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: David.Dolinger@finddx.org

Paolo Miotto: miotto.paolo@hsr.it

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