Publications

Year 4 Publications

25 Mar 2024
Diarrhea Case Surveillance in the Enterics for Global Health Shigella Surveillance Study: Epidemiologic Methods
Atlas HE, Conteh B, Islam MT, Jere KC, Omore R, Sanogo D, Schiaffino F, Yousafzai MT, Ahmed N, Awuor AO, Badji H, Cornick J, Feutz E, Galagan SR, Haidara FC, Horne B, Hossen MI, Hotwani A, Houpt ER, Jallow AF, Karim M, Keita AM, Keita Y, Khanam F, Liu J, Malemia T, Manneh A, McGrath CJ, Nasrin D, Ndalama M, Ochieng JB, Ogwel B, Paredes Olortegui M, Zegarra Paredes LF, Pinedo Vasquez T, Platts-Mills JA, Qudrat-E-Khuda S, Qureshi S, Hasan Rajib MN, Rogawski McQuade ET, Sultana S, Tennant SM, Tickell KD, Witte D, Peñataro Yori P, Cunliffe NA, Hossain MJ, Kosek MN, Kotloff KL, Qadri F, Qamar FN, Tapia MD, Pavlinac PB

25 Mar 2024
Quantifying the Cost of Shigella Diarrhea in the Enterics for Global Health (EFGH) Shigella Surveillance Study
Morozoff C, Ahmed N, Chinkhumba J, Islam MT, Jallow AF, Ogwel B, Zegarra Paredes LF, Sanogo D, Atlas HE, Badji H, Bar-Zeev N, Conteh B, Güimack Fajardo M, Feutz E, Haidara FC, Karim M, Mamby Keita A, Keita Y, Khanam F, Kosek MN, Kotloff KL, Maguire R, Mbutuka IS, Ndalama M, Ochieng JB, Okello C, Omore R, Perez Garcia KF, Qamar FN, Qudrat-E-Khuda S, Qureshi S, Rajib MNH, Shapiama Lopez WV, Sultana S, Witte D, Yousafzai MT, Awuor AO, Cunliffe NA, Jahangir Hossain M, Paredes Olortegui M, Tapia MD, Zaman K, Means AR

25 Mar 2024
Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study
Liu J, Garcia Bardales PF, Islam K, Jarju S, Juma J, Mhango C, Naumanga Q, Qureshi S, Sonye C, Ahmed N, Aziz F, Bhuiyan MTR, Charles M, Cunliffe NA, Abdou M, Galagan SR, Gitteh E, Guindo I, Jahangir Hossain M, Jabang AMJ, Jere KC, Kawonga F, Keita M, Keita NY, Kotloff KL, Shapiama Lopez WV, Munga S, Paredes Olortegui M, Omore R, Pavlinac PB, Qadri F, Qamar FN, Azadul Alam Raz SM, Riziki L, Schiaffino F, Stroup S, Traore SN, Pinedo Vasquez T, Yousafzai MT, Antonio M, Cornick JE, Kabir F, Khanam F, Kosek MN, Ochieng JB, Platts-Mills JA, Tennant SM, Houpt ER

25 Mar 2024
Exploring Natural Immune Responses to Shigella Exposure Using Multiplex Bead Assays on Dried Blood Spots in High-Burden Countries: Protocol From a Multisite Diarrhea Surveillance Study
Benedicto-Matambo P, Avolio LN, Badji H, Batool R, Khanam F, Munga S, Tapia MD, Peñataro Yori P, Awuor AO, Ceesay BE, Cornick J, Cunliffe NA, Garcia Bardales PF, Heaney CD, Hotwani A, Ireen M, Taufiqul Islam M, Jallow O, Kaminski RW, Shapiama Lopez WV, Maiden V, Ikumapayi UN, Nyirenda R, Ochieng JB, Omore R, Paredes Olortegui M, Pavlinac PB, Pisanic N, Qadri F, Qureshi S, Rahman N, Rogawski McQuade ET, Schiaffino F, Secka O, Sonye C, Sultana S, Timite D, Traore A, Yousafzai MT, Taufiqur Rahman Bhuiyan M, Jahangir Hossain M, Jere KC, Kosek MN, Kotloff KL, Qamar FN, Sow SO, Platts-Mills JA

