Contexts

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
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000630
- 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
https://www.mdpi.com/2076-2607/9/9/1868
- 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 crookpm@ndm.ac.ox.uk 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
https://www.thelancet.com/journals/eclinm/article/PIIS2589-5370(21)00190-5/fulltext
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
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000391
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
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
https://academic.oup.com/jac/article/75/4/873/5710700
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
https://academic.oup.com/cid/article/73/12/2276/6067638
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
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00947-2
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
https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00128-2/fulltext
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
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000453
Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection
Lipworth S, Peto T, Crook D, Walker A, Stoesser N
https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00151-8/fulltext
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
https://www.nature.com/articles/s41396-021-00926-w
Flanker: a tool for comparative genomics of gene flanking regions
Matlock W, Lipworth S, Constantinides B, Peto T, Walker A, Crook D, Stoesser N
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000634
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
https://journals.asm.org/doi/10.1128/AEM.01715-20
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
https://www.science.org/doi/10.1126/sciadv.abe3868