The TB diagnostic pipeline

– a realistic view

Claudia Denkinger, MD PhD MSc

Head of TB Programme at FIND

26th October 2016, Union Meeting, Liverpool

Understanding diagnostic needs:

Diagnostics gaps in the care cascade

All Patients Patients with MDR TB

4.3 million undiagnosed

or not reported >80% not diagnosed

and treated

WHO Global TB report 2016

Understanding diagnostic needs:

Where do patients seek and receive care?

Reference

Labs

District Labs

Microscopy

Centers

6 million tests (LPA/Cx)

5 million tests (Xpert, smear)

60 million tests (smear,

rapid serology)

Diagnosis Treatment for DS-TB Treatment for DR-TB

Microscopy

Centers

Reference

District

Microscopy

Centers

Reference

District

MDR or pre-

XDR or XDR

or more

TB or not TB

DS or not DS HRZE

Short course or

standard or

individualized

regimen

Microscopy

Centers

Reference

Labs

District Labs

Microscopy

Centers

Community/

Health Posts

Community/

Health Posts

Community/

Health Posts

Health care seeking

High risk for

TB

31 October 2016 4

Non-sputum based tests for

diagnosis or triage

Note: Blood-based markers in separate talk

Goal: Early identification of patients with TB or at high-risk

of TB on easy to access samples ideally at level 0

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

Antibodies (b) Proteins

(s, b, u)

Nucleic

Acids (u, b) Mycolic acids/

Iipids (s)

VOC

(breath)

microRNA

(b, u)

McNerney

Moody

Dobos

Moritz

Walt/Ahmed

Feldheim

Campos-Neto

Somalogic

Kaufmann

Walzl/Chegou

Laal

Krishna

Drain

Lawn

Li

Bradbury

Hust

Blackburn

FIND…

Several

LMU

Levin (host RNA)

Zak (host RNA)

Cirillo (sRNA)

Cannas (tr-DNA)

Joosten/Ottenhoff (hostRNA)

Sweeney (hostRNA)

O’Garra/Bloom (RNA signatures)

Vlaminck (cfDNA)

The biomarker landscape

Cellular,

stimulation (b) Geldmacher

Pantaleo

Modlin

Lewinsohn

Rengerajan

Schaller

Walzl

Bruchfeld

Cirillo/Miotto

Zhou

Xu

Goa/Nyrolles

Zhang

Meyerhans

The eNose Company

Rapid Biosensor Systems

Avisa

Menssana BreathLink

Hill, Dartmouth

s – sputum

u – urine

b –whole blood

LAM (u, b, s)

FIND/Fujifilm

Pinter

Brennan/Chatterjee

Hamasur/Källenius

Global Good/IVT

Swanson/Mukundan

A lot of work for little clinical benefit

Poste, Nature, 2011

FIND Systematic Review unpublished

Science stops at exploratory

studies with limited sample size

Limited knowledge sharing among

researchers

Concerns about revealing IP

Accelerating path to success

- a TB Biomarker Database

Goal:

• Overcome data and IP sharing barriers

• Enable comparison of markers and

assessment of combinations of markers

to identify signatures

• Drive biomarker research towards use-

case focused test development

Includes:

• Published literature from an ongoing

systematic search for evidence

• Unpublished results from the

assessment of ongoing R&D efforts

using banked patient specimens

FIND IJID unpublished

Current LAM assay –a niche test

Peter et al. The Lancet 2016 387, 1187-1197DOI: (10.1016/S0140-6736(15)01092-2)

Absolute reduction in mortality – 4%

Peter Lancet 2016

Can we do better with LAM?

31 October 2016 9

Matrix Advantages Challanges and

Disadvantages

Urine • Potential in

EPTB &

paediatric TB

• LAM might be

related to GU TB

• Immunocompetent–

concentrations may

be low or absent

Serum • More direct

correlation to

MTB load

expected

• Potential in

EPTB &

paediatric TB

• Complex formation

with anti-LAM Abs in

systemic circulation

requires sample

treatment

Sputum • Correlation to

Mtb load in

lungs (useful

in treatment

monitoring?)

• Probably

highest LAM

concentrations

• Only useful for PTB

• Complex sample

matrix

Graphic confidential

Detection on breath

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]

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

31 October 2016 11

Smear replacement tests

Goal: ENABLE TEST and TREAT through

• Accurate, rapid, easy detection

• Universal DST

What do we need to overcome diagnostic gaps?

Reference

Labs

District Labs

Microscopy

Centers

6 million tests (LPA/Cx)

5 million tests (Xpert, smear)

60 million tests (smear,

rapid serology)

