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Iqbal Group

Algorithms and analysis for microbial genomes

Publications

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Genomic perspective on the bacillus causing paratyphoid B fever.

Hawkey J, Frézal L, Tran Dien A, Zhukova A, Brown D, Chattaway MA, Simon S, Izumiya H, Fields PI, De Lappe N, Kaftyreva L, Xu X, Isobe J, Clermont D, Njamkepo E, Akeda Y, Issenhuth-Jeanjean S, Makarova M, Wang Y, Hunt M, Jenkins BM, Ravel M, Guibert V, Serre E, Matveeva Z, Fabre L, Cormican M, Yue M, Zhu B, Morita M, Iqbal Z, Silva Nodari C, Pardos de la Gandara M, Weill FX.

Nature communications, 2024

doi:10.1038/s41467-024-54418-4.

Whole genome sequencing of M. tuberculosis for disease control in high-burden settings: study protocol for a cluster randomized controlled trial evaluating different community-wide intervention strategies in rural Madagascar.

Ametepe ESA, Andriamanoha N, Andrianomanana FR, Point F, Mangahasimbola RT, Dyachenko A, Hall M, Gamana TM, Knoblauch AM, Razafindrasoa YY, Nimalan A, Behr M, Durand M, Johri M, Iqbal Z, Rakotoarivelo AR, Randremanana RV, Rakotosamimanana N, Lapierre SG.

Trials, 2024

doi:10.1186/s13063-024-08537-4.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Barkham T, Bashton M, Batty EM, Bediako Y, Belder DD, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Chen YYC, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao N, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Mora JAM, Morang’a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sessions OM, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, Zair X, IMSSC2 Laboratory Network Consortium, de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z.

Preprint, 2024

doi:10.1101/2024.04.29.591666.

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

Amoako D, Anh NT, Bastable J, Brouard M, Campano Romero C, Castillo Ramirez A, Constantinides B, Crook DW, Cuong PM, Diagne MM, Diallo A, Dung NT, Dunn L, Duyet LV, Everatt J, Fletcher K, Fowler PW, Gall M, Gentry J, Gharbia S, Hospital for Tropical Diseases SARS-CoV-2 testing team, Hong NTT, Hunt M, Iqbal Z, Jeffery K, Kekana D, Kesteman T, Knaggs J, Lopes Alves M, Man DNH, Mathers A, Ngoc NM, Oakley S, Parikh H, Peto TE, Quan P, Rojas Herrera M, Sanderson N, Sintchenko V, Swann J, Takata J, Tam NT, Tan LV, Thach PN, Top NM, Trang NT, Trang VD, Turner R, Van Doorn HR, von Gottberg A, Westhead J, Wolter N, Young BC.

Preprint, 2023

doi:10.1101/2023.11.27.23298986.

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Rahman N, O’Cathail C, Zyoud A, Sokolov A, Munnink BO, Grüning B, Cummins C, Amid C, Nieuwenhuijse D, Visontai D, Yuan DY, Gupta D, Prasad D, Gulyás GM, Rinck G, McKinnon J, Rajan J, Knaggs J, Skiby JE, Stéger J, Szarvas J, Gueye K, Papp K, Hoek M, Kumar M, Ventouratou M, Bouquieaux M, Koliba M, Mansurova M, Haseeb M, Worp N, Harrison PW, Leinonen R, Thorne R, Selvakumar S, Hunt S, Venkataraman S, Jayathilaka S, Cezard T, Maier W, Waheed Z, Iqbal Z, Aarestrup FM, Csabai I, Koopmans M, Burdett T, Cochrane G.

Preprint, 2023

doi:10.1101/2023.04.19.537514.

The 2021 WHO catalogue of <i>Mycobacterium tuberculosis</i> complex mutations associated with drug resistance: A genotypic analysis.

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

The Lancet. Microbe, 2022

doi:10.1016/s2666-5247(21)00301-3.

Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of <i>M. tuberculosis</i>

The CRyPTIC Consortium, Fowler PW, Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Gibertoni Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin W, Liu C, Liu D, Malone KM, Mandal A, Mansjö M, Matias D, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, Okozi N, Oliveira RS, Omar SV, Paton N, Peto TE, Watanabe Pinhata JM, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PM, Rathod P, Robinson E, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Kohl TA, Smith G, Solano W, Spitaleri A, Supply P, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker TM, Walker AS, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao Y, Yang Y, Yanlin Z, Yao S, Zhu B.

Preprint, 2021

doi:10.1101/2021.02.24.21252386.

Antibiotic resistance prediction for &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; from genome sequence data with Mykrobe.

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 P, 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.

Wellcome open research, 2019

doi:10.12688/wellcomeopenres.15603.1.

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B.

The New England journal of medicine, 2018

doi:10.1056/nejmoa1800474.

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