2024
Microbiological Methods Used in the Enterics for Global Health <i>Shigella</i> Surveillance Study. (Journal article)
Horne, B., Badji, H., Bhuiyan, M. T. R., Romaina Cachique, L., Cornick, J., Hotwani, A., . . . Tennant, S. M. (2024). Microbiological Methods Used in the Enterics for Global Health <i>Shigella</i> Surveillance Study.. Open forum infectious diseases, 11(Suppl 1), S25-S33. doi:10.1093/ofid/ofad576DOI: 10.1093/ofid/ofad576
Mategula, D., Ndalama, M., Lefu, C., Chinkhumba, J., Ndeketa, L., Munthali, V., . . . Cornick, J. (2024). The Enterics for Global Health (EFGH) <i>Shigella</i> Surveillance Study in Malawi.. Open forum infectious diseases, 11(Suppl 1), S101-S106. doi:10.1093/ofid/ofae050DOI: 10.1093/ofid/ofae050
Agapov, A., Baker, K. S., Bedekar, P., Bhatia, R. P., Blower, T. R., Brockhurst, M. A., . . . Wright, R. (2024). Multi-layered genome defences in bacteria.. Current opinion in microbiology, 78, 102436. doi:10.1016/j.mib.2024.102436DOI: 10.1016/j.mib.2024.102436
2023
A sensor histidine kinase from a plant-endosymbiont bacterium restores the virulence of a mammalian intracellular pathogen. (Journal article)
Chaves-Olarte, E., Meza-Torres, J., Herrera-Rodríguez, F., Lizano-González, E., Suárez-Esquivel, M., Baker, K. S., . . . Guzmán-Verri, C. (2023). A sensor histidine kinase from a plant-endosymbiont bacterium restores the virulence of a mammalian intracellular pathogen.. Microbial pathogenesis, 185, 106442. doi:10.1016/j.micpath.2023.106442DOI: 10.1016/j.micpath.2023.106442
Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces. (Journal article)
Muloi, D. M., Jauneikaite, E., Anjum, M. F., Essack, S. Y., Singleton, D. A., Kasudi, M. R., . . . SEDRIC Genomics Surveillance Working Group. (2023). Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces.. The Lancet. Microbe, 4(12), e1056-e1062. doi:10.1016/s2666-5247(23)00284-7DOI: 10.1016/s2666-5247(23)00284-7
Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities. (Journal article)
Jauneikaite, E., Baker, K. S., Nunn, J. G., Midega, J. T., Hsu, L. Y., Singh, S. R., . . . SEDRIC Genomics Surveillance Working Group. (2023). Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities.. The Lancet. Microbe, 4(12), e1040-e1046. doi:10.1016/s2666-5247(23)00282-3DOI: 10.1016/s2666-5247(23)00282-3
Genomics for public health and international surveillance of antimicrobial resistance. (Journal article)
Baker, K. S., Jauneikaite, E., Hopkins, K. L., Lo, S. W., Sánchez-Busó, L., Getino, M., . . . SEDRIC Genomics Surveillance Working Group. (2023). Genomics for public health and international surveillance of antimicrobial resistance.. The Lancet. Microbe, 4(12), e1047-e1055. doi:10.1016/s2666-5247(23)00283-5DOI: 10.1016/s2666-5247(23)00283-5
Wheeler, N. E., Price, V., Cunningham-Oakes, E., Tsang, K. K., Nunn, J. G., Midega, J. T., . . . SEDRIC Genomics Surveillance Working Group. (2023). Innovations in genomic antimicrobial resistance surveillance.. The Lancet. Microbe, 4(12), e1063-e1070. doi:10.1016/s2666-5247(23)00285-9DOI: 10.1016/s2666-5247(23)00285-9
Stenhouse, G. E., Keddy, K. H., Bengtsson, R. J., Hall, N., Smith, A. M., Thomas, J., . . . Baker, K. S. (2023). The genomic epidemiology of shigellosis in South Africa.. Nature communications, 14(1), 7715. doi:10.1038/s41467-023-43345-5DOI: 10.1038/s41467-023-43345-5
Baker, K. S., Jauneikaite, E., Nunn, J. G., Midega, J. T., Atun, R., Holt, K. E., . . . SEDRIC Genomics Surveillance Working Group. (2023). Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group.. The Lancet. Microbe, S2666-5247(23)00281-1. doi:10.1016/s2666-5247(23)00281-1DOI: 10.1016/s2666-5247(23)00281-1
De Silva, P. M., Bennett, R. J., Kuhn, L., Ngondo, P., Debande, L., Njamkepo, E., . . . Baker, K. S. (2023). Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins.. EBioMedicine, 97, 104822. doi:10.1016/j.ebiom.2023.104822DOI: 10.1016/j.ebiom.2023.104822