Diagnosis Treatment for DS-TB Treatment for DR-TB

Microscopy

Centers

Reference

Labs

District Labs

Microscopy

Centers

Reference

Labs

District

Labs

Expanded

DST

HRZE/ new

regimens

Short course or

standard or

individualized

regimen

Microscopy

Centers

Reference

Labs

District Labs

Microscopy

Centers

Community/

Health Posts

Community/

Health Posts

Community/

Health Posts

Health care seeking

TB or not TB

DS or not DS TB or not TB

Which regimen

Greatest progress - NAAT for smear

replacement and DST

New NAAT platforms

Universal DST

Needs to be addressed

Decentralization

Improving MTB

detection

Improving time to

diagnosis

Detection of EPTB

Move tests to lower levels or samples to higher levels

Higher throughput,

broad portfolio

Improvements on the Cepheid platform

Level 0

Community/POC

Level 1

Microscopy centre

Level 2

District hospital

Level 3

Reference centre

Tuberculosis

Patient

Established in LMICs

>21’600 installed modules Roll-out starts in Q4/2016

GeneXpert Omni

Xpert

cartridges

Data

reporting

Omni platform

• Anticipated for Q3 2017

• Studies planned to

assess impact in

settings of intended

use

Expanded portfolio: Xpert, Ultra, XDR, other

diseases (HIV, HCV, NG/CT, Ebola)

Xpert vs Ultra

Xpert Ultra Benefits

Target Single copy

rpoB

Multi-copy

IS6110 &

IS1081 + rpoB

Increased sensitivity: 20 CFU/ml vs 130

CFU/ml

Cartridge 25mcl tube 50 mcl tube

Analysis Real time

PCR curves

Melt curve

analysis

• Improved ability to detect mutations in

mixtures.

• Robust detection of all mutations

associated to Rifampin resistance (i.e.

rpoB 533 C to G mutations).

• Avoid false + for Rifampin resistance in

samples with low bacterial load

31 October 2016 15

Rif -Susceptible Rif-Resistant

Results to date & ongoing work

Beta-study with 364 patients

• Ultra: Sensitivity of 92.4% (Smear-: 86.4%); Specificity: 99.2%

• Xpert: Sensitivity of 85.9% (Smear-: 72.7%); Specificity: 99.0%

• RIF on Ultra:

-4 FP: 3 with disputed mutations or heteroresistance

-3 FN: G4 and Ultra are WT, likely mutation outside of rpoB

Ongoing: 10 sites; 8 country study

• Reference standard: 4-6 cultures

• Direct comparison to Xpert

• Subgroup analysis by smear status, TB history, HIV status

• Results expected in Q1 2017

31 October 2016 16 FIND unpublished data

Cepheid Xpert XDR

31 October 2016 17

Cepheid Xpert XDR – promising early results

TB/RIF

RIFs

TB detected/FL regimen

RIFr

FQ/AG/INH S

Short regimen

R Individualized Rx/

further testing

D. Alland unpublished data

Table confidential

Graphic confidential

Expansion of the utility beyond sputum

for children & in the diagnosis of EPTB

18

Xpert vs. Culture Sensitivity Specificity

Respiratory 71.4%

(29.0%, 96.3%)

98.1%

(94.5%, 99.6%)

Swab rectal 42.9%

(9.9%, 81.6%)

100.0%

(97.7%, 100.0%)

0.6 g stool 71.4%

(29.0%, 96.3%)

98.7%

(95.5%, 99.8%)

Xpert for MTB detection on stool

FIND unpublished; Banada PLOSone 2016

Is there a limit to the sensitivity we can

achieve with molecular tests?

Steingart Cochrane 2014; Theron CID 2016; Metcalfe ERJ 2014

Xpert (G4) specificity in patients with past

history of TB (from Theron et al).

Graphic confidential

Expanded drug susceptibility testing

Goal: ENABLE individualized therapy

What is the drug pipeline telling us

about the diagnostic needs?

31 October 2016 21

TPP: Drug prioritization: RIF > FQ (incl. Mox)> INH = PZA

Revised prioritization?: RIF > FQ > PZA>BDQ >LZD= PA

Uncertainties:

• Success of regimens

• For DS, MDR, XDR? > defines level

of implementation

• Barrier to resistance; cross-

resistance

In use In pipeline

PRETOMANID

WHO report 2014; TB Alliance pipeline

SNP

WGS

Exp

ert P

an

el

Re

vie

w

Genotypic

data

Phenotypi

c data

Clinical

trial data

DR study

data

Surveillanc

e data

Original

WGS SNP

reports

New SNP

reports from

Unified

Pipeline

Contributed Data

Unified Pipeline

Our understanding of the genotypic

basis of resistance is improving

Starks CID 2015, Salamon JID 2015

Both integrated platforms & more flexible,

comprehensive platforms are necessary

23

Integrated Platform

• Define number of

target resistance

mutations

• Sample to result

• Changes to

targets require

revalidation of

entire assay

Sequencing

• Modular with

extraction, PCR,

sequencer

• Possible directly

from sputum

• Targeted or

whole genome

• Flexible targets

Regimen selection at level 1 Individualized care at level 2/3

Vision for TB diagnostic in 2020

First point of contact

Level 0/Level 1

Dedicated unit

Level 1/Level 2

Reference level/

Level 3

ICT supported solutions; Systems strengthening; Active case finding; Integration across diseases;

TB

1.Comprehensive DST that

covers the extended

portfolio of drugs

1.TB confirmation with rapid

integrated DST for critical

drugs that drive regimen

decisions

2. Latent to active progression

1.Triage test

And what we can and should achieve!

MDR

Undx’d TB

All cases of TB

• Minimal undiagnosed or not

reported TB

• No undiagnosed MDR TB

WHO Global TB report 2016

26

Thank you/ Questions?

FIND

Tobias Broger

David Dolinger

Catharina Boehme

Samuel Schumacher