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Oxford University Lead: Dr Nicole Stoesser

UKHSA co-lead: Dr Matt Ellington


We aim to understand how healthcare associated and antimicrobial resistant infections can be affected by what happens on farms, and in both the general and hospital environment. Our strategy is to increase our understanding on what the important factors to drive AMR and HAI infections,  how these factors are influenced by different environments and how they are passed onto and disseminated in humans.  We hope this will provide understanding on how AMR genes are shared between humans, animals and the environment, identify what systems contribute to the to the spread of microbes in hospitals and work towards minimising this and optimise resistance prediction for certain microbes using whole genome sequencing and molecular techniques.


Contexts Theme Publications

  • A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage

AbuOun M, Jones H, Stubberfield E, Gilson D, Shaw LP, Hubbard ATM, Chau K, Sebra R, Peto TEA, Crook DW, Read DS, Gweon HS, Walker AS, Stoesser N, Smith RP, Anjum MF


  • Migration of Escherichia coli and Klebsiella pneumoniae Carbapenemase (KPC)-Producing Enterobacter cloacae through Wastewater Pipework and Establishment in Hospital Sink Waste Traps in a Laboratory Model System

Aranega-Bou P, Ellaby N, Ellington M, Moore G


  • A splash-reducing clinical handwash basin reduces droplet-mediated dispersal from a sink contaminated with Gram-negative bacteria in a laboratory model system

Aranega-Bou P, Cornbill C, Verlander N, Moore G

Please contact for a copy of the paper.


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

Auguet O, Niehus R, Gweon HS, Berkley JA, Waichungo J, Njim T, Edgeworth JD, Batra R, Chau K, Swann J, Walker AS, Peto TE, Crook DW, Lamble S, Turner P, Cooper BS, Stoesser N


Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

Constantinides B, Chau KK, Quan TP, Rodger G, Andersson MI, Jeffery K, Lipworth S, Hyun S, Peniket A, Pike G, Millo J, Byukusenge M, Holdaway M, Gibbons C, Mathers A, Crook D, Peto T, Walker A, Stoesser N


Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

Davies T, Stoesser N, Sheppard A, Abuoun M, Fowler P, Swann J, Quan P, Griffiths D, Vaugahn A, Morgan M, Phan H, Jeffery K, Andersson M, Ellington M, Ekelund O, Woodford N, Mathers A, Bonomo R, Crook D, Peto T, Anjum M, Walker S

Reconciling the Potentially Irreconcilable? Genotypic and Phenotypic Amoxicillin-Clavulanate Resistance in Escherichia coli | Antimicrobial Agents and Chemotherapy (


Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital

Kizny GA, Phan H, Lipworth S, Cheong E, Gottlieb T, George S, Peto T, Mathers A, Walker A, Crook D, Stoesser N


Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

Lipworth S, Vihta K, Chau K, Kavanagh J, Davies T, George S,  Barker L, Vaughan A,  Anderson M, Jeffrey K, Oakley S, Morgan M, Peto T, Crook D, Walker A, Stoesser N


Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK

Lipworth S, Vihta K, 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


Epidemiology of Mycobacterium abscessus in England: an observational study

Lipworth S, Hough N, Weston N, Muller-Pebody B, Phin N, Myers R, Chapman S, Flight W, Alexander E, Smith E, Robinson E, Peto T, Crook D, Walker A, Hopkins S, Eyre D, Walker T


Optimized use of Oxford Nanopore flowcells for hybrid assemblies

Lipworth S, Pickford H, Sanderson N, Chau K, Kavanagh J, Barker L, Vaughan A, Swann J, Anderson M, Jeffery K, Morgan M, Peto T, Crook D, Stoesser N, Walker A


Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection

Lipworth S, Peto T, Crook D, Walker A, Stoesser N


Genomic network analysis of environmental and livestock F-type plasmid populations

Matlock W, Chau K, AbuOun M, Stubberfield E, Barker L, Kavanagh J, Pickford H, Gilson D, Smith R, Gweon H, Hoosdally S, Swann J, Sebra R, Bailey M, Peto T, Crook D, Anjum M, Read D, Walker A, Stoesser N, Shaw L, REHAB Consortium


Flanker: a tool for comparative genomics of gene flanking regions

Matlock W, Lipworth S, Constantinides B, Peto T, Walker A, Crook D, Stoesser N


Risk factors associated with carbapenemase-producing Enterobacterales (CPE) positivity in the hospital wastewater environment

Park S, Parikh H, Vegesana K, Stoesser N, Barry K, Kotay S, Dudley S, Peto T, Crook D, Walker A, Mathers A


Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Shaw L, Chau K, 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