Presentation on theme: "The Abbott Plex-ID and RIPL Tim Brooks, Carrie Turner & Jackie Duggan Rare & Imported Pathogens Laboratory, PHE Porton Down."— Presentation transcript:
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
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
The breadth of the problem
In time of need… Single phone number 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
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
Next generation assays Array cards for panels of PCR’s Plex ID Will extend range and fill gaps Intelligent algorithms for patterns
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
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
Overview of process SampleNucleic 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
Triangulating the answers Primer pair 1 Product = 95% p of B. pseudomallei Primer pair 2 Product = 90% p of B. pseudomallei Primer pair 3 Product = 90% p of B. pseudomallei Primers 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
What you can use it on Anything you can extract!
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
How does it perform -1 SampleExpected resultFront end reportSummary report EQA P12/1185 (RG3-01) B. pseudomallei & S. aureus Burkholderia mallei, Burkholderia pseudomallei Staphylococcus hominis, Staphylococcus aureus, Streptococcus sp. EQA P12/1185 (RG3-01) B. pseudomallei & S. aureus Burkholderia mallei, Burkholderia pseudomallei Staphylococcus hominis, Staphylococcus aureus, Streptococcus sp. EQA P12/1186 (RG3-02) B. anthracis (pX01 -) & P. aeruginosa Bacillus anthracis, Ba-pX02Pseudomonas aeruginosa EQA P12/1187 (RG3-03) B. melitensis & S. hominis Brucella ovis, Brucella abortus, Brucella suis, Brucella melitensis, Burkholderia thailandensis, Vibrio cholerae Francisella tularensis Note additional detections over intended result reveal contents of, and issues in, originators lab!
How does it perform -2 Intended resultFront end reportSummary report EQA P12/1190 (RG3-06) B. abortus & Y. enterocolitica Brucella ovis, Brucella abortus, Brucella suis, Brucella melitensis Shewanella sediminis† EQA P12/1190 (RG3-06) B. abortus & Y. enterocolitica Brucella ovis, Brucella abortus, Brucella suis, Brucella melitensis Shewanella sediminis EQA P12/1191 (RG3-07) B. thailandensis & E.coli Burkholderia thailandensisEscherichia coli † This organism was best hit; Y enterocolitica came up as alternative; 1 base difference!
Behind the data -1 Result *Score Quality score Level EQA P12/1185Burkholderia mallei/ Burkholderia pseudomallei 2 of Staphylococcus hominis/ Staphylococcus aureus/ Streptococcus sp. 1 of EQA P12/1191 Burkholderia thailandensis 2 of Escherichia coli K-12 1 of *Relevant Primer pairs in this assay well
Unintended results: Food sample intended to demonstrate Brucella contamination Organism ScoreQualityLevel Coxiella burnetii 1 of 1 & 1 of Brucella ovis/ Brucella abortus/ Brucella suis/ Brucella melitensis 2 of bacterium EF 1 of Pseudomonas syringae/ Pseudomonas fluorescens/ Pseudomonas putida 1 of 2
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.
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!)