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Cambridge Public Health

 

Stephen Baker is a director of research for global health in the Department of Medicine at the University of Cambridge. His research focusses on studying the mechanisms and epidemiological influences of antimicrobial resistant Gram-negative bacteria. His group used various genomic and laboratory techniques to understand how antimicrobial resistant bacterial emerge and spread and how best they can be combatted through antimicrobials and vaccines.

He has published over 300 scientific articles and is a recognized name in global health with a portfolio of work ranging from typhoid fever and other enteric diseases to hospital acquired infections and zoonoses.

Publications from Elements

Theses / dissertations

2021 (No publication date)

  • Sridhar, S., 2021 (No publication date). An integrated approach to ciprofloxacin susceptibility analysis and high-throughput bacterial phenotyping in Salmonella
  • Journal articles

    2021 (Accepted for publication)

  • Bergamaschi, L., Mescia, F., Turner, L., Hanson, AL., Kotagiri, P., Dunmore, BJ., Ruffieux, H., De Sa, A., Huhn, O., Morgan, MD., Gerber, PP., Wills, MR., Baker, S., Calero‐Nieto, FJ., Doffinger, R., Dougan, G., Elmer, A., Goodfellow, IG., Gupta, RK., Hosmillo, M., Hunter, K., Kingston, N., Lehner, PJ., Matheson, NJ., Nicholson, JK., Petrunkina, AM., Richardson, S., Saunders, C., Thaventhiran, JED., Toonen, EJM., Weekes, MP., Göttgens, B., Toshner, M., Hess, C., Bradley, JR., Lyons, PA. and Smith, KGC., 2021 (Accepted for publication). Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease. Immunity,
    Doi: http://doi.org/10.1016/j.immuni.2021.05.010
  • Maes, M., Higginson, E., Pereira-Dias, J., Curran, MD., Parmar, S., Khokhar, F., Cuchet-Lourenço, D., Lux, J., Sharma-Hajela, S., Ravenhill, B., Hamed, I., Heales, L., Mahroof, R., Solderholm, A., Forrest, S., Sridhar, S., Brown, NM., Baker, S., Navapurkar, V., Dougan, G., Bartholdson Scott, J. and Conway Morris, A., 2021 (Accepted for publication). Ventilator-associated pneumonia in critically ill patients with COVID-19 Critical Care (UK),
  • 2021

  • Will, RC., Ramamurthy, T., Sharma, NC., Veeraraghavan, B., Sangal, L., Haldar, P., Pragasam, AK., Vasudevan, K., Kumar, D., Das, B., Heinz, E., Melnikov, V., Baker, S., Sangal, V., Dougan, G. and Mutreja, A., 2021. Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae. Nat Commun, v. 12
    Doi: http://doi.org/10.1038/s41467-021-21870-5
  • Carey, ME., Jain, R., Yousuf, M., Maes, M., Dyson, ZA., Thu, TNH., Nguyen Thi Nguyen, T., Ho Ngoc Dan, T., Nhu Pham Nguyen, Q., Mahindroo, J., Thanh Pham, D., Sandha, KS., Baker, S. and Taneja, N., 2021. Spontaneous Emergence of Azithromycin Resistance in Independent Lineages of Salmonella Typhi in Northern India. Clin Infect Dis, v. 72
    Doi: http://doi.org/10.1093/cid/ciaa1773
  • Sridhar, S., Forrest, S., Warne, B., Maes, M., Baker, S., Dougan, G. and Bartholdson Scott, J., 2021. High-Content Imaging to Phenotype Antimicrobial Effects on Individual Bacteria at Scale. mSystems, v. 6
    Doi: http://doi.org/10.1128/mSystems.00028-21
  • Thuy, DB., Campbell, J., Thuy, CT., Hoang, NVM., Voong Vinh, P., Nguyen, TNT., Nguyen Ngoc Minh, C., Pham, DT., Rabaa, MA., Lan, NPH., Hao, NV., Thwaites, GE., Thwaites, CL., Baker, S., Chau, NVV. and Chung The, H., 2021. Colonization with Staphylococcus aureus and Klebsiella pneumoniae causes infections in a Vietnamese intensive care unit. Microb Genom, v. 7
    Doi: http://doi.org/10.1099/mgen.0.000514
  • Chung The, H., Bodhidatta, L., Pham, DT., Mason, CJ., Ha Thanh, T., Voong Vinh, P., Turner, P., Hem, S., Dance, DAB., Newton, PN., Phetsouvanh, R., Davong, V., Thwaites, GE., Thomson, NR., Baker, S. and Rabaa, MA., 2021. Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia. Commun Biol, v. 4
    Doi: http://doi.org/10.1038/s42003-021-01905-9
  • Maes, M., Dyson, ZA., Smith, SE., Goulding, DA., Ludden, C., Baker, S., Kellam, P., Reece, ST., Dougan, G. and Bartholdson Scott, J., 2021. Publisher Correction: A novel therapeutic antibody screening method using bacterial high-content imaging reveals functional antibody binding phenotypes of Escherichia coli ST131. Sci Rep, v. 11
    Doi: http://doi.org/10.1038/s41598-021-86902-y
  • Tu, NTK., Deng, X., Hong, NTT., Ny, NTH., Phuc, TM., Tam, PTT., Han, DA., Ha, LTT., Thwaites, G., Doorn, HRV., Virtala, A-MK., Delwart, E., Baker, S., Vapalahti, O., Tan, LV. and On Behalf Of The Vizions Consortium, , 2021. Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission. Viruses, v. 13
    Doi: http://doi.org/10.3390/v13040533
  • Argimón, S., Yeats, CA., Goater, RJ., Abudahab, K., Taylor, B., Underwood, A., Sánchez-Busó, L., Wong, VK., Dyson, ZA., Nair, S., Park, SE., Marks, F., Page, AJ., Keane, JA., Baker, S., Holt, KE., Dougan, G. and Aanensen, DM., 2021. A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. Nat Commun, v. 12
    Doi: http://doi.org/10.1038/s41467-021-23091-2
  • Mylona, E., Sanchez-Garrido, J., Hoang Thu, TN., Dongol, S., Karkey, A., Baker, S., Shenoy, AR. and Frankel, G., 2021. Very long O-antigen chains of Salmonella Paratyphi A inhibit inflammasome activation and pyroptotic cell death. Cell Microbiol, v. 23
    Doi: http://doi.org/10.1111/cmi.13306
  • Warne, B., Enright, J., Metaxaki, M., Fuller, S., Samworth, R., Weale, G., Holgate, J., Samtani, V., Brierley, C., Aggarwal, D., Hilborne, S., Kahkeshi, MB., Berry, S., Douthwaite, J., Orton, A., Clarke, R., Danaei, D., Dyer, R., Glew, R., Lambson, O., Dahal, A., Margolis, B., Murphy, E., Russell, M., Braithwaite, V., Faulkner, K., Wright, E., Chaudhry, A., Mactavous, L., Dhada, M., Parlikad, A., Greatorex, J., Leslie, I., Neely, A., Rees, S., Shaw, A., Vinnell, M., Sheridan, L., Watkins, E., Baker, S., Goodfellow, I., Lehner, P., Liddell, K., Clark, R., Howes, R., Weekes, M., McFarlane, D., Maxwell, P., Matheson, N. and University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium, , 2021. Feasibility and efficacy of mass testing for SARS-CoV-2 in a UK university using swab pooling and PCR
    Doi: http://doi.org/10.21203/rs.3.rs-520626/v1
  • de Alwis, R., Liang, L., Taghavian, O., Werner, E., The, HC., Thu, TNH., Duong, VT., Davies, DH., Felgner, PL. and Baker, S., 2021. The identification of novel immunogenic antigens as potential Shigella vaccine components. Genome Med, v. 13
    Doi: http://doi.org/10.1186/s13073-020-00824-4
  • Baker, S., 2021. Challenges and opportunities in antimicrobial resistance research. Microbiology (Reading), v. 167
    Doi: http://doi.org/10.1099/mic.0.000999
  • Manandhar, S., Amatya, P., Ansari, I., Joshi, N., Maharjan, N., Dongol, S., Basnyat, B., Dixit, SM., Baker, S. and Karkey, A., 2021. Risk factors for the development of neonatal sepsis in a neonatal intensive care unit of a tertiary care hospital of Nepal. BMC Infect Dis, v. 21
    Doi: http://doi.org/10.1186/s12879-021-06261-x
  • Anh, NT., Nhu, LNT., Hong, NTT., Phuc, TM., Tam, PTT., Huong, DT., Anh, TT., Deng, X., Nghia, HDT., Nguyen, TT., Van Hung, N., Thuan, ND., Phuong, PTH., Chau, NVV., Baker, S., Delwart, E., Thwaites, G., Van Tan, L. and VIZIONS Consortium1, , 2021. Viral Metagenomic Analysis of Cerebrospinal Fluid from Patients with Acute Central Nervous System Infections of Unknown Origin, Vietnam. Emerg Infect Dis, v. 27
    Doi: http://doi.org/10.3201/eid2701.202723
  • Sridhar, S., Forrest, S., Pickard, D., Cormie, C., Lees, EA., Thomson, NR., Dougan, G. and Baker, S., 2021. Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium. mBio, v. 12
    Doi: http://doi.org/10.1128/mBio.01093-21
  • Qumar, S., Nguyen, TH., Nahar, S., Sarker, N., Baker, S., Bulach, D., Ahmed, N. and Rahman, M., 2021. A comparative whole genome analysis of Helicobacter pylori from a human dense South Asian setting. Helicobacter, v. 26
    Doi: http://doi.org/10.1111/hel.12766
  • Sridhar, S., Forrest, S., Warne, B., Maes, M., Baker, S., Dougan, G. and Scott, JB., 2021. High-content imaging to phenotype antimicrobial effects on individual bacteria at scale
    Doi: http://doi.org/10.1101/2021.01.11.426307
  • Stephenson, E., Reynolds, G., Botting, RA., Calero-Nieto, FJ., Morgan, MD., Tuong, ZK., Bach, K., Sungnak, W., Worlock, KB., Yoshida, M., Kumasaka, N., Kania, K., Engelbert, J., Olabi, B., Spegarova, JS., Wilson, NK., Mende, N., Jardine, L., Gardner, LCS., Goh, I., Horsfall, D., McGrath, J., Webb, S., Mather, MW., Lindeboom, RGH., Dann, E., Huang, N., Polanski, K., Prigmore, E., Gothe, F., Scott, J., Payne, RP., Baker, KF., Hanrath, AT., Schim van der Loeff, ICD., Barr, AS., Sanchez-Gonzalez, A., Bergamaschi, L., Mescia, F., Barnes, JL., Kilich, E., de Wilton, A., Saigal, A., Saleh, A., Janes, SM., Smith, CM., Gopee, N., Wilson, C., Coupland, P., Coxhead, JM., Kiselev, VY., van Dongen, S., Bacardit, J., King, HW., Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, , Rostron, AJ., Simpson, AJ., Hambleton, S., Laurenti, E., Lyons, PA., Meyer, KB., Nikolić, MZ., Duncan, CJA., Smith, KGC., Teichmann, SA., Clatworthy, MR., Marioni, JC., Göttgens, B. and Haniffa, M., 2021. Single-cell multi-omics analysis of the immune response in COVID-19. Nat Med, v. 27
    Doi: http://doi.org/10.1038/s41591-021-01329-2
  • Collier, DA., De Marco, A., Ferreira, IATM., Meng, B., Datir, RP., Walls, AC., Kemp, SA., Bassi, J., Pinto, D., Silacci-Fregni, C., Bianchi, S., Tortorici, MA., Bowen, J., Culap, K., Jaconi, S., Cameroni, E., Snell, G., Pizzuto, MS., Pellanda, AF., Garzoni, C., Riva, A., CITIID-NIHR BioResource COVID-19 Collaboration, , Elmer, A., Kingston, N., Graves, B., McCoy, LE., Smith, KGC., Bradley, JR., Temperton, N., Ceron-Gutierrez, L., Barcenas-Morales, G., COVID-19 Genomics UK (COG-UK) Consortium, , Harvey, W., Virgin, HW., Lanzavecchia, A., Piccoli, L., Doffinger, R., Wills, M., Veesler, D., Corti, D. and Gupta, RK., 2021. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies Nature, v. 593
    Doi: http://doi.org/10.1038/s41586-021-03412-7
  • Hawkey, J., Paranagama, K., Baker, KS., Bengtsson, RJ., Weill, F-X., Thomson, NR., Baker, S., Cerdeira, L., Iqbal, Z., Hunt, M., Ingle, DJ., Dallman, TJ., Jenkins, C., Williamson, DA. and Holt, KE., 2021. Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nat Commun, v. 12
    Doi: http://doi.org/10.1038/s41467-021-22700-4
  • Giri, A., Karkey, A., Dangol, S., Arjyal, A., Pokharel, S., Rijal, S., Gajurel, D., Sharma, R., Lamsal, K., Shrestha, P., Prajapati, G., Pathak, S., Shrestha, SR., K C, RK., Pandey, S., Thapa, A., Shrestha, N., Thapa, RK., Poudyal, B., Phuong, DNT., Baker, S., Kestelyn, E., Geskus, R., Thwaites, G. and Basnyat, B., 2021. Trimethoprim-sulfamethoxazole Versus Azithromycin for the Treatment of Undifferentiated Febrile Illness in Nepal: A Double-blind, Randomized, Placebo-controlled Trial. Clin Infect Dis, v. 73
    Doi: http://doi.org/10.1093/cid/ciaa1489
  • Devaraj, A., González, JF., Eichar, B., Thilliez, G., Kingsley, RA., Baker, S., Allard, MW., Bakaletz, LO., Gunn, JS. and Goodman, SD., 2021. Enhanced biofilm and extracellular matrix production by chronic carriage versus acute isolates of Salmonella Typhi. PLoS Pathog, v. 17
    Doi: http://doi.org/10.1371/journal.ppat.1009209
  • de Alwis, R., Phuc, TM., Bai, BYH., Quynh, NLT., Tam, PTT., Dung, TTN., Nhan, NTT., Vinh, C., Hien, HV., Nhat, LTH., Hong, NTT., Tuyen, NTM., Trang, HTT., Thao, LP., Diep, VTN., Chau, PTH., Thinh, LQ., Thu, HTN., Hang, NN., Danh, MC., Hao, TD., Dao, TA., Dai, L., Diu, VTH., En, NT., Hanh, NTT., Hanh, LT., Hien, HPT., Linh, NTT., Darton, TC., Thwaites, GE., Kestelyn, E., Vi, LL., Tien, BTT., Tuyet, HTD., Anderson, C. and Baker, S., 2021. The influence of human genetic variation on early transcriptional responses and protective immunity following immunization with Rotarix vaccine in infants in Ho Chi Minh City in Vietnam: A study protocol for an open single-arm interventional trial Wellcome Open Research, v. 5
    Doi: http://doi.org/10.12688/WELLCOMEOPENRES.16090.1
  • Nguyen, NT., Phuong Yen, NT., Ky Thien, NV., Van Cuong, N., Kiet, BT., Campbell, J., Thwaites, G., Baker, S., Geskus, RB. and Carrique-Mas, J., 2021. A novel method for measuring phenotypic colistin resistance in Escherichia coli populations from chicken flocks. Appl Environ Microbiol, v. 87
    Doi: 10.1128/AEM.02597-20
  • 2020 (Accepted for publication)

