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The TB diagnostic pipeline
Claudia Denkinger, MD PhD MSc
Head of TB Programme at FIND
3rd December 2015, Union Meeting Cape Town
The Global TB Epidemic
MDR
Undiagnosed TB Undiagnosed TB
Untreated TB
All cases of TB
Facts TB:
• 9.6 million TB cases
• 1.5 million TB deaths
• 3.6 million undiagnosed
• Up to 30% of cases
diagnosed never get treated
Facts MDR:
• 480 000 with MDR
• <25% were diagnosed and
reported
WHO Global TB report 2015
Diagnostic cascade – the patient
perspective
Community health
worker/ Health post/
primary health care
First symptoms
Microscopy
center/District
hospital
Referral/persistent symptoms
Second test/results
Follow-up/test of cure
Expanded testing
Target Product
Profiles
http://apps.who.int/iris/bitstream/10665/135617/1/WHO
_HTM_TB_2014.18_eng.pdf?ua=1
Prioritized TPPs:
• Point-of-care, non-sputum based test
• Point-of-care triage test
• Point-of-care sputum based test for
microscopy replacement
• Point-of-care DST -microscopy center
Iterative process with input from many
stakeholders
WHO Consensus Meeting
• Delphi process leading up to the meeting
• > 75% agreement amongst stakeholders
Diagnostic cascade – the patient
perspective
Community health
worker/ Health post/
primary health care
First symptoms
Microscopy
center/District
hospital
Referral/persistent symptoms
Second test/results
Follow-up/test of cure
Expanded testing
POC test for diagnosis
POC Triage test POC test for diagnosis
POC Triage test
Smear replacement test
DST for regimen selection
Expanded DST for patients
suffering from resistant TB
Treatment monitoring test
Test of cure
Test that predicts
progression from TBI
15 December 2015 6
Non-sputum based tests for
diagnosis or triage
Diagnostic cascade – the patient
perspective
Community health
worker/ Health post/
primary health care
First symptoms
Microscopy
center/District
hospital
Referral/persistent symptoms
Second test/results
Follow-up/test of cure
Expanded testing
POC test for diagnosis
POC Triage test:
• Easy-to-use
• Non-sputum sample
• Rapid result
• Very resilient to dust, challenging
environmental conditions, shocks
• If any instrumentation battery
operated
• Cost 4-6USD
Level of certainty in Biomarker
Ea
se
of
tra
nsla
tin
g o
nto
a p
oin
t o
f ca
re p
latf
orm
Whole Bug (s)
Nucleic Acids (s)
Antibodies (b)
Proteins
(s, b, u)
Nucleic
Acids (u, b) Mycolic acids/
Iipids (u)
Metabolites (s, b, u)
VOC
(breath)
microRNA
(b, u)
Alere
Molbio
Quidel
Epistem
Belisle
Dobos
Moritz
Feldheim
Campos-Neto
Somalogic
Kaufmann
Laal
Proteinlogic
Krishna
Bradbury
Hust
Blackburn
GBD
FIND…
FIND
Anderson
Lowary
Feldheim
LMU
Levin (host RNA)
Cirillo (sRNA)
Cannas (tr-DNA)
O’Garra/Bloom (RNA signatures)
Ongoing Biomarker work
Cellular,
stimulation (b) Geldmacher
Pantaleo
Modlin
Lewinsohn
Rengerajan
Schaller
Cirillo
Zhou
Xu
Goa/Nyrolles
Zhang
The eNose Company
Technion
Menssana BreathLink
Next Dimensions
Rapid Biosensor Systems
Metabolomx/Specific Technol.
