Eccmid 2015 Mykrobe Predictor - A desktop application identifying species and antibiotic resistance...

Wellcome Trust Centre for Human Genetics

Mykrobe predictorA desktop application identifying species

and antibiotic resistance from S. aureus

and M. tuberculosis raw genome

sequence data.

Phelim Bradley

phelimb@well.ox.ac.uk

Zamin Iqbal zam@well.ox.ac.uk

How can we make clinical genomics a practical

reality?

Mykrobe predictor is clinical

grade software to enable

sequencing data to be used to

identify species and test for drug

susceptibility.

Mykrobe predictor is:

• Quick

• Usable by non informatics-experts

• Scalable

• As accurate as comparable drug susceptibility tests.

Mykrobe replaces post culture DST with whole genome sequencing + software analysis.

Mykrobe predictor fits into clinical workflow.

Drag and drop demo

Drag and drop demo

Drag and drop demo

Drag and drop demo

Drag and drop demo

Drag and drop demo

Drag and drop demo

Drag and drop demo

Future advances may decrease required

culture times

Can we also be robust to decreased culture times?

SequencingCulture

Mykrobe

Future advances may decrease required

culture times

Can we also be robust to decreased culture times?

SequencingCulture

Mykrobe

Mykrobe has been trained and tested on

1000s of samples

• 987 S. aureus and 3529 M. tuberculosis samples (Illumina HiSeq)

S. aureus:

• Resistance predictions for 12 drugs: Penicillin, Erythromycin,

Ciprofloxacin, Methicillin, Fusidic Acid, Tetracycline, Rifampicin,

Gentamycin, Mupirocin and Vancomycin.

• Gold-standard phenotype = a consensus of antibiotic BSAC disc,

Phoenix™ and Etest.

M. tuberculosis:

• Resistance predictions for 10 1st and 2nd line drugs: Isoniazid,

Rifampicin, Ethambutol, Streptomycin, Amoxicillin, Ofloxacin,

Amikacin, Capreomycin, Kanamycin.

• Gold-standard phenotype = proportion method via Löwenstein-

Jensen slope-based testing.

Results – toy example

Sample Predict Truth

1 R R

2 R R

3 R R

4 S R

5 S R

6 S R

7 S R

8 S R

9 S R

10 S R

0123456789

10

dru

g

Resis

tan

t S

am

ple

s

VME = Very major error(incorrect S prediction)

(Correct R predictions)

0123456789

10

dru

g

Resis

tan

t S

am

ple

s

Results – toy example

Sample Predict Truth

1 R R

2 R R

3 R R

4 R R

5 R R

6 R R

7 R R

8 S R

9 S R

10 S R

VME = Very major error(incorrect S prediction)

TP (Correct R predictions)

0123456789

10

dru

g

Resis

tan

t S

am

ple

s

Results – toy example

Sample Predict Truth

1 R R

2 R R

3 R R

4 R R

5 R R

6 R R

7 R R

8 R R

9 R R

10 R R

TP (Correct R predictions)

0123456789

10

dru

g

Resis

tan

t S

am

ple

s

Results – toy example

Sample Predict Truth

11 S S

12 S S

13 S S

14 R S

15 R S

16 R S

17 R S

18 R S

19 R S

20 R S

0123456789

10

dru

g

Su

sce

ptible

Sam

ple

s

TN

ME = Major error(incorrect R prediction)

0123456789

10

dru

g

Resis

tan

t S

am

ple

s

Results – toy example

Sample Predict Truth

11 S S

12 S S

13 S S

14 S S

15 S S

16 S S

17 S S

18 R S

19 R S

20 R S

TN

ME = Major error(incorrect R prediction)

0123456789

10

dru

g

Su

sce

ptible

Sam

ple

s

0123456789

10

dru

g

Su

sce

ptible

Sam

ple

s

0123456789

10

dru

g

Resis

tan

t S

am

ple

s

Results – toy example

Sample Predict Truth

11 S S

12 S S

13 S S

14 S S

15 S S

16 S S

17 S S

18 S S

19 S S

20 S S

TN

Mykrobe predictor is as sensitive and specific

as Disc and Phoenix for S. aureus DST .

• We achieved an overall 0.7% VME rate and 0.5% ME

rate across all antibiotics in S. aureus.

VME – missed R

predictions

ME – missed S

predictions

Comparison to comparable MTB DST

• Gold standard resistance predictions are slow.

• Faster options:

• PCR based test (e.g. CEPHEID GeneXpert)

• Limited scope (Only RIF predictions)

• Line probe assay (e.g. HAIN MTBDR)

• Static, difficult to update targets.

• Sequencing (e.g. Mykrobe predictor)

• Flexible, updatable panel.

• Single, quantitative test

Ability to detect minor populations has

potential clinical