Torraca, V., Brokatzky, D., Miles, S. L., Chong, C. E., De Silva, P. M., Baker, S., . . . Mostowy, S. (2023). Shigella Serotypes Associated With Carriage in Humans Establish Persistent Infection in Zebrafish. JOURNAL OF INFECTIOUS DISEASES. doi:10.1093/infdis/jiad326DOI: 10.1093/infdis/jiad326
Thorley, K., Charles, H., Greig, D. R., Prochazka, M., Mason, L. C. E., Baker, K. S., . . . Jenkins, C. (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. LANCET INFECTIOUS DISEASES, 23(6), 732-739. doi:10.1016/S1473-3099(22)00807-6DOI: 10.1016/S1473-3099(22)00807-6
Mason, L. C. E., Greig, D. R., Cowley, L. A., Partridge, S. R., Martinez, E., Blackwell, G. A., . . . Baker, K. S. (2023). The evolution and international spread of extensively drug resistant <i>Shigella sonnei</i> (vol 14, 1983, 2023). NATURE COMMUNICATIONS, 14(1). doi:10.1038/s41467-023-38041-3DOI: 10.1038/s41467-023-38041-3
Mason, L. C. E., Greig, D. R., Cowley, L. A., Partridge, S. R., Martinez, E., Blackwell, G. A., . . . Baker, K. S. (2023). The evolution and international spread of extensively drug resistant Shigella sonnei.. Nature communications, 14(1), 1983. doi:10.1038/s41467-023-37672-wDOI: 10.1038/s41467-023-37672-w
Bengtsson, R. J., Baker, K. S., Cunningham, A. A., Greig, D. R., John, S. K., Macgregor, S. K., . . . Lawson, B. (2023). The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain.. Nature communications, 14(1), 1707. doi:10.1038/s41467-023-37312-3DOI: 10.1038/s41467-023-37312-3
Price, V., Ngwira, L. G., Lewis, J. M., Baker, K. S., Peacock, S. J., Jauneikaite, E., & Feasey, N. (2023). A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens.. Microbial genomics, 9(2). doi:10.1099/mgen.0.000947DOI: 10.1099/mgen.0.000947
2022
Azarian, T., Sherry, N. L., Baker, K., Holt, K. E., & Okeke, I. N. (2022). Making microbial genomics work for clinical and public health microbiology. MICROBIAL GENOMICS, 8(9). doi:10.1099/mgen.0.000900DOI: 10.1099/mgen.0.000900
Malaka De Silva, P., Stenhouse, G. E., Blackwell, G. A., Bengtsson, R. J., Jenkins, C., Hall, J. P. J., & Baker, K. S. (2022). A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella.. Proceedings. Biological sciences, 289(1980), 20220581. doi:10.1098/rspb.2022.0581DOI: 10.1098/rspb.2022.0581
Bengtsson, R. J., Simpkin, A. J., Pulford, C. V., Low, R., Rasko, D. A., Rigden, D. J., . . . Baker, K. S. (2022). Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. NATURE MICROBIOLOGY. doi:10.1038/s41564-021-01054-zDOI: 10.1038/s41564-021-01054-z
2021
Perez-Sepulveda, B. M., Heavens, D., Pulford, C. V., Predeus, A. V., Low, R., Webster, H., . . . Hall, N. (2021). An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. GENOME BIOLOGY, 22(1). doi:10.1186/s13059-021-02536-3DOI: 10.1186/s13059-021-02536-3
A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among <i>Shigella</i> (Journal article)
De Silva, M., Stenhouse, G., Blackwell, G., Bengtsson, R., Jenkins, C., Hall, J. P. J., & Baker, K. (2021). A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among <i>Shigella</i>. doi:10.1101/2021.12.17.473221DOI: 10.1101/2021.12.17.473221
Singleton, D. A., Pongchaikul, P., Smith, S., Bengtsson, R. J., Baker, K., Timofte, D., . . . Williams, N. J. (n.d.). Temporal, Spatial, and Genomic Analyses of Enterobacteriaceae Clinical Antimicrobial Resistance in Companion Animals Reveals Phenotypes and Genotypes of One Health Concern. Frontiers in Microbiology, 12, 2160. doi:10.3389/fmicb.2021.700698DOI: 10.3389/fmicb.2021.700698
Hawkey, J., Paranagama, K., Baker, K. S., Bengtsson, R. J., Weill, F. -X., Thomson, N. R., . . . Holt, K. E. (2021). Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, <i>Shigella sonnei</i>. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-22700-4DOI: 10.1038/s41467-021-22700-4