Hill, Dartmouth
Avisa
s – sputum
u – urine
b –whole blood
LAM (u, b, s)
FIND
Wenk/MacAry
Brennan/Chatterjee
Hamasur/Källenius
Global Good
Swanson/Mukundan
Nigou/Gilleron
LAM –a niche test
Niche test: Only a subset
of patients benefits
Model:
5 Host markers
1 IgG marker
Promising biomarker sets towards POC assay:
SomaLogic - FIND
10
SomaLogic - FIND
• Combination of SomaLogic Host Markers and
FIND Antibody Detection
• Number of required markers reduced from 9 to 6
• 6-marker model showed promising performance
to distinguish TB from non-TB close to minimal
targets as defined in TPPs in well-characterized
samples (N=480) from FIND
• Potential to measure biomarkers on a relatively
simple, and patient near platform
Sensitivity: 93 %
Specificity: 75%
AUC: 0.91
Preliminary Data
Promising biomarker sets towards POC assay:
ProteinLogic - FIND
11
ProteinLogic - FIND
• Combination of soluble biomarkers in blood
• 6-marker classification tree model showed
promising performance above minimal targets as
defined in WHO endorsed TPPs (N=300)
• Potential to measure the biomarkers on a simple,
and patient near platform
Sensitivity: 88%
Specificity: 95%
AUC: 0.94
TPP minimal
Preliminary Data
Promising biomarker sets: Transcriptional
profiles in blood
Anderson NEJM 2014
Bloom et al. 2013
• Unbiased system biology revealed type I
IFN/inflammatory transcriptional signature in
blood during pulmonary TB (Berry et al. 2010)
• Class prediction of 144 transcripts (validation
set, TB vs. Non-TB)
• The signature was validated in different
populations (Lu et al. 2011; Maertzdorf et al.
2011, 2012, Bloom et al. 2013)
• The signature also increases with disease activity
and diminishes with treatment (Bloom 2012).
Sensitivity: 88%
Specificity: 92%
C. Bloom et al.
Translation
into POC?
Promising biomarker sets: Host mRNA
signature
Using host RNA
• Signature
51-transcript signature
Assessed across 3
• Cohorts of children:
-South Africa (655)
-Malawi (701)
-Kenya (1599)
Anderson NEJM 2014
Translation
into POC?
Promising biomarker sets: Detection on
breath/VOCs
Overview of the processes involved in breath testing.
Metal-oxide-based
olfactory sensor
[Bruins et al. 2013]
Portable GC
coupled to surface
acoustic wave
(SAW) detector
[Phillips et al. 2013]
New sensors based
on array of chemical
films: VOC leads to
changes in electrical
conduction
Ligand coated
monolayer gold
nanoparticles
to analyze breath
(in an adhesive
patch)
Colorimetric
sensor array
for odour
visualization.
Cough/aerosol
collection combined
with immunoassay
based antigen
detection
[McNerney et al. 2010]
13C-urea is converted
to 13CO2 in the patients
lung if bacteria is
present and detected
in a spectrometer
[Jassal et al. 2010]
Proof-of-principle data from feasibility studies available for some technologies (performance thus far
not meeting TPP, limited independent study data)
[Konvalina and
Haick 2014]
Detection versus triage tests
Treatment
High Sensitivity
& specificity
Further testing
High Sensitivity
Lower specificity
Treatment
Biomarker
TPP
Triage TPP
15 December 2015 16
Smear replacement tests and DST
Diagnostic cascade – the patient
perspective
Community health
worker/ Health post/
primary health care
First symptoms
Microscopy
center/District
hospital
Referral/persistent symptoms
Second test/results
Follow-up/test of cure
Expanded testing
POC test for diagnosis
• Easy-to-use
• Sputum sample
• Rapid result
• Resilient to dust,
environmentally challenging
conditions
• Limited instrumentation (if any
battery operated)
• Lost cost (4-6USD)
POC DST:
• Enabling regimen selection
at the site of patient care
• Decreasing ToT
• Easy-to-use
DST centralized settings:
• Expanding DST portfolio
• Decreasing ToT
• Easy-to-use
• Increasing throughput
Automated smear microscopy
Automated reading
• TBDx (Applied Visual Sciences)
• CellScope TB Microscope (UCSF)
• Fluorobot
Combined staining and readng
• New imaging platform (BD)
Increasing throughput
Decreasing reader dependency
Decreasing human resource needs
? Decreasing cost in comparison to
Xpert MTB/RIF
? Performance
UNITAID 2015 Landscape
Molecular Pipeline for TB
Molecular highlight 1:
Bringing molecular closer to patients
20
Alere™ q in late development
• Fully integrated
• Alere™ q TB/DST will detect MTB and
resistance to RIF, INH, FQ, & potentially PZA
• Time to result 20min for MTB, 40 min for
DST
GeneXpert OMNI platform, Cepheid, Q1
2016
• Fully integrated. Same cartridge
• Will run Xpert, Ultra, HIV, HCV
• Time to result 90min with Ultra for MTB/RIF
Molecular highlight 2:
Improving MTB detection
Xpert® MTB/Rif Ultra completed development, with the goal of closing the sensitivity gap with culture
• Sensitivity as low as 10 cfu/ml, depending on strain
• Runs on existing systems
• Cost is the same at $9.98
• Trials as of Q1 2016
Xpert® XDR in development, which will detect resistance to INH, fluoroquinolones, and aminoglycosides
• Alpha study ongoing in 2 countries
• Runs on existing systems (10 color)
• Trials as of Q1 2017
21
Rapid diagnosis of additional 30% Sm-Cul+ patients (or >
in HIV+ and children); addressing overtreatment.
