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P I O N E E R I N G D I A G N O S T I C S
New Opportunities in Pathogen Mitigation
Stan Bailey, PhDSr. Director Scientific AffairsbioMereiux Industry
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Marcel Mérieux1897 - Creation of Institut Mérieux
Dr Charles Mérieux1937 - Dr Charles Mérieux took up the reins
Dr Alain Mérieux1963 - Creation of bioMérieux
Alexandre Mérieux
A HISTORIC FAMILY COMMITMENT TO MEDICINE AND PUBLIC HEALTH WORLDWIDE
A pasteurian tradition: Marcel Mérieux worked with Louis Pasteur in 1894.
Marcel Mérieux,student of Louis Pasteur in 1894.
A commitment that transcends generations:Ever since the creation of Institut Mérieux, a generation has worked one after another to expand its legacy.
3
OUR FACTS & FIGURES
Sales amounting to
€2.421 billion
A large installed base of
86,900 systems
90% of international sales
About
11,000employees worldwide
1,600 peopleworking at
20 R&D centers
2 LEADERSHIP POSITIONS IN
MICROBIOLOGY GENERATE 2/3 OF SALES
+ 20 YEARS OF EXPERTISE IN INDUSTRIAL MICROBIOLOGY CONTROL
+ 50 YEARSOF EXPERTISE IN
IN VITRO DIAGNOSTICS
4
CHANGE IS THE NEW CONSTANT..
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MOORE’S LAW
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TRANSLATION…?
[Today] you would be able to go with that car
300,000 miles per hour. You would get two
million miles per gallon of gas, and all that for
the mere cost of 4 cents!
-Brian Krzanich, Intel CEO
https://www.nytimes.com/2015/05/13/opinion/thomas-friedman-moores-law-turns-50.html
1971
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WHAT DOES NORMAL LOOK LIKE?
FOOD INDUSTRY CUSTOMER CONSUMERSUPPLIER
RAW MATERIALSPRODUCTION
FINISHED PRODUCT
Maintenance
CONSUMER EXPERIENCECONFORMITY
DATA
RAW MATERIAL
VERIFICATIONIN-PRODUCTION DATA
FINISHED PRODUCT TESTING
MAINTENANCE DATA
ENVIRONMENTAL MONITORING DATA
R&DR&D DATA
COMPLAINTS
ENVIRONMENT
ENVIRONMENT MONITORING DATA
Laboratory Testing
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COMPONENTS OF LINEAR TESTING..
Total Solution Partner
Performance Solutions and Lab Optimization
Optimized space layout and sample flow
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CHALLENGES: LINEAR TESTING
• Data in silos with limited scope i.e. lot/situation specific
• Heavy reliance on sampling plans
• “Plateau effect” from technology adding value
• Proactive is still not predictive
• Mundane: often comes down to meeting regulatory compliance
• Answers the What but not “WHY” and definitely not “HOW”
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LABORATORY TRANSFORMATION
Laboratory• Advanced and
comprehensive analysis
• Centers for Predictive Analytics
In field testing:• Real-time data • Actionable • Less reliance on sampling plans• Usually simple workflows• Cost effective • Labs are pushing out the testing
VIDAS
V itek
I mmuno
D iagnostic
A ssay
S ystem
System Overview
VIDAS® IMMUNO ASSAY
CAPTURE OFANTIGENS
SANDWICH TEST DETECTION
The antibody or proteincaptures the target
pathogens
A second antibodyconjugated with an enzymebinds to specific antigens
The intensity of thereaction is interpreted
by the system
370 nm 450 nm
VIDAS evolution
LMO2 LSXNextDay
SET2
Fragment Fab ELFA
1992 1996
ImmunoConcentration
2002 2003 2004 2006
LDUOICS+ SLM
Listeria
2009
SLMXLMX
1993
ECO
2008
ECPT
Protéine Recombinante de phage
2007
VIDASHeat & Go
GENE-UP®
BioMérieux Real Time PCR Solution For Foodborne Pathogen Detection
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GENE-UP ADVANTAGES
3 Levels of Specificity with FRET Technology Internal Control with every test Rapid, Standardized Workflow for all assay parameters
- 30 minutes sample prep time for 96 tests
Ultra Fast and Efficient mechanical lysis procedure Only two enrichment broths used:
- BPW for GENE-UP E. coli O157:H7, STEC, and Salmonella spp- LPT Broth for GENE-UP Listeria spp. and L. monocytogenes
Assay Mix & Match Capability Open Platform
- Capability for foodborne virus detection, GMO testing, allergen testing, etc.
