Year 3 Publications
01 Oct 2023
Outbreak of sexually transmitted, extensively drug-resistant Shigella sonnei in the UK, 2021-22: a descriptive epidemiological study
Hannah Charles, Mateo Prochazka, Katie Thorley, Adam Crewdson, David R Greig, Claire Jenkins, Anais Painset, Helen Fifer, Lynda Browning, Paul Cabrey, Robert Smith, Daniel Richardson, Laura Waters, Katy Sinka, Gauri Godbole; Outbreak Control Team
29 Mar 2023
Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi
Edward Cunningham-Oakes, Christina Bronowski, End Chinyama, Khuzwayo C. Jere,
Kulandaipalayam Natarajan C. Sindhu, Gagandeep Kang, Miren Iturriza-Gómara, Alistair C Darby, Edward P. K. Parker; on behalf of the RoVI study group
15 Mar 2023
DiD IT?: a differences-in-differences investigation tool to quantify the impact of local incidents on public health using real-time syndromic surveillance health data
Morbey R, Todkill D, DeAngelis D, Charlett A, Elliot A
01 Mar 2023
Rapid antigen testing in COVID-19 management for school-aged children: an observational study in Cheshire and Merseyside, UK
David M. Hughes, Sheila M. Bird, Christopher P Cheyne, Matthew Ashton, Melisa C. Campbell, Marta García-Fiñana, Iain Buchan
19 Feb 2023
Predicting Norovirus in England Using Existing and Emerging Syndromic Data: Infodemiology Study
Nikola Ondrikova, John P Harris, Amy Douglas, Helen E Hughes, Miren Iturriza-Gomara, Roberto Vivancos, Alex J Elliot, Nigel A Cunliffe, Helen E Clough
01 Feb 2023
Socioeconomic and ethnic inequalities in incidence and severity of enteric fever in England 2015–2019: analysis of a national enhanced surveillance system
Matylda Buczkowska, Claire Jenkins, Jeremy Hawker, Daniel Hungerford, Parisha Katwa, Hilary Kirkbride, Lisa Byrne
31 Jan 2023
Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012–2020
Marie Anne Chattaway, Anaïs Painset, Gauri Godbole, Saheer Gharbia, Claire Jenkins
30 Jan 2023
Isolation of Salmonella species of public health concern from commonly fed dried meat dog treats
Genever Morgan, Mikhela Saal, Aoife Corr, Claire Jenkins, Marie Anne Chattaway, Gina Pinchbeck, Nicola Williams
26 Jan 2023
Association of SARS-CoV-2 viral load distributions with individual demographics and suspected variant type: results from the Liverpool community testing pilot, England, 6 November 2020 to 8 September 2021
David M Hughes, Christopher P Cheyne, Matthew Ashton, Emer Coffey, Alex Crozier, Malcolm G Semple, Iain Buchan, Marta García-Fiñana
07 Jan 2023
Patterns of reported infection and reinfection of SARS-CoV-2 in England
Matt J Keeling
05 Jan 2023
Informing antimicrobial stewardship with explainable AI
Massimo Cavallaro, Ed Moran, Benjamin Collyer, Noel D. McCarthy, Christopher Green, Matt J. Keeling
01 Jan 2023
Epidemiology of respiratory syncytial virus in children younger than 5 years in England during the COVID-19 pandemic, measured by laboratory, clinical, and syndromic surveillance: a retrospective observational study
Bardsley M, Morbey RA, Hughes HE, Beck CR, Watson CH, Zhao H, Ellis J, Smith GE, Elliot AJ
01 Jan 2023
Estimating hospital admissions due to respiratory syncytial virus in children
Megan Bardsley, Roger A Morbey, Helen E Hughes, Charles R Beck, Conall H Watson, Hongxin Zhao, Gillian E Smith, Alex J Elliot
01 Jan 2023
Two Outbreaks of Foodborne Gastrointestinal Infection Linked to Consumption of Imported Melons, United Kingdom, March to August 2021
Yung-Wai Chan, Ann Hoban, Hannah Moore, David R Greig, Anais Painset, Frieda Jorgensen, Marie A Chattaway, Claire Jenkins, Sooria Balasegaram, Jacquelyn McCormick, Lesley Larkin; Incident Management Teams
01 Jan 2023
Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease
Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca
01 Jan 2023
Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: A cross-sectional study at the UK's largest sexual health service
Holly D Mitchell, Gary Whitlock, Jey Zdravkov, Jenny Olsson, Panida Silalang, Megan Bardsley, Paula B Blomquist, Claire Jenkins, Nicholas R Thomson, Nigel Field, Gwenda Hughes
19 Dec 2022
Representativeness, Vaccination Uptake, and COVID-19 Clinical Outcomes 2020-2021 in the UK Oxford-Royal College of General Practitioners Research and Surveillance Network: Cohort Profile Summary
Leston M, Elson W, Watson C, Lakhani A, Aspden C, Bankhead C, Borrow R, Button E, Byford R, Elliot A, Fan X, Hoang U, Linley E, Macartney J, Nicholson B, Okusi C, Ramsay M, Smith G, Smith S, Thomas M, Todkill D, Tsang R, Victor W, Williams A, Williams J, Zambon M, Howsam G, Amirthalingam G, Lopez-Bernal J, Hobbs F, de Lusignan S
05 Dec 2022
Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi
David R. Greig, Matthew T. Bird, Marie Anne Chattaway, Gemma C. Langridge, Emma V. Waters, Paolo Ribeca, Claire Jenkins, Satheesh Nair
30 Nov 2022
Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease
Massimo Cavallaro, Juliana Coelho, Derren Ready, Valerie Decraene, Theresa Lamagni, Noel D. McCarthy, Dan Todkill, Matt J. Keeling
28 Nov 2022
Tracking outbreak dynamics using within-host variation
I'ah Donovan-Banfield, Edward Cunningham-Oakes
26 Nov 2022
Changing patterns of SARS-CoV-2 infection through Delta and Omicron waves by vaccination status, previous infection and neighbourhood deprivation: a cohort analysis of 2.7 M people
Mark A. Green, Daniel J. Hungerford, David M. Hughes, Marta Garcia‑Fiñana, Lance Turtle,
Christopher Cheyne, Matthew Ashton, Gary Leeming, Malcolm G. Semple, Alex Singleton, Iain Buchan
24 Nov 2022
Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis
Edward Cunningham-Oakes, Tom Pointon, Barry Murphy, Stuart Campbell-Lee, Thomas R Connor, Eshwar Mahenthiralingam
23 Nov 2022
A blueprint for synthetic control methodology: a causal inference tool for evaluating natural experiments in population health
Ben Barr, Xingna Zhang, Mark Green, Iain Buchan
23 Nov 2022
Impact of community asymptomatic rapid antigen testing on covid-19 related hospital admissions: synthetic control study
Zhang X, Barr B, Green M, Hughes D, Ashton M, Charalampopoulos D, García-Fiñana M, Buchan I
22 Nov 2022
Estimation of reproduction numbers in real time: Conceptual and statistical challenges
Lorenzo Pellis, Paul J. Birrell, Joshua Blake, Christopher E. Overton, Francesca Scarabel, Helena B. Stage, Ellen Brooks‐Pollock, Leon Danon, Ian Hall, Thomas A. House, Matt J. Keeling, Jonathan M. Read, JUNIPER Consortium, Daniela De Angelis
01 Nov 2022
Daily use of lateral flow devices by contacts of confirmed COVID-19 cases to enable exemption from isolation compared with standard self-isolation to reduce onward transmission of SARS-CoV-2 in England: a randomised, controlled, non-inferiority trial
Nicola K Love, Derren R Ready, Charlie Turner, Neville Q Verlander, Clare E French, Alex F Martin, Tina B Sorensen, Soeren Metelmann, Sarah Denford, G James Rubin, Lucy Yardley, Richard Amlôt, Susan Hopkins, Isabel Oliver
01 Nov 2022
The association between family structure and adolescent physical activity levels: a systematic review
Mylona E, Kletter M, Jones HM, Murphy M, Lampard R, Oyebode O
27 Oct 2022
Retrospectively modeling the effects of increased global vaccine sharing on the COVID-19 pandemic
Sam Moore, Edward M. Hill, Louise Dyson, Michael J. Tildesley, Matt J. Keeling
10 Oct 2022
A scalable analytical approach from bacterial genomes to epidemiology
Xavier Didelot, Julian Parkhill
15 Sep 2022
