 6 (3). 327-+.

Peel, Alison J, Baker, Kate S ORCID: 0000-0001-5850-1949, Hayman, David TS, Broder, Christopher C, Cunningham, Andrew A, Fooks, Anthony R, Garnier, Romain, Wood, James LN and Restif, Olivier (2018) Support for viral persistence in bats from age-specific serology and models of maternal immunity. SCIENTIFIC REPORTS, 8 (1). 3859-.

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Baker, Kate S ORCID: 0000-0001-5850-1949, Dallman, Timothy J, Behar, Adi, Weill, Francois-Xavier, Gouali, Malika, Sobel, Jeremy, Fookes, Maria, Valinsky, Lea, Gal-Mor, Ohad, Connor, Thomas R et al (show 6 more authors) , Nissan, Israel, Bertrand, Sophie, Parkhill, Julian, Jenkins, Claire, Cohen, Dani and 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.

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Stenhouse, George E, Jere, Khuzwayo C ORCID: 0000-0003-3376-8529, Peno, Chikondi, Bengtsson, Rebecca J, Chinyama, End, Mandolo, Jonathan, Cain, Amy, Iturriza-Gomara, Miren ORCID: 0000-0001-5816-6423, Bar-Zeev, Naor ORCID: 0000-0003-0570-4624, Cunliffe, Nigel A ORCID: 0000-0002-5449-4988 et al (show 2 more authors) , Cornick, Jennifer and Baker, Kate S ORCID: 0000-0001-5850-1949 (2021) Whole genome sequence analysis of Shigella from Malawi identifies fluoroquinolone resistance. MICROBIAL GENOMICS, 7 (5).

Rew, Vanessa, Mook, Piers, Trienekens, Suzan, Baker, Kate S ORCID: 0000-0001-5850-1949, Dallman, Timothy J, Jenkins, Claire, Crook, Paul D and 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).

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Perez-Sepulveda, Blanca M, Heavens, Darren, Pulford, Caisey V, Predeus, Alexander V ORCID: 0000-0002-2750-1599, Low, Ross, Webster, Hermione, Dykes, Gregory F, Schudoma, Christian, Rowe, Will, Lipscombe, James et al (show 8 more authors) , Watkins, Chris, Kumwenda, Benjamin, Shearer, Neil, Costigan, Karl, Baker, Kate S ORCID: 0000-0001-5850-1949, Feasey, Nicholas A, Hinton, Jay CD ORCID: 0000-0003-2671-6026 and Hall, Neil (2021) An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. GENOME BIOLOGY, 22 (1). 349-.

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Mason, Lewis CE ORCID: 0000-0001-5049-1352, Greig, David R, Cowley, Lauren A, Partridge, Sally R, Martinez, Elena, Blackwell, Grace A, Chong, Charlotte E, De Silva, P Malaka, Bengtsson, Rebecca J, Draper, Jenny L et al (show 13 more authors) , Ginn, Andrew N, Sandaradura, Indy, Sim, Eby M, Iredell, Jonathan R, Sintchenko, Vitali, Ingle, Danielle J, Howden, Benjamin P, Lefèvre, Sophie, Njampeko, Elisabeth, Weill, François-Xavier, Ceyssens, Pieter-Jan, Jenkins, Claire and Baker, Kate S ORCID: 0000-0001-5850-1949 (2023) The evolution and international spread of extensively drug resistant Shigella sonnei. Nature communications, 14 (1). p. 1983.

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Bengtsson, Rebecca J, Baker, Kate S ORCID: 0000-0001-5850-1949, Cunningham, Andrew A ORCID: 0000-0002-3543-6504, Greig, David R ORCID: 0000-0001-9436-067X, John, Shinto K, Macgregor, Shaheed K, Seilern-Moy, Katharina, Spiro, Simon, Chong, Charlotte C, De Silva, P Malaka ORCID: 0000-0002-0579-0131 et al (show 2 more authors) , Jenkins, Claire and Lawson, Becki (2023) The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain. Nature communications, 14 (1). 1707-.

Baker, Kate S ORCID: 0000-0001-5850-1949, Dallman, Timothy J, Thomson, Nicholas R and 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).

Price, Vivien, Ngwira, Lucky Gift, Lewis, Joseph M ORCID: 0000-0002-3837-5188, Baker, Kate S ORCID: 0000-0001-5850-1949, Peacock, Sharon J, Jauneikaite, Elita and Feasey, Nicholas (2023) A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens. Microbial genomics, 9 (2).

Malaka De Silva, P, Stenhouse, George E, Blackwell, Grace A, Bengtsson, Rebecca J, Jenkins, Claire, Hall, James PJ ORCID: 0000-0002-4896-4592 and Baker, Kate S ORCID: 0000-0001-5850-1949 (2022) A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella. Proceedings. Biological sciences, 289 (1980). p. 20220581.