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26
Chau KK, Barker L, Budgell EP, Vihta KD, Sims N, Kasprzyk-Hordern B, Harriss E, Crook DW, Read DS, Walker AS, Stoesser N. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. ENVIRONMENT INTERNATIONAL 2022;162:107171. [PMID: 35290866 PMCID: PMC8960996 DOI: 10.1016/j.envint.2022.107171] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/23/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
27
Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat MR, Cirillo DM, Comas I, Posey J, Omar SV, Peto TEA, Suresh A, Uplekar S, Laurent S, Colman RE, Nathanson CM, Zignol M, Walker AS, Crook DW, Ismail N, Rodwell TC. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis. THE LANCET. MICROBE 2022;3:e265-e273. [PMID: 35373160 PMCID: PMC7612554 DOI: 10.1016/s2666-5247(21)00301-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
28
Lee LYW, Rozmanowski S, Pang M, Charlett A, Anderson C, Hughes GJ, Barnard M, Peto L, Vipond R, Sienkiewicz A, Hopkins S, Bell J, Crook DW, Gent N, Walker AS, Peto TEA, Eyre DW. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity by Viral Load, S Gene Variants and Demographic Factors, and the Utility of Lateral Flow Devices to Prevent Transmission. Clin Infect Dis 2022;74:407-415. [PMID: 33972994 PMCID: PMC8136027 DOI: 10.1093/cid/ciab421] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 11/28/2022]  Open
29
Lee LYW, Rozmanowski S, Pang M, Charlett A, Anderson C, Hughes GJ, Barnard M, Peto L, Vipond R, Sienkiewicz A, Hopkins S, Bell J, Crook DW, Gent N, Walker AS, Peto TEA, Eyre DW. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity by Viral Load, S Gene Variants and Demographic Factors, and the Utility of Lateral Flow Devices to Prevent Transmission. Clin Infect Dis 2022;74:407-415. [PMID: 33972994 DOI: 10.1101/2021.03.31.21254687] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 05/27/2023]  Open
30
Wang W, Balfe P, Eyre DW, Lumley SF, O'Donnell D, Warren F, Crook DW, Jeffery K, Matthews PC, Klerman EB, McKeating JA. Time of Day of Vaccination Affects SARS-CoV-2 Antibody Responses in an Observational Study of Health Care Workers. J Biol Rhythms 2021;37:124-129. [PMID: 34866459 PMCID: PMC8825702 DOI: 10.1177/07487304211059315] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
31
Yang Y, Walker TM, Kouchaki S, Wang C, Peto TEA, Crook DW, Clifton DA. An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction. Brief Bioinform 2021;22:6355133. [PMID: 34414415 PMCID: PMC8575050 DOI: 10.1093/bib/bbab299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/28/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022]  Open
32
Young BC, Wu CH, Charlesworth J, Earle S, Price JR, Gordon NC, Cole K, Dunn L, Liu E, Oakley S, Godwin H, Fung R, Miller R, Knox K, Votintseva A, Quan TP, Tilley R, Scarborough M, Crook DW, Peto TE, Walker AS, Llewelyn MJ, Wilson DJ. Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study. Microb Genom 2021;7:000700. [PMID: 34812717 PMCID: PMC8743558 DOI: 10.1099/mgen.0.000700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022]  Open
33
Wei J, Matthews PC, Stoesser N, Maddox T, Lorenzi L, Studley R, Bell JI, Newton JN, Farrar J, Diamond I, Rourke E, Howarth A, Marsden BD, Hoosdally S, Jones EY, Stuart DI, Crook DW, Peto TEA, Pouwels KB, Walker AS, Eyre DW. Anti-spike antibody response to natural SARS-CoV-2 infection in the general population. Nat Commun 2021;12:6250. [PMID: 34716320 PMCID: PMC8556331 DOI: 10.1038/s41467-021-26479-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/06/2021] [Indexed: 01/08/2023]  Open
34