  • Weekes, M., rivett, L., Sridhar, S., sparkes, D., routledge, M., jones, N., forrest, S., young, J., Pereira-Dias, J., hamilton, W., torok, E., Meredith, L., curran, M., fuller, S., Samworth, R., Bradley, J., Dougan, G., Smith, K., Lehner, P., Matheson, N., Goodfellow, I. and Baker, S., 2020 (Accepted for publication). Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission eLife,
  • Weekes, M., 2020 (Accepted for publication). Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 eLife,
    Doi: http://doi.org/10.7554/eLife.59391
  • 2020

  • Manandhar, S., Zellweger, RM., Maharjan, N., Dongol, S., Prajapati, KG., Thwaites, G., Basnyat, B., Dixit, SM., Baker, S. and Karkey, A., 2020. A high prevalence of multi-drug resistant Gram-negative bacilli in a Nepali tertiary care hospital and associated widespread distribution of Extended-Spectrum Beta-Lactamase (ESBL) and carbapenemase-encoding genes. Ann Clin Microbiol Antimicrob, v. 19
    Doi: http://doi.org/10.1186/s12941-020-00390-y
  • Sridhar, S., Forrest, S., Kean, I., Young, J., Bartholdson Scott, J., Maes, M., Pereira-Dias, J., Parmar, S., Routledge, M., Sparkes, D., Rivett, L., Dougan, G., Weekes, M., Curran, M., Goodfellow, I. and Baker, S., 2020. A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities. Wellcome Open Res, v. 5
    Doi: http://doi.org/10.12688/wellcomeopenres.15937.2
  • Parisi, A., Le Thi Phuong, T., Mather, AE., Jombart, T., Thanh Tuyen, H., Phu Huong Lan, N., Hoang Thu Trang, N., Carrique-Mas, J., Campbell, JI., Glass, K., Kirk, MD. and Baker, S., 2020. Differential antimicrobial susceptibility profiles between symptomatic and asymptomatic non-typhoidal Salmonella infections in Vietnamese children. Epidemiol Infect, v. 148
    Doi: http://doi.org/10.1017/S0950268820001168
  • Minh, NNQ., Toi, PV., Qui, LM., Tinh, LBB., Ngoc, NT., Kim, LTN., Uyen, NH., Hang, VTT., Chinh B'Krong, NTT., Tham, NT., Khoa, TD., Khuong, HD., Vi, PQ., Phuc, NNH., Vien, LTM., Pouplin, T., Khanh, DV., Phuong, PN., Lam, PK., Wertheim, HFL., Campbell, JI., Baker, S., Parry, CM., Bryant, JE., Schultsz, C., Hung, NT., de Jong, MD. and van Doorn, HR., 2020. Antibiotic use and prescription and its effects on Enterobacteriaceae in the gut in children with mild respiratory infections in Ho Chi Minh City, Vietnam. A prospective observational outpatient study. PLoS One, v. 15
    Doi: http://doi.org/10.1371/journal.pone.0241760
  • Thanh Duy, P., Thi Nguyen, TN., Vu Thuy, D., Chung The, H., Alcock, F., Boinett, C., Dan Thanh, HN., Thanh Tuyen, H., Thwaites, GE., Rabaa, MA. and Baker, S., 2020. Commensal Escherichia coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei. Nat Microbiol, v. 5
    Doi: http://doi.org/10.1038/s41564-019-0645-9
  • Maes, M., Dyson, ZA., Smith, SE., Goulding, DA., Ludden, C., Baker, S., Kellam, P., Reece, ST., Dougan, G. and Bartholdson Scott, J., 2020. A novel therapeutic antibody screening method using bacterial high-content imaging reveals functional antibody binding phenotypes of Escherichia coli ST131. Sci Rep, v. 10
    Doi: http://doi.org/10.1038/s41598-020-69300-8
  • Gallagher, P. and Baker, S., 2020. Developing new therapeutic approaches for treating infections caused by multi-drug resistant Acinetobacter baumannii: Acinetobacter baumannii therapeutics. J Infect, v. 81
    Doi: http://doi.org/10.1016/j.jinf.2020.10.016
  • Carey, ME., MacWright, WR., Im, J., Meiring, JE., Gibani, MM., Park, SE., Longley, A., Jeon, HJ., Hemlock, C., Yu, AT., Soura, A., Aiemjoy, K., Owusu-Dabo, E., Terferi, M., Islam, S., Lunguya, O., Jacobs, J., Gordon, M., Dolecek, C., Baker, S., Pitzer, VE., Yousafzai, MT., Tonks, S., Clemens, JD., Date, K., Qadri, F., Heyderman, RS., Saha, SK., Basnyat, B., Okeke, IN., Qamar, FN., Voysey, M., Luby, S., Kang, G., Andrews, J., Pollard, AJ., John, J., Garrett, D. and Marks, F., 2020. r Studies: A Review of Methodological Similarities and Differences. ... Clin Infect Dis, v. 71
    Doi: http://doi.org/10.1093/cid/ciaa367
  • Tuan-Anh, T., Tuyen, HT., Minh Chau, NN., Toan, ND., Triet, TH., Triet, LM., Trang, NHT., To, NTN., Bartholdson Scott, J., The, HC., Thanh, DP., Clapham, H. and Baker, S., 2020. Pathogenic Escherichia coli Possess Elevated Growth Rates under Exposure to Sub-Inhibitory Concentrations of Azithromycin. Antibiotics (Basel), v. 9
    Doi: http://doi.org/10.3390/antibiotics9110735
  • da Silva, KE., Baker, S., Croda, J., Nguyen, TNT., Boinett, CJ., Barbosa, LS., Tetila, A. and Simionatto, S., 2020. Risk factors for polymyxin-resistant carbapenemase-producing Enterobacteriaceae in critically ill patients: An epidemiological and clinical study. Int J Antimicrob Agents, v. 55
    Doi: http://doi.org/10.1016/j.ijantimicag.2020.105882
  • Andrews, JR., Yu, AT., Saha, S., Shakya, J., Aiemjoy, K., Horng, L., Qamar, F., Garrett, D., Baker, S., Saha, S. and Luby, SP., 2020. Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission. Clin Infect Dis, v. 71
    Doi: http://doi.org/10.1093/cid/ciaa513
  • Mlcochova, P., Collier, D., Ritchie, A., Assennato, SM., Hosmillo, M., Goel, N., Meng, B., Chatterjee, K., Mendoza, V., Temperton, N., Kiss, L., James, LC., Ciazynska, KA., Xiong, X., Briggs, JAG., Nathan, JA., Mescia, F., Bergamaschi, L., Zhang, H., Barmpounakis, P., Demeris, N., Skells, R., Lyons, PA., Bradley, J., Baker, S., Allain, JP., Smith, KGC., Bousfield, R., Wilson, M., Sparkes, D., Amoroso, G., Gkrania-Klotsas, E., Hardwick, S., Boyle, A., Goodfellow, I., Gupta, RK. and Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, , 2020. Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Cell Rep Med, v. 1
    Doi: http://doi.org/10.1016/j.xcrm.2020.100099
  • Baker, S., Kellam, P., Krishna, A. and Reece, S., 2020. Protecting intubated patients from the threat of antimicrobial resistant infections with monoclonal antibodies. Lancet Microbe, v. 1
    Doi: http://doi.org/10.1016/S2666-5247(20)30126-9
  • Diaz-Guevara, P., Montaño, LA., Duarte, C., Zabaleta, G., Maes, M., Martinez Angarita, JC., Thanh, DP., León-Quevedo, W., Castañeda-Orjuela, C., Alvarez Alvarez, CJ., Guerrero, J., Moroni, M., Campos, J., Pérez, E. and Baker, S., 2020. Surveillance of Salmonella enterica serovar  Typhi in Colombia, 2012-2015. PLoS Negl Trop Dis, v. 14
    Doi: http://doi.org/10.1371/journal.pntd.0008040
  • Baker, S., Blohmke, CJ., Maes, M., Johnston, PI. and Darton, TC., 2020. The Current Status of Enteric Fever Diagnostics and Implications for Disease Control. Clin Infect Dis, v. 71
    Doi: http://doi.org/10.1093/cid/ciaa503
  • Xiong, X., Qu, K., Ciazynska, KA., Hosmillo, M., Carter, AP., Ebrahimi, S., Ke, Z., Scheres, SHW., Bergamaschi, L., Grice, GL., Zhang, Y., CITIID-NIHR COVID-19 BioResource Collaboration, , Nathan, JA., Baker, S., James, LC., Baxendale, HE., Goodfellow, I., Doffinger, R. and Briggs, JAG., 2020. A thermostable, closed SARS-CoV-2 spike protein trimer. Nature Structural and Molecular Biology, v. 27
    Doi: http://doi.org/10.1038/s41594-020-0478-5
  • Collier, DA., Assennato, SM., Warne, B., Sithole, N., Sharrocks, K., Ritchie, A., Ravji, P., Routledge, M., Sparkes, D., Skittrall, J., Smielewska, A., Ramsey, I., Goel, N., Curran, M., Enoch, D., Tassell, R., Lineham, M., Vaghela, D., Leong, C., Mok, HP., Bradley, J., Smith, KGC., Mendoza, V., Demiris, N., Besser, M., Dougan, G., Lehner, PJ., Siedner, MJ., Zhang, H., Waddington, CS., Lee, H., Gupta, RK. and Collaboration, CCB., 2020. Point of Care Nucleic Acid Testing for SARS-CoV-2 in Hospitalized Patients: A Clinical Validation Trial and Implementation Study Cell Rep Med, v. 1
    Doi: http://doi.org/10.1016/j.xcrm.2020.100062
