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Publications

Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam.
Silcocks, M; Chang, X; Thuong Thuong, NT; Qin, Y; Minh Ha, DT; Khac Thai, PV; Vijay, S; Anh Thu, DD; Ngoc Ha, VT; Ngoc Nhung, H; Huu Lan, N; Quynh Nhu, NT; Edwards, D; Nath, A; Pham, K; Duc Bang, N; Hong Chau, TT; Thwaites, G; Heemskerk, AD; Chuen Khor, C; Teo, YY; Inouye, M; Ong, RT-H; Caws, M; HOLT, KE; ... Dunstan, SJ.
2023
Microbiology spectrum, (2023).11 6 10.1128/spectrum.02562-23.
Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities.
Jauneikaite, E; Baker, KS; Nunn, JG; Midega, JT; Hsu, LY; Singh, SR; Halpin, AL; Hopkins, KL; Price, JR; Srikantiah, P; Egyir, B; Okeke, IN; HOLT, KE; Peacock, SJ; Feasey, NA; SEDRIC Genomics Surveillance Working Group,;
2023
The Lancet. Microbe, (2023).4 12 10.1016/S2666-5247(23)00282-3.
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, LC E; Rodgus, J; Hendriksen, RS; Essack, SY; Egyir, B; Halpin, AL; MacCannell, DR; Campos, J; Srikantiah, P; ... SEDRIC Genomics Surveillance Working Group,
2023
The Lancet. Microbe, (2023).4 12 10.1016/S2666-5247(23)00281-1.
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; SEDRIC Genomics Surveillance Working Group,;
2023
The Lancet. Microbe, (2023).4 12 10.1016/s2666-5247(23)00283-5.
aj-clements/Vivli-AMR-KG.
KNIGHT, GM; Waterlow, N; WILDFIRE, J; Clements, AJ;
2023
, Github (2023).
AHHME: A model for estimating the holistic cost-effectiveness of antimicrobial resistance interventions in food animal production.
Emes, ET; WAAGE, J; KNIGHT, GM; NAYLOR, NR;
2023
One health, (2023).17, 10.1016/j.onehlt.2023.100629.
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.
CAREY, ME; DYSON, ZA; Ingle, DJ; Amir, A; Aworh, MK; Chattaway, MA; Chew, KL; Crump, JA; Feasey, NA; Howden, BP; Keddy, KH; Maes, M; Parry, CM; Van Puyvelde, S; Webb, HE; Afolayan, AO; Alexander, AP; Anandan, S; Andrews, JR; Ashton, PM; Basnyat, B; Bavdekar, A; Bogoch, II; Clemens, JD; Da Silva, KE; ... Global Typhoid Genomics Consortium Group Authorshi,
2023
eLife, (2023).12, 10.7554/eLife.85867.
Quantifying patient- and hospital-level antimicrobial resistance dynamics in Staphylococcus aureus from routinely collected data.
Leclerc, Q; CLEMENTS, A; Dunn, H; Hatcher, J; Lindsay, JA; Grandjean, L; KNIGHT, GM;
2023
Journal of medical microbiology, (2023).72 7 10.1099/jmm.0.001724.
Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization.
CAREY, ME; DYSON, ZA; Argimón, S; CERDEIRA, L; Yeats, C; Aanensen, D; Mboowa, G; Baker, S; Tessema, SK; Smith, AM; Okeke, IN; HOLT, KE;
2023
Open forum infectious diseases, (2023).10 Suppl 10.1093/ofid/ofad044.
Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17.
Hetland, MA K; Hawkey, J; Bernhoff, E; Bakksjø, R-J; Kaspersen, H; Rettedal, SI; Sundsfjord, A; HOLT, KE; Löhr, IH;
2023
Microbial genomics, (2023).9 5 10.1099/mgen.0.001005.