Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC)

Lead Research Organisation: University of Oxford

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

Our aim is to achieve sufficiently accurate genetic prediction of resistance to all anti-tuberculosis
drugs for whole genome sequencing (WGS) to replace slow, cumbersome, culture-based drug
susceptibility testing (DST) for Mycobacterium tuberculosis complex (MTBC). This would enable
rapid-turnaround near-to-patient assays to revolutionize drug-resistant TB identification and
management.

This multidisciplinary collaboration including TB experts from five continents, WHO,
statisticians/mathematicians and software engineers will integrate machine-learning, statistical
genetics and molecular genetics methods to uncover all genomic variation causing at least 1%
resistance to first- and second-line anti-TB drugs with >1% resistance prevalence. We will use largescale
global and clade-representative WGS (>90,000), with initially >37,000 isolates with extended DST. Approaches include better WGS assembly to identify more variants with more precision,
improved statistical methods to detect associations between variants and DST, and selected
molecular validation of predicted resistant variants.

The project will create an automatically-updating, free, publically accessible, comprehensive data
repository of resistance-conferring variants. This will provide accurate genetic resistance prediction
for all drugs for any new MTBC WGS; superior design of near-to-patient amplification-based
molecular drug-resistance tests as alternatives to ‘WGS-only’ solutions; and better, faster and more
targeted drug-resistant TB treatment, facilitating improved control and WHO’s initiative to eliminate
TB by 2050.

Organisations

Publications

10 25 50
 
Title Pipeline developed to analyse TB WGS including SNPs and indels 
Description A pipeline has been developed improving existing pipelines to identify both SNPs and Indels in TB WGS., 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact None yet 
 
Title CliRes database hosted at OUCRU to collect DST and epidemiological data from across the world 
Description A database hosted at Oxford University Clinical Research Unit which allows all sites acros the world to record DST results and epidemiological data relating to the patients and isolates which can be accessed by the analyses team. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact ability to record data from all sites in a formatted way to allow analyses team to systematically align WGS with DST data 
 
Description China CDC collaboration 
Organisation Chinese Center for Disease Control and Prevention (China CDC)
Country China 
Sector Public 
PI Contribution Coordination of project and analyses of DST and WGS from approximately 100,000 clinical TB isolates across the world to determine whether antimicrobial resistance can be predicted through whole genome sequencing.
Collaborator Contribution Contribute ~3100 WGS and DST from TB clinical isolates. Contibute to the analyses of the data and help identify further research questions and opportunties arising from the dataset. Member of the General Assembly
Impact No outcome as yet, project just started.
Start Year 2016
 
Description Collaboration Aldolfo Lutz 
Organisation Instituto Adolfo Lutz
Country Brazil 
Sector Public 
PI Contribution Co-ordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical isoaltes across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution Contribute DST and WGS from 400 TB isolates. Contibute to analyses and help identify research opportunities and questions from dataset. Member of the general assembly
Impact None, project just started
Start Year 2016
 
Description Collaboration CPTR 
Organisation Critical Path to TB Drug Regimens (CPTR)
Country United States 
Sector Public 
PI Contribution Co-ordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS.
Collaborator Contribution Assistance with co-ordination at the start of project. Financial assistance to sequence 1000 TB genomes Work closely on data interoperability with regards to TB
Impact None, project just started
Start Year 2016
 
Description Collaboration EBI 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution co-ordination ofthe project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted from WGS.
Collaborator Contribution Co-applicant Zamin Iqbal has moved to EBI. EBI will be developing and and hosting the "data warehouse" allowing the upload of sequences generated across the world for view initially by the research team and them open access. Will be developing variant calling software for the sequences.
Impact None, project just started.
Start Year 2017
 
Description Collaboration Janssen 
Organisation Janssen Pharmaceutica NV
Country Belgium 
Sector Private 
PI Contribution Co-ordination of project and analyse of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution Provide research service to allow bedaquiline testing in Taiwan using microtitre plates. Provide bedaquiline for inclusion of the CRyPTIC generated DST plates. Provide general advice regarding microtitre DST and bedaquiline.
Impact Microtitre DST plate for use under CRyPTIC project
Start Year 2016
 
Description Collaboration NICD 
Organisation Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, National Health Laboratory Service in Johannesburg
Country South Africa 
Sector Hospitals 
PI Contribution Coodination of project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution Contribute WGS and DST from 2300 TB clinical isolates. Contribute to the analyses and help identify further research opportunities and questions arising from the data. Member of the General Assembly
Impact No output, project just started
Start Year 2016
 
Description Collaboration with Atlanta CDC 
Organisation Centers for Disease Control and Prevention (CDC)
Country United States 
Sector Public 
PI Contribution Co-ordination of project and analyses of DST and WGS from approximately 100,000 TB Clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution validation of novel gene variants conferring resistance to antimicrobials. Member of the General Assembly
Impact No outputs, project just started.
Start Year 2016
 