Stenhouse, G. E., Jere, K. C., Peno, C., Bengtsson, R. J., Chinyama, E., Mandolo, J., . . . Baker, K. S. (2021). Whole genome sequence analysis of<i> Shigella</i> from Malawi identifies fluoroquinolone resistance. MICROBIAL GENOMICS, 7(5). doi:10.1099/mgen.0.000532DOI: 10.1099/mgen.0.000532
Bengtsson, R. J., Dallman, T. J., Allen, H., De Silva, P. M., Stenhouse, G., Pulford, C. V., . . . Baker, K. S. (2021). Accessory Genome Dynamics and Structural Variation of <i>Shigella</i> from Persistent Infections.. mBio, 12(2), e00254-e00221. doi:10.1128/mbio.00254-21DOI: 10.1128/mbio.00254-21
Evidence for re-infection and persistent carriage of Shigella species in adult males reporting domestically acquired infection in England (Journal article)
Allen, H., Mitchell, H. D., Simms, I., Baker, K. S., Foster, K., Hughes, G., . . . Jenkins, C. (2021). Evidence for re-infection and persistent carriage of Shigella species in adult males reporting domestically acquired infection in England. CLINICAL MICROBIOLOGY AND INFECTION, 27(1). doi:10.1016/j.cmi.2020.03.036DOI: 10.1016/j.cmi.2020.03.036
2020
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa (Journal article)
Pulford, C., Perez-Sepulveda, B. M., Canals, R., Bevington, J. A., Bengtsson, R. J., Wenner, N., . . . Hinton, J. (2020). Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology. doi:10.1038/s41564-020-00836-1DOI: 10.1038/s41564-020-00836-1
Baker, K. S., Tachedjian, M., Barr, J., Marsh, G. A., Todd, S., Crameri, G., . . . Wang, L. -F. (2020). Achimota Pararubulavirus 3: A New Bat-Derived Paramyxovirus of the Genus <i>Pararubulavirus</i>. VIRUSES-BASEL, 12(11). doi:10.3390/v12111236DOI: 10.3390/v12111236
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, <i>Shigella sonnei</i> (Journal article)
Hawkey, J., Paranagama, K., Baker, K., Bengtsson, R., Weill, F. -X., Thomson, N., . . . Holt, K. (2020). Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, <i>Shigella sonnei</i>. doi:10.1101/2020.10.29.360040DOI: 10.1101/2020.10.29.360040
Microbe hunting in the modern era: reflecting on a decade of microbial genomic epidemiology (Journal article)
Baker, K. S. (2020). Microbe hunting in the modern era: reflecting on a decade of microbial genomic epidemiology. CURRENT BIOLOGY, 30(19), R1124-R1130. Retrieved from https://www.webofscience.com/
Bardsley, M., Jenkins, C., Mitchell, H. D., Mikhail, A. F. W., Baker, K. S., Foster, K., . . . Dallman, T. J. (2020). Persistent Transmission of Shigellosis in England Is Associated with a Recently Emerged Multidrug-Resistant Strain of <i>Shigella sonnei</i>. JOURNAL OF CLINICAL MICROBIOLOGY, 58(4). doi:10.1128/JCM.01692-19DOI: 10.1128/JCM.01692-19
2019
Pulford, C. V., Perez-Sepulveda, B. M., Rodwell, E. V., Weill, F. -X., Baker, K. S., & Hinton, J. C. D. (2019). <i>Salmonella enterica</i> Serovar Panama, an Understudied Serovar Responsible for Extraintestinal Salmonellosis Worldwide. INFECTION AND IMMUNITY, 87(9). doi:10.1128/IAI.00273-19DOI: 10.1128/IAI.00273-19
Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth <i>Brucella</i> sp. BCCN84.3 (vol 6, 175, 2019) (Journal article)
Guzman-Verri, C., Suarez-Esquivel, M., Ruiz-Villalobos, N., Zygmunt, M. S., Gonnet, M., Campos, E., . . . Moreno, E. (2019). Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth <i>Brucella</i> sp. BCCN84.3 (vol 6, 175, 2019). FRONTIERS IN VETERINARY SCIENCE, 6. doi:10.3389/fvets.2019.00253DOI: 10.3389/fvets.2019.00253
Bianco, C., Baker, K. S., Pazzini, L., Cafiso, A., Suu-Ire, R. D., Cunningham, A. A., . . . Nunez, A. (2019). Demodicosis in a captive African straw-coloured fruit bat (Eidolon helvum). EXPERIMENTAL AND APPLIED ACAROLOGY, 78(4), 547-554. doi:10.1007/s10493-019-00399-9DOI: 10.1007/s10493-019-00399-9
Hinton, J. C. D. (2019). The diversity, evolution and ecology of Salmonella in venomous snakes. PLoS Neglected Tropical Diseases.
