ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads by Hunt, M, Swann, J, Constantinides, B, Fowler, PW, Iqbal, Z

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads by Hunt, M, Swann, J, Constantinides, B, Fowler, PW, Iqbal, Z

GM-CSF drives dysregulated hematopoietic stem cell activity and pathogenic extramedullary myelopoiesis in experimental spondyloarthritis by Regan-Komito, D, Swann, J, Demetriou, P, Cohen, S, Horwood, N, Sansom, S, Griseri, T

Scalable Pathogen Pipeline Platform (SP^3): enabling unified genomic data analysis with elastic cloud computing by Yang-Turner, F, Volk, D, Fowler, P, Swann, J, Bull, M, Hoosdally, S, Connor, T, Peto, T, Crook, D

Prospective trial of different antimicrobial treatment durations for presumptive canine urinary tract infections by Pouwels, KB, Allerton, F, Bazelle, J, Caddy, S, Cauvin, A, De Risio, L, Swann, J, Warland, J, Kent, A

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing by Sanderson, ND, Swann, J, Barker, L, Kavanagh, J, Hoosdally, S, Crook, D, GonFast Investigators Group, Street, TL, Eyre, DW

An Open-source Azure Solution for Scalable Genomics Workflows by Yang-Turner, F, Gripper, L, Swann, J, Do, T, Foster, D, Volk, D, Ramanan, A, Robinson, M, Peto, T, Crook, D

Postnatal prebiotic supplementation in rats affects adult anxious behaviour, hippocampus electrophysiology, metabolomics and gut microbiota by Spitzer, S, Tkacz, A, Savignac, H, Cooper, M, Giallourou, N, Edward, M, Bannerman, D, Swann, J, Anthony, D, Poole, P, Burnet, PW

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices by Sanderson, N, Street, T, Foster, D, Swann, J, Atkins, B, Brent, A, McNally, M, Oakley, S, Taylor, A, Peto, T, Crook, D, Eyre, D

Penicillin binding protein substitutions co-occur with fluoroquinolone resistance in ‘epidemic’ lineages of multi drug-resistant Clostridioides difficile by Dingle, K, Freeman, J, Didelot, X, Quan, TP, Eyre, DW, Swann, J, Spittal, WD, Clark, EV, Jolley, KA, Walker, AS, Wilcox, MH, Crook, DW

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli by Davies, TJ, Swann, J, Sheppard, AE, Pickford, H, Lipworth, S, AbuOun, M, Ellington, MJ, Fowler, PW, Hopkins, S, Hopkins, KL, Crook, DW, Peto, TEA, Anjum, MF, Walker, AS, Stoesser, N

Optimised use of Oxford nanopore flowcells for hybrid assemblies by Lipworth, S, Pickford, H, Sanderson, N, Chau, KK, Kavanagh, J, Barker, L, Vaughan, A, Swann, J, Andersson, M, Jeffery, K, Morgan, M, Peto, TEA, Crook, DW, Stoesser, N, Walker, AS

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples by Gweon, H, Shaw, L, Swann, J, De Maio, N, AbuOun, M, Hubbard, A, Bowes, M, Bailey, M, Peto, T, Hoosdally, S, Walker, A, Sebra, R, Crook, D, Anjum, M, Read, D, Stoesser, N

Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Ca... by Auguet, OT, Niehus, R, Gweon, HS, Berkley, JA, Waichungo, J, Njim, T, Edgeworth, JD, Batra, R, Chau, K, Swann, J, Walker, SA, Peto, TEA, Crook, DW, Lamble, S, Turner, P, Cooper, BS, Stoesser, N

Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Entero... by Stoesser, N, George, R, Aiken, Z, Phan, HTT, Lipworth, S, Quan, TP, Mathers, AJ, De Maio, N, Seale, AC, Eyre, DW, Vaughan, A, Swann, J, Peto, TEA, Crook, DW, Cawthorne, J, Dodgson, A, Walker, AS

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes by De Maio, N, Shaw, L, Hubbard, A, George, S, Sanderson, N, Swann, J, Wick, R, Abuoun, M, Stubberfield, E, Hoosdally, S, Crook, D, Peto, T, Sheppard, A, Bailey, M, Read, D, Anjum, M, Walker, A, Stoesser, N

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

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli by Davies, TJ, Stoesser, N, Sheppard, AE, Abuoun, M, Fowler, P, Swann, J, Quan, TP, Griffiths, D, Vaughan, A, Morgan, M, Phan, HTT, Jeffery, KJ, Andersson, M, Ellington, MJ, Ekelund, O, Woodford, N, Mathers, AJ, Bonomo, RA, Crook, DW, Peto, TEA, Anjum, MF, Walker, AS

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 individua... by Lumley, SF, Constantinides, B, Sanderson, N, Rodger, G, Street, TL, Swann, J, Chau, KK, O'Donnell, D, Warren, F, Hoosdally, S, OUH Microbiology laboratory, OUH Infection Prevention and Control team, O'Donnell, A-M, Walker, TM, Stoesser, NE, Butcher, L, Peto, TE, Crook, DW, Jeffery, K, Matthews, PC, Eyre, DW

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. by 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, REHAB consortium