Description Collaboration with Germany 
Organisation Borstel Research Centre
Country Germany 
Sector Private 
PI Contribution Co-ordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical isolates across the world to determine whether antimicrobial resistacnce can be predicted through WGS.
Collaborator Contribution Contribute WGS and DST from 2000 TB clinical isolates. Contribute to analyses and help identify further research questions from dataset. Members of the General Assembly
Impact No output, project just started.
Start Year 2016
 
Description Collaboration with Germany 
Organisation IML red GmbH
Department Institute of Microbiology and Laboratory Medicine
Country Germany 
Sector Learned Society 
PI Contribution Co-ordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical isolates across the world to determine whether antimicrobial resistacnce can be predicted through WGS.
Collaborator Contribution Contribute WGS and DST from 2000 TB clinical isolates. Contribute to analyses and help identify further research questions from dataset. Members of the General Assembly
Impact No output, project just started.
Start Year 2016
 
Description Collaboration with National University of Singapore 
Organisation National University of Singapore
Country Singapore 
Sector Academic/University 
PI Contribution Analyses of WGS and DST data from samples collected as part of clinical trial in Philippines
Collaborator Contribution Contribution of WGS and DST data from samples collected as part of clinical trail in Philliipines. Funding provided by collaborator.
Impact No outputs yet
Start Year 2017
 
Description Collaboration with Otsuka 
Organisation Otsuka Pharmaceutical
Country Japan 
Sector Private 
PI Contribution Coordination of project and analses of DST and WGS from approximately 100,000 TB clinical samples from across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution provided Delamind for the microtitre DST plates used under the project which is not commercially available.
Impact Microtitre plate containing delamanid manufactured by Thermofisher for research use only.
Start Year 2016
 
Description Collaboration with Public Health Sweden 
Organisation Stockholm University
Department Public Health
Country Sweden 
Sector Academic/University 
PI Contribution Analyses of the WGS and DST data generated on clinical isolates from Sweden as part of the CRyPTIC objectives.
Collaborator Contribution Contibution of DST and DST data generated from clinical isolates.
Impact No outputs to date
Start Year 2017
 
Description Collaboration with SRI 
Organisation San Raffaele Hospital
Country Italy 
Sector Hospitals 
PI Contribution Co-ordination of project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution Contribute to WGS and DST from 2000 clinical isolates. Contribute to the analyses and help identify further research quesitons and opportunity from data. Member of the General Assembly
Impact No output, project just started.
Start Year 2016
 
Description Collaboration with South Africa 
Organisation Wits Health Consortium
Country South Africa 
Sector Private 
PI Contribution Co-ordination of the project and analyses of DST and WGS fro approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution Legal entity for National Institute of Communicable Diseases, Johannesberg, South Africa
Impact No output yet, project only just started.
Start Year 2016
 
Description Collaboration with Taiwan 
Organisation Centers for Disease Control Taiwan
Country Taiwan, Province of China 
Sector Public 
PI Contribution Analyses DST and WGS data of clinical isolates from Taiwan as part of worldwide dataset
Collaborator Contribution Contributing DST and WGS data from Taiwan
Impact No output yet
Start Year 2017
 
Description Collaboration with Uni Peruana Cayetano Heredia 
Organisation Cayetano Heredia University
Country Peru 
Sector Academic/University 
PI Contribution Co-ordination of project and analyses of DAT and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution Contribute 3100 WGS and DST data from TB clinical isolates. Contibute to analyses and help identify further research opportunities and questions arising from the dataset.
Impact None as yet as project just started.
Start Year 2016
 
Description Collaboration with sites providing existing data and advisors 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-ordination of the project and analyses of WGS and DST from approximately 100,000 TB clinical isolates across the world to determine whether antimicrobial resistance can be predicted through whole genome sequencing
Collaborator Contribution Contibution of existing WGS and DST from TB isolates. Contribution to analyses and help identify further research questions from the dataset. Members of the General Assembly
Impact None, project just started
Start Year 2016
 
Description Collaboration with sites providing existing data and advisors 
Organisation NHS Lothian
Country United Kingdom 
Sector Public 
PI Contribution Co-ordination of the project and analyses of WGS and DST from approximately 100,000 TB clinical isolates across the world to determine whether antimicrobial resistance can be predicted through whole genome sequencing
Collaborator Contribution Contibution of existing WGS and DST from TB isolates. Contribution to analyses and help identify further research questions from the dataset. Members of the General Assembly
Impact None, project just started
Start Year 2016
 
