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The Abbott Plex -ID and RIPL

The Abbott Plex -ID and RIPL. Tim Brooks, Carrie Turner & Jackie Duggan Rare & Imported Pathogens Laboratory, PHE Porton Down. Overview. Our lab and why we want the Plex-ID The instrument & how it works Performance in trials Topics for the Tropics Future steps Summary. Systemic anthrax.

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The Abbott Plex -ID and RIPL

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  1. The Abbott Plex-ID and RIPL Tim Brooks, Carrie Turner & Jackie Duggan Rare & Imported Pathogens Laboratory, PHE Porton Down

  2. Overview • Our lab and why we want the Plex-ID • The instrument & how it works • Performance in trials • Topics for the Tropics • Future steps • Summary Systemic anthrax

  3. RIPL service & needs • Acute diagnostic services for unusual and imported fevers • 24/7 helpline for clinicians • Same day telephone results for critical diagnoses • 24/7 service with 2-6 hour turn around for emergencies e.g. VHF • Main hub for National Imported Fever Service • PCR: real time and some block assays • Serology (mostly automated) • Culture Primary pneumonia from Leptospirosis, Malaysia

  4. The breadth of the problem

  5. In time of need… • Single phone number 0844 77 88 990 • Manned 24/7 • Working hours -> IFS SpR • Out of hours -> on-call Consultant rota • HPA/NHS - RIPL; Liverpool TIDU; HTD/UCLH; HPA • Weekly IFS teleconference • For discussion of interesting cases, get help with differentials • Bi-monthly IFS steering committee • Governance & service development Imported Fever Service Imported Fever Service

  6. Differential Diagnosis Algorithms Divided into 10 world regions Divided into 8 broad symptom categories: Undifferentiated fever Fever with haemorrhage Fever with rash Fever with skin/soft tissue involvement Fever with respiratory symptoms Fever with GI symptoms Fever with jaundice or hepato/splenomegaly Fever with neurological symptoms

  7. Next generation assays • Array cards for panels of PCR’s • Plex ID • Will extend range and fill gaps • Intelligent algorithms for patterns

  8. The Plex-ID • Developed by IBIS for detection of designated Biothreat agents • IBIS acquired by Abbott and device rebranded as Plex-ID • Additional panels developed for wide range of pathogens • Theoretical capability: • All bacteria • All viruses • All fungi } Known & Unknown Dengue haemorrhagic fever

  9. Plex-ID Features • Broad range PCR combined with Electrospray-Ionisation Time of Flight Mass Spectrometry (ESI TOF MS) • Broad identification of microbes (bacteria, viruses, fungi, protozoa) • Can detect complex mixtures of microbes • No culture required • Expected and unexpected pathogens in a single sample • High resolution genotyping, strain identification and drug resistance testing Cowpox, UK

  10. Overview of process Sample Nucleic acid extraction Broad range PCR with multiple primers (8 or 16 well assays) Determination of the amplicon weights by MS Calculation of the base compositions (A:G:T:C) Automated bioinformatics analysis

  11. Triangulating the answers Primer pair 1 Primer pair 2 Primer pair 3 Product = 90% p of B. pseudomallei Product = 95% p of B. pseudomallei Product = 90% p of B. pseudomallei Primers 1 + 2 results =p 98%B pseudomallei Primers 1, 2 and 3 results combined = p 99.5% B. pseudomallei Additional wells/plates can be used to give increased resolution depending on assay

  12. Assay panels • Bacterial, antibiotic resistance, candida (6024 species, 10205 strains detected) • Broad bacterial identification (5885 species, 10561 strains detected) • Broad viral (human) (173 species, 2611 strains detected) • Broad fungal (2108 species, 3044 strains detected) • Food borne (89 species, 2573 strains detected) • Respiratory virus (116 species, 13080 strains detected) • Vector borne (324 species, 1020 strains detected) • Biothreat (177 species, 3997 strains detected) • Flu (2 species, 14980 strains detected) • MDR TB (25 species, 127 strains, drug resistance) Courtesy Abbott

  13. What you can use it on • Anything you can extract!

  14. RIPL sample evaluation • 3 assay panels • Biothreat (anthrax, plague, tularaemia, Rickettsia, Q fever, alphaviruses, filoviruses) • Vector-borne panel (Borrelia, Rickettsia, malaria, Anaplasma, Babesia) • Custom designed Tropical fever panel (Alphaviruses, flaviviruses, bunyaviruses, hantaviruses, malaria etc) • In development subject to contract Rattus norvegicus, reservoir of Seoul virus in current UK outbreak

  15. How does it perform -1 Note additional detections over intended result reveal contents of, and issues in, originators lab!

  16. How does it perform -2 † This organism was best hit; Y enterocolitica came up as alternative; 1 base difference!

  17. Behind the data -1 *Relevant Primer pairs in this assay well

  18. Behind the data- detail • Sample P12C001185 Burkholderia data

  19. Unintended results: • Food sample intended to demonstrate Brucella contamination

  20. Future steps • Evaluate Plex in comparison with extant tests for whole range of samples • Work up tropical fever panel • Generate data to support future validation for marketing • Determine the relative frequency of different pathogens • Evaluate large sample extraction e.g. for typhoid • Long term: • If commercially available, use Plex as 2nd line diagnostic system across full range of capability.

  21. Summary • Versatile & capable system • Single instrument has massive coverage • Needs multiple plates to achieve full potential • Currently relatively slow & expensive • Ideal for lower throughput assays and unusual problems • Can be used as basic typing tool • With thanks to: • ABBOTT staff, especially Ranga Sampath • RIPL staff At risk of glanders? (not a case this time!)

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