Presentation on theme: "The Abbott Plex-ID and RIPL"— Presentation transcript:
1The Abbott Plex-ID and RIPL Tim Brooks, Carrie Turner & Jackie DugganRare & Imported Pathogens Laboratory, PHE Porton Down
2OverviewOur lab and why we want the Plex-ID The instrument & how it works Performance in trials Topics for the Tropics Future steps SummarySystemic anthrax
3RIPL service & needsAcute 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) CulturePrimary pneumonia from Leptospirosis, Malaysia
5In time of need… Single phone number 0844 77 88 990 Manned 24/7 Working hours -> IFS SpROut of hours -> on-call Consultant rotaHPA/NHS - RIPL; Liverpool TIDU; HTD/UCLH; HPAWeekly IFS teleconferenceFor discussion of interesting cases, get help with differentialsBi-monthly IFS steering committeeGovernance & service developmentImported Fever ServiceImported Fever Service
6Differential Diagnosis Algorithms Divided into 10 world regionsDivided into 8 broad symptom categories:Undifferentiated feverFever with haemorrhageFever with rashFever with skin/soft tissue involvementFever with respiratory symptomsFever with GI symptomsFever with jaundice or hepato/splenomegalyFever with neurological symptoms
7Next generation assays Array cards for panels of PCR’s Plex ID Will extend range and fill gaps Intelligent algorithms for patterns
8The Plex-IDDeveloped 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 & UnknownDengue haemorrhagic fever
9Plex-ID FeaturesBroad 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 microbesNo culture requiredExpected and unexpected pathogens in a single sampleHigh resolution genotyping, strain identification and drug resistance testingCowpox, UK
10Overview of process Sample Nucleic acid extraction Broad range PCR with multiple primers (8 or 16 well assays)Determination of the amplicon weights by MSCalculation of the base compositions (A:G:T:C)Automated bioinformatics analysis
11Triangulating the answers Primer pair 1Product = 95% p of B. pseudomalleiPrimer pair 2Product = 90% p of B. pseudomalleiPrimer pair 3Product = 90% p of B. pseudomalleiPrimers results =p 98% B pseudomalleiPrimers 1, 2 and 3 results combined = p 99.5%B. pseudomalleiAdditional wells/plates can be used to give increased resolution depending on assay
14RIPL sample evaluation 3 assay panelsBiothreat (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 contractRattus norvegicus, reservoir of Seoul virus in current UK outbreak
15How does it perform -1SampleExpected resultFront end reportSummary reportEQA P12/1185 (RG3-01)B. pseudomallei & S. aureusBurkholderia mallei, Burkholderia pseudomalleiStaphylococcus hominis, Staphylococcus aureus, Streptococcus sp.EQA P12/1186 (RG3-02)B. anthracis (pX01 -) & P. aeruginosaBacillus anthracis, Ba-pX02Pseudomonas aeruginosaEQA P12/1187 (RG3-03)B. melitensis & S. hominisBrucella ovis, Brucella abortus, Brucella suis, Brucella melitensis, Burkholderia thailandensis, Vibrio choleraeFrancisella tularensisNote additional detections over intended result reveal contents of, and issues in, originators lab!
16How does it perform -2 Intended result Front end report Summary report EQA P12/1190 (RG3-06)B. abortus & Y. enterocoliticaBrucella ovis, Brucella abortus, Brucella suis, Brucella melitensisShewanella sediminis†Shewanella sediminisEQA P12/1191 (RG3-07)B. thailandensis & E.coliBurkholderia thailandensisEscherichia coli† This organism was best hit; Y enterocolitica came up as alternative; 1 base difference!
17Behind the data -1 Result *Score Quality score Level EQA P12/1185 Burkholderia mallei/ Burkholderia pseudomallei2 of 21.003089Staphylococcus hominis/ Staphylococcus aureus/ Streptococcus sp.1 of 1635EQA P12/1191Burkholderia thailandensis1344Escherichia coli K-1263*Relevant Primer pairs in this assay well
19Unintended results:Food sample intended to demonstrate Brucella contaminationOrganismScoreQualityLevelCoxiella burnetii1 of 1 & 1 of 20.98166Brucella ovis/ Brucella abortus/ Brucella suis/ Brucella melitensis2 of 21.001226bacterium EF1 of 10.86167Pseudomonas syringae/ Pseudomonas fluorescens/ Pseudomonas putida1 of 2
20Future stepsEvaluate 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.
21At risk of glanders? (not a case this time!) SummaryVersatile & 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 staffAt risk of glanders? (not a case this time!)