  • Thanh, LT., Toffaletti, DL., Tenor, JL., Giamberardino, C., Sempowski, GD., Asfaw, Y., Phan, HT., Van Duong, A., Trinh, NM., Thwaites, GE., Ashton, PM., Chau, NVV., Baker, SG., Perfect, JR. and Day, JN., 2020. Assessing the virulence of Cryptococcus neoformans causing meningitis in HIV infected and uninfected patients in Vietnam. Med Mycol, v. 58
    Doi: http://doi.org/10.1093/mmy/myaa013
  • da Silva, KE., Thi Nguyen, TN., Boinett, CJ., Baker, S. and Simionatto, S., 2020. Molecular and epidemiological surveillance of polymyxin-resistant Klebsiella pneumoniae strains isolated from Brazil with multiple mgrB gene mutations. Int J Med Microbiol, v. 310
    Doi: http://doi.org/10.1016/j.ijmm.2020.151448
  • Duong, VT., The, HC., Nhu, TDH., Tuyen, HT., Campbell, JI., Minh, PV., Phuc, HL., Chau, TTH., Ngoc, NM., Vi, LL., Mather, AE. and Baker, S., 2020. Genomic Serotyping, Clinical Manifestations, and Antimicrobial Resistance of Nontyphoidal Salmonella Gastroenteritis in Hospitalized Children in Ho Chi Minh City, Vietnam. J Clin Microbiol, v. 58
    Doi: http://doi.org/10.1128/JCM.01465-20
  • Nhung, NT., Yen, NTP., Cuong, N., Kiet, BT., Hien, VB., Campbell, J., Thwaites, G., Baker, S., Geskus, R., Ashton, P. and Carrique-Mas, J., 2020. Carriage of the zoonotic organism Streptococcus suis in chicken flocks in Vietnam. Zoonoses Public Health, v. 67
    Doi: http://doi.org/10.1111/zph.12711
  • Thi Kha Tu, N., Thi Thu Hong, N., Thi Han Ny, N., My Phuc, T., Thi Thanh Tam, P., Doorn, HRV., Dang Trung Nghia, H., Thao Huong, D., An Han, D., Thi Thu Ha, L., Deng, X., Thwaites, G., Delwart, E., Virtala, A-MK., Vapalahti, O., Baker, S. and Van Tan, L., 2020. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses, v. 12
    Doi: http://doi.org/10.3390/v12090960
  • Peacock, S., Meredith, L., Dougan, G., Torok, ME., Baker, S., Brwon, N. and Gouliouris, T., 2020. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study Lancet Infectious Diseases,
    Doi: http://doi.org/10.1016/S1473-3099(20)30562-4
  • Duy, PT., Dongol, S., Giri, A., Nguyen To, NT., Dan Thanh, HN., Nhu Quynh, NP., Duc Trung, P., Thwaites, GE., Basnyat, B., Baker, S., Rabaa, MA. and Karkey, A., 2020. The emergence of azithromycin-resistant Salmonella Typhi in Nepal. JAC Antimicrob Resist, v. 2
    Doi: http://doi.org/10.1093/jacamr/dlaa109
  • Parisi, A., Phuong, TLT., Mather, AE., Jombart, T., Tuyen, HT., Lan, NPH., Trang, NHT., Carrique-Mas, J., Campbell, JI., Trung, NV., Glass, K., Kirk, MD. and Baker, S., 2020. The role of animals as a source of antimicrobial resistant nontyphoidal Salmonella causing invasive and non-invasive human disease in Vietnam. Infect Genet Evol, v. 85
    Doi: http://doi.org/10.1016/j.meegid.2020.104534
  • Yen, NTP., Nhung, NT., Van, NTB., Cuong, NV., Tien Chau, LT., Trinh, HN., Tuat, CV., Tu, ND., Phu Huong Lan, N., Campbell, J., Thwaites, G., Baker, S. and Carrique-Mas, J., 2020. Antimicrobial residues, non-typhoidal Salmonella, Vibrio spp. and associated microbiological hazards in retail shrimps purchased in Ho Chi Minh city (Vietnam). Food Control, v. 107
    Doi: http://doi.org/10.1016/j.foodcont.2019.106756
  • Nguyen, TTK., Ngo, TT., Tran, PM., Pham, TTT., Vu, HTT., Nguyen, NTH., Thwaites, G., Virtala, A-MK., Vapalahti, O., Baker, S. and Le Van, T., 2020. Respiratory viruses in individuals with a high frequency of animal exposure in southern and highland Vietnam. J Med Virol, v. 92
    Doi: http://doi.org/10.1002/jmv.25640
  • Lu, L., Robertson, G., Ashworth, J., Pham Hong, A., Shi, T., Ivens, A., Thwaites, G., Baker, S. and Woolhouse, M., 2020. Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam. Front Microbiol, v. 11
    Doi: http://doi.org/10.3389/fmicb.2020.00833
  • Robertson, G., Perry, M., Vinh, PV., Ngoc, DTT., Thanh, TPT., My, PT., Thao, HD., Rabaa, M., Baker, S., Woolhouse, M. and VIZIONS consortium, , 2020. Pig Exposure and Health Outcomes in Hospitalized Infectious Disease Patients in Vietnam. Ecohealth, v. 17
    Doi: http://doi.org/10.1007/s10393-019-01460-0
  • Duong, VT., Tu, LTP., Tuyen, HT., Nhi, LTQ., Campbell, JI., Van Minh, P., Le Phuc, H., Chau, TTH., Ngoc, NM., Vi, LL., Jenkins, C., Okeke, I., Higginson, E. and Baker, S., 2020. Novel multiplex real-time PCR assays reveal a high prevalence of diarrhoeagenic Escherichia coli pathotypes in healthy and diarrhoeal children in the south of Vietnam. BMC Microbiol, v. 20
    Doi: http://doi.org/10.1186/s12866-020-01878-5
  • Browne, AJ., Kashef Hamadani, BH., Kumaran, EAP., Rao, P., Longbottom, J., Harriss, E., Moore, CE., Dunachie, S., Basnyat, B., Baker, S., Lopez, AD., Day, NPJ., Hay, SI. and Dolecek, C., 2020. Drug-resistant enteric fever worldwide, 1990 to 2018: a systematic review and meta-analysis. BMC Med, v. 18
    Doi: http://doi.org/10.1186/s12916-019-1443-1
  • Im, J., Balasubramanian, R., Ouedraogo, M., Wandji Nana, LR., Mogeni, OD., Jeon, HJ., van Pomeren, T., Haselbeck, A., Lim, JK., Prifti, K., Baker, S., Meyer, CG., Kim, JH., Clemens, JD., Marks, F. and Soura, AB., 2020. The epidemiology of dengue outbreaks in 2016 and 2017 in Ouagadougou, Burkina Faso. Heliyon, v. 6
    Doi: http://doi.org/10.1016/j.heliyon.2020.e04389
  • Maes, M., Dyson, ZA., Higginson, EE., Fernandez, A., Araya, P., Tennant, SM., Baker, S., Lagos, R., Levine, MM., Hormazabal, JC. and Dougan, G., 2020. Multiple Introductions of Salmonella enterica Serovar Typhi H58 with Reduced Fluoroquinolone Susceptibility into Chile. Emerg Infect Dis, v. 26
    Doi: http://doi.org/10.3201/eid2611.201676
  • Wyres, KL., Nguyen, TNT., Lam, MMC., Judd, LM., van Vinh Chau, N., Dance, DAB., Ip, M., Karkey, A., Ling, CL., Miliya, T., Newton, PN., Lan, NPH., Sengduangphachanh, A., Turner, P., Veeraraghavan, B., Vinh, PV., Vongsouvath, M., Thomson, NR., Baker, S. and Holt, KE., 2020. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med, v. 12
    Doi: http://doi.org/10.1186/s13073-019-0706-y
  • Thanh Duy, P., Thieu, NTV., Nguyen Thi Nguyen, T., Ngoc Dan Thanh, H., Dongol, S., Karkey, A., Carey, M., Basnyat, B., Dougan, G., Rabaa, MA. and Baker, S., 2020. Gallbladder carriage generates genetic variation and genome degradation in Salmonella Typhi. PLoS Pathog, v. 16
    Doi: http://doi.org/10.1371/journal.ppat.1008998
  • Carrique-Mas, JJ., Choisy, M., Van Cuong, N., Thwaites, G. and Baker, S., 2020. An estimation of total antimicrobial usage in humans and animals in Vietnam. Antimicrob Resist Infect Control, v. 9
    Doi: http://doi.org/10.1186/s13756-019-0671-7
  • Darton, TC., Chau, TTH., Parry, CM., Campbell, JI., Ngoc, NM., Ngoc, TLC., Tuyen, HT., Duong, VT., Nhat, LTH., van Minh, P., Kestelyn, E., Thwaites, GE., Tung, TH. and Baker, S., 2020. The CIPAZ study protocol: an open label randomised controlled trial of azithromycin versus ciprofloxacin for the treatment of children hospitalised with dysentery in Ho Chi Minh City, Vietnam [version 1; peer review: 2 approved with reservations] Wellcome Open Research, v. 5
    Doi: http://doi.org/10.12688/wellcomeopenres.16093.1
  • Iqbal, J., Dehraj, IF., Carey, ME., Dyson, ZA., Garrett, D., Seidman, JC., Kabir, F., Saha, S., Baker, S. and Qamar, FN., 2020. A Race against Time: Reduced Azithromycin Susceptibility in Salmonella enterica Serovar Typhi in Pakistan. mSphere, v. 5
    Doi: http://doi.org/10.1128/mSphere.00215-20
  • 2019 (No publication date)

  • Dougan, G., Ashton, PM., Thanh, LT., Trieu, PH., Van Anh, D., Trinh, NM., Beardsley, J., Kibengo, F., Chierakul, W., Dance, DAB., Hung, LQ., Chau, NVV., Tung, NLN., Chan, AK., Thwaites, GE., Lalloo, DG., Anscombe, C., Nhat, LTH., Perfect, J., Baker, S., Harris, S. and Day, JN., 2019 (No publication date). Three phylogenetic groups have driven the recent population 2 expansion of C. neoformans Nature Communications,
  • 2019