The evolution and international spread of extensively drug resistant Shigella sonnei
Mason L, Greig D, Cowley L, Partridge S, Martinez E, Blackwell G, Chong C, De Silva M, Bengtsson R, Draper J, Ginn A, SandaraduraI, Sim E, Iredell J, Sintchenko V, Ingle D, Howden B, Lefevre S, Njamkepo E, Weill F, Ceyssens P, Jenkins C, Baker K
07 Sep 2022
The bounded coalescent model: Conditioning a genealogy on a minimum root date
Jake Carson, Alice Ledda, Luca Ferretti, Matt Keeling, Xavier Didelot
06 Sep 2022
A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic
Joe Hilton, Heather Riley, Lorenzo Pellis, Rabia Aziza, Samuel P. C. Brand, Ivy K. Kombe, John Ojal, Andrea Parisi, Matt J. Keeling, D. James Nokes, Robert Manson-Sawko, Thomas House
24 Aug 2022
Shiga toxin-producing Escherichia coli clonal complex 32, including serotype O145:H28, in the UK and Ireland
Ella V. Rodwell, Yung-Wai Chan, Clare Sawyer, Anne Carroll, Eleanor McNamara, Lesley Allison, Lynda Browning, Anne Holmes, Gauri Godbole, Noel McCarthy, Claire Jenkins
22 Aug 2022
Comparison of the 2021 COVID-19 roadmap projections against public health data in England
Matt J. Keeling, Louise Dyson, Michael J. Tildesley, Edward M. Hill, Samuel Moore
10 Aug 2022
Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study
Michael J. Tildesley, Anna Vassall, Steven Riley, Mark Jit, Frank Sandmann, Edward M. Hill, Robin N. Thompson, Benjamin D. Atkins, John Edmunds, Louise Dyson, Matt J. Keeling
10 Aug 2022
A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella
P. Malaka De Silva, George E. Stenhouse, Grace A. Blackwell, Rebecca J. Bengtsson, Claire Jenkins, James P. J. Hall and Kate S. Baker
01 Aug 2022
Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya
Stacey Orangi, John Ojal, Samuel PC Brand, Cameline Orlendo, Angela Kairu, Rabia Aziza, Morris Ogero, Ambrose Agweyu, George M Warimwe, Sophie Uyoga, Edward Otieno, Lynette I Ochola-Oyier, Charles N Agoti, Kadondi Kasera, Patrick Amoth, Mercy Mwangangi,
Rashid Aman, Wangari Ng'ang'a, Ifedayo MO Adetifa, J Anthony G Scott, Philip Bejon, Matt J Keeling, Stefan Flasche, D James Nokes, Edwine Barasa
27 Jul 2022
Measuring multimorbidity in research: Delphi consensus study
Iris S S Ho, Amaya Azcoaga-Lorenzo, Ashley Akbari, Jim Davies, Kamlesh Khunti, Umesh T Kadam, Ronan A Lyons, Colin McCowan, Stewart W Mercer, Krishnarajah Nirantharakumar, Sophie Staniszewska, Bruce Guthrie
22 Jul 2022
Can cases and outbreaks of norovirus in children provide an early warning of seasonal norovirus infection: an analysis of nine seasons of surveillance data in England UK
Anna L. Donaldson, John P. Harris, Roberto Vivancos, Sarah J. O’Brien
14 Jul 2022
Modelling livestock infectious disease control policy under differing social perspectives on vaccination behaviour
Edward M. Hill, Naomi S. Prosser, Eamonn Ferguson, Jasmeet Kaler, Martin J. Green, Matt J. Keeling, Michael J. Tildesley
01 Jul 2022
Daily testing of contacts of SARS-CoV-2 infected cases as an alternative to quarantine for key workers in Liverpool: A prospective cohort study
Lucy Marsden, David M Hughes, Rhiannon Corcoran, Christopher P Cheyne, Matt Ashton, Iain Buchan, Emer Coffey, Marta García-Fiñana
01 Jul 2022
Long-term impact of pre-incision antibiotics on children born by caesarean section: a longitudinal study based on UK electronic health records
Šumilo D, Nirantharakumar K, Willis BH, Rudge GM, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Harris IM, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P
01 Jul 2022
Increase in extensively drug resistant Shigella sonnei in Europe
Hannah Trivett
30 Jun 2022
Symptom profiling for infectious intestinal disease (IID): Do symptom profiles alter with age?
