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Publications

A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis.
Deelder, W; Napier, G; CAMPINO, S; Palla, L; PHELAN, J; CLARK, TG;
2022
BMC genomics, (2022).23 1 10.1186/s12864-022-08291-4.
Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial.
Pickering, H; HART, JD; Burr, S; STABLER, R; Maleta, K; Kalua, K; BAILEY, RL; HOLLAND, MJ;
2022
Gut pathogens, (2022).14 1 10.1186/s13099-021-00478-6.
Quantifying the Relationship between Antibiotic Use in Food-Producing Animals and Antibiotic Resistance in Humans.
EMES, D; NAYLOR, N; WAAGE, J; KNIGHT, G;
2022
Antibiotics (Basel, Switzerland), (2022).11 1 10.3390/antibiotics11010066.
TyphiNET: An online dashboard for global genomic surveillance of Salmonella Typhi.
DYSON, Z; Cerdeira, L; Chattaway, MA; Weill, F-X; Ingle, DJ; Williamson, DA; Argimon, S; Aanensen, D; Baker, S; HOLT, KE;
2022
(2022).
The Strategic Typhoid Alliance Across Africa and Asia (STRATAA): Genetic epidemiology of typhoidal Salmonella in Blantyre, Kathmandu and Dhaka.
DYSON, ZA; Ashton, PM; Meiring, JE; Duchene, S; Khanam, F; Chirambo, A; Msefula, CL; Karkey, A; Shakya, M; Tonks, S; Dunstan, SJ; Clemens, J; Pitzer, VE; Qadri, F; Basnyat, B; Gordon, MA; Heyderman, RS; Dougan, G; Baker, S; Pollard, AJ; HOLT, KE; STRATAA Consortium,;
2022
(2022).
TyphiNET: An online dashboard for global genomic surveillance of Salmonella Typhi.
DYSON, Z; Cerdeira, L; Chattaway, MA; Weill, F-X; Ingle, DJ; Williamson, DA; Argimon, S; Aanensen, D; Baker, S; HOLT, KE;
2022
(2022).
TyphiNET: An online dashboard for global genomic surveillance of Salmonella Typhi.
DYSON, Z; Cerdeira, L; Chattaway, MA; Weill, F-X; Ingle, DJ; Williamson, DA; Argimon, S; Aanensen, D; Baker, S; HOLT, KE;
2022
(2022).
A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307.
Fostervold, A; Hetland, MA K; Bakksjø, R; Bernhoff, E; HOLT, KE; Samuelsen, Ø; Simonsen, GS; Sundsfjord, A; Wyres, KL; Löhr, IH; Norwegian Study Group on Klebsiella pneumoniae,;
2021
The Journal of antimicrobial chemotherapy, (2021).77 3 10.1093/jac/dkab463.
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae.
Viehweger, A; Blumenscheit, C; Lippmann, N; Wyres, KL; Brandt, C; Hans, JB; Hölzer, M; Irber, L; Gatermann, S; Lübbert, C; Pletz, MW; HOLT, KE; König, B;
2021
Microbial genomics, (2021).7 12 10.1099/mgen.0.000741.
Linear plasmids in <i>Klebsiella</i> and other Enterobacteriaceae.
Hawkey, J; Cottingham, H; Tokolyi, A; Wick, R; Judd, L; CERDEIRA, L; De Oliveira Garcia, D; Wyres, K; HOLT, K;
2021
bioRxiv (2021). 10.1101/2021.12.14.472703.