  • Boinett, CJ., Cain, AK., Hawkey, J., Do Hoang, NT., Khanh, NNT., Thanh, DP., Dordel, J., Campbell, JI., Lan, NPH., Mayho, M., Langridge, GC., Hadfield, J., Chau, NVV., Thwaites, GE., Parkhill, J., Thomson, NR., Holt, KE. and Baker, S., 2019. Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microb Genom, v. 5
    Doi: http://doi.org/10.1099/mgen.0.000246
  • Jeon, HJ., Im, J., Haselbeck, A., Holm, M., Rakotozandrindrainy, R., Bassiahi, AS., Panzner, U., Mogeni, OD., Seo, HJ., Lunguya, O., Jacobs, J., Okeke, IN., Terferi, M., Owusu-Dabo, E., Dougan, G., Carey, M., Steele, AD., Kim, JH., Clemens, JD., Andrews, JR., Park, SE., Baker, S. and Marks, F., 2019. How Can the Typhoid Fever Surveillance in Africa and the Severe Typhoid Fever in Africa Programs Contribute to the Introduction of Typhoid Conjugate Vaccines? Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz629
  • Le Ngoc, C., Tran Thi Thanh, T., Tran Thi Lan, P., Nguyen Mai, T., Nguyen Hoa, T., Nghiem My, N., Le Van, T., Le Manh, H., Le Thanh, P., Nguyen Van Vinh, C., Thwaites, G., Cooke, G., Heilek, GM., Shikuma, C., Le, T., Baker, S., Rahman, M. and VIZIONS consortium, , 2019. Differential prevalence and geographic distribution of hepatitis C virus genotypes in acute and chronic hepatitis C patients in Vietnam. PLoS One, v. 14
    Doi: http://doi.org/10.1371/journal.pone.0212734
  • Huynh, TTN., Nguyen, HQ., Vinh, PV., Baker, S. and Pathirana, A., 2019. Enteric pathogens in flood-related waters in urban areas of the Vietnamese Mekong Delta: a case study of Ninh Kieu district, Can Tho city Urban Water Journal, v. 16
    Doi: http://doi.org/10.1080/1573062X.2020.1713381
  • Carrique-Mas, J., Van Cuong, N., Truong, BD., Phu, DH., Phuc, TM., Turner, H., Thwaites, G. and Baker, S., 2019. Affordability of antimicrobials for animals and humans in Vietnam: A call to revise pricing policies. Int J Antimicrob Agents, v. 54
    Doi: http://doi.org/10.1016/j.ijantimicag.2019.05.009
  • Toy, T., Pak, GD., Duc, TP., Campbell, JI., El Tayeb, MA., Von Kalckreuth, V., Im, J., Panzner, U., Cruz Espinoza, LM., Eibach, D., Dekker, DM., Park, SE., Jeon, HJ., Konings, F., Mogeni, OD., Cosmas, L., Bjerregaard-Andersen, M., Gasmelseed, N., Hertz, JT., Jaeger, A., Krumkamp, R., Ley, B., Thriemer, K., Kabore, LP., Niang, A., Raminosoa, TM., Sampo, E., Sarpong, N., Soura, A., Owusu-Dabo, E., Teferi, M., Yeshitela, B., Poppert, S., May, J., Kim, JH., Chon, Y., Park, JK., Aseffa, A., Breiman, RF., Schütt-Gerowitt, H., Aaby, P., Adu-Sarkodie, Y., Crump, JA., Rakotozandrindrainy, R., Meyer, CG., Sow, AG., Clemens, JD., Wierzba, TF., Baker, S. and Marks, F., 2019. Multicountry Distribution and Characterization of Extended-spectrum β-Lactamase-associated Gram-negative Bacteria From Bloodstream Infections in Sub-Saharan Africa. Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz450
  • Nadjm, B., Dat, VQ., Campbell, JI., Dung, VTV., Torre, A., Tu, NTC., Van, NTT., Trinh, DT., Lan, NPH., Trung, NV., Hang, NTT., Hoi, LT., Baker, S., Wolbers, M., Chau, NVV., Van Kinh, N., Thwaites, GE., van Doorn, HR. and Wertheim, HFL., 2019. erial and fungal infections in Vietnam. ... J Infect, v. 78
    Doi: http://doi.org/10.1016/j.jinf.2019.03.010
  • Saha, S., Tanmoy, AM., Andrews, JR., Sajib, MSI., Yu, AT., Baker, S., Luby, SP. and Saha, SK., 2019. Evaluating PCR-Based Detection of Salmonella Typhi and Paratyphi A in the Environment as an Enteric Fever Surveillance Tool. American Journal of Tropical Medicine and Hygiene, v. 100
    Doi: http://doi.org/10.4269/ajtmh.18-0428
  • de Alwis, R., Tu, LTP., Quynh, NLT., Thompson, CN., Anders, KL., Van Thuy, NT., Hieu, NT., Vi, LL., Chau, NVV., Duong, VT., Chau, TTH., Tuyen, HT., Nga, TVT., Minh, PV., Tan, TV., Thu, TNH., Nhu, TDH., Thwaites, GE., Simmons, C. and Baker, S., 2019. The Role of Maternally Acquired Antibody in Providing Protective Immunity Against Nontyphoidal Salmonella in Urban Vietnamese Infants: A Birth Cohort Study. J Infect Dis, v. 219
    Doi: http://doi.org/10.1093/infdis/jiy501
  • Park, SE., Toy, T., Cruz Espinoza, LM., Panzner, U., Mogeni, OD., Im, J., Poudyal, N., Pak, GD., Seo, H., Chon, Y., Schütt-Gerowitt, H., Mogasale, V., Ramani, E., Dey, A., Park, JY., Kim, J-H., Seo, HJ., Jeon, HJ., Haselbeck, A., Conway Roy, K., MacWright, W., Adu-Sarkodie, Y., Owusu-Dabo, E., Osei, I., Owusu, M., Rakotozandrindrainy, R., Soura, AB., Kabore, LP., Teferi, M., Okeke, IN., Kehinde, A., Popoola, O., Jacobs, J., Lunguya Metila, O., Meyer, CG., Crump, JA., Elias, S., Maclennan, CA., Parry, CM., Baker, S., Mintz, ED., Breiman, RF., Clemens, JD. and Marks, F., 2019. The Severe Typhoid Fever in Africa Program: Study Design and Methodology to Assess Disease Severity, Host Immunity, and Carriage Associated With Invasive Salmonellosis. Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz715
  • Crellen, T., Turner, P., Pol, S., Baker, S., Nguyen Thi Nguyen, T., Stoesser, N., Day, NP., Turner, C. and Cooper, BS., 2019. Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country. Elife, v. 8
    Doi: http://doi.org/10.7554/eLife.50468
  • Baker, S., Ali, M., Deerin, JF., Eltayeb, MA., Cruz Espinoza, LM., Gasmelseed, N., Im, J., Panzner, U., Kalckreuth, VV., Keddy, KH., Pak, GD., Park, JK., Park, SE., Sooka, A., Sow, AG., Tall, A., Luby, S., Meyer, CG. and Marks, F., 2019. The Typhoid Fever Surveillance in Africa Program: Geospatial Sampling Frames for Household-based Studies: Lessons Learned From a Multicountry Surveillance Network in Senegal, South Africa, and Sudan. Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz755
  • Nguyen-Hoang, T-P., Nguyen Hoa, T., Nguyen, T-H., Baker, S., Rahman, M. and Nguyen, T-V., 2019. Complete Genome Sequence of Helicobacter pylori Strain GD63, Isolated from a Vietnamese Patient with a Gastric Ulcer. Microbiol Resour Announc, v. 8
    Doi: http://doi.org/10.1128/MRA.01412-18
  • Popoola, O., Kehinde, A., Ogunleye, V., Adewusi, OJ., Toy, T., Mogeni, OD., Aroyewun, EO., Agbi, S., Adekanmbi, O., Adepoju, A., Muyibi, S., Adebiyi, I., Elaturoti, OO., Nwimo, C., Adeoti, H., Omotosho, T., Akinlabi, OC., Adegoke, PA., Adeyanju, OA., Panzner, U., Baker, S., Park, SE., Marks, F. and Okeke, IN., 2019. Bacteremia Among Febrile Patients Attending Selected Healthcare Facilities in Ibadan, Nigeria. Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz516
  • Yeung, A., Hale, C., Clare, S., Palmer, S., Bartholdson Scott, J., Baker, S. and Dougan, G., 2019. Using a Systems Biology Approach To Study Host-Pathogen Interactions. Microbiol Spectr, v. 7
    Doi: http://doi.org/10.1128/microbiolspec.BAI-0021-2019
  • Mogeni, OD., Cruz Espinoza, LM., Im, J., Panzner, U., Toy, T., Pak, GD., Haselbeck, A., Ramani, E., Schütt-Gerowitt, H., Jacobs, J., Metila, OL., Adewusi, OJ., Okeke, IN., Ogunleye, VI., Owusu-Dabo, E., Rakotozandrindrainy, R., Soura, AB., Teferi, M., Roy, KC., Macwright, W., Breiman, RF., Kim, JH., Mogasale, V., Baker, S., Park, SE. and Marks, F., 2019. The Monitoring and Evaluation of a Multicountry Surveillance Study, the Severe Typhoid Fever in Africa Program. Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz597
  • Nguyen, LV., Ta, QV., Dang, TB., Nguyen, PH., Nguyen, T., Pham, TVH., Nguyen, TH., Baker, S., Le Tran, T., Yang, DJ., Kim, KW. and Doan, KV., 2019. Carvedilol improves glucose tolerance and insulin sensitivity in treatment of adrenergic overdrive in high fat diet-induced obesity in mice. PLoS One, v. 14
    Doi: http://doi.org/10.1371/journal.pone.0224674
  • Parry, CM., Ribeiro, I., Walia, K., Rupali, P., Baker, S. and Basnyat, B., 2019. Multidrug resistant enteric fever in South Asia: unmet medical needs and opportunities. BMJ, v. 364
    Doi: http://doi.org/10.1136/bmj.k5322
  • Barkham, T., Zadoks, RN., Azmai, MNA., Baker, S., Bich, VTN., Chalker, V., Chau, ML., Dance, D., Deepak, RN., van Doorn, HR., Gutierrez, RA., Holmes, MA., Huong, LNP., Koh, TH., Martins, E., Mehershahi, K., Newton, P., Ng, LC., Phuoc, NN., Sangwichian, O., Sawatwong, P., Surin, U., Tan, TY., Tang, WY., Thuy, NV., Turner, P., Vongsouvath, M., Zhang, D., Whistler, T. and Chen, SL., 2019. One hypervirulent clone, sequence type 283, accounts for a large proportion of invasive Streptococcus agalactiae isolated from humans and diseased tilapia in Southeast Asia. PLoS Negl Trop Dis, v. 13
    Doi: http://doi.org/10.1371/journal.pntd.0007421
  • Mahindroo, J., Thanh, DP., Nguyen, TNT., Mohan, B., Thakur, S., Baker, S. and Taneja, N., 2019. Endemic fluoroquinolone-resistant Salmonellaenterica serovar Kentucky ST198 in northern India. Microb Genom, v. 5
    Doi: http://doi.org/10.1099/mgen.0.000275
  • Tu, NTK., Tue, NT., Vapalahti, O., Virtala, A-MK., Van Tan, L., Rabaa, MA., Carrique-Mas, J., Thwaites, GE., Baker, S. and VIZIONS consortium, , 2019. Occupational Animal Contact in Southern and Central Vietnam. Ecohealth, v. 16
    Doi: http://doi.org/10.1007/s10393-019-01444-0
  • Balasubramanian, R., Im, J., Lee, J-S., Jeon, HJ., Mogeni, OD., Kim, JH., Rakotozandrindrainy, R., Baker, S. and Marks, F., 2019. The global burden and epidemiology of invasive non-typhoidal Salmonella infections. Hum Vaccin Immunother, v. 15
    Doi: http://doi.org/10.1080/21645515.2018.1504717
  • Woolhouse, M., Ashworth, J., Bogaardt, C., Tue, NT., Baker, S., Thwaites, G. and Phuc, TM., 2019. Sample descriptors linked to metagenomic sequencing data from human and animal enteric samples from Vietnam. Sci Data, v. 6
    Doi: http://doi.org/10.1038/s41597-019-0215-2
  • Msefula, CL., Olgemoeller, F., Jambo, N., Segula, D., Van Tan, T., Nyirenda, TS., Nedi, W., Kennedy, N., Graham, M., Henrion, MYR., Baker, S., Feasey, N., Gordon, M. and Heyderman, RS., 2019. Ascertaining the burden of invasive Salmonella disease in hospitalised febrile children aged under four years in Blantyre, Malawi. PLoS Negl Trop Dis, v. 13
    Doi: http://doi.org/10.1371/journal.pntd.0007539
  • Shakya, M., Colin-Jones, R., Theiss-Nyland, K., Voysey, M., Pant, D., Smith, N., Liu, X., Tonks, S., Mazur, O., Farooq, YG., Clarke, J., Hill, J., Adhikari, A., Dongol, S., Karkey, A., Bajracharya, B., Kelly, S., Gurung, M., Baker, S., Neuzil, KM., Shrestha, S., Basnyat, B., Pollard, AJ. and TyVAC Nepal Study Team, , 2019. Phase 3 Efficacy Analysis of a Typhoid Conjugate Vaccine Trial in Nepal. N Engl J Med, v. 381
    Doi: http://doi.org/10.1056/NEJMoa1905047
  • Andrews, JR., Baker, S., Marks, F., Alsan, M., Garrett, D., Gellin, BG., Saha, SK., Qamar, FN., Yousafzai, MT., Bogoch, II., Antillon, M., Pitzer, VE., Kim, J-H., John, J., Gauld, J., Mogasale, V., Ryan, ET., Luby, SP. and Lo, NC., 2019. Typhoid conjugate vaccines: a new tool in the fight against antimicrobial resistance. Lancet Infect Dis, v. 19
    Doi: http://doi.org/10.1016/S1473-3099(18)30350-5
  • Blohmke, CJ., Muller, J., Gibani, MM., Dobinson, H., Shrestha, S., Perinparajah, S., Jin, C., Hughes, H., Blackwell, L., Dongol, S., Karkey, A., Schreiber, F., Pickard, D., Basnyat, B., Dougan, G., Baker, S., Pollard, AJ. and Darton, TC., 2019. Diagnostic host gene signature for distinguishing enteric fever from other febrile diseases. EMBO Mol Med, v. 11
    Doi: http://doi.org/10.15252/emmm.201910431
  • Kestelyn, E., Le Phuong, C., Ilo Van Nuil, J., Dong Thi, HT., Minh Nguyen, N., Dinh The, T., Chambers, M., Simmons, CP., Nguyen Trong, T., Nguyen The, D., Phuong, LT., Do Van, D., Duc Anh, D., Nguyen Van, VC., Baker, S., Wills, B. and OUCRU Controlled Human Infection Models workshop and focus group participants, , 2019. Expert voices and equal partnerships: establishing Controlled Human Infection Models (CHIMs) in Vietnam. Wellcome Open Res, v. 4
    Doi: http://doi.org/10.12688/wellcomeopenres.15337.1
  • Pitzer, VE., Meiring, J., Martineau, FP., Watson, CH., Kang, G., Basnyat, B. and Baker, S., 2019. The Invisible Burden: Diagnosing and Combatting Typhoid Fever in Asia and Africa. Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz611
  • Chung The, H., Boinett, C., Pham Thanh, D., Jenkins, C., Weill, F-X., Howden, BP., Valcanis, M., De Lappe, N., Cormican, M., Wangchuk, S., Bodhidatta, L., Mason, CJ., Nguyen, TNT., Ha Thanh, T., Voong, VP., Duong, VT., Nguyen, PHL., Turner, P., Wick, R., Ceyssens, P-J., Thwaites, G., Holt, KE., Thomson, NR., Rabaa, MA. and Baker, S., 2019. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nat Commun, v. 10
    Doi: http://doi.org/10.1038/s41467-019-12823-0
  • Teferi, M., Desta, M., Yeshitela, B., Beyene, T., Cruz Espinoza, LM., Im, J., Jeon, HJ., Kim, J-H., Konings, F., Kwon, SY., Pak, GD., Park, JK., Park, SE., Yedenekachew, M., Kim, J., Baker, S., Sir, WS., Marks, F., Aseffa, A. and Panzner, U., 2019. Acute Febrile Illness Among Children in Butajira, South-Central Ethiopia During the Typhoid Fever Surveillance in Africa Program. Clin Infect Dis, v. 69
    Doi: http://doi.org/10.1093/cid/ciz620
  • Napolitani, G., Kurupati, P., Teng, KWW., Gibani, MM., Rei, M., Aulicino, A., Preciado-Llanes, L., Wong, MT., Becht, E., Howson, L., de Haas, P., Salio, M., Blohmke, CJ., Olsen, LR., Pinto, DMS., Scifo, L., Jones, C., Dobinson, H., Campbell, D., Juel, HB., Thomaides-Brears, H., Pickard, D., Bumann, D., Baker, S., Dougan, G., Simmons, A., Gordon, MA., Newell, EW., Pollard, AJ. and Cerundolo, V., 2019. Publisher Correction: Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses. Nat Immunol, v. 20
    Doi: http://doi.org/10.1038/s41590-019-0357-6
  • 2018 (Published online)