Description Collaboration with sites providing existing data and advisors 
Organisation University of British Columbia
Country Canada 
Sector Academic/University 
PI Contribution Co-ordination of the project and analyses of WGS and DST from approximately 100,000 TB clinical isolates across the world to determine whether antimicrobial resistance can be predicted through whole genome sequencing
Collaborator Contribution Contibution of existing WGS and DST from TB isolates. Contribution to analyses and help identify further research questions from the dataset. Members of the General Assembly
Impact None, project just started
Start Year 2016
 
Description Collaboration with sites providing existing data and advisors 
Organisation University of Cape Town
Country South Africa 
Sector Academic/University 
PI Contribution Co-ordination of the project and analyses of WGS and DST from approximately 100,000 TB clinical isolates across the world to determine whether antimicrobial resistance can be predicted through whole genome sequencing
Collaborator Contribution Contibution of existing WGS and DST from TB isolates. Contribution to analyses and help identify further research questions from the dataset. Members of the General Assembly
Impact None, project just started
Start Year 2016
 
Description External Advisory Board 
Organisation Foundation for Innovative New Diagnostics (FIND)
Country Switzerland 
Sector Charity/Non Profit 
PI Contribution Coordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution External Advisory Board i) providing advice on resolution of problems identified by the Executive Committee; and ii) reviewing and monitoring overall progress of the project and providing advice to the Executive Committee with regards to achieving deliverables; and iii) providing strategic oversight of effective dissemination, publication and deployment of project aims and outputs.
Impact No output project just started.
Start Year 2016
 
Description External Advisory Board 
Organisation Indian Council of Medical Research (ICMR)
Country India 
Sector Public 
PI Contribution Coordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution External Advisory Board i) providing advice on resolution of problems identified by the Executive Committee; and ii) reviewing and monitoring overall progress of the project and providing advice to the Executive Committee with regards to achieving deliverables; and iii) providing strategic oversight of effective dissemination, publication and deployment of project aims and outputs.
Impact No output project just started.
Start Year 2016
 
Description External Advisory Board 
Organisation University of Lille
Country France 
Sector Academic/University 
PI Contribution Coordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution External Advisory Board i) providing advice on resolution of problems identified by the Executive Committee; and ii) reviewing and monitoring overall progress of the project and providing advice to the Executive Committee with regards to achieving deliverables; and iii) providing strategic oversight of effective dissemination, publication and deployment of project aims and outputs.
Impact No output project just started.
Start Year 2016
 
Description External Advisory Board 
Organisation World Health Organization (WHO)
Country Global 
Sector Public 
PI Contribution Coordination of the project and analyses of DST and WGS from approximately 100,000 TB clinical samples across the world to determine whether antimicrobial resistance can be predicted through WGS
Collaborator Contribution External Advisory Board i) providing advice on resolution of problems identified by the Executive Committee; and ii) reviewing and monitoring overall progress of the project and providing advice to the Executive Committee with regards to achieving deliverables; and iii) providing strategic oversight of effective dissemination, publication and deployment of project aims and outputs.
Impact No output project just started.
Start Year 2016
 
Description FMR Collaboration 
Organisation Fidelity Management & Research
Country India 
Sector Private 
PI Contribution Lead institution contributing to analysis of the TB WGS and DST results from the project
Collaborator Contribution Providing ~6000 WGS on TB clinical samples and some DST results. Contribute to analyses and help identify research questions from dataset. Member of the General Assembly
Impact The project has just started, DNA extracted from clinical TB samples and sent for sequencing. PZA DST results generated by FMR
Start Year 2016
 
Description Hinduja Hosp Collaboration 
Organisation P. D. Hinduja Hospital and Medical Research Centre
Country India 
Sector Hospitals 
PI Contribution Lead Insitution, coordinator and analyses of WGS and DST from TB clinical samples across the world.
Collaborator Contribution Will provide DST information on ~6000 clinical TB isolates. Contribute to analyses and help identify further research questions from data. Member of the General Assembly
Impact None yet, project just started.
Start Year 2016
 
Description PacBio sequencing 
Organisation Icahn School of Medicine at Mount Sinai
Country United States 
Sector Academic/University 
PI Contribution Investigation of plasmid structure
Collaborator Contribution Sequencing and analysis Member of the CRyPTIC General Assembly. Member of REHAB Steering Committee
Impact Two publications
Start Year 2014
 
Description Public Health England (PHE) 
Organisation Public Health England
Country United Kingdom 
Sector Public 
PI Contribution Access to sequencing data and research results.
Collaborator Contribution Access to S. aureus, Norovirus, C. difficile and TB samples and related epidemiological data. Staff to collect the samples and data and to ship this to Oxford and the Wellcome Trust Sanger Institute for sequencing. As well as intellectual input into the research. Member of REHAB Steering Committee
Impact Successful translation of next generation sequencing into public health microbiology
Start Year 2009
 