Remote Access Software Room Temperature reagent storage bioMérieux Service and Support
- Scientific Affairs validation/verification services- Applications support
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Amplification & Detection
SPIN DOWN(10 sec)
ENRICHMENT in X mL Broth
Selective Broth
ConfirmationSample Prep
Transfer 5µl Lysate intoPCR TUBES
PCR MIX (Blue Dye)
Transfer20µL into
LYSIS TUBES(Red Dye)
MECHANICAL LYSIS(5 min) PCR
(<1 h)
GENE-UP ROUTINE METHOD: SIMPLIFIED WORKFLOW
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FRET TECHNOLOGY PRINCIPLE
Target
640 nm detection
470 nm light
Internal Amplification
Control
705 nm detection
470 nm light
640 nm detection
705 nm detection
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GENE-UP PROBE-BASED MELT PEAK ANALYSIS
Melt peak analysis is more sensitive than other real time PCR and is
valuable for detecting low level samples.
IncreaseTemperature
Cool PCR reaction
Probes bind DNA
Probes melt off DNA
High Fluorescence
Low Fluorescence
negative derivative
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GENE-UP PROBE-BASED MELT PEAK ANALYSIS
Sample 13 amplified poorly during PCR but was called positive by melt and confirmed by culture
Low level sample + negatives
Amplification Curves
Melting peaks
This is Confidence
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• Amplifies all O157 isolates target DNA (and not from other E. coli)
• Probe melting peak analysis differentiates H7 (SNP) from non-H7 isolates
GENE-UP PERFORMANCE: E. COLI O157:H7 ASSAY
Inc. Temp
Cool PCR Reaction
Probes bind DNA
Probes melt off DNA
High Fluorescence
Low Fluorescence
Inc. Temp
Cool PCR Reaction
O157:H7 O157:non-H7
~ 62 C ~ 58 C
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O157:H7O157: non-H7
E. coli O157:H7 and O157:non H7
isolates can be amplified
GENE-UP PERFORMANCE: E. COLI O157:H7 VS. O157:NON H7
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GENE-UP VALIDATED MATRICES
GENE-UPSalmonella spp.(AOAC)
Fresh Raw ground Beef (25g & 375g)Raw beef trim (25g & 375g)Raw ground pork (375g)Raw ground bison (375g)Fresh Raw chicken breast (25g)Raw ground chicken (25g)Chicken carcass rinse (30mL)Fresh Raw fish (25g)Creamy peanut butter (25g & 375g)Vanilla ice cream (25g)Dry pet food (25g & 375g)Pasteurized liquid whole egg (25g & 100g)Powdered egg (100g)Cooked ham (25g)Lettuce (25g)Chocolate (25g)Whey protein powder (375g)Garlic powder (375g)Onion powder (375g)Dark chocolate (375g)Stainless steel (sponge)
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Work Flow
AOAC RI ValidatedProtocol
FOOD 25g
AOAC RI ValidatedProtocol
FRESH BEEF 25g
AOAC RI ValidatedProtocol
FRESH BEEF 375g
AOAC RI ValidatedProtocol
DRY PET FOOD 375g
GENE-UPSalmonella
GENE-UPSalmonella
GENE-UPSalmonella
GENE-UPSalmonella
Enrichment Broth BPWPre-warmed
BPWPre-warmed
BPW (1:4)Pre-warmed
BPW (1:4)
Enrichment Time42°C for
18-24 h42°C for
8-24 h42°C for
10-24 h42°C for
22-26 h
Sample Prep Time 25 min 25 min 25 min 25 min
No Pipetting Steps 4 4 4 4
Run Time on System 58 min 58 min 58 min 58 min
Min TTR 19.5 h 9.5 h 11.5 h 23.5 h
GENE-UP WORK FLOW & TIME-TO-RESULT
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WHAT DOES NORMAL LOOK LIKE?
Linear testing Dynamic testing
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$1K GENOME WITH $$$ COST ANALYSIS
https://www.researchgate.net/publication/320044302_
Next gen sequencing
$1K genome
Commun ACM. 2016 Aug; 59(8): 72–80.
Moore’s
Kryder’s
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SEQUENCING APPLICATIONS: TODAY
• Identification• Typing and subtyping• Serotyping • AMR• Virulence typing
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EVOLVING SEQUENCING APPLICATIONS
In Greek “meta” means “transcendent”…..
= Meta.. Genomics • WGS • Amplicon (targeted)• .• .• .• .
= Meta.. Transcriptomics
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SOLVING PROBLEMS: DYNAMIC TESTING
Sequence type
Physiological PhysicalChemical Attributes
S. cer. Var Diastaticus Positive
Sequencing ComputationPredictive analytics &
Probability %
Population structure
SourceSpoilage Shelf lifeOthers…
In-field/Lab test
Laboratory Analysis
MACHINE LEARNING
P I O N E E R I N G D I A G N O S T I C S