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The Abbott Plex-ID and RIPL
Tim Brooks, Carrie Turner & Jackie DugganRare & Imported Pathogens Laboratory, PHE Porton Down
OverviewOur lab and why we want the Plex-ID
The instrument & how it works
Performance in trials
Topics for the Tropics
Future steps
SummarySystemic anthrax
RIPL 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)
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 Service 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 assaysArray cards for panels of PCR’s
Plex ID
Will extend range and fill gaps
Intelligent algorithms for patterns
The 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 & 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 processSample 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
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
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 onAnything 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 & 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-pX02 Pseudomonas 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 result Front end report Summary 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 thailandensis Escherichia 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 P12/1185 Burkholderia mallei/ Burkholderia pseudomallei
2 of 2 1.00 3089
Staphylococcus hominis/ Staphylococcus aureus/ Streptococcus sp.
1 of 1 1.00 635
EQA P12/1191 Burkholderia thailandensis
2 of 2 1.00 1344
Escherichia coli K-12 1 of 1 1.00 63
*Relevant Primer pairs in this assay well
Behind the data- detail
Sample P12C001185 Burkholderia data
QuantityConfidence Row Type Match
1214.2531 1PrimerNumber 1214.2531 1PrimerName 1214.2531 1Observed 1214.2531 1GenomeCounts 1214.2531 1Matched Burkholderia mallei NCTC102471214.2531 1Matched Burkholderia pseudomallei 1710b1214.2531 1Matched Burkholderia pseudomallei 1106a1214.2531 1Matched Burkholderia mallei NCTC102291214.2531 1Matched Burkholderia mallei ATCC233441214.2531 1Matched Burkholderia mallei SAVP1
Unintended results:Food sample intended to demonstrate Brucella
contamination
OrganismScore Quality Level
Coxiella burnetii1 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
Pseudomonas syringae/ Pseudomonas fluorescens/ Pseudomonas putida
1 of 2
Future 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.
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 staff
At risk of glanders? (not a case this
time!)