One Health Data at Bristol Andrew Dowsey

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1 One Health Data at Bristol Andrew Dowsey School of Social & Community Medicine (Oakfield House, Bristol) + School of Veterinary Sciences (Langford) Amateur Cage Fighter 1

2 Antimicrobial Resistance Transmission Dynamics of Infections Veterinary Sciences Epidemiology & Public Health Immunology Environmental Sciences One Health Human Sciences Animal Welfare Food Security Animal Models of Human Disease

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4 The OH-STAR Project One Health Selection and Transmission of Antimicrobial Resistance One Health Questions What are the risk factors for acquisition of AMR E. coli in the faecal microbiota of dairy cattle? Do AMR E. coli found in cattle faecal samples make their way to pasture? Are the same AMR E. coli isolates found in human UTI in the same locale? 80 dairy farms, their vets, dogs walked on farms, local GP clinics On-farm antimicrobial use and farm management practices E. coli isolates from cows and pasture, and their resistance to 5 antimicrobials E. coli isolates from farm footpaths and dogs walked on the footpaths Human primary care UTI samples PCR and WGS to track movement of bacterial AMR genes 4

5 Point-of-use Auditing MedicineRecorder app Make auditing easier & less error-prone No barcodes on bottles OCR Pattern Matchin g VMD Lookup User Confirm

6 Surveillience at Scale Measure what is being prescribed (by vets) Extract from Veterinary Practice Management Software (PMS) Inconsistencies between PMS/Practice/Individual Staff No data standards for recording/reporting PMS data structure small animal oriented Over 20 PMS products in regular use in UK Partnering with

7 Surveillance of AMR at scale Auditing vs routine lab results? Bias For underlying bacterial type, rare to test for resistance 7

8 Sharing sensitive data Remote Analysis Differential Privacy Synthetic Data 8

9 Surveillance at scale Measure what is being prescribed (by vets) Prescription is to farmer, not animal Variance: Missing/incorrect data at source Bias: Courses not completed / used on multiple animals Many products licensed for multiple species Off-label usage does happen UoB to provide independent data quality assessment Will data be good enough to satisfy regulatory bodies? Can sparse point-of-use and audit data correct/calibrate the prescription data?

10 Diagnostics with Mass Spectrometry (MS) Origins in the late 1890s, developments led to 5 Nobels Market now $3.9b, will be worth $5.9b by 2018 Environmental (water, air and petroleum quality) Food safety, drug testing and forensics All stages of Pharma, including lead compound discovery, structural analysis, pharmacokinetics and pharmacodynamics Life sciences/biotech: assaying and sequencing proteins and metabolites Clinical biomarker discovery and screening Flexible platform from 0.5m+ biological research instruments to portable devices

11 Clinical Tech: MALDI Bacterial Identification

12 Gas Chromatography Mass Spectrometry Clinical Tech: Volatile Organic Compounds Human urine, 30 vs 30 study, mean image log intensity Impact Accelerator

13 Clinical Tech: Point-of-care monitoring of VOCs Impact Accelerator Impact Accelerator

14 Discovery proteomics: 2-40Gb per sample 14

15 Discovery proteomics: 2-40Gb per sample

16 Bayesian Wavelet Functional Mixed Model Probability fc ± % percentile posterior mean 97.5% percentile

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18 Peptide basis functions Scantime m/z

19 Peptide basis functions Scantime m/z

20 seamass with Peptide Simplex raw spectrum baseline factor1 factor2 factor3 spectrum minus baseline isotopes

21 seamass with Peptide Simplex raw spectrum baseline factor1 factor2 factor3 spectrum minus baseline isotopes

22 seamass with Peptide Simplex raw spectrum baseline factor1 factor2 factor3 spectrum minus baseline isotopes

23 Bayesian Protein Quantification 23

24 Proteomics Data Science at Scale Stoller Biomarker Discovery Centre Case-control studies: too many limitations?

25 Acknowledgments Research Team Ranjeet Bhamber Andris Jankevics Hanqing Liao Jon Massey Alex Phillips Academic Collaborators Stoller Biomarker Discovery Centre Research funded by: Industrial Collaborators

26 Antimicrobial Resistance Force The University of Bristol School of Veterinary Science's interdisciplinary working group actively researching key topics around veterinary antimicrobial resistance. Follow