25 Mar 2024
Evaluation of Fecal Inflammatory Biomarkers to Identify Bacterial Diarrhea Episodes: Systematic Review and Protocol for the Enterics for Global Health Shigella Surveillance Study
Babb C, Badji H, Bhuiyan MTR, Cornick J, Qureshi S, Sonye C, Shapiama Lopez WV, Adnan M, Atlas HE, Begum K, Brennhofer SA, Ceesay BE, Ceesay AK, Cunliffe NA, Garcia Bardales PF, Haque S, Horne B, Hossain MJ, Iqbal J, Islam MT, Islam S, Khanam F, Kotloff KL, Malemia T, Manzanares Villanueva K, Million GM, Munthali V, Ochieng JB, Ogwel B, Paredes Olortegui M, Omore R, Pavlinac PB, Platts-Mills JA, Sears KT, Secka O, Tennant SM, Peñataro Yori P, Yousafzai MT, Jere KC, Kosek MN, Munga S, Ikumapayi UN, Qadri F, Qamar FN, Rogawski McQuade ET

25 Mar 2024
Population Enumeration and Household Utilization Survey Methods in the Enterics for Global Health (EFGH): Shigella Surveillance Study
Dodd R, Awuor AO, Garcia Bardales PF, Khanam F, Mategula D, Onwuchekwa U, Sarwar G, Yousafzai MT, Ahmed N, Atlas HE, Amirul Islam Bhuiyan M, Colston JM, Conteh B, Diawara M, Dilruba N, Elwood S, Fatima I, Feutz E, Galagan SR, Haque S, Taufiqul Islam M, Karim M, Keita B, Kosek MN, Kotloff KL, Lefu C, Mballow M, Ndalama M, Ndeketa L, Ogwel B, Okonji C, Paredes Olortegui M, Pavlinac PB, Pinedo Vasquez T, Platts-Mills JA, Qadri F, Qureshi S, Rogawski McQuade ET, Sultana S, Traore MO, Cunliffe NA, Jahangir Hossain M, Omore R, Qamar FN, Tapia MD, Peñataro Yori P, Zaman K, McGrath CJ

25 Mar 2024
The Enterics for Global Health (EFGH) Shigella Surveillance Study in Malawi
Mategula D, Ndalama M, Lefu C, Chinkhumba J, Ndeketa L, Munthali V, Chitala C, Malemia T, Million G, Mbutuka I, Mhone R, Makwenda E, James M, Bwanali C, Kazembe G, Manundo A, Chauluka E, Chitalo S, Alumando E, Longwe D, Matandika M, Jonasi P, Thindwa A, Phiri D, Wachepa R, Kawonga F, Maiden V, Charles M, Kapindula I, Witte D, Turner AM, Bronowski C, Baker K, Bar-Zeev N, Gordon MA, Dube Q, Cunliffe NA, Jere KC, Cornick J

25 Mar 2024
Microbiological Methods Used in the Enterics for Global Health Shigella Surveillance Study
Horne B, Badji H, Bhuiyan MTR, Romaina Cachique L, Cornick J, Hotwani A, Juma J, Ochieng JB, Abdou M, Apondi E, Atlas HE, Awuor AO, Baker KS, Ceesay BE, Charles M, Cunliffe NA, Feutz E, Galagan SR, Guindo I, Hossain MJ, Iqbal J, Jallow F, Keita NY, Khanam F, Kotloff KL, Maiden V, Manzanares Villanueva K, Mito O, Mosharraf MP, Nkeze J, Ikumapayi UN, Paredes Olortegui M, Pavlinac PB, Pinedo Vasquez T, Qadri F, Qamar FN, Qureshi S, Rahman N, Sangare A, Sen S, Peñataro Yori P, Yousafzai MT, Ahmed D, Jere KC, Kosek MN, Omore R, Permala-Booth J, Secka O, Tennant SM

20 Mar 2024
Listeria monocytogenes: the silent assassin
Fotopoulou ET, Jenkins C, Painset A, Amar C

09 Mar 2024
Re-analysis of an outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with raw drinking milk using Nanopore sequencing
Greig DR, Nascimento V, Gally DL, Gharbia, SE, Dallman TJ, Jenkins C

26 Feb 2024
Shedding and exclusion from childcare in children with Shiga toxin-producing Escherichia coli, 2018–2022
Vusirikala, A., Rowell, S., Dabke, G., Fox, G., Bell, J., Manuel, R., Jenkins, C., Love, N., McCarthy, N., Sumilo, D., & Balasegaram, S

16 Feb 2024
Yersinia enterocolitica biovar 1A: An underappreciated potential pathogen in the food chain
Palau R, Bloomfield SJ, Jenkins C, Greig DR, Jorgensen F, Mather AE