Description collaboration with LSHTM 
Organisation London School of Hygiene and Tropical Medicine (LSHTM)
Department Malaria Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Coordination of project and analyses of DST and WGS from approximately 100,000 WGS TB clinical isolates. across the world to determine whether antimicrobial resisatnce can be predicted through WGS.
Collaborator Contribution Subcontracting to Universidad Peruana Cayetano Heredia. Member of the General Assembly
Impact No output as yet as project just started.
Start Year 2016
 
Title AMyGDA -Automated Detection of Bacterial Growth on 96-well plates (AMyGDA) 
Description This software automatically identifies whether there is Mtb growth in each well of a 96 well plate containing a range of anti-microbials to establish the minimum inhibitory concentration per drug for each isolate using plate images taken by Vizion (from Thermofisher). As the project progresses, we will be using this as a method of quality control and will re-evaluate any plates where the manual MIC reading for any drug has more than 1 doubling dilution difference to determine reading errors. Additionally, this software can be expanded to other plates and other drugs for other bacteria so is transferrable. 
IP Reference  
Protection Copyrighted (e.g. software)
Year Protection Granted 2017
Licensed Yes
Impact None yet.
 
Title Software to automatically read CRyPTIC anti-tuberculosis microtitre plate (CRyPTIC_DST) 
Description One goal of CRyPTIC is to pursue a validation for regulatory approval of 96 well microtitre pates developed under CRyPTIC (UKMYC5 plates; Trek Sensititre manufactured in collaboration with Thermo Fisher) offering standardized minimum inhibitory concentrations (MIC) for 14 anti-tuberculosis drugs. Seven CRyPTIC collaborators across the world have performed intitial evaluation of this microtitre plate by performing extensive DST on a laboratory-adapted H37Rv MTBC strain followed by evaluation of a panel of well characterized drug resistant strains which were shipped for simultaneous testing by all sites. This initial evaluation involved reading the plates by three different methods: Inverted microscope, mirrored plate reader and Sensititre™ Vizion™ Digital MIC Viewing System (Vizion). Vizion allows the user to capture images which are analysed by the team in Oxford, however, all three methods of reading are subject to user interpretation which is likely to be dependent on experience reading anti-tuberculosis microtitre plates. CRyPTIC_DST is a Python module that analyses photographs of 96 well plates and determines the growth of bacteria in each well. Since each well contains a different concentration of antibiotic and there are 14 antibiotics on the plate, this data can be used to determine the minimum inhibitory concentrations of each antibiotic and hence the drug susceptibility profile of the M.tuberculosis pathogen. The code maintains a local copy of all the metadata for each plate locally in a filesystem-based tree, stored in JSON files. Data and image are automatically downloaded from the CRyPTIC SQL database using its WebService, thereby bypassing the browser. The photograph of each plate is first cleaned up by applying a mean shift algorithm and locally equalising the histograms. The code then iteratively searches for circles in the image using a Hough transform and stops if and only if 96 circles of approximately the correct radius are found. This defines the locations of the wells. A square of pixels in the middle of each well is analysed; specifically the proportion of pixels below a threshold are counted, and if there are sufficient, the well is classified as containing growth. Since the metadata are also stored locally, the results of the image algorithm can be directly compared to the human measurements. The code can be run on a consumer grade laptop and each image takes around 5 seconds to analyse. It is currently stored as a private GitHub repository and will be made public upon publication of the first CRyPTIC validation paper. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2017 
Impact This has only just been developed and is currently being tested. Impact of this could minimise interlab and intralab variation of microtitre plate readings due and allow MIC determination irrespective of user experience 
 
Description New Scientist publication 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Project described in New Scientist magazine focussing on the machine learning element.
Year(s) Of Engagement Activity 2016
URL https://www.newscientist.com/article/mg23130923-000-genereading-software-to-cut-tb-diagnosis-from-mo...
 
Description Bash the Bug 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact "Bash the bug" is a website which encourages members of the public to identify whether there is Mtb bacterial growth in a specific well of a 96 well plate containing anti-microbial drugs. These plates are being used as part of the CRyPTIC project, and the objective of this is to use multiple opinions to "call" growth or no growth in a well which is proving problematic to the experts.
Year(s) Of Engagement Activity 2017,2018
URL https://www.zooniverse.org/projects/mrniaboc/bash-the-bug
 
Description Press release 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Press release for CRyPTIC project
Year(s) Of Engagement Activity 2016
 
Description Set up patient panels 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact We circulated an advert inviting members of the public to join patient panels to inform all aspects of the groups' work. Over 100 individuals responded, and we held two open meetings where different aspects of the work were presented. Following this smaller groups have been set up to review and advise on different projects.

Members of the public have really valued the opportunity to get involved.
Year(s) Of Engagement Activity 2014,2016