MDR/XDR triaging in high DR settings; addressing INH
concerns; preparedness for new FQ-based regimens
Molecular highlight 3:
Making molecular local
Molbio - Truenat; India. In late development.
• Realtime-PCR
• A more automated TB assay developed, RIF integration planned.
• Improved assay under evaluation as of Q3 15
Ustar – Easynat; China. In development.
• Cross-priming amplification
• Started work on more automated
version
• Trials planned for 2016.
If successful, could save costs and ease access
(shipment, import)
Molecular highlight 4:
Expanding centralized DST
HAIN Fluorotype® MTBDR – CE-
marked
• RIF/INH resistance detection
• Trials planned for WHO review in Q1 2016
Others: Abbott (CE-Marked), BD, Roche
• Detects resistance to RIF, INH
HAIN Fluorotype® XDR; in development
• Detects resistance to RIF, INH, FQ, PZA
and possibly AG/CAP
• Trials planned for WHO review in Q1 2017
Molecular highlight 5: Expanding utility
beyond sputum
Xpert for MTB detection on stool
24
Improving detection
of Extrapulmonary &
Pediatric TB
Trans-renal DNA detection
What is coming next? - Sequencing
Needs to be resolved:
• Specimen processing
• Data interpretation
• Cost, batching
• Genotypic basis of
resistance
A joint effort toward a common goal: providing
effective diagnostic
tools where are mostly needed
If interested please contact:
David Dolinger: [email protected]
Paolo Miotto: [email protected]
Culture-based technologies
Remains gold standard
Correlation: Genotype
Phenotype (MIC)
Outcome
Innovation needs
Miniaturization
Acceleration
Improved information
flow/connectivity
Adaptable to new drugs
for DST
DNA-delivery particles cause live
bacteria to produce light faster
detection compared to culture
B-SMART™
Detection of phage RNA on a
Nucleic Acid Lateral Flow Assay
(NLFA) after isothermal
amplification
Smarticles™
15 December 2015 27
Other diagnostic needs
Community health
worker/ Health post/
primary health care
First symptoms
Diagnostic cascade – the patient
perspective
Microscopy
center/District
hospital
Referral/persistent symptoms
Second test/results
Follow-up/test of cure
Expanded testing
Treatment monitoring and test-of-cure
• Enables identification of relapse free
cure (test-of-cure)
• Or monitors treatment response,
assess infectiousness and allow early
identification of treatment failure
• Easy-to-use
• Ideally same test as used for
diagnosis
Tests for treatment monitoring
Smear with 57% sensitivity and 81% specificity at 2 months for treatment monitoring; culture with long TOT
Markers:
• IP-10: most promising but requires further validation in different patient groups
• Pathogen mRNA
• Host RNA
Molecular tests:
• EMA/PMA: with variable results & complex
• Different interpretation algorithms
15 December 2015 29
Test for TB infection
Barry Nature Reviews 2009
Pulmonary vs Extrapulmonary
Identifies TBI that
never progresses
Identifies infection
that progresses
Detects cure/
predicts
relapse/useful in re-
exposure
On pathway to WHO evaluation Late or completed development Early development
New TruArray MDR-TB (Akkoni)
COBAS TaqMan MTB + DST(Roche)
Hydra 1K (Insilixa)
Mycobacterium Real-time MDR (CapitalBio)
MTB Detect (Great Basin Scientific)
Aries (Luminex)
PNAClamp (Panagene)
AccuPower TB&MDR (Bioneer)
BNP Middlebrook (NanoLogix)
Rapid colorimetric DST
TRC Rapid MTB (Tosoh)
VereMTB (Veredus Laboratories)
LiPA Pyrazinamide (Nipro)
Fluorotype MTBDR (Hain)
TBMDx (Abbott)
Meltpro (Zeesan)
Mycobacteria RT PCR (CapitalBio)
REBA MTB-XDR (YD Diagnostics)
EasyNAT TB (Ustar)
BD Max (BD)
TREK Sensitive MYCOTB (Trek)
GenoTYPE MTBDRsl (Hain)
REBA MTB-Rifa (YD Diagnostics)
Xtend XDR (Cepheid)
Alere Q (Alere)
Enigma ML (Enigma Diagnostics)
Q-POC (QuantuMDx)
EOSCAPE (Wave80)
TBDx system (KGI)
X1 (Xagenic)
MTB Detection (Tangen Biosciences)
TB POC (Qiagen)
Savanna (NWGHF/Quidel)
BreathLink (Menssana)
Prototype breathanalyzer (Next Dimensions Tech)
TB Breathalyser (Rapid Biosensor Systems)
Aeonose (The eNose Company)
Breath analysis instrument (Metabolomx)
TBDx (Applied Visual Sciences)
Fluorescent microscopy (ID-FISH Tech.)
Automatic TB Screener (Fluorobot)
Cellscope (UCSF)
Genedrive MTB/RIF (Epistem)
Truelab/Truenat MTB (Molbio)
Xpert Ultra/Omni platform (Cepheid)
Microimager (BD)
CAD4TB (Delft Imaging Systems)
LAM in sputum (Standard Diagnostics)
IRISA-TB -pleural/pericardial/ascitic fluid (Antrum Biotec)
Alere Determine TB-LAM in urine (Alere)
-lactamase reporter (Global BioDiagnostics)
Molecular - Detection/DST
Molecular Detection/DST
Culture-based - Detection/DST
Breath biomarker - Detection
Automated Microscopy & Imaging - Detection
Antigen, Antibody and Biomarker detection- Detection
Enzymatic - Detection/DST
Low
complexity
assays
High
complexity
assays
Moderate
complexity
assays
TB LAMP (Eiken)
T-Track TB (Lophius)
TAM-TB (LMU/Alere)
ESAT-6/CFP-10 skin test (SSI)
QuantiFERON-TB PLUS (Qiagen)
Diaskin (Generium)
Cellular Response - Detection/Latent and latent to active progression
Smear replacement test
DST for regimen selection
Expanded DST
Smear replacement test
(non molecular)
POC diagnosis/triage test
TB infection
The need for novel testing strategies
32
Fever, cough,
weight loss Bacterial, viral,
TB
Severity
Resistance
Targeted
therapy
Reduction in
antibiotic use and
preservation of
drugs
Po
ten
tia
l im
pac
t
Integrated care Primary
care
TB
HIV
RPS Diagnostics obtains CE mark for
test to differentiate viral and bacterial
acute febrile respiratory infection
based on Myxovirus Resistance
Protein A (MxA) and C-reactive Protein
(CRP)
Example 1: Fever point-of-care tests
FIND & Cepheid announcement
Broadening collaboration between FIND and Cepheid.
Most immediate priority of the collaboration is the independent field evaluation of Cepheid’s new GX-Omni diagnostics platform
Request for applications from experienced clinical trial sites for pragmatic trials that assess potential impact. www.finddx.org/resource-centre/news/151203.html
Agreement covers additional aspects including implementation planning with a special focus on connectivity.
Pave the path for the introduction of novel tests that aim the microscopy center level or below.
34
Thank you/Ke a leboga/Enkosi/Ngiyabonga/Danke
FIND
Tobias Broger
David Dolinger
Catharina Boehme