AMR Open Data Initiative AMR Surveillance in Pharma: a case-study for data sharingauthor by Professor Barry Cookson External Consultant to Project eLibrary • Division of Infection and Immunity, Univ. College London ESCMID• Dept. of Microbiology, © St Thomas’ Hospital Background of “90 day Project” Addressed some recommendations of the first Wellcome funded multi-disciplinary workshop (included Pharma Academia & Public Health invitees: 27thauthor July 2017 (post the Davos Declaration): by 1) Review the landscape of existing Pharma AMR programmes, their protocols,eLibrary data standards and sets 2) Develop a "portal" (register/platform) to access currently available AMR Surveillance data ESCMID Important ©to emphasise that this is a COLLABORATION between Pharma and others Overview of Questionnaire Content • General information - including name,author years active, countries, antimicrobials, microorganisms.by • Methodology - including accreditation, methodology for; surveillance, isolate collection, organism identification, breakpointseLibrary used, • Dataset - including data storage methodology, management and how accessed. ESCMID © 13 Company Responses author 7 by 3 3 eLibrary ESCMID © Structure of register Companies can have different ways of referring to their activities: We had to choose a consistent framework. author Companies Companyby 1 Programmes Programme A Programme B eLibrary Antimicrobials 1 2 3 4 5 company’s product comparator company’s product antimicrobials Programmes canESCMID contain multiple studies (e.g. Pfizer has© single global programme "ATLAS" containing all studies) Open-Access Register https://amr.theodi.org/6 Structure: author by eLibrary ESCMID © author by eLibrary ESCMID © What sort of data Pharmaceutical activities: - High-quality standardised data are collected? - Large Antimicrobial panel Lab Based - Many countries Surveillance - Stored in spreadsheets or (a WHO GLASS databases (integration a massive Category) author Reported challenge) by Culture-confirmed Lab tests for organisms Specimens obtained eLibrary People who seek healthcare People who become ill People infected with AMR bacteria ESCMID AMR surveillance© ‘pyramid’ What sort of data Programmes vary in: are collected? - Infection sites - Microorganisms and - Antimicrobials tested Issues can relateauthor to: Reported - Ability to identify Hospital- versus Community-by Acquired infections Culture-confirmed as inconsistently recorded or defined Lab tests for organisms - Denominator data: usually % susceptible organisms Specimens obtained BUT many variations: eLibrary e.g . limiting % per site or People who seek healthcare organism numbers People who become ill People infected with AMR bacteria ESCMID Resonates with SUSPIRE study: AMR surveillance© ‘pyramid’ CMI, 2018;24:105-9 Surveillance targets vary considerably between companies: in aggregate…… Microorganisms Antimicrobials Infection sites Acinetobacter baumannii author Burkholderia cepacia Amikacin Blood stream Citrobacter spp. Amoxicillin/clavulanateby Intra-abdominal Enterobacter spp. Ampicillin/sulbactam Skin Enterococcus spp. Azithromycin Soft tissue Escherichia coli Aztreonam/avibactam Respiratory tract Haemophilus influenzae Bedaquiline Urinary tract Klebsiella pneumoniae BenzylpenicillineLibrary Moraxella catarrhalis Biapenem Mycobacterium tuberculosis Capreomycin Pseudomonas aeruginosa Cefaclor/Cefazolin/Cefcapene Streptococcus pneumoniae Cefdinir/Cefditoren/Cefepime Serratia spp. Cefiderocol etc. Staphylococcus aureusESCMID N.B. not comprehensive list Staphylococcus spp.© and not all equally Stenotrophomonas maltophilia represented What is the scale of the data? author by No. of eLibrary ProgrammesESCMID in register have data on isolates from a total of © 93 countries and 85 antimicrobials. Sub Saharan Africa Poor Datasets: format, management, access Format Databases (7/12) - managed by specialised companies e.g. Micron, JMI, IHMA (via SLDN), LGC. author Spreadsheets (5/12) - managed internally by Access • Online password-protected to centre participants • Some datasets are public to some extent: ATLAS (Pfizer) - www.atlas-surveillance.comeLibrary (updated every 6-9 months) SMART (Merck) - www.globalsmartsite.com SOAR (GSK) - raw data are now available ScientificESCMID Publications - often include tabulated MIC distributions © Example of use MICs for cefuroxime against Streptococcus pneumoniae from China SOAR 114620 (GSK) • Downloaded author anonymized data from register for all isolates from India andby China N.B. this distribution ~2011-2014 was published as • Subsetted to S. Table 4 in the pneumoniae and cefuroxime in China associated GSK • Generated distribution SOAR publication: • Plotted Hu et al. (2016) JAC doi: 10.1093/jac/dkw065 % of isolates eLibrary Here Liam Shaw generated it from the raw data ESCMID © Second Workshop March 2018: Four Key Actions • Develop a public–private partnership between industry, public health organisations and other AMR initiatives for a more informative, coherent and openly accessible AMR data landscape author • Enable open innovation and catalyse databy sharing within the AMR community by encouraging reuse of shared industry AMR data with case studies (Wellcome to launch a Data Reuse prize ~Jan. 2019) • Facilitate development of commoneLibrary methodological and metadata standards and data governance frameworks so enabling the scientific and public health communities to utilise and compare data use with existing in-country datasets • Online portal ESCMIDlaunch managed and© governed by an independent party ` Collaboration Personnel (and Acknowledgements) Steering group 10 Company Nominated David Beardmore (ODI), Chair Lead Collaborators Pauline L’Henaff (ODI), Project Manager Seamus O’Brien (Pfizer now GARDP) Achaogen: Tiffany Keepers Didem Torumkuney (GSK) Allergan: author Ian Critchley Andrew Freeman (GSK) GSK: Didem Torumkuney Seamus O’Brien (Pfizer now GARDP) J&J: by Karen Grosser Najib Rehman (Pfizer now Merck: Mary Motyl, Kokoro & Farma Trust) Silas Holland Barry Cookson (Consultant: UCL) Novartis: Susana Goncalves Liam Shaw (Scientist: UCL) Pfizer: Michael Dowzicky Nandini Shetty (PHE) Roche: Claudia Zampaloni Allison Holt (Longitude 174) eLibrarySanofi: Christine Luxemburger Wellcome: Francesca Chiara, Shionogi: Yoshiri Yamano, Joanna Wiecek, Ghada Zoubiane Gareth Morgan &Tim Jinks One Data Institute technical team (IT)ESCMID Phil Lang, Olivier Thereaux & Myriam Wiesenfeld© .