08 Feb 2024
‘A system that is struggling’: understanding health protection resilience in England during the COVID-19 pandemic through the experiences of local health protection responders
Rotheram S, Clayton S, Buchan I, Ghebrehewet S, Barr B

01 Feb 2024
Clinical and public health implications of increasing notifications of LEE-negative Shiga toxin-producing Escherichia coli in England, 2014–2022
Rodwell EV, Greig DR, Godbole G, Jenkins C.J

26 Jan 2024
Inequalities in local funding cuts to environmental and regulatory service expenditure in England from 2009 to 2020
Murrell L, Fahy H, Clough HE, Gibb R, Zhang X, Chattaway M, Green MA, Buchan I, Barr B, Hungerford D

05 Jan 2024
Understanding the impact funding cuts on Environmental and regulatory services and gastrointestinal infections: a longitudinal ecological study
Murrell, Lauren, Helen Clough, Roger Gibb, Xingna Zhang, Mark Green, Marie Chattaway, Iain Buchan, Benjamin Barr, Daniel Hungerford

03 Jan 2024
Thoughts and perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study
Trivett H, Darby A, Oyebode O

02 Jan 2024
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK
Fotopoulou ET, Jenkins C, Barker CR, Painset A, Didelot X, Simbo A, Douglas A, Godbole G, Jorgensen F, Gharbia S, McLauchlin J

05 Dec 2023
Comparison of statistical approaches to predicting norovirus laboratory reports before and during COVID-19: insights to inform public health surveillance
Ondrikova N, Clough H, Douglas A, Vivancos R, Itturiza-Gomara M, Cunliffe N, Harris JP

18 Nov 2023
Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi
Cunningham-Oakes E, Bronowski C, Chinyama E, Jere KC, Sindhu KNC, Kang G, Iturriza-Gómara M, Darby AC, Parker EPK

14 Nov 2023
Genomics for public health and international surveillance of antimicrobial resistance
Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden, BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, Midega JT, Feasey NA, Peacock SJ

14 Nov 2023
Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group
Baker KS, Jauneikaite E, Nunn JG, Midega JT, Atun R, Holt KE, Walia K, Howden BP, Tate H, Okeke IN, Carattoli A, Hsu LY, Hopkins KL, Muloi DM, Wheeler NE, Aanensen DM, Mason LCE, Rodgus J, Hendriksen RS, Essack SY, Egyir B, Halpin AL, MacCannell DR, Campos J, Srikanthia P, Feasey NA, Peacock SJ

14 Nov 2023
Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities
Jauneikaite E, Baker KS, Nunn J, Midega J, Hsu LY, Singh SR, Halpin AL, Hopkins KL, Price JR, Srikantiah P, Egyir B, Okeke IN, Holt KE, Peacock SJ, Feasey NA

14 Nov 2023
Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces
Muloi DM, Jauneikaite E, Anjum M, Essack SY, Singleton D, Kasudi M, Wade M , Egyir B, Nunn JG, Midega J, Peacock SJ, Feasey NA, Baker KS, Zadoks R, The SEDRIC Genomics Surveillance Working Group

14 Nov 2023
Innovations in genomic antimicrobial resistance surveillance
Wheeler NE, Price V, Cunningham-Oakes E, Tsang KK, Nunn JG, Midega JT, Anjum MF, Wade MJ, Feasey NA, Peacock SJ, Jaunekaite E, Baker KS, The SEDRIC Genomics Surveillance Working Group

27 Oct 2023
The Epidemiology of Chickenpox in England, 2016–2022: An Observational Study Using General Practitioner Consultations
Bardsley M, Loveridge P, Bednarska NG, Smith S, Morbey RA, Amirthalingam G, Elson WH, Bates C, de Lusignan S, Todkill D, Elliot AJ

25 Oct 2023
Preliminary investigation of a significant national Cryptosporidium exceedance in the United Kingdom, August 2023 and ongoing
Peake L, Inns T, Jarvis C, King G, Rabie H, Henderson J, Wensley A, Jarratt R, Roberts C, Williams C, Orife O, Browning L, Neilson M, McCarthy C, Millar P, Love N, Elwin K, Robinson G, Mannes T, Young N, Chalmers R, Elson R, Vivancos R

18 Oct 2023
Shigella Serotypes Associated With Carriage in Humans Establish Persistent Infection in Zebrafish
Torraca V, Brokatzky D, Miles SL, Chong CE, De Silva PM, Baker S, Jenkins C, Holt KE, Baker KS, Mostowy S