  • Thi Ty Hang, V., Thi Han Ny, N., My Phuc, T., Thi Thanh Tam, P., Thao Huong, D., Dang Trung Nghia, H., Tran Anh Vu, N., Thi Hong Phuong, P., Van Xang, N., Dong, N., Nhu Hiep, P., Van Hung, N., Tinh Hien, T., Rabaa, M., Thwaites, GE., Baker, S., Van Tan, L. and van Doorn, HR., 2018 (Published online). Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam Wellcome Open Research, v. 2
    Doi: 10.12688/wellcomeopenres.12429.2
  • Ny, NTH., Anh, NT., Hang, VTT., Nguyet, LA., Thanh, TT., Ha, DQ., Minh, NNQ., Ha, DLA., McBride, A., Tuan, HM., Baker, S., Tam, PTT., Phuc, TM., Huong, DT., Loi, TQ., Vu, NTA., Hung, NV., Minh, TTT., Xang, NV., Dong, N., Nghia, HDT., Chau, NVV., Thwaites, G., van Doorn, HR., Anscombe, C. and Le Van, T., 2018 (Published online). Enterovirus D68 in Viet Nam (2009-2015) Wellcome Open Research, v. 2
    Doi: 10.12688/wellcomeopenres.11558.2
  • 2018

  • Duong, VT., Tuyen, HT., Van Minh, P., Campbell, JI., Phuc, HL., Nhu, TDH., Tu, LTP., Chau, TTH., Nhi, LTQ., Hung, NT., Ngoc, NM., Huong, NTT., Vi, LL., Thompson, CN., Thwaites, GE., de Alwis, R. and Baker, S., 2018. No Clinical Benefit of Empirical Antimicrobial Therapy for Pediatric Diarrhea in a High-Usage, High-Resistance Setting. Clin Infect Dis, v. 66
    Doi: http://doi.org/10.1093/cid/cix844
  • Klemm, EJ., Shakoor, S., Page, AJ., Qamar, FN., Judge, K., Saeed, DK., Wong, VK., Dallman, TJ., Nair, S., Baker, S., Shaheen, G., Qureshi, S., Yousafzai, MT., Saleem, MK., Hasan, Z., Dougan, G. and Hasan, R., 2018. Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins. mBio, v. 9
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  • 2016

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  • 2013

  • Karkey, A., Thompson, CN., Tran Vu Thieu, N., Dongol, S., Le Thi Phuong, T., Voong Vinh, P., Arjyal, A., Martin, LB., Rondini, S., Farrar, JJ., Dolecek, C., Basnyat, B. and Baker, S., 2013. Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: a matched case control investigation in a highly endemic enteric fever setting. PLoS Negl Trop Dis, v. 7
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    Doi: http://doi.org/10.1128/mBio.00231-13
  • Campbell, JI., Lan, NPH., Qui, PT., Dung, LT., Farrar, JJ. and Baker, S., 2013. A successful antimicrobial regime for Chromobacterium violaceum induced bacteremia. BMC Infect Dis, v. 13
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  • Kolader, M-E., Vinh, H., Ngoc Tuyet, PT., Thompson, C., Wolbers, M., Merson, L., Campbell, JI., Ngoc Dung, TT., Manh Tuan, H., Vinh Chau, NV., Farrar, J., van Doorn, HR. and Baker, S., 2013. An oral preparation of Lactobacillus acidophilus for the treatment of uncomplicated acute watery diarrhoea in Vietnamese children: study protocol for a multicentre, randomised, placebo-controlled trial. Trials, v. 14
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  • Castonguay-Vanier, J., Davong, V., Bouthasavong, L., Sengdetka, D., Simmalavong, M., Seupsavith, A., Dance, DAB., Baker, S., Le Thi Phuong, T., Vongsouvath, M. and Newton, PN., 2013. Evaluation of a simple blood culture amplification and antigen detection method for diagnosis of Salmonella enterica serovar typhi bacteremia. J Clin Microbiol, v. 51
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  • Liang, L., Juarez, S., Nga, TVT., Dunstan, S., Nakajima-Sasaki, R., Davies, DH., McSorley, S., Baker, S. and Felgner, PL., 2013. Immune profiling with a Salmonella Typhi antigen microarray identifies new diagnostic biomarkers of human typhoid. Sci Rep, v. 3
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  • Trang, NHT., Nga, TVT., Campbell, JI., Hiep, NT., Farrar, J., Baker, S. and Duy, PT., 2013. The characterization of ESBL genes in Escherichia coli and Klebsiella pneumoniae causing nosocomial infections in Vietnam. J Infect Dev Ctries, v. 7
    Doi: http://doi.org/10.3855/jidc.2938
  • Holt, KE., Thieu Nga, TV., Thanh, DP., Vinh, H., Kim, DW., Vu Tra, MP., Campbell, JI., Hoang, NVM., Vinh, NT., Minh, PV., Thuy, CT., Nga, TTT., Thompson, C., Dung, TTN., Nhu, NTK., Vinh, PV., Tuyet, PTN., Phuc, HL., Lien, NTN., Phu, BD., Ai, NTT., Tien, NM., Dong, N., Parry, CM., Hien, TT., Farrar, JJ., Parkhill, J., Dougan, G., Thomson, NR. and Baker, S., 2013. Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proc Natl Acad Sci U S A, v. 110
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  • Koirala, S., Basnyat, B., Arjyal, A., Shilpakar, O., Shrestha, K., Shrestha, R., Shrestha, UM., Agrawal, K., Koirala, KD., Thapa, SD., Karkey, A., Dongol, S., Giri, A., Shakya, M., Pathak, KR., Campbell, J., Baker, S., Farrar, J., Wolbers, M. and Dolecek, C., 2013. Gatifloxacin versus ofloxacin for the treatment of uncomplicated enteric fever in Nepal: an open-label, randomized, controlled trial. PLoS Negl Trop Dis, v. 7
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  • My, PVT., Thompson, C., Phuc, HL., Tuyet, PTN., Vinh, H., Hoang, NVM., Minh, PV., Vinh, NT., Thuy, CT., Nga, TTT., Hau, NTT., Campbell, J., Chinh, NT., Thuong, TC., Tuan, HM., Farrar, J. and Baker, S., 2013. Endemic norovirus infections in children, Ho Chi Minh City, Vietnam, 2009-2010. Emerg Infect Dis, v. 19
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  • Pham Thanh, D., Tran Vu Thieu, N., Tran Thuy, C., Lodén, M., Tuin, K., Campbell, JI., Van Minh Hoang, N., Voong Vinh, P., Farrar, JJ., Holt, KE., Dougan, G. and Baker, S., 2013. Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification. J Clin Microbiol, v. 51
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  • Day, JN., Chau, TTH., Wolbers, M., Mai, PP., Dung, NT., Mai, NH., Phu, NH., Nghia, HD., Phong, ND., Thai, CQ., Thai, LH., Chuong, LV., Sinh, DX., Duong, VA., Hoang, TN., Diep, PT., Campbell, JI., Sieu, TPM., Baker, SG., Chau, NVV., Hien, TT., Lalloo, DG. and Farrar, JJ., 2013. Combination antifungal therapy for cryptococcal meningitis. N Engl J Med, v. 368
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  • Baker, S., Duy, PT., Nga, TVT., Dung, TTN., Phat, VV., Chau, TT., Keith Turner, A., Farrar, J. and Boni, MF., 2013. Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure eLife, v. 2013
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  • Shieh, M., Thompson, C., Phan, VTM., Van, TTL., Tediosi, F., Merson, L., Farrar, JJ., Ha, MT., Ho, LV., Pham, TNT. and Baker, S., 2013. The policy of free healthcare for children under the age of 6 years in Vietnam: assessment of the uptake for children hospitalised with acute diarrhoea in Ho Chi Minh City. Trop Med Int Health, v. 18
    Doi: http://doi.org/10.1111/tmi.12208
  • Charles, RC., Sultana, T., Alam, MM., Yu, Y., Wu-Freeman, Y., Bufano, MK., Rollins, SM., Tsai, L., Harris, JB., LaRocque, RC., Leung, DT., Brooks, WA., Nga, TVT., Dongol, S., Basnyat, B., Calderwood, SB., Farrar, J., Khanam, F., Gunn, JS., Qadri, F., Baker, S. and Ryan, ET., 2013. Identification of immunogenic Salmonella enterica serotype Typhi antigens expressed in chronic biliary carriers of S. Typhi in Kathmandu, Nepal. PLoS Negl Trop Dis, v. 7
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  • Andrews, JR., Prajapati, KG., Eypper, E., Shrestha, P., Shakya, M., Pathak, KR., Joshi, N., Tiwari, P., Risal, M., Koirala, S., Karkey, A., Dongol, S., Wen, S., Smith, AB., Maru, D., Basnyat, B., Baker, S., Farrar, J., Ryan, ET., Hohmann, E. and Arjyal, A., 2013. Evaluation of an electricity-free, culture-based approach for detecting typhoidal Salmonella bacteremia during enteric fever in a high burden, resource-limited setting. PLoS Negl Trop Dis, v. 7
    Doi: http://doi.org/10.1371/journal.pntd.0002292
  • Thompson, CN., Phan, VTM., Le, TPT., Pham, TNT., Hoang, LP., Ha, V., Nguyen, VMH., Pham, VM., Nguyen, TV., Cao, TT., Tran, TTN., Nguyen, TTH., Dao, MT., Campbell, JI., Nguyen, TC., Tang, CT., Ha, MT., Farrar, J. and Baker, S., 2013. Epidemiological features and risk factors of Salmonella gastroenteritis in children resident in Ho Chi Minh City, Vietnam. Epidemiol Infect, v. 141
    Doi: http://doi.org/10.1017/S0950268812002014
  • Tra My, PV., Lam, HM., Thompson, CN., Phuc, HL., Tuyet, PTN., Vinh, H., Hoang, NVM., Minh, P., Vinh, NT., Thuy, CT., Nga, TTT., Hau, NTT., Chinh, NT., Thuong, TC., Tuan, HM., Campbell, JI., Clements, ACA., Farrar, J., Boni, MF. and Baker, S., 2013. The dynamics of GII.4 Norovirus in Ho Chi Minh City, Vietnam. Infect Genet Evol, v. 18
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  • Phu, NH., Hoang Mai, NT., Nghia, HDT., Chau, TTH., Loc, PP., Thai, LH., Phuong, TM., Thai, CQ., Man, DNH., Van Vinh Chau, N., Nga, TVT., Campbell, J., Baker, S. and Whitehorn, J., 2013. Fatal consequences of freshwater pearl diving. Lancet, v. 381
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  • 2012

