Publications

A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology

Daniel Amoako, Nguyen To Anh, Jasmine Bastable, Marc Brouard, Constanza Campano Romero, Andres Castillo Ramirez, Bede Constantinides, Derrick W. Crook, Phan Manh Cuong, Moussa Moise Diagne, Amadou Diallo, Nguyen Thanh Dung, Laura Dunn, Le Van Duyet, Josie Everatt, Katherine Fletcher, View ORCID ProfilePhilip W. Fowler, Mailie Gail, Jessica Gentry, Saheer Gharbia, Hospital for Tropical Diseases SARS-CoV-2 testing team, Nguyen Thi Thu Hong, View ORCID ProfileMartin Hunt, View ORCID ProfileZam Iqbal, Katie Jeffery, Dikeledi Kekana, Thomas Kesteman, Jeff Knaggs, Marcela Lopes Alves, Dinh Nguyen Huy Man, Amy (pre-print) J. Mathers, Nghiem My Ngoc, Sarah Oakley, Hardik Parikh, Tim E.A. Peto, Phuong Quan, Marcelo Rojas Herrera, Nicholas Sanderson, Vitali Sintchenko, Jeremy Swann, View ORCID ProfileJunko Takata, Nguyen Thi Tam, View ORCID ProfileLe Van Tan, Pham Ngoc Thach, Ndeye Marieme Top, Nguyen Thu Trang, Van Dinh Trang, Robert Turner, H. Rogier van Doorn, Anne von Gottberg, Jeremy Westhead, Nicole Wolter, Bernadette C. Young

A consensus statement on dual purpose pathogen surveillance systems: The always on approach

Helene-Mari van der Westhuizen, Srinidhi Soundararajan, Tamsin Berry, David Agus, Sergio Carmona, Philip Ma, Jessica Davis, Sarah Walker, Jolynne Mokaya, Stephen D. Bentley, Nick R. Thomson, John Silitoe, Andrew Singer, Ines Hassan, Romina Mariano, Megan Akodu, Gabriel Seidman, Nabihah Sachedina, Jonathan Edgeworth, Reshania Naidoo, Tariro Makadzange, Vladimir Choi, Renuka Gadde, Samuel V. Scarpino, Corinna Bull, Kumeren Govender, Belinda Ngongo, Hinda Ruton, Paul Pronyk, Kate Smolina, Henry Li, Dylan Barry, Sven Schaffer, Vanessa Moeder, George Gao, Derrick Crook, John Bell.

Transforming clinical microbiology with bacterial genome sequencing

Xavier Didelot, Rory Bowden, Daniel J. Wilson, Tim E. A. Peto and Derrick W. Crook

Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe Wellcome Open Research 4:191

Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler PW, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z. (2019)

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz M, Ramakrishnan S, The CRyPTIC Consortium, Iqbal Z (2022) Genome Biology 23:147

Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance in M. tuberculosis

Brankin AE, Fowler PW (2024) J Antimicrob Chemother AMR 5:dlad039

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A new global standard for molecular diagnostics

Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey JE, Omar SV, Peto TEA, Suresh A, Uplekar S, Laurent S, Colman R, Nathanson CM, Zignol M, Walker AS, the CRyPTIC Consortium, the Seq&Treat Consortium, Crook DW, Ismail N, Rodwell TC (2022)

Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, 2nd ed

World Health Organisation (2023) Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, second edition ISBN: 978-92-4-008241-0

WHO

Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, 1st ed

World Health Organisation (2021) Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance ISBN: 978-92-4-002817-3

WHO