Guzman-Verri, C., Suarez-Esquivel, M., Ruiz-Villalobos, N., Zygmunt, M. S., Gonnet, M., Campos, E., . . . Moreno, E. (2019). Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth <i>Brucella</i> sp. BCCN84.3. FRONTIERS IN VETERINARY SCIENCE, 6. doi:10.3389/fvets.2019.00175DOI: 10.3389/fvets.2019.00175
Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes (Journal article)
Bennett, R. J., & Baker, K. S. (2019). Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes. Journal of Clinical Microbiology, 57(8). doi:10.1128/JCM.00100-19DOI: 10.1128/JCM.00100-19
2018
Barr, J., Todd, S., Crameri, G., Foord, A., Marsh, G., Frazer, L., . . . Wang, L. -F. (2018). Animal infection studies of two recently discovered African bat paramyxoviruses, Achimota 1 and Achimota 2. SCIENTIFIC REPORTS, 8, 10 pages. doi:10.1038/s41598-018-31193-zDOI: 10.1038/s41598-018-31193-z
Baker, K. S., Dallman, T. J., Thomson, N. R., & Jenkins, C. (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). doi:10.1099/mgen.0.000181DOI: 10.1099/mgen.0.000181
Behar, A., Baker, K. S., Bassal, R., Ezernitchi, A., Valinsky, L., Thomson, N. R., & Cohen, D. (2018). Microevolution and Patterns of Transmission of <i>Shigella sonnei</i> within Cyclic Outbreaks of Shigellosis, Israel. EMERGING INFECTIOUS DISEASES, 24(7), 1335-1339. doi:10.3201/eid2407.171313DOI: 10.3201/eid2407.171313
Hayman, D. T. S., Luis, A. D., Restif, O., Baker, K. S., Fooks, A. R., Leach, C., . . . Webb, C. T. (2018). Maternal antibody and the maintenance of a lyssavirus in populations of seasonally breeding African bats. PLoS One, 13(6). doi:10.1371/journal.pone.0198563DOI: 10.1371/journal.pone.0198563
Baker, K. S., Dallman, T. J., Field, N., Childs, T., Mitchell, H., Day, M., . . . Thomson, N. (n.d.). Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance. SCIENTIFIC REPORTS, 8, 8 pages. doi:10.1038/s41598-018-25764-3DOI: 10.1038/s41598-018-25764-3
Baker, K. S., Dallman, T., Field, N., Childs, T., Mitchell, H., Day, M., . . . Thomson, N. (2018). Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species. Nature Communications, 9. doi:10.1038/s41467-018-03949-8DOI: 10.1038/s41467-018-03949-8
Peel, A. J., Baker, K. S., Hayman, D. T. S., Broder, C. C., Cunningham, A. A., Fooks, A. R., . . . Restif, O. (2018). Support for viral persistence in bats from age-specific serology and models of maternal immunity. SCIENTIFIC REPORTS, 8. doi:10.1038/s41598-018-22236-6DOI: 10.1038/s41598-018-22236-6
Rew, V., Mook, P., Trienekens, S., Baker, K. S., Dallman, T. J., Jenkins, C., . . . Thomson, N. R. (2018). Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of <i>Shigella sonnei</i> from Israel. MICROBIAL GENOMICS, 4(3). doi:10.1099/mgen.0.000170DOI: 10.1099/mgen.0.000170
2017
Baker, K. S., Campos, J., Pichel, M., Della Gaspera, A., Duarte-Martinez, F., Campos-Chacon, E., . . . Thomson, N. R. (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), 845-853. doi:10.1016/j.cmi.2017.03.021DOI: 10.1016/j.cmi.2017.03.021
Suarez-Esquivel, M., Baker, K. S., Ruiz-Villalobos, N., Hernandez-Mora, G., Barquero-Calvo, E., Gonzalez-Barrientos, R., . . . Guzman-Verri, C. (2017). Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution. Genome Biology and Evolution, 9(7), 1901-1912. doi:10.1093/gbe/evx137DOI: 10.1093/gbe/evx137