Lumley SF, Richens N, Lees E, Cregan J, Kalimeris E, Oakley S, Morgan M, Segal S, Dawson M, Walker AS, Eyre DW, Crook DW, Beer S, Novak A, Stoesser NE, Matthews PC. Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic. J Infect 2021;84:40-47. [PMID: 34757137 PMCID: PMC8591975 DOI: 10.1016/j.jinf.2021.10.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 01/21/2023]
35
AbuOun M, Jones H, Stubberfield E, Gilson D, Shaw LP, Hubbard ATM, Chau KK, Sebra R, Peto TEA, Crook DW, Read DS, Gweon HS, Walker AS, Stoesser N, Smith RP, Anjum MF, On Behalf Of The Rehab Consortium. A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Microb Genom 2021;7. [PMID: 34609275 PMCID: PMC8627209 DOI: 10.1099/mgen.0.000630] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
36
Lipworth S, Peto TE, Crook DW, Walker AS, Stoesser N. Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection. THE LANCET. MICROBE 2021;2:e492. [PMID: 35544174 DOI: 10.1016/s2666-5247(21)00151-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 11/29/2022]
37
Lipworth S, Hough N, Weston N, Muller-Pebody B, Phin N, Myers R, Chapman S, Flight W, Alexander E, Smith EG, Robinson E, Peto TEA, Crook DW, Walker AS, Hopkins S, Eyre DW, Walker TM. Epidemiology of Mycobacterium abscessus in England: an observational study. THE LANCET. MICROBE 2021;2:e498-e507. [PMID: 34632432 PMCID: PMC8481905 DOI: 10.1016/s2666-5247(21)00128-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
38
Eyre DW, Lumley SF, Wei J, Cox S, James T, Justice A, Jesuthasan G, O'Donnell D, Howarth A, Hatch SB, Marsden BD, Jones EY, Stuart DI, Ebner D, Hoosdally S, Crook DW, Peto TEA, Walker TM, Stoesser NE, Matthews PC, Pouwels KB, Walker AS, Jeffery K. Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status. Clin Microbiol Infect 2021;27:1516.e7-1516.e14. [PMID: 34111577 PMCID: PMC8180449 DOI: 10.1016/j.cmi.2021.05.041] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 10/31/2022]
39
Lumley SF, Constantinides B, Sanderson N, Rodger G, Street TL, Swann J, Chau KK, O'Donnell D, Warren F, Hoosdally S, O'Donnell AM, Walker TM, Stoesser NE, Butcher L, Peto TE, Crook DW, Jeffery K, Matthews PC, Eyre DW. Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals. J Infect 2021;83:473-482. [PMID: 34332019 PMCID: PMC8316632 DOI: 10.1016/j.jinf.2021.07.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022]
40
Liu D, Huang F, Zhang G, He W, Ou X, He P, Zhao B, Zhu B, Liu F, Li Z, Liu C, Xia H, Wang S, Zhou Y, Walker TM, Liu L, Crook DW, Zhao Y. Whole-genome sequencing for surveillance of tuberculosis drug resistance and determination of resistance level in China. Clin Microbiol Infect 2021;28:731.e9-731.e15. [PMID: 34600118 DOI: 10.1016/j.cmi.2021.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 01/07/2023]
41
Lipworth S, Vihta KD, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Genome Med 2021;13:144. [PMID: 34479643 PMCID: PMC8414751 DOI: 10.1186/s13073-021-00947-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022]  Open
42
Wei J, Stoesser N, Matthews PC, Ayoubkhani D, Studley R, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Rourke E, Howarth A, Marsden BD, Hoosdally S, Jones EY, Stuart DI, Crook DW, Peto TEA, Pouwels KB, Eyre DW, Walker AS. Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom. Nat Microbiol 2021;6:1140-1149. [PMID: 34290390 PMCID: PMC8294260 DOI: 10.1038/s41564-021-00947-3] [Citation(s) in RCA: 199] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
43
Moloney G, Eyre DW, Mac Aogáin M, McElroy MC, Vaughan A, Peto TE, Crook DW, Rogers TR. Human and Porcine Transmission of Clostridioides difficile Ribotype 078, Europe. Emerg Infect Dis 2021;27:2294-2300. [PMID: 34423760 PMCID: PMC8386809 DOI: 10.3201/eid2709.203468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
