SSI ACTIVITIES ON SALMONELLA FOR ECDC

Transcription

1 SSI ACTIVITIES ON SALMONELLA FOR ECDC EQA organizer and Database curators Head of Typing Laboratory Mia Torpdahl Food borne infections, SSI

2 TWO ECDC FRAMEWORK CONTRACTS Two contracts in European EQA programs - Molecular typing database curator Salmonella, VTEC and Listeria Maximum of 4 years

3 EQA PROGRAMME FOR SALMONELLA Yearly program (ECDC funded ) PFGE - 10 test strains - 1 standard - Using PulseNet International protocol - Provide trouble shooting MLVA - 10 test strains - 33 reference strains upon request Phage typing (FOOD, DTU) - 10 Typhimurium strains - 10 Enteritidis strains Molecular typing service including data analysis and strain storage - Divided on all three organisms - Approximately per year 350 PFGE and 50 MLVA strains Protocols Trouble-shooting Individual feedback Final report Publication

4 TYPHIMURIUM PHAGE TYPING 11 participating laboratories

5 ENTERITIDIS PHAGE TYPING 12 participating laboratories

6 MLVA RESULTS FOR 15 LABORATORIES Three laboratories responsible for all results outside expected change * 1 Accepted changes are one repeat change in one of the loci STTR5, STTR6 or STTR10 * 2 Measurements for strain 19 gives a total of 120%. This is caused by 3 different laboratories identifying two different MLVA profiles for this strain.

7 PFGE Tiff grading (Maximum 28) 25 laboratories average 23 BioNumerics analysis (Maximum 20) 14 laboratories average 18

8 CELL SUSPENSIONS AND LANES Salmonella average - Cell suspensions Lanes Restriction Gel background DNA degradation 3.3 All between excellent and good

9 IMAGE AQUISITION AND RUNNING CONDITIONS

10 PROBLEMS Wells not included in tiff Running conditions not as described in protocol Not cropped as described and run too far

11 BANDS

12 PROBLEMS Bands to thick caused by overexposure Fuzzy bands Remember to focus during image aquisition

13 SALMONELLA CLUSTER ANALYSIS PFGE_XbaI PFGE_XbaI

14 SALMONELLA CLUSTER ANALYSIS PFGE_XbaI PFGE_XbaI

15 SALMONELLA BN NORMALIZATION

16 SALMONELLA BN NORMALISATION

17 SALMONELLA BN NORMALIZATION

18 CONCLUSIONS Results are encouraging MLVA improvements - Make sure to check your reference run - It is useful to have the same strain (known alleles) on each run Should this be standardised in Europe? PFGE - Room for improvement - Make sure to use your image acquisition equipment correct - Run according to protocol - Washing! Plugs De-staining of gel - Laboratories could benefit from PFGE training

19 ECDC S MOLECULAR SURVEILLANCE ROADMAP ECDC has just starting to integrate molecular methods into the surveillance on a European level with a five year plan ( ) Objectives - Fast international cluster detection - Emergence of new virulent strains, including resistance - Identify Transmission routes, sources and risk factors Method requirements - Results must be comparable between labs - Data should be interpreted by typing experts

20 TESSY 3.0 MSS TESSy: Surveillance system of infectious diseases Detailed flow of isolate-related data between Member States, TESSy 3.0 MSS, Curators and EPIS

21 FWD PILOT Member States Consultation on Pilot project protocol (AF, NMFP and NSFP) Review SOPs, sample data (pilot participants) Data submission (pilot participants) Coordination of laboratory support; EQA, data validation, expert advice, regular cluster reports (outsourced to SSI, Denmark) ECDC Invitation of min. 3-5 voluntary labs 14 labs! Finalisation of supporting IT systems Validation of historical data Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr Advisory Forum 29 Update on pilot phase Workshop Review of metadataset 2013: routine operation

22 TESSY TYPING DATA Salmonella - PFGE: XbaI, BlnI, SpeI. - MLVA: Typhimurium. - AST (Antimicrobial Susceptibility Typing): MIC, zone, etest. Both raw test result and interpreted resistance. Listeria - PFGE: AscI, ApaI, SmaI. E. coli - PFGE: XbaI, BlnI, SpeI, XbaI non O157, BlnI non O157, SpeI non O AST (Antimicrobial Susceptibility Typing): MIC, zone, etest. Both raw test result and interpreted resistance. All: text only results like serotype, presence of toxicity genes,...

23 CURATOR TASK Pilot phase Response time 4h for critical tasks Expected number of PFGE profiles - Listeria: 1 st year isolates; then 500 isolates yearly - VTEC: 400 isolates yearly - Salmonella: 1 st year isolates; then 3000 yearly

24 LAB EXPERT TASKS - CURATION Databases are managed by ECDC SSI secures the quality and integrity - Senior curators Cluster analysis at least weekly Expert advice to ECDC - Data interpretation - Outbreak integrity - Database setup etc - Junior curators Correct normalisation Naming and managing profiles Feedback to laboratories - Gel quality etc. - Help for improvement

25 ROUTINE OPERATION DATA SUBMISSION - Reporting when and how? Ideally, reporting should be part of the regular analysis in BN - Plug-in for direct submission through the TESSy web service (preferred option) - Also possible to create XML for TESSy file upload Curators and ECDC will review non-urgent data on a weekly basis - More often if an urgent need emerges In an outbreak situation, Member States may be asked to provide additional data - PFGE data should normally be submitted through TESSy, but can additionally be uploaded as an image file in EPIS if needed System only supports human samples! - Discussions with EFSA, EC and EURLs are on-going on how to make it possible to co-analyse typing data

26 TESSY MSS WORKFLOW Laboratory Experiment Protocols Quality Control Submission Upload Approval Cluster Analysis Web interface Escalation Processes will be described fully by Standard Operating Procedures, now v1.0 Constant drive to improve efficiency and achieve/maintain acceptable quality. Curation Quality Control Nomenclature Cluster Detection Link to notified cases

27 FIRST CLUSTER Distribution of Salmonella Stanley cases by Member States and week of onset of disease, week 20 to Hungary Germany Belgium Austria

28 EPIS

29 TESSY TO EPIS Actions Visible by Curator detects a cluster in TESSy and inform ECDC TESSy ECDC/curator ECDC opens an MTCI EPIS ECDC/curator and affected Member States ECDC opens an urgent inquiry EPIS All FWD network

30 THANK YOU For listening