  • Vien, LTM., Minh, NNQ., Thuong, TC., Khuong, HD., Nga, TVT., Thompson, C., Campbell, JI., de Jong, M., Farrar, JJ., Schultsz, C., van Doorn, HR. and Baker, S., 2012. The co-selection of fluoroquinolone resistance genes in the gut flora of Vietnamese children. PLoS One, v. 7
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  • Koirala, KD., Thanh, DP., Thapa, SD., Arjyal, A., Karkey, A., Dongol, S., Shrestha, UM., Farrar, JJ., Basnyat, B. and Baker, S., 2012. Highly resistant Salmonella enterica serovar Typhi with a novel gyrA mutation raises questions about the long-term efficacy of older fluoroquinolones for treating typhoid fever. Antimicrob Agents Chemother, v. 56
    Doi: http://doi.org/10.1128/AAC.06414-11
  • Wijedoru, LPM., Kumar, V., Chanpheaktra, N., Chheng, K., Smits, HL., Pastoor, R., Nga, TVT., Baker, S., Wuthiekanun, V., Peacock, SJ., Putchhat, H. and Parry, CM., 2012. Typhoid fever among hospitalized febrile children in Siem Reap, Cambodia. J Trop Pediatr, v. 58
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  • Seth-Smith, HMB., Fookes, MC., Okoro, CK., Baker, S., Harris, SR., Scott, P., Pickard, D., Quail, MA., Churcher, C., Sanders, M., Harmse, J., Dougan, G., Parkhill, J. and Thomson, NR., 2012. Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae. J Bacteriol, v. 194
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  • 2011

  • Karavolos, MH., Bulmer, DM., Spencer, H., Rampioni, G., Schmalen, I., Baker, S., Pickard, D., Gray, J., Fookes, M., Winzer, K., Ivens, A., Dougan, G., Williams, P. and Khan, CMA., 2011. Salmonella Typhi sense host neuroendocrine stress hormones and release the toxin haemolysin E. EMBO Rep, v. 12
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  • Hoa, NT., Chieu, TTB., Nghia, HDT., Mai, NTH., Anh, PH., Wolbers, M., Baker, S., Campbell, JI., Chau, NVV., Hien, TT., Farrar, J. and Schultsz, C., 2011. The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008. BMC Infect Dis, v. 11
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  • Vinh, H., Anh, VTC., Anh, ND., Campbell, JI., Hoang, NVM., Nga, TVT., Nhu, NTK., Minh, PV., Thuy, CT., Duy, PT., Phuong, LT., Loan, HT., Chinh, MT., Thao, NTT., Tham, NTH., Mong, BL., Bay, PVB., Day, JN., Dolecek, C., Lan, NPH., Diep, TS., Farrar, JJ., Chau, NVV., Wolbers, M. and Baker, S., 2011. A multi-center randomized trial to assess the efficacy of gatifloxacin versus ciprofloxacin for the treatment of shigellosis in Vietnamese children. PLoS Negl Trop Dis, v. 5
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  • Croucher, NJ., Harris, SR., Fraser, C., Quail, MA., Burton, J., van der Linden, M., McGee, L., von Gottberg, A., Song, JH., Ko, KS., Pichon, B., Baker, S., Parry, CM., Lambertsen, LM., Shahinas, D., Pillai, DR., Mitchell, TJ., Dougan, G., Tomasz, A., Klugman, KP., Parkhill, J., Hanage, WP. and Bentley, SD., 2011. Rapid pneumococcal evolution in response to clinical interventions. Science, v. 331
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  • Baker, S., Holt, KE., Clements, ACA., Karkey, A., Arjyal, A., Boni, MF., Dongol, S., Hammond, N., Koirala, S., Duy, PT., Nga, TVT., Campbell, JI., Dolecek, C., Basnyat, B., Dougan, G. and Farrar, JJ., 2011. Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission. Open Biol, v. 1
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  • Tra My, PV., Rabaa, MA., Vinh, H., Holmes, EC., Hoang, NVM., Vinh, NT., Phuong, LT., Tham, NT., Bay, PVB., Campbell, JI., Farrar, J. and Baker, S., 2011. The emergence of rotavirus G12 and the prevalence of enteric viruses in hospitalized pediatric diarrheal patients in southern Vietnam. Am J Trop Med Hyg, v. 85
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  • Arjyal, A., Basnyat, B., Koirala, S., Karkey, A., Dongol, S., Agrawaal, KK., Shakya, N., Shrestha, K., Sharma, M., Lama, S., Shrestha, K., Khatri, NS., Shrestha, U., Campbell, JI., Baker, S., Farrar, J., Wolbers, M. and Dolecek, C., 2011. Gatifloxacin versus chloramphenicol for uncomplicated enteric fever: an open-label, randomised, controlled trial. Lancet Infect Dis, v. 11
    Doi: http://doi.org/10.1016/S1473-3099(11)70089-5
  • Holt, KE., Phan, MD., Baker, S., Duy, PT., Nga, TVT., Nair, S., Turner, AK., Walsh, C., Fanning, S., Farrell-Ward, S., Dutta, S., Kariuki, S., Weill, F-X., Parkhill, J., Dougan, G. and Wain, J., 2011. Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid. PLoS Negl Trop Dis, v. 5
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  • Day, JN., Hoang, TN., Duong, AV., Hong, CTT., Diep, PT., Campbell, JI., Sieu, TPM., Hien, TT., Bui, T., Boni, MF., Lalloo, DG., Carter, D., Baker, S. and Farrar, JJ., 2011. Most cases of cryptococcal meningitis in HIV-uninfected patients in Vietnam are due to a distinct amplified fragment length polymorphism-defined cluster of Cryptococcus neoformans var. grubii VN1. J Clin Microbiol, v. 49
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  • 2010

  • Karkey, A., Arjyal, A., Anders, KL., Boni, MF., Dongol, S., Koirala, S., My, PVT., Nga, TVT., Clements, ACA., Holt, KE., Duy, PT., Day, JN., Campbell, JI., Dougan, G., Dolecek, C., Farrar, J., Basnyat, B. and Baker, S., 2010. The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu. PLoS One, v. 5
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  • Nga, TVT., Karkey, A., Dongol, S., Thuy, HN., Dunstan, S., Holt, K., Tu, LTP., Campbell, JI., Chau, TT., Chau, NVV., Arjyal, A., Koirala, S., Basnyat, B., Dolecek, C., Farrar, J. and Baker, S., 2010. The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens. BMC Infect Dis, v. 10
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  • Parry, CM., Thuy, CT., Dongol, S., Karkey, A., Vinh, H., Chinh, NT., Duy, PT., Thieu Nga, TV., Campbell, JI., Van Minh Hoang, N., Arjyal, A., Bhutta, ZA., Bhattacharya, SK., Agtini, MD., Dong, B., Canh, DG., Naheed, A., Wain, J., Tinh Hien, T., Basnyat, B., Ochiai, L., Clemens, J., Farrar, JJ., Dolecek, C. and Baker, S., 2010. Suitable disk antimicrobial susceptibility breakpoints defining Salmonella enterica serovar Typhi isolates with reduced susceptibility to fluoroquinolones. Antimicrob Agents Chemother, v. 54
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  • Chau, TT., Mai, NH., Phu, NH., Nghia, HD., Chuong, LV., Sinh, DX., Duong, VA., Diep, PT., Campbell, JI., Baker, S., Hien, TT., Lalloo, DG., Farrar, JJ. and Day, JN., 2010. A prospective descriptive study of cryptococcal meningitis in HIV uninfected patients in Vietnam - high prevalence of Cryptococcus neoformans var grubii in the absence of underlying disease. BMC Infect Dis, v. 10
    Doi: http://doi.org/10.1186/1471-2334-10-199
  • Nguyen, NTK., Ha, V., Tran, NVT., Stabler, R., Pham, DT., Le, TMV., van Doorn, HR., Cerdeño-Tárraga, A., Thomson, N., Campbell, J., Nguyen, VMH., Tran, TTN., Pham, MV., Cao, TT., Wren, B., Farrar, J. and Baker, S., 2010. The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam. PLoS Negl Trop Dis, v. 4
    Doi: http://doi.org/10.1371/journal.pntd.0000702
  • Chau, TTH., Campbell, JI., Schultsz, C., Chau, NVV., Diep, TS., Baker, S., Chinh, NT., Farrar, JJ. and van Doorn, HR., 2010. Three adult cases of Listeria monocytogenes meningitis in Vietnam. PLoS Med, v. 7
    Doi: http://doi.org/10.1371/journal.pmed.1000306
  • Holt, KE., Baker, S., Dongol, S., Basnyat, B., Adhikari, N., Thorson, S., Pulickal, AS., Song, Y., Parkhill, J., Farrar, JJ., Murdoch, DR., Kelly, DF., Pollard, AJ. and Dougan, G., 2010. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children. BMC Infect Dis, v. 10
    Doi: http://doi.org/10.1186/1471-2334-10-144
  • 2009