10 Oct 2023
Comparison of surveillance systems for monitoring COVID-19 in England: a retrospective observational study
Brainard J, Lake IR, Morbey RA, Jones NR, Elliot AJ, Hunter PR

06 Oct 2023
Evaluating the impact of using mobile vaccination units to increase COVID-19 vaccination uptake in Cheshire and Merseyside, UK: a synthetic control analysis
Zhang X, Tulloch JSP, Knott S, Allison R, Parvulescu P, Buchan IE, Garcia-Finana M, Piroddi R, Green MA, Baird S, Barr B

06 Oct 2023
Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins
De Silva PM, Bennett RJ, Kuhn L, Ngondo P, Debande L, Njamkepo E, Ho B, Weill FX, Marteyn BS, Jenkins C, Baker KS

28 Sep 2023
Draft genomes of Aeromonas caviae from patients with cholera-like illness during the 2022–2023 cholera outbreak in Malawi
Jere KC, Chibwe I, Chaima D, Kasambala W, Mhango C, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Kamng'ona AW, Steele AD, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga MM, Dube Q, French N, Cunliffe NA, Msefula CL, Chaguza C

06 Sep 2023
Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health
Chase-Topping M, Dallman TJ, Allison L, Lupolova N, Matthews L, Mitchell S, Banks CJ, Prentice J, Brown H, Tongue S, Henry M, Evans J, Gunn G, Hoyle D, McNeilly TN, Fitzgerald S, Smith-Palmer A, Shaaban S, Holmes A, Hanson M, Woolhouse M, Didelot X, Jenkins C, Gally DL

05 Sep 2023
Surveillance of antimicrobial resistant Shiga toxin-producing E. coli O157:H7 in England, 2016-2020
Greig DR, Do Nascimento V, Olonade I, Swift C, Nair S, Jenkins C

01 Sep 2023
Haemolytic uraemic syndrome in children England, Wales, Northern Ireland, and Ireland: A prospective cohort study
Byrne L, Douglas A, Launders N, Godbole G, Lynn R, Inward C, Jenkins C

31 Aug 2023
Association Between Maternal Breastmilk Microbiota Composition and Rotavirus Vaccine Response in African, Asian, and European Infants: A Prospective Cohort Study
Mandolo J, Parker EPK, Bronowski C, Sindhu KNC, Darby AC, Cunliffe NA, Kang G, Iturriza-Gómara M, Kamng'ona AW, Jere KC

25 Aug 2023
Understanding the impact of the COVID-19 pandemic response on GI infection surveillance trends in England, January 2020–April 2022
Love NK, Douglas A, Gharbia S, Hughes H, Morbey R, Oliver I, Smith GE, Elliot AJ

17 Aug 2023
Prevalence and Persistence of Antibiotic Resistance Determinants in the Gut of Travelers Returning to the United Kingdom is Associated with Colonization by Pathogenic Escherichia coli
Dallman TJ, Neuert S, Fernandez Turienzo C, Berin M, Richardson E, Fuentes-Utrilla P, Loman N, Gharbia S, Jenkins C, Behrens RH, Godbole G, Brown M

26 Jul 2023
A Systematic Review of the Prevalence of Persistent Gastrointestinal Symptoms and Incidence of New Gastrointestinal Illness after Acute SARS-CoV-2 Infection
Hawkings MJ, Vaselli NM, Charalampopoulos D, Brierley L, Elliot AJ, Buchan I, Hungerford D

14 Jun 2023
Association between socioeconomic deprivation and incidence of infectious intestinal disease by pathogen and linked transmission route: An ecological analysis in the UK
Matylda Buczkowska, Saira Butt, Claire Jenkins, Dan Hungerford, Jeremy Hawker, Neville Q. Verlander, Anne-Marie O’Connell, Lisa Byrne

14 Jun 2023
Association between socioeconomic deprivation and incidence of infectious intestinal disease by pathogen and linked transmission route: An ecological analysis in the UK
Buczkowska M, Butt S, Jenkins C, Hungerford D, Hawker J, Verlander NQ, O'Connell AM, Byrne L

09 Jun 2023
Escherichia coli encoding Shiga toxin subtype Stx2f causing human infections in England, 2015–2022
Den Ouden A, Greig DR, Rodwell EV, Tripodo F, Olonade I, Swift C, Jenkins C