Anna L. Donaldson , John P. Harris, Roberto Vivancos, Sarah J. O’Brien
02 Jun 2022
Community transmission of monkeypox in the United Kingdom, April to May 2022
Vivancos R, Anderson C, Blomquist P, Balasegaram S, Bell A, Bishop L, Brown CS, Chow Y, Edeghere O, Florence I, Logan S, Manley P, Crowe W, McAuley A, Shankar AG, Mora-Peris B, Paranthaman K, Prochazka M, Ryan C, Simons D, Vipond R, Byers C, Watkins NA
01 Jun 2022
Prospective validation of the 4C prognostic models for adults hospitalised with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol
Stephen R Knight, Rishi K Gupta, Antonia Ho, Riinu Pius, Iain Buchan, Gail Carson, Thomas M Drake, Jake Dunning, Cameron J Fairfield, Carrol Gamble, Christopher A Green, Sophie Halpin, Hayley E Hardwick, Karl A Holden, Peter W Horby, Clare Jackson, Kenneth A Mclean, Laura Merson, Jonathan S Nguyen-Van-Tam, Lisa Norman, Piero L Olliaro, Mark G Pritchard, Clark D Russell, Catherine A Shaw, Aziz Sheikh, Tom Solomon, Cathie Sudlow, Olivia V Swann, Lance C W Turtle, Peter J M Openshaw, J Kenneth Baillie, Annemarie Docherty, Malcolm G Semple, Mahdad Noursadeghi, Ewen M Harrison; ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) Investigators; ISARIC4C investigators
27 May 2022
Assessing the impact of lateral flow testing strategies on within-school SARS-CoV-2 transmission and absences: A modelling study
Trystan Leng, Edward M. Hill, Robin N. Thompson, Michael J. Tildesley, Matt J. Keeling, Louise Dyson
19 May 2022
Factors influencing decisions about whether to participate in health research by people of diverse ethnic and cultural backgrounds: a realist review
Eleanor Jayne Hoverd, George Hawker-Bond, Sophie Staniszewska, Jeremy Dale
18 May 2022
Outbreak of STEC O157:H7 linked to a milk pasteurisation failure at a dairy farm in England, 2019
Claire Jenkins, Philippa K. Bird, Adrian Wensley, Jarrod Wilkinson, Heather Aird, Adrienne Mackintosh, David R. Greig, Alex Simpson, Lisa Byrne, Rachel Wilkinson, Gauri Godbole,
Nachi Arunachalam, Gareth J. Hughes
18 May 2022
An assessment of the vaccination of school-aged children in England against SARS-CoV-2
Matt J. Keeling, Sam E. Moore
17 May 2022
Long term impact of prophylactic antibiotic use before incision versus after cord clamping on children born by caesarean section: longitudinal study of UK electronic health records
Šumilo D, Nirantharakumar K, Willis BH, Rudge GM, Martin J, Gokhale K, Thayakaran R, Adderley NJ, Chandan JS, Okoth K, Harris IM, Hewston R, Skrybant M, Deeks JJ, Brocklehurst P
13 May 2022
Public acceptability of a technology-mediated stool sample collection platform to inform community-based surveillance of infectious intestinal disease: a pilot study
Rowan Davies, Miren Iturriza-Gómara, Rebecca Glennon-Alty, Alex J. Elliot, Roberto Vivancos, Anica Alvarez Nishio, Nigel A. Cunliffe & Daniel Hungerford
21 Apr 2022
The impact of community asymptomatic rapid antigen testing on COVID-19 hospital admissions: a synthetic control study
Xingna Zhang, Ben Barr, Mark Green, David Hughes, Matthew Ashton, Dimitrios Charalampopoulos, Marta García-Fiñana, Iain Buchan
20 Apr 2022
Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399
Alice Ledda, Martina Cummins, Liam P. Shaw, Elita Jauneikaite, Kevin Cole, Florent Lasalle, Deborah Barry, Jane Turton, Caryn Rosmarin, Sudy Anaraki, David Wareham, Nicole Stoesser, John Paul, Rohini Manuel, Benny P. Cherian, Xavier Didelot
12 Apr 2022
Evaluating the impacts of tiered restrictions introduced in England, during October and December 2020 on COVID-19 cases: a synthetic control study
Xingna Zhang, Gwilym Owen, Mark A Green, Iain Buchan, Ben Barr
01 Apr 2022
Patient and Public Involvement in research: A journey to co-production
Amy Price, Mike Clarke, Sophie Staniszewska, Larry Chu, Doreen Tembo, Marjorie Kirkpatrick, Yasmine Nelken