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 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 Imported Service 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 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 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 1 + 2 results =p 98% B pseudomallei Additional wells/plates can be used to give increased resolution depending on assay Primers 1, 2 and 3 results combined = p 99.5% B. pseudomallei 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 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 Sample Expected result Front end report Summary report EQA P12/1185 (RG3-01) B. pseudomallei Burkholderia mallei, & S. Burkholderia pseudomallei aureus Staphylococcus hominis, Staphylococcus aureus, Streptococcus sp. EQA P12/1185 (RG3-01) B. pseudomallei Burkholderia mallei, & S. Burkholderia pseudomallei aureus Staphylococcus hominis, Staphylococcus aureus, Streptococcus sp. EQA P12/1186 (RG3-02) B. anthracis (pX01 -) & P. aeruginosa Bacillus anthracis, Ba-pX02 Pseudomonas aeruginosa B. melitensis & S. hominis Brucella ovis, Brucella abortus, Brucella suis, Brucella Francisella tularensis melitensis, Burkholderia thailandensis, Vibrio cholerae EQA P12/1187 (RG3-03) Note additional detections over intended result reveal contents of, and issues in, originators lab! How does it perform -2 Intended result Front end report EQA P12/1190 (RG3-06) EQA P12/1190 (RG3-06) EQA P12/1191 (RG3-07) B. abortus & Y. enterocolitica B. abortus & Y. enterocolitica B. thailandensis & E.coli Brucella ovis, Brucella abortus, Brucella suis, Brucella melitensis Brucella ovis, Brucella abortus, Brucella suis, Brucella melitensis Summary report Shewanella sediminis† Shewanella sediminis Burkholderia thailandensis Escherichia coli † This organism was best hit; Y enterocolitica came up as alternative; 1 base difference! Behind the data -1 Result EQA P12/1185 Burkholderia mallei/ Burkholderia pseudomallei Staphylococcus hominis/ Staphylococcus aureus/ Streptococcus sp. EQA P12/1191 Burkholderia thailandensis Escherichia coli K-12 *Relevant Primer pairs in this assay well *Score Quality Level score 2 of 2 1.00 3089 1 of 1 1.00 2 of 2 1.00 1344 1 of 1 1.00 635 63 Behind the data- detail Sample P12C001185 Burkholderia data Quantity 1214.2531 1214.2531 1214.2531 1214.2531 1214.2531 1214.2531 1214.2531 1214.2531 1214.2531 1214.2531 Confide nce Row Type 1PrimerNumber 1PrimerName 1Observed 1GenomeCounts 1Matched 1Matched 1Matched 1Matched 1Matched 1Matched Match Burkholderia mallei NCTC10247 Burkholderia pseudomallei 1710b Burkholderia pseudomallei 1106a Burkholderia mallei NCTC10229 Burkholderia mallei ATCC23344 Burkholderia mallei SAVP1 Unintended results: Food sample intended to demonstrate Brucella contamination Score Quality Level 1 of 1 & 1 of 2 0.98 166 Brucella ovis/ Brucella abortus/ Brucella suis/ Brucella melitensis 2 of 2 1.00 1226 bacterium EF 1 of 1 0.86 167 Organism Coxiella burnetii 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!)