  • Minh Vien, LT., Baker, S., Phuong Thao, LT., Phuong Tu, LT., Thu Thuy, C., Thu Nga, TT., Minh Hoang, NV., Campbell, JI., Minh Yen, L., Trong Hieu, N., Vinh Chau, NV., Farrar, J. and Schultsz, C., 2009. High prevalence of plasmid-mediated quinolone resistance determinants in commensal members of the Enterobacteriaceae in Ho Chi Minh City, Vietnam. J Med Microbiol, v. 58
    Doi: http://doi.org/10.1099/jmm.0.010033-0
  • Campbell, JI., Lam, TMY., Huynh, TL., To, SD., Tran, TTN., Nguyen, VMH., Le, TS., Nguyen, VVC., Parry, C., Farrar, JJ., Tran, TH. and Baker, S., 2009. Microbiologic characterization and antimicrobial susceptibility of Clostridium tetani isolated from wounds of patients with clinically diagnosed tetanus. Am J Trop Med Hyg, v. 80
  • Vinh, H., Baker, S., Campbell, J., Hoang, NVM., Loan, HT., Chinh, MT., Anh, VTC., Diep, TS., Phuong, LT., Schultsz, C. and Farrar, J., 2009. Rapid emergence of third generation cephalosporin resistant Shigella spp. in Southern Vietnam. J Med Microbiol, v. 58
    Doi: http://doi.org/10.1099/jmm.0.002949-0
  • Vinh, H., Nhu, NTK., Nga, TVT., Duy, PT., Campbell, JI., Hoang, NVM., Boni, MF., My, PVT., Parry, C., Nga, TTT., Van Minh, P., Thuy, CT., Diep, TS., Phuong, LT., Chinh, MT., Loan, HT., Tham, NTH., Lanh, MN., Mong, BL., Anh, VTC., Bay, PVB., Chau, NVV., Farrar, J. and Baker, S., 2009. A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation. BMC Infect Dis, v. 9
    Doi: http://doi.org/10.1186/1471-2334-9-204
  • Khatri, NS., Maskey, P., Poudel, S., Jaiswal, VK., Karkey, A., Koirala, S., Shakya, N., Agrawal, K., Arjyal, A., Basnyat, B., Day, J., Farrar, J., Dolecek, C. and Baker, S., 2009. Gallbladder carriage of Salmonella paratyphi A may be an important factor in the increasing incidence of this infection in South Asia. Ann Intern Med, v. 150
    Doi: http://doi.org/10.7326/0003-4819-150-8-200904210-00017
  • 2008

  • Baker, S., Holt, K., van de Vosse, E., Roumagnac, P., Whitehead, S., King, E., Ewels, P., Keniry, A., Weill, F-X., Lightfoot, D., van Dissel, JT., Sanderson, KE., Farrar, J., Achtman, M., Deloukas, P. and Dougan, G., 2008. High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia. J Clin Microbiol, v. 46
    Doi: http://doi.org/10.1128/JCM.02249-07
  • Baker, S., Campbell, JI., Stabler, R., Nguyen, HVM., To, DS., Nguyen, DV. and Farrar, J., 2008. Fatal wound infection caused by Chromobacterium violaceum in Ho Chi Minh City, Vietnam. J Clin Microbiol, v. 46
    Doi: http://doi.org/10.1128/JCM.01068-08
  • Baker, S., Pickard, D., Whitehead, S., Farrar, J. and Dougan, G., 2008. Mobilization of the incQ plasmid R300B with a chromosomal conjugation system in Salmonella enterica serovar typhi. J Bacteriol, v. 190
    Doi: http://doi.org/10.1128/JB.00065-08
  • Bishop, A., House, D., Perkins, T., Baker, S., Kingsley, RA. and Dougan, G., 2008. Interaction of Salmonella enterica serovar Typhi with cultured epithelial cells: roles of surface structures in adhesion and invasion. Microbiology (Reading), v. 154
    Doi: http://doi.org/10.1099/mic.0.2008/016998-0
  • Pickard, D., Thomson, NR., Baker, S., Wain, J., Pardo, M., Goulding, D., Hamlin, N., Choudhary, J., Threfall, J. and Dougan, G., 2008. Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1. J Bacteriol, v. 190
    Doi: http://doi.org/10.1128/JB.01654-07
  • Karkey, A., Aryjal, A., Basnyat, B. and Baker, S., 2008. Kathmandu, Nepal: still an enteric fever capital of the world. J Infect Dev Ctries, v. 2
    Doi: http://doi.org/10.3855/jidc.162
  • Holt, KE., Parkhill, J., Mazzoni, CJ., Roumagnac, P., Weill, F-X., Goodhead, I., Rance, R., Baker, S., Maskell, DJ., Wain, J., Dolecek, C., Achtman, M. and Dougan, G., 2008. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet, v. 40
    Doi: http://doi.org/10.1038/ng.195
  • 2007

  • Baker, S., Hardy, J., Sanderson, KE., Quail, M., Goodhead, I., Kingsley, RA., Parkhill, J., Stocker, B. and Dougan, G., 2007. A novel linear plasmid mediates flagellar variation in Salmonella Typhi. PLoS Pathog, v. 3
    Doi: http://doi.org/10.1371/journal.ppat.0030059
  • Baker, S., Holt, K., Whitehead, S., Goodhead, I., Perkins, T., Stocker, B., Hardy, J. and Dougan, G., 2007. A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. Mol Microbiol, v. 66
    Doi: http://doi.org/10.1111/j.1365-2958.2007.05995.x
  • Baker, S. and Dougan, G., 2007. The genome of Salmonella enterica serovar Typhi. Clin Infect Dis, v. 45 Suppl 1
    Doi: http://doi.org/10.1086/518143
  • Baker, S., Hardy, J., Sanderson, KE., Quail, M., Goodhead, I., Kingsley, RA., Parkhill, J., Stocker, B. and Dougan, G., 2007. A novel linear plasmid mediates flagellar variation in Salmonella Typhi PLoS Pathogens, v. 3
    Doi: http://doi.org/10.1371/journal.ppat.0030059
  • 2006

  • Roumagnac, P., Weill, F-X., Dolecek, C., Baker, S., Brisse, S., Chinh, NT., Le, TAH., Acosta, CJ., Farrar, J., Dougan, G. and Achtman, M., 2006. Evolutionary history of Salmonella typhi. Science, v. 314
    Doi: http://doi.org/10.1126/science.1134933
  • Sebaihia, M., Wren, BW., Mullany, P., Fairweather, NF., Minton, N., Stabler, R., Thomson, NR., Roberts, AP., Cerdeño-Tárraga, AM., Wang, H., Holden, MTG., Wright, A., Churcher, C., Quail, MA., Baker, S., Bason, N., Brooks, K., Chillingworth, T., Cronin, A., Davis, P., Dowd, L., Fraser, A., Feltwell, T., Hance, Z., Holroyd, S., Jagels, K., Moule, S., Mungall, K., Price, C., Rabbinowitsch, E., Sharp, S., Simmonds, M., Stevens, K., Unwin, L., Whithead, S., Dupuy, B., Dougan, G., Barrell, B. and Parkhill, J., 2006. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet, v. 38
    Doi: http://doi.org/10.1038/ng1830
  • 2005

  • Bishop, AL., Baker, S., Jenks, S., Fookes, M., Gaora, PO., Pickard, D., Anjum, M., Farrar, J., Hien, TT., Ivens, A. and Dougan, G., 2005. Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX). J Bacteriol, v. 187
    Doi: http://doi.org/10.1128/JB.187.7.2469-2482.2005
  • Wain, J., House, D., Zafar, A., Baker, S., Nair, S., Kidgell, C., Bhutta, Z., Dougan, G. and Hasan, R., 2005. Vi antigen expression in Salmonella enterica serovar Typhi clinical isolates from Pakistan. J Clin Microbiol, v. 43
    Doi: http://doi.org/10.1128/JCM.43.3.1158-1165.2005
  • Baker, S., Sarwar, Y., Aziz, H., Haque, A., Ali, A., Dougan, G., Wain, J. and Haque, A., 2005. Detection of Vi-negative Salmonella enterica serovar typhi in the peripheral blood of patients with typhoid fever in the Faisalabad region of Pakistan. J Clin Microbiol, v. 43
    Doi: http://doi.org/10.1128/JCM.43.9.4418-4425.2005
  • Anjum, MF., Marooney, C., Fookes, M., Baker, S., Dougan, G., Ivens, A. and Woodward, MJ., 2005. Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray. Infect Immun, v. 73
    Doi: http://doi.org/10.1128/IAI.73.12.7894-7905.2005
  • 2004

  • Liu, M., Gingery, M., Doulatov, SR., Liu, Y., Hodes, A., Baker, S., Davis, P., Simmonds, M., Churcher, C., Mungall, K., Quail, MA., Preston, A., Harvill, ET., Maskell, DJ., Eiserling, FA., Parkhill, J. and Miller, JF., 2004. Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes. J Bacteriol, v. 186
    Doi: http://doi.org/10.1128/JB.186.5.1503-1517.2004
  • Thomson, N., Baker, S., Pickard, D., Fookes, M., Anjum, M., Hamlin, N., Wain, J., House, D., Bhutta, Z., Chan, K., Falkow, S., Parkhill, J., Woodward, M., Ivens, A. and Dougan, G., 2004. The role of prophage-like elements in the diversity of Salmonella enterica serovars. J Mol Biol, v. 339
    Doi: http://doi.org/10.1016/j.jmb.2004.03.058
  • 2003