09 Jun 2023
Investigating association between inflammatory bowel disease and rotavirus vaccination in a paediatric cohort in the UK
Flatt A, Inns T, Fleming KM, Iturriza-Gómara M, Hungerford D

02 Jun 2023
Acute rotavirus infection is associated with the induction of circulating memory CD4+ T cell subsets
Malamba-Banda C, Mhango C, Benedicto-Matambo P, Mandolo JJ, Chinyama E, Kumwenda O, Barnes KG, Cunliffe NA, Iturriza-Gomara M, Jambo KC, Jere KC

01 Jun 2023
Emergence of extensively drug-resistant and multidrug-resistant Shigella flexneri serotype 2a associated with sexual transmission among gay, bisexual, and other men who have sex with men, in England: a descriptive epidemiological study
Thorley K, Charles H, Greig DR, Prochazka M, Mason LCE, Baker KS, Godbole G, Sinka K, Jenkins C

01 Jun 2023
Foodborne Outbreak of Extended Spectrum Beta-lactamase Producing Shigella sonnei Associated with Contaminated Spring Onions in the United Kingdom
Jenkins C, Griddith P, Hoban A, Brown C, Garner J, Bardsley M, Willis C, Jorgensen F, Bird M, Greig DR, Edmunds M, Beck C, Larkin L, Incident Management Teams

01 Jun 2023
Histo-blood group antigen profile of Australian Aboriginal children and seropositivity following oral rotavirus vaccination
Middleton BF, Danchin M, Cunliffe NA, Jones MA, Boniface K, Kirkwood CD, Gallagher S, Kirkham LA, Granland C, McNeal M, Donato C, Bogdanovic-Sakran N, Handley A, Bines JE, Snelling TL

22 May 2023
Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi
Mhango C, Banda A, Chinyama E, Mandolo JJ, Kumwenda O, Malamba-Banda C, Barnes KG, Kumwenda B, Jambo KC, Donato CM, Esona MD, Mwangi PN, Steele AD, Iturriza-Gomara M, Cunliffe NA, Ndze VN, Kamng'ona AW, Dennis FE, Nyaga MM, Chaguza C, Jere KC

08 May 2023
Predicting Norovirus in England Using Existing and Emerging Syndromic Data: Infodemiology Study
Ondrikova N, Harris JP, Douglas A, Hughes HE, Iturriza-Gomara M, Vivancos R, Elliot AJ, Cunliffe NA, Clough HE

13 Apr 2023
The epidemiology of Shiga toxin-producing Escherichia coli O26:H11 (clonal complex 29) in England, 2014-2021
Rodwell EV, Simpson A, Chan YW, Godbole G, McCarthy ND, Jenkins C.J

12 Apr 2023
Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning
Bayliss SC, Locke RK, Jenkins C, Chattaway MA, Dallman TJ, Cowley LA

08 Apr 2023
The evolution and international spread of extensively drug resistant Shigella sonnei
Mason LCE, Greig DR, Cowley LA, Partridge SR, Martinez E, Blackwell GA, Chong CE, De Silva PM, Bengtsson RJ, Draper JL, Ginn AN, Sandaradura I, Sim EM, Iredell JR, Sintchenko V, Ingle DJ, Howden BP, Lefèvre S, Njamkepo E, Weill FX, Ceyssens PJ, Jenkins C, Baker KS

06 Apr 2023
Forgotten but not gone: Yersinia infections in England, 1975 to 2020
Šumilo D, Love NK, Manuel R, Dabke G, Paranthaman K, Jenkins C, McCarthy ND

05 Apr 2023
Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile
Dingle KE, Freeman J, Didelot X, Quan TP, Eyre DW, Swann J, Spittal WD, Clark EV, Jolley KA, Walker AS, Wilcox MH, Crook DW

04 Apr 2023
Health inequalities in infectious diseases: a systematic overview of reviews
Abimbola Ayorinde, Iman Ghosh, Ifra Ali, Iram Zahair, Olajumoke Olarewaju, Megha Singh, Edward Meehan, Seun Stephen Anjorin, Suzanne Rotheram, Ben Barr, Noel McCarthy , Oyinlola Oyebode

04 Apr 2023
Metatranscriptomics improves the laboratory diagnosis of infectious intestinal disease from human diarrhoeal samples
Cunningham-Oakes E, Li Y, Perez-Sepulveda B, Hinton JCD, Nelson CA, McIntyre KM, Wardeh M, Iturriza-Gómara M, Hertz-Fowler C, O’Brien SJ, Cunliffe NA, Darby AC, the INTEGRATE consortium