Suarez-Esquivel, M., Ruiz-Villalobos, N., Jimenez-Rojas, C., Barquero-Calvo, E., Chacon-Diaz, C., Viquez-Ruiz, E., . . . Guzman-Verri, C. (2017). <i>Brucella neotomae</i> Infection in Humans, Costa Rica. EMERGING INFECTIOUS DISEASES, 23(6), 997-1000. doi:10.3201/eid2306.162018DOI: 10.3201/eid2306.162018
How does Africa's most hunted bat vary across the continent? Population traits of the straw-coloured fruit bat (<i>Eidolon helvum</i>) and its interactions with humans (Journal article)
Peel, A. J., Wood, J. L. N., Baker, K. S., Breed, A. C., de Carvalho, A., Fernandez-Loras, A., . . . Hayman, D. T. S. (2017). How does Africa's most hunted bat vary across the continent? Population traits of the straw-coloured fruit bat (<i>Eidolon helvum</i>) and its interactions with humans. ACTA CHIROPTEROLOGICA, 19(1), 77-92. doi:10.3161/15081109ACC2017.19.1.006DOI: 10.3161/15081109ACC2017.19.1.006
Common determinants of antimicrobial resistance in sequential episodes of sexually transmitted shigellosis in men who have sex with men: a cross-sectional study (Conference Paper)
Baker, K. S., Dallman, T. J., Field, N., Childs, T., Were, J., Hughes, G., . . . Thomson, N. R. (2017). Common determinants of antimicrobial resistance in sequential episodes of sexually transmitted shigellosis in men who have sex with men: a cross-sectional study. In LANCET Vol. 389 (pp. 24). Retrieved from https://www.webofscience.com/
How do epidemics become endemic? Lessons from shigellosis in men who have sex with men (Scholarly edition)
Baker, K. (2017). How do epidemics become endemic? Lessons from shigellosis in men who have sex with men.
2016
Suarez-Esquivel, M., Ruiz-Villalobos, N., Castillo-Zeledon, A., Jimenez-Rojas, C., Roop, R. M. I. I., Comerci, D. J., . . . Guzman-Verri, C. (2016). <i>Brucella abortus</i> Strain 2308 Wisconsin Genome: Importance of the Definition of Reference Strains. FRONTIERS IN MICROBIOLOGY, 7. doi:10.3389/fmicb.2016.01557DOI: 10.3389/fmicb.2016.01557
Baker, K. S., Dallman, T. J., Behar, A., Weill, F. -X., Gouali, M., Sobel, J., . . . Thomson, N. R. (2016). Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities. EMERGING INFECTIOUS DISEASES, 22(9), 1545-1553. doi:10.3201/eid2209.151953DOI: 10.3201/eid2209.151953
Peel, A. J., Baker, K. S., Hayman, D. T. S., Suu-Ire, R., Breed, A. C., Gembu, G. -C., . . . Wood, J. L. N. (2016). Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, <i>Eidolon</i> <i>helvum</i>. SCIENTIFIC DATA, 3. doi:10.1038/sdata.2016.49DOI: 10.1038/sdata.2016.49
2015
The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource (Journal article)
Baker, K. S., Burnett, E., McGregor, H., Deheer-Graham, A., Boinett, C., Langridge, G. C., . . . Parkhill, J. (2015). The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource. GENOME MEDICINE, 7. doi:10.1186/s13073-015-0222-7DOI: 10.1186/s13073-015-0222-7
Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri (Journal article)
Connor, T. R., Barker, C. R., Baker, K. S., Weill, F. -X., Talukder, K. A., Smith, A. M., . . . Thomson, N. R. (2015). Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife, 4. doi:10.7554/eLife.07335DOI: 10.7554/eLife.07335
Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study (Journal article)
Baker, K. S., Dallman, T. J., Ashton, P. M., Day, M., Hughes, G., Crook, P. D., . . . Thomson, N. R. (2015). Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. Lancet Infectious Diseases, 15(8), 913-921. doi:10.1016/S1473-3099(15)00002-XDOI: 10.1016/S1473-3099(15)00002-X