  • Parkhill, J., Sebaihia, M., Preston, A., Murphy, LD., Thomson, N., Harris, DE., Holden, MTG., Churcher, CM., Bentley, SD., Mungall, KL., Cerdeño-Tárraga, AM., Temple, L., James, K., Harris, B., Quail, MA., Achtman, M., Atkin, R., Baker, S., Basham, D., Bason, N., Cherevach, I., Chillingworth, T., Collins, M., Cronin, A., Davis, P., Doggett, J., Feltwell, T., Goble, A., Hamlin, N., Hauser, H., Holroyd, S., Jagels, K., Leather, S., Moule, S., Norberczak, H., O'Neil, S., Ormond, D., Price, C., Rabbinowitsch, E., Rutter, S., Sanders, M., Saunders, D., Seeger, K., Sharp, S., Simmonds, M., Skelton, J., Squares, R., Squares, S., Stevens, K., Unwin, L., Whitehead, S., Barrell, BG. and Maskell, DJ., 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet, v. 35
    Doi: http://doi.org/10.1038/ng1227
  • Chan, K., Baker, S., Kim, CC., Detweiler, CS., Dougan, G. and Falkow, S., 2003. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. J Bacteriol, v. 185
    Doi: http://doi.org/10.1128/JB.185.2.553-563.2003
  • Wood, V., Gwilliam, R., Rajandream, MA., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., Basham, D., Bowman, S., Brooks, K., Brown, D., Brown, S., Chillingworth, T., Churcher, C., Collins, M., Connor, R., Cronin, A., Davis, P., Feltwell, T., Fraser, A., Gentles, S., Goble, A., Hamlin, N., Harris, D., Hidalgo, J., Hodgson, G., Holroyd, S., Hornsby, T., Howarth, S., Huckle, EJ., Hunt, S., Jagels, K., James, K., Jones, L., Jones, M., Leather, S., McDonald, S., McLean, J., Mooney, P., Moule, S., Mungall, K., Murphy, L., Niblett, D., Odell, C., Oliver, K., O'Neil, S., Pearson, D., Quail, MA., Rabbinowitsch, E., Rutherford, K., Rutter, S., Saunders, D., Seeger, K., Sharp, S., Skelton, J., Simmonds, M., Squares, R., Squares, S., Stevens, K., Taylor, K., Taylor, RG., Tivey, A., Walsh, S., Warren, T., Whitehead, S., Woodward, J., Volckaert, G., Aert, R., Robben, J., Grymonprez, B., Weltjens, I., Vanstreels, E., Rieger, M., Schafer, M., Muller-Auer, S., Gabel, C., Fuchs, M., Dusterhoft, A., Fritzc, C., Holzer, E., Moestl, D., Hilbert, H., Borzym, K., Langer, I., Beck, A., Lehrach, H., Reinhardt, R., Pohl, TM., Eger, P., Zimmermann, W., Wedler, H., Wambutt, R., Purnelle, B., Goffeau, A., Cadieu, E., Dreano, S., Gloux, S., Lelaure, V., Mottier, S., Galibert, F., Aves, SJ., Xiang, Z., Hunt, C., Moore, K., Hurst, SM., Lucas, M., Rochet, M., Gaillardin, C., Tallada, VA., Garzon, A., Thode, G., Daga, RR., Cruzado, L., Jimenez, J., Sanchez, M., del Rey, F., Benito, J., Dominguez, A., Revuelta, JL., Moreno, S., Armstrong, J., Forsburg, SL., Cerutti, L., Lowe, T., McCombie, WR., Paulsen, I., Potashkin, J., Shpakovski, GV., Ussery, D., Barrell, BG. and Nurse, P., 2003. The genome sequence of Schizosaccharomyces pombe (vol 415, pg 871, 2002) NATURE, v. 421
    Doi: http://doi.org/10.1038/nature01203
  • Wood, V., Gwilliam, R., Rajandream, MA., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., Basham, D., Bowman, S., Brooks, K., Brown, D., Brown, S., Chillingworth, T., Churcher, C., Collins, M., Connor, R., Cronin, A., Davis, P., Feltwell, T., Fraser, A., Gentles, S., Goble, A., Hamlin, N., Harris, D., Hidalgo, J., Hodgson, G., Holroyd, S., Hornsby, T., Howarth, S., Huckle, EJ., Hunt, S., Jagels, K., James, K., Jones, L., Jones, M., Leather, S., McDonald, S., McLean, J., Mooney, P., Moule, S., Mungall, K., Murphy, L., Niblett, D., Odell, C., Oliver, K., O'Neil, S., Pearson, D., Quail, MA., Rabbinowitsch, E., Rutherford, K., Rutter, S., Saunders, D., Seeger, K., Sharp, S., Skelton, J., Simmonds, M., Squares, R., Squares, S., Stevens, K., Taylor, K., Taylor, RG., Tivey, A., Walsh, S., Warren, T., Whitehead, S., Woodward, J., Volckaert, G., Aert, R., Robben, J., Grymonprez, B., Weltjens, I., Vanstreels, E., Rieger, M. and Schäfer, M., 2003. Erratum: The genome sequence of Schizosaccharomyces pombe (Nature (2002) 415 (871-880)) Nature, v. 421
    Doi: http://doi.org/10.1038/nature01203
  • Pickard, D., Wain, J., Baker, S., Line, A., Chohan, S., Fookes, M., Barron, A., Gaora, PO., Chabalgoity, JA., Thanky, N., Scholes, C., Thomson, N., Quail, M., Parkhill, J. and Dougan, G., 2003. Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. J Bacteriol, v. 185
    Doi: http://doi.org/10.1128/JB.185.17.5055-5065.2003
  • 2002

  • Wood, V., Gwilliam, R., Rajandream, M-A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., Basham, D., Bowman, S., Brooks, K., Brown, D., Brown, S., Chillingworth, T., Churcher, C., Collins, M., Connor, R., Cronin, A., Davis, P., Feltwell, T., Fraser, A., Gentles, S., Goble, A., Hamlin, N., Harris, D., Hidalgo, J., Hodgson, G., Holroyd, S., Hornsby, T., Howarth, S., Huckle, EJ., Hunt, S., Jagels, K., James, K., Jones, L., Jones, M., Leather, S., McDonald, S., McLean, J., Mooney, P., Moule, S., Mungall, K., Murphy, L., Niblett, D., Odell, C., Oliver, K., O'Neil, S., Pearson, D., Quail, MA., Rabbinowitsch, E., Rutherford, K., Rutter, S., Saunders, D., Seeger, K., Sharp, S., Skelton, J., Simmonds, M., Squares, R., Squares, S., Stevens, K., Taylor, K., Taylor, RG., Tivey, A., Walsh, S., Warren, T., Whitehead, S., Woodward, J., Volckaert, G., Aert, R., Robben, J., Grymonprez, B., Weltjens, I., Vanstreels, E., Rieger, M., Schäfer, M., Müller-Auer, S., Gabel, C., Fuchs, M., Düsterhöft, A., Fritzc, C., Holzer, E., Moestl, D., Hilbert, H., Borzym, K., Langer, I., Beck, A., Lehrach, H., Reinhardt, R., Pohl, TM., Eger, P., Zimmermann, W., Wedler, H., Wambutt, R., Purnelle, B., Goffeau, A., Cadieu, E., Dréano, S., Gloux, S., Lelaure, V., Mottier, S., Galibert, F., Aves, SJ., Xiang, Z., Hunt, C., Moore, K., Hurst, SM., Lucas, M., Rochet, M., Gaillardin, C., Tallada, VA., Garzon, A., Thode, G., Daga, RR., Cruzado, L., Jimenez, J., Sánchez, M., del Rey, F., Benito, J., Domínguez, A., Revuelta, JL., Moreno, S., Armstrong, J., Forsburg, SL., Cerutti, L., Lowe, T., McCombie, WR., Paulsen, I., Potashkin, J., Shpakovski, GV., Ussery, D., Barrell, BG. and Nurse, P., 2002. The genome sequence of Schizosaccharomyces pombe. Nature, v. 415
    Doi: http://doi.org/10.1038/nature724
  • Hall, N., Pain, A., Berriman, M., Churcher, C., Harris, B., Harris, D., Mungall, K., Bowman, S., Atkin, R., Baker, S., Barron, A., Brooks, K., Buckee, CO., Burrows, C., Cherevach, I., Chillingworth, C., Chillingworth, T., Christodoulou, Z., Clark, L., Clark, R., Corton, C., Cronin, A., Davies, R., Davis, P., Dear, P., Dearden, F., Doggett, J., Feltwell, T., Goble, A., Goodhead, I., Gwilliam, R., Hamlin, N., Hance, Z., Harper, D., Hauser, H., Hornsby, T., Holroyd, S., Horrocks, P., Humphray, S., Jagels, K., James, KD., Johnson, D., Kerhornou, A., Knights, A., Konfortov, B., Kyes, S., Larke, N., Lawson, D., Lennard, N., Line, A., Maddison, M., McLean, J., Mooney, P., Moule, S., Murphy, L., Oliver, K., Ormond, D., Price, C., Quail, MA., Rabbinowitsch, E., Rajandream, M-A., Rutter, S., Rutherford, KM., Sanders, M., Simmonds, M., Seeger, K., Sharp, S., Smith, R., Squares, R., Squares, S., Stevens, K., Taylor, K., Tivey, A., Unwin, L., Whitehead, S., Woodward, J., Sulston, JE., Craig, A., Newbold, C. and Barrell, BG., 2002. Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13. Nature, v. 419
    Doi: http://doi.org/10.1038/nature01095
  • 2001

  • Parkhill, J., Dougan, G., James, KD., Thomson, NR., Pickard, D., Wain, J., Churcher, C., Mungall, KL., Bentley, SD., Holden, MT., Sebaihia, M., Baker, S., Basham, D., Brooks, K., Chillingworth, T., Connerton, P., Cronin, A., Davis, P., Davies, RM., Dowd, L., White, N., Farrar, J., Feltwell, T., Hamlin, N., Haque, A., Hien, TT., Holroyd, S., Jagels, K., Krogh, A., Larsen, TS., Leather, S., Moule, S., O'Gaora, P., Parry, C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S. and Barrell, BG., 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature, v. 413
    Doi: http://doi.org/10.1038/35101607
  • Parkhill, J., Wren, BW., Thomson, NR., Titball, RW., Holden, MT., Prentice, MB., Sebaihia, M., James, KD., Churcher, C., Mungall, KL., 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. and Barrell, BG., 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature, v. 413
    Doi: http://doi.org/10.1038/35097083
  • Prentice, MB., James, KD., Parkhill, J., Baker, SG., Stevens, K., Simmonds, MN., Mungall, KL., Churcher, C., Oyston, PC., Titball, RW., Wren, BW., Wain, J., Pickard, D., Hien, TT., Farrar, JJ. and Dougan, G., 2001. Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid. J Bacteriol, v. 183
    Doi: http://doi.org/10.1128/JB.183.8.2586-2594.2001
  • Townsend, SM., Kramer, NE., Edwards, R., Baker, S., Hamlin, N., Simmonds, M., Stevens, K., Maloy, S., Parkhill, J., Dougan, G. and Bäumler, AJ., 2001. Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences. Infect Immun, v. 69
    Doi: http://doi.org/10.1128/IAI.69.5.2894-2901.2001
  • Book chapters

    2020

  • Yeung, A., Hale, C., Clare, S., Palmer, S., Scott, JB., Baker, S. and Dougan, G., 2020. Using a systems biology approach to study host-pathogen interactions
    Doi: http://doi.org/10.1128/9781683670261.ch24
  • Internet publications

    2020

  • Meredith, L., Hamilton, W., Warne, B., Houldcroft, C., Hosmillo, M., Jahun, A., Curran, M., Parmar, S., Caller, L., Caddy, S., Khokhar, F., Yakovleva, A., Hall, G., Feltwell, T., Forrest, S., Sridhar, S., Weekes, M., Baker, S., Brown, N., Moore, E., Popay, A., Roddick, I., Reacher, M., Gouliouris, T., Peacock, S., Dougan, G., Török, E. and Goodfellow, I., 2020. Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections
    Doi: http://doi.org/10.1101/2020.05.08.20095687
  • Other publications

    2019

  • Weinert, LA., Chaudhuri, RR., Wang, J., Peters, SE., Corander, J., Jombart, T., Baig, A., Howell, KJ., Vehkala, M., Välimäki, N., Harris, D., Chieu, TTB., Van Vinh Chau, N., Campbell, J., Schultsz, C., Parkhill, J., Bentley, SD., Langford, PR., Rycroft, AN., Wren, BW., Farrar, J., Baker, S., Hoa, NT., Holden, MTG., Tucker, AW., Maskell, DJ. and BRaDP1T Consortium, , 2019. Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nat Commun, v. 10
    Doi: http://doi.org/10.1038/s41467-019-13138-w
  • Conference proceedings

    2016

  • Wong, VK., Baker, S., Pickard, D., Page, AJ., Feasey, NA., Dougan, G. and Holt, KE., 2016. The emergence and intercontinental spread of a multidrug-resistant clade of typhoid agent <i>Salmonella enterica</i> serovar Typhi LANCET, v. 387
  • 2015

  • Van Cuong, N., Carrique-Mas, J., Vo Be, H., An, NN., Tue, NT., Anh, NL., Anh, PH., Phuc, NT., Baker, S., Voutilainen, L., Jääskeläinen, A., Huhtamo, E., Utriainen, M., Sironen, T., Vaheri, A., Henttonen, H., Vapalahti, O., Chaval, Y., Morand, S. and Bryant, JE., 2015. Rodents and risk in the Mekong Delta of Vietnam: seroprevalence of selected zoonotic viruses in rodents and humans. Vector Borne Zoonotic Dis, v. 15
    Doi: http://doi.org/10.1089/vbz.2014.1603
  • Books

    2014

  • Dougan, G. and Baker, S., 2014. Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever.
    Doi: http://doi.org/10.1146/annurev-micro-091313-103739
  • Subject: