rapid point-of-care breath test for tuberculosis point... · 2016. 10. 4. · rapid point-of-care...
TRANSCRIPT
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Rapid point-of-care breath
test for tuberculosis
Michael Phillips MD, FACP, FRCP
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• High-risk hospitalized
patients sputum
cultures for MTB (52)
• Healthy controls (59)
Collect breath VOCs
SBIR Phase I pilot study – NIH/NIAID
New York University, New York Medical College
HUMAN IN VITRO
Culture reference
strains of
M. tuberculosis
Collect VOCs from
head-space air
above culture
Analyze VOCs with gas
chromatography/mass
spectrometry (GC/MS)
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The BCA 5.0
- All-electronic controls
- Digital display guides the user through every step
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Library ID:
Undecane
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C:\HPCHEM\1\DATA\NHSSB19.DNorm. Hum. Study, Breath 1, Tube #173
RT VOC Area Quality
1 1.76112 Butane 1.47E+06 49
2 2.0959 Ethanol 219710 86
3 2.19635 Butane, 2-methyl- 2.00E+06 91
4 2.39722 2-Propanone 6.18E+06 86
5 2.58135 1,3-Butadiene, 2-methyl- 2.14E+07 93
6 2.76548 1-Butene, 2-methyl- 998209 91
7 2.86592 1,2-Pentadiene 208507 86
8 2.93288 Ethane, 1,1,2-trichloro-1,2,2-trifluoro- 183187 43
9 3.08353 2,3-Pentadiene 105270 93
10 3.3681 Cyclopentene 156352 91
11 3.4518 Pentane, 3-methylene- 87692 70
12 3.56898 Butane, 2,3-dimethyl- 404068 78
13 3.71963 Pentane, 2-methyl- 1.48E+06 87
14 3.82007 Propane, 2-methoxy-2-methyl- 2.72E+06 42
15 4.12138 Pentane, 3-methyl- 1.04E+06 87
16 4.42268 1-Pentene, 2-methyl- 428950 83
17 4.75748 Hexane 998527 91
18 4.94162 Furan, 2-methyl- 683458 90
19 5.09228 2-Hexene, (E)- 270476 91
20 5.17597 2-Pentene, 2-methyl- 995042 80
192 51.4271 Octadecane 110167 90
193 51.695 2-(Methylamino)anthraquinone 41043 11
194 51.9963 Heptacosane 845932 99
195 52.4482 Octacosane 172853 91
196 52.5487 Nonadecane, 9-methyl- 207177 93
197 52.6826 AZADIBENZOPYRENE 50624 56
198 52.9169 1,2-Benzenedicarboxylic acid, bis(2-ethylhexyl) ester70140 68
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Culture (in vitro)
2-Hexene
Naphthalene, 1-methyl-
3-Heptanone
Methylcyclododecane
Heptane, 2,2,4,6,6-pentamethyl-
Benzene, 1-methyl-4-(1-methylethyl)-
Cyclohexane, 1,4-dimethyl-
3,5-dimethylamphetamine
Butanal, 3-methyl-
Trans-anti-1-methyl-decahydronaphthalene
IN VITRO
Breath (fuzzy logic)
Cyclohexane, 1,3-dimethyl-, trans-
Benzene, 1,4-dichloro-
Cyclohexane, 1,4-dimethyl-
1-Octanol, 2-butyl-
2-Butanone
Naphthalene, 1-methyl-
Camphene
Decane, 4-methyl-
Heptane, 3-ethyl-2-methyl-
Octane, 2,6-dimethyl-
Benzene, 1,2,3,4-tetramethyl-
Bicyclo_3_1_1_hept-2-ene, 3,6,6-trimethyl-
Cyclohexane, 1-ethyl-4-methyl-, trans-
l-_beta_-Pinene
HUMAN
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Culture (in vitro)
2-Hexene
Naphthalene, 1-methyl-
3-Heptanone
Benzene, 1-methyl-4-(1-methylethyl)-
Cyclohexane, 1,4-dimethyl-
Methylcyclododecane
Heptane, 2,2,4,6,6-pentamethyl-
Trans-anti-1-methyl-decahydronaphthalene
3,5-dimethylamphetamine
Butanal, 3-methyl-
Breath (fuzzy logic)
Cyclohexane, 1,3-dimethyl-, trans-
Benzene, 1,4-dichloro-
Cyclohexane, 1,4-dimethyl-
1-Octanol, 2-butyl-
2-Butanone
Naphthalene, 1-methyl-
Camphene
Decane, 4-methyl-
Heptane, 3-ethyl-2-methyl-
Octane, 2,6-dimethyl-
Benzene, 1,2,3,4-tetramethyl-
Bicyclo_3_1_1_hept-2-ene, 3,6,6-trimethyl-
Cyclohexane, 1-ethyl-4-methyl-, trans-
l-_beta_-Pinene
Identical VOCs
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Culture (in vitro)
2-Hexene
Naphthalene, 1-methyl-
3-Heptanone
Methylcyclododecane
Heptane, 2,2,4,6,6-pentamethyl-
Benzene, 1-methyl-4-(1-methylethyl)-
Cyclohexane, 1,4-dimethyl-
3,5-dimethylamphetamine
Trans-anti-1-methyl-decahydronaphthalene
Butanal, 3-methyl-
Benzene, 1,2,3,4-tetramethyl-
Bicyclo_3_1_1_hept-2-ene, 3,6,6-trimethyl-
Cyclohexane, 1-ethyl-4-methyl-, trans-
l-_beta_-Pinene
Heptane, 3-ethyl-2-methyl-
Octane, 2,6-dimethyl-
Camphene
Decane, 4-methyl-
Naphthalene, 1-methyl-
Cyclohexane, 1,4-dimethyl-
1-Octanol, 2-butyl-
Breath (fuzzy logic)
Cyclohexane, 1,3-dimethyl-, trans-
2-Butanone
Benzene, 1,4-dichloro-
Identical and Similar VOCs
VOC manufactured
by Mycobacteria
Excreted in breath:
unchanged or as a
metabolite
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Culture (in vitro)
2-Hexene
Naphthalene, 1-methyl-
3-Heptanone
Methylcyclododecane
Heptane, 2,2,4,6,6-pentamethyl-
Benzene, 1-methyl-4-(1-methylethyl)-
Cyclohexane, 1,4-dimethyl-
3,5-dimethylamphetamine
Trans-anti-1-methyl-decahydronaphthalene
Butanal, 3-methyl-
Benzene, 1,2,3,4-tetramethyl-
Bicyclo_3_1_1_hept-2-ene, 3,6,6-trimethyl-
Cyclohexane, 1-ethyl-4-methyl-, trans-
l-_beta_-Pinene
Heptane, 3-ethyl-2-methyl-
Octane, 2,6-dimethyl-
Camphene
Decane, 4-methyl-
Naphthalene, 1-methyl-
Cyclohexane, 1,4-dimethyl-
1-Octanol, 2-butyl-
Breath (fuzzy logic)
Cyclohexane, 1,3-dimethyl-, trans-
2-Butanone
Benzene, 1,4-dichloro-
Breath signal derived from two sources:
Bacterial metabolites AND host response
Oxidative stress products in breath
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Collaboration:
• University of California San Diego
International multicenter study:
• USA – San Diego
• UK - London
• Philippines – Manila and Cavite
Phillips M, et al. Breath biomarkers of active pulmonary tuberculosis. Tuberculosis
(Edinburgh: 2010 Mar;90(2):145-51. Epub 2010 Feb 26.
SBIR Phase II study – NIH/NIAID
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INVESTIGATIONS
Sputum culture (Bactec 460, Becton Dickinson)
Sputum microscopy (AFB staining)
Chest X-ray
226 high-risk patients
All symptomatic
e.g. cough, fever, night sweats, weight loss
BREATH TEST
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Breath VOCs:
Correlation with different
diagnostic criteria
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1-specificity
Sen
sitiv
ity
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0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0 0.5 1
1-specificity (FPR)
Sen
sit
ivit
y (
TP
R) sensitivity =84.0%
specificity =64.7%
Positive for sputum smear
and sputum culture
and chest x-ray
AUC = 0.85
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2010: Lab-based breath test for TB
Advantages:
• ID biomarkers with GC/MS
• ID disease - 85% accuracy
Disadvantages:
• Inconvenient – ship samples to lab
• Expensive – GC/MS ~$200K + highly trained staff
• Slow turnaround time
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Point-of-care breath test
for active pulmonary TB
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Point-of-care test
Lab Test
Personal test
The evolution of a successful diagnostic test
1927 Ascheim Zondek test
Slow Cost $$$
1960 Immunological tests
Faster Cost $$
1976 First home test kit
Fastest Cost~$10
Pregnancy tests
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Point-of-care test
Lab Test
Personal test
Basic R&D (GC/MS)
identify biomarkers
Migrate biomarkers to
POC instrument
cheaper, quicker
Shrink the instrument
cell phone app?
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BreathLink system
Point-of-care breath testing
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BreathLink system
Point-of-care breath testing
• Collects breath volatile organic
compounds (VOCs)
• Concentrates VOCs
• Separates VOCs with GC
• Detects VOCs with SAW
• Interpretation in <10 minutes
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BreathLink ™
• Rapid, safe, and painless
• Patient-friendly and user-friendly
• Works anywhere in world - internet or phone
• Near real-time monitoring of patient
and instrument
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London
Mumbai Manila
Cavite
Menssana
Newark, NJ
Study: Active pulmonary TB
Results available in USA within 10 minutes
of breath sample collection anywhere in the
world
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Overview
• Recruit controls and disease group
279 patients
• Breath test in ~6 min
upload data to US lab via internet
• Monte Carlo analysis of data
biomarker identification
• Combine biomarkers
multivariate algorithm
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Criteria for active pulmonary TB
Positive sputum culture
and/or
positive sputum smear microscopy
and/or
chest x-ray consistent with active
pulmonary TB.
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Control group Technical quality of breath test
Site No. recruited Unsatisfactory Satisfactory
Cavite 47 5 42
London 17 4 13
Manila 52 6 46
Mumbai 22 2 20
Total 138 17 121
Male 53
Female 68
Total 121
Control group Technical quality of breath test
Site No. recruited Unsatisfactory Satisfactory
Cavite 47 5 42
London 17 4 13
Manila 52 6 46
Mumbai 22 2 20
Total 138 17 121
Male 53
Female 68
Total 121
Technical quality of breath test
Site No. recruited Unsatisfactory Satisfactory
Cavite 47 5 42
London 17 4 13
Manila 52 6 46
Mumbai 22 2 20
Total 138 17 121
Control group
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Control group Technical quality of breath test
Site No. recruited Unsatisfactory Satisfactory
Cavite 47 5 42
London 17 4 13
Manila 52 6 46
Mumbai 22 2 20
Total 138 17 121
Male 53
Female 68
Total 121
Control group Technical quality of breath test
Site No. recruited Unsatisfactory Satisfactory
Cavite 47 5 42
London 17 4 13
Manila 52 6 46
Mumbai 22 2 20
Total 138 17 121
Male 53
Female 68
Total 121
Technical quality
of breath test Smear
positive
Culture
positive
Chest x-
ray
positive
Total
positive*
* Site No.
recruited Not OK OK
Cavite 30 0 30 30 30 30 30
London 3 0 3 1 3 3 3
Manila 60 4 56 56 55 56 56
Mumbai 48 7 41 38 7 41 41
Total 141 11 130 126 96 130 130
Disease group
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Analysis of data
Segment the chromatograms into series of 100
candidate biomarkers by retention times
compared to alkane standards
Kovats Index (KI) windows
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Is it a new biomarker?
Or is it just a face in the clouds?
• Costs of assays falling
• BUT…costs of human and animal studies rising
• > 1,000 candidate biomarkers, <100 subjects
high risk of over-fitting data in statistical models
false-positive IDs of biomarkers
- seeing “faces in the clouds”
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A rigorous method for biomarker
identification
1. What was the experimental accuracy of a candidate VOC?
Area under curve (AUC) of receiver operating characteristic (ROC)
curve
Range: 0.5 (coin-flip) to 1.0 (perfect accuracy)
2. What was its accuracy by chance alone?
Multiple Monte Carlo simulations
Assign random diagnosis (disease or no disease)
determine AUC of the ROC curve
repeat 40 times
mean chance accuracy
3. Compare the outcomes
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0.5
No. candidate
biomarkers
AUC of biomarker ROC curve 1.0
Chance accuracy with random diagnosis
True accuracy with correct diagnosis
Biomarkers with accuracy better than chance
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Disease group Technical quality of breath test Smear
positive
Culture
positive
Chest x-ray
positive
Total
positive** Site No. recruited Unsatisfactory Satisfactory
Cavite 30 0 30 30 30 30 30
London 3 0 3 1 3 3 3
Manila 60 4 56 56 55 56 56
Mumbai 48 7 41 38 7 41 41
Total 141 11 130 126 96 130 130
Disease group Technical quality of breath test Smear
positive
Culture
positive
Chest x-ray
positive
Total
positive** Site No. recruited Unsatisfactory Satisfactory
Cavite 30 0 30 30 30 30 30
London 3 0 3 1 3 3 3
Manila 60 4 56 56 55 56 56
Mumbai 48 7 41 38 7 41 41
Total 141 11 130 126 96 130 130
Disease group Technical quality of breath test Smear
positive
Culture
positive
Chest x-ray
positive
Total
positive** Site No. recruited Unsatisfactory Satisfactory
Cavite 30 0 30 30 30 30 30
London 3 0 3 1 3 3 3
Manila 60 4 56 56 55 56 56
Mumbai 48 7 41 38 7 41 41
Total 141 11 130 126 96 130 130
05
10
15
20
0.5 0.55 0.6 0.65 0.7 0.75
No
. K
I w
ind
ow
s
C-statistic cutoff value
Mean of multiple
Monte Carlo simulations
Correct
Random
Random + 1 SD
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Biomarker
number
KI
window Breath biomarker VOCs
M. tuberculosis
in vitro VOCs
1 & 2
965-
1030
camphene ; l-beta-pinene ; benzene, 1,3,5-
trimethyl-
heptane,2,2,4,6,
6-pentamethyl-
3 & 4
1243-
1313
naphthalene,1-methyl- ; tridecane ; 1-octanol, 2-
butyl ; dodecane, 4-methyl
naphthalene, 1-
methyl-
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0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0 0.2 0.4 0.6 0.8 1
Sen
sit
ivit
y
1-Specificity
AUC
Accuracy = 84%
in age-matched
subgroups
Sensitivity =84.7%
Specificity =66.7%
Is that good
enough for
clinical use?
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Clinical role of BreathLink
“Rule out” test for
primary screening
NOT a “rule in” test
for final diagnosis
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Predicted outcome
of using BreathLink
Screen 10,000 people
Assume prevalence of active TB = 5%
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Screen 10,000 people
Assume prevalence of active TB = 5%
Breath
test
No disease: 9,500 Disease: 500
True positives 424
False negatives 76
True negatives 6,337
False positives 3164
Predictive
values
Positive PV
= 424/3588
= 11.8%
Negative PV
= 6337/6413
= 98.8%
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Staged case finding
Screen population
with BreathLink
breath test
If negative: reassure
– no further testing
If positive:
sputum testing
Step 1 Step 2
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Staged diagnosis with two sequential tests
Test 1
Test 2
Screened
population
Disease
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Number of sputum tests
0 2000 4000 6000 8000 10000 12000
With BreathLink
Without BreathLink
3,588
10,000
Reduction: 64%
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Breath tests and sputum tests
are complementary,
NOT competitive
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Comparison: BreathLink breath test
and Xpert sputum test
* O’Grady et al: Clin Infect Dis. 2012 Nov;55(9):1171-8. doi:
10.1093/cid/cis631. Epub 2012 Jul 17.
BreathLink Xpert *
Sensitivity 84.7 86.1
Specificity 66.7 95.0
Speed Fast Slow
Cost Low High
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Current practice:
Sputum testing in everyone
A safe alternative strategy:
BreathLink breath test in everyone
• If negative: reassure retest in future
• If positive: sputum testing
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Outcome
Case discovery rate: No change
Cost of case finding: Reduced +++
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Other potential applications
of BreathLink
Prospective studies
– response to treatment?
MDR strains
– ID infections?
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Does the breath VOC signal
change with treatment?
Rationale: VOC products of MTB in breath
Proposal: Perform prospective study
of BreathLink in treated patients
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Is the breath VOC signal
changed in MDR infection?
Proposal: Planned in-vitro study
of MDR strains
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Two-dimensional
gas
chromatography
and time-of-flight
mass spectrometry
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• Comparing Media & MG, BCG – Response in MG & BCG has higher level than Media
Conhydrin 1-Methylpentyl cyclopropane
BCG and M. gordonii
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Thanks for
listening!