44
Lumley SF, Wei J, O'Donnell D, Stoesser NE, Matthews PC, Howarth A, Hatch SB, Marsden BD, Cox S, James T, Peck LJ, Ritter TG, de Toledo Z, Cornall RJ, Jones EY, Stuart DI, Screaton G, Ebner D, Hoosdally S, Crook DW, Conlon CP, Pouwels KB, Walker AS, Peto TEA, Walker TM, Jeffery K, Eyre DW. The Duration, Dynamics, and Determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Responses in Individual Healthcare Workers. Clin Infect Dis 2021;73:e699-e709. [PMID: 33400782 DOI: 10.1101/2020.11.02.20224824] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Indexed: 05/20/2023]  Open
45
Lumley SF, Wei J, O’Donnell D, Stoesser NE, Matthews PC, Howarth A, Hatch SB, Marsden BD, Cox S, James T, Peck LJ, Ritter TG, de Toledo Z, Cornall RJ, Jones EY, Stuart DI, Screaton G, Ebner D, Hoosdally S, Crook DW, Conlon CP, Pouwels KB, Walker AS, Peto TEA, Walker TM, Jeffery K, Eyre DW. The Duration, Dynamics, and Determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Responses in Individual Healthcare Workers. Clin Infect Dis 2021;73:e699-e709. [PMID: 33400782 PMCID: PMC7929225 DOI: 10.1093/cid/ciab004] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Indexed: 12/13/2022]  Open
46
Matlock W, Chau KK, AbuOun M, Stubberfield E, Barker L, Kavanagh J, Pickford H, Gilson D, Smith RP, Gweon HS, Hoosdally SJ, Swann J, Sebra R, Bailey MJ, Peto TEA, Crook DW, Anjum MF, Read DS, Walker AS, Stoesser N, Shaw LP. Genomic network analysis of environmental and livestock F-type plasmid populations. THE ISME JOURNAL 2021;15:2322-2335. [PMID: 33649550 PMCID: PMC8319146 DOI: 10.1038/s41396-021-00926-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/08/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022]
47
Buchanan J, Roope LSJ, Morrell L, Pouwels KB, Robotham JV, Abel L, Crook DW, Peto T, Butler CC, Walker AS, Wordsworth S. Preferences for Medical Consultations from Online Providers: Evidence from a Discrete Choice Experiment in the United Kingdom. APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2021;19:521-535. [PMID: 33682065 PMCID: PMC7937442 DOI: 10.1007/s40258-021-00642-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
48
Auguet OT, Niehus R, Gweon HS, Berkley JA, Waichungo J, Njim T, Edgeworth JD, Batra R, Chau K, Swann J, Walker SA, Peto TE, Crook DW, Lamble S, Turner P, Cooper BS, Stoesser N. Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK. EClinicalMedicine 2021;36:100910. [PMID: 34124634 PMCID: PMC8173267 DOI: 10.1016/j.eclinm.2021.100910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 01/04/2023]  Open
49
Shaw LP, Chau KK, Kavanagh J, AbuOun M, Stubberfield E, Gweon HS, Barker L, Rodger G, Bowes MJ, Hubbard ATM, Pickford H, Swann J, Gilson D, Smith RP, Hoosdally SJ, Sebra R, Brett H, Peto TEA, Bailey MJ, Crook DW, Read DS, Anjum MF, Walker AS, Stoesser N. Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. SCIENCE ADVANCES 2021;7:eabe3868. [PMID: 33837077 PMCID: PMC8034854 DOI: 10.1126/sciadv.abe3868] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/22/2021] [Indexed: 05/07/2023]
50
Reynolds ME, Phan HTT, George S, Hubbard ATM, Stoesser N, Maciuca IE, Crook DW, Timofte D. Occurrence and characterization of Escherichia coli ST410 co-harbouring blaNDM-5, blaCMY-42 and blaTEM-190 in a dog from the UK. J Antimicrob Chemother 2021;74:1207-1211. [PMID: 30753576 DOI: 10.1093/jac/dkz017] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 12/14/2022]  Open
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