Rowe, W., Baker, K. S., Verner-Jeffreys, D., Baker-Austin, C., Ryan, J. J., Maskell, D., & Pearce, G. (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). doi:10.1371/journal.pone.0133492DOI: 10.1371/journal.pone.0133492
Characterization of Pre-Antibiotic Era <i>Klebsiella pneumoniae</i> Isolates with Respect to Antibiotic/Disinfectant Susceptibility and Virulence in <i>Galleria mellonella</i> (Journal article)
Wand, M. E., Baker, K. S., Benthall, G., McGregor, H., McCowen, J. W. I., Deheer-Graham, A., & Sutton, J. M. (2015). Characterization of Pre-Antibiotic Era <i>Klebsiella pneumoniae</i> Isolates with Respect to Antibiotic/Disinfectant Susceptibility and Virulence in <i>Galleria mellonella</i>. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 59(7), 3966-3972. doi:10.1128/AAC.05009-14DOI: 10.1128/AAC.05009-14
Draft genomes of <i>Shigella</i> strains used by the STOPENTERICS consortium (Journal article)
Rossi, O., Baker, K. S., Phalipon, A., Weill, F. -X., Citiulo, F., Sansonetti, P., . . . Thomson, N. R. (2015). Draft genomes of <i>Shigella</i> strains used by the STOPENTERICS consortium. GUT PATHOGENS, 7. doi:10.1186/s13099-015-0061-5DOI: 10.1186/s13099-015-0061-5
Draft Genome Sequence of 24570, the Type Strain of <i>Shigella flexneri</i> (Journal article)
Baker, K. S., Parkhill, J., & Thomson, N. R. (2015). Draft Genome Sequence of 24570, the Type Strain of <i>Shigella flexneri</i>. GENOME ANNOUNCEMENTS, 3(3). doi:10.1128/genomeA.00393-15DOI: 10.1128/genomeA.00393-15
A high‐resolution genomic analysis of multidrug‐resistant hospital outbreaks of Klebsiella pneumoniae (Journal article)
Chung The, H., Karkey, A., Pham Thanh, D., Boinett, C. J., Cain, A. K., Ellington, M., . . . Baker, S. (2015). A high‐resolution genomic analysis of multidrug‐resistant hospital outbreaks of Klebsiella pneumoniae. EMBO Molecular Medicine, 7(3), 227-239. doi:10.15252/emmm.201404767DOI: 10.15252/emmm.201404767
GENOME WATCH Demystifying <i>Escherichia coli</i> pathovars (Journal article)
Baker, K. S. (2015). GENOME WATCH Demystifying <i>Escherichia coli</i> pathovars. NATURE REVIEWS MICROBIOLOGY, 13(1), 5. doi:10.1038/nrmicro3411DOI: 10.1038/nrmicro3411
2014
Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection (Journal article)
Mather, A. E., Baker, K. S., McGregor, H., Coupland, P., Mather, P. L., Deheer-Graham, A., . . . Thomson, N. R. (2014). Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection. LANCET, 384(9955), 1720. doi:10.1016/S0140-6736(14)61790-6DOI: 10.1016/S0140-6736(14)61790-6
The extant World War 1 dysentery bacillus NCTC1: a genomic analysis (Journal article)
Baker, K. S., Mather, A. E., McGregor, H., Coupland, P., Langridge, G. C., Day, M., . . . Thomson, N. R. (2014). The extant World War 1 dysentery bacillus NCTC1: a genomic analysis. The Lancet, 384(9955), 1691-1697. doi:10.1016/S0140-6736(14)61789-XDOI: 10.1016/S0140-6736(14)61789-X
Emerging risks from bat bushmeat in West Africa (Chapter)
Kamins, A., Baker, K., Restif, O., Cunningham, A., & Wood, J. L. N. (2014). Emerging risks from bat bushmeat in West Africa. In TRENDS IN GAME MEAT HYGIENE: FROM FOREST TO FORK (pp. 91-105). doi:10.3920/978-90-8686-238-2_5DOI: 10.3920/978-90-8686-238-2_5
Poxviruses in Bats ... so What? (Journal article)
Baker, K. S., & Murcia, P. R. (2014). Poxviruses in Bats ... so What?. VIRUSES-BASEL, 6(4), 1564-1577. doi:10.3390/v6041564DOI: 10.3390/v6041564
Draft genome sequences of the type strains of <i>Shigella flexneri</i> held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence (Journal article)
Ashton, P. M., Baker, K. S., Gentle, A., Wooldridge, D. J., Thomson, N. R., Dallman, T. J., & Jenkins, C. (2014). Draft genome sequences of the type strains of <i>Shigella flexneri</i> held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence. GUT PATHOGENS, 6. doi:10.1186/1757-4749-6-7DOI: 10.1186/1757-4749-6-7
Viral antibody dynamics in a chiropteran host (Journal article)
Baker, K. S., Suu-Ire, R., Barr, J., Hayman, D. T. S., Broder, C. C., Horton, D. L., . . . Wood, J. L. N. (2014). Viral antibody dynamics in a chiropteran host. JOURNAL OF ANIMAL ECOLOGY, 83(2), 415-428. doi:10.1111/1365-2656.12153DOI: 10.1111/1365-2656.12153
GENOME WATCH TB or not TB? Genomic portraits provide answers (Journal article)
Baker, K. S., & Ellington, M. J. (2014). GENOME WATCH TB or not TB? Genomic portraits provide answers. NATURE REVIEWS MICROBIOLOGY, 12(6), 398. doi:10.1038/nrmicro3273DOI: 10.1038/nrmicro3273
2013
Continent-wide panmixia of an African fruit bat facilitates transmission of potentially zoonotic viruses (Journal article)
Peel, A. J., Sargan, D. R., Baker, K. S., Hayman, D. T. S., Barr, J. A., Crameri, G., . . . Cunningham, A. A. (2013). Continent-wide panmixia of an African fruit bat facilitates transmission of potentially zoonotic viruses. NATURE COMMUNICATIONS, 4. doi:10.1038/ncomms3770DOI: 10.1038/ncomms3770
Use of cross-reactive serological assays for detecting novel pathogens in wildlife: Assessing an appropriate cutoff for henipavirus assays in African bats (Journal article)
Peel, A. J., McKinley, T. J., Baker, K. S., Barr, J. A., Crameri, G., Hayman, D. T. S., . . . Wood, J. L. N. (2013). Use of cross-reactive serological assays for detecting novel pathogens in wildlife: Assessing an appropriate cutoff for henipavirus assays in African bats. JOURNAL OF VIROLOGICAL METHODS, 193(2), 295-303. doi:10.1016/j.jviromet.2013.06.030DOI: 10.1016/j.jviromet.2013.06.030
Metagenomic study of the viruses of African straw-coloured fruit bats: Detection of a chiropteran poxvirus and isolation of a novel adenovirus (Journal article)
Baker, K. S., Leggett, R. M., Bexfield, N. H., Alston, M., Daly, G., Todd, S., . . . Murcia, P. R. (2013). Metagenomic study of the viruses of African straw-coloured fruit bats: Detection of a chiropteran poxvirus and isolation of a novel adenovirus. VIROLOGY, 441(2), 95-106. doi:10.1016/j.virol.2013.03.014DOI: 10.1016/j.virol.2013.03.014
Novel, Potentially Zoonotic Paramyxoviruses from the African Straw-Colored Fruit Bat <i>Eidolon helvum</i> (Journal article)
Baker, K. S., Todd, S., Marsh, G. A., Crameri, G., Barr, J., Kamins, A. O., . . . Wang, L. -F. (2013). Novel, Potentially Zoonotic Paramyxoviruses from the African Straw-Colored Fruit Bat <i>Eidolon helvum</i>. JOURNAL OF VIROLOGY, 87(3), 1348-1358. doi:10.1128/JVI.01202-12DOI: 10.1128/JVI.01202-12
2012
Endemic Lagos bat virus infection in <i>Eidolon helvum</i> (Journal article)
Hayman, D. T. S., Fooks, A. R., Rowcliffe, J. M., McCrea, R., Restif, O., Baker, K. S., . . . Wood, J. L. N. (2012). Endemic Lagos bat virus infection in <i>Eidolon helvum</i>. EPIDEMIOLOGY AND INFECTION, 140(12), 2163-2171. doi:10.1017/S0950268812000167DOI: 10.1017/S0950268812000167
A framework for the study of zoonotic disease emergence and its drivers: spillover of bat pathogens as a case study (Journal article)
Wood, J. L. N., Leach, M., Waldman, L., MacGregor, H., Fooks, A. R., Jones, K. E., . . . Cunningham, A. A. (2012). A framework for the study of zoonotic disease emergence and its drivers: spillover of bat pathogens as a case study. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 367(1604), 2881-2892. doi:10.1098/rstb.2012.0228DOI: 10.1098/rstb.2012.0228
Co-circulation of diverse paramyxoviruses in an urban African fruit bat population (Journal article)
Baker, K. S., Todd, S., Marsh, G., Fernandez-Loras, A., Suu-Ire, R., Wood, J. L. N., . . . Cunningham, A. A. (2012). Co-circulation of diverse paramyxoviruses in an urban African fruit bat population. JOURNAL OF GENERAL VIROLOGY, 93, 850-856. doi:10.1099/vir.0.039339-0DOI: 10.1099/vir.0.039339-0
<i>Bartonella</i> species in bat flies (Diptera: Nycteribiidae) from western Africa (Journal article)
Billeter, S. A., Hayman, D. T. S., Peel, A. J., Baker, K., Wood, J. L. N., Cunningham, A., . . . Kosoy, M. Y. (2012). <i>Bartonella</i> species in bat flies (Diptera: Nycteribiidae) from western Africa. PARASITOLOGY, 139(3), 324-329. doi:10.1017/S0031182011002113DOI: 10.1017/S0031182011002113
Henipavirus Neutralising Antibodies in an Isolated Island Population of African Fruit Bats (Journal article)
Peel, A. J., Baker, K. S., Crameri, G., Barr, J. A., Hayman, D. T. S., Wright, E., . . . Wood, J. L. N. (2012). Henipavirus Neutralising Antibodies in an Isolated Island Population of African Fruit Bats. PLOS ONE, 7(1). doi:10.1371/journal.pone.0030346DOI: 10.1371/journal.pone.0030346
2011
Antibodies to Henipavirus or Henipa-Like Viruses in Domestic Pigs in Ghana, West Africa (Journal article)
Hayman, D. T. S., Wang, L. -F., Barr, J., Baker, K. S., Suu-Ire, R., Broder, C. C., . . . Wood, J. L. N. (2011). Antibodies to Henipavirus or Henipa-Like Viruses in Domestic Pigs in Ghana, West Africa. PLOS ONE, 6(9). doi:10.1371/journal.pone.0025256DOI: 10.1371/journal.pone.0025256
Evidence of Henipaviruses and Lyssaviruses in Isolated Island Populations of African Fruit Bats (Conference Paper)
Peel, A. J., Loras, A. F., Baker, K. S., Hayman, D. T. S., Kamins, A., Rossiter, S. J., . . . Cunningham, A. A. (2011). Evidence of Henipaviruses and Lyssaviruses in Isolated Island Populations of African Fruit Bats. In ECOHEALTH Vol. 7 (pp. S40). Retrieved from https://www.webofscience.com/
Next Generation Surveillance? A metaviromic Study of a West African Bat Population Using Next Generation Sequencing (Conference Paper)
Baker, K., Kellam, P., Suu-Ire, R., Cunningham, A., Wood, J., Caccamo, M., & Murcia, P. (2011). Next Generation Surveillance? A metaviromic Study of a West African Bat Population Using Next Generation Sequencing. In ECOHEALTH Vol. 7 (pp. S41-S42). Retrieved from https://www.webofscience.com/
2009
Design and evaluation of consensus PCR assays for henipaviruses (Journal article)
Feldman, K. S., Foord, A., Heine, H. G., Smith, I. L., Boyd, V., Marsh, G. A., . . . Wang, L. -F. (2009). Design and evaluation of consensus PCR assays for henipaviruses. JOURNAL OF VIROLOGICAL METHODS, 161(1), 52-57. doi:10.1016/j.jviromet.2009.05.014DOI: 10.1016/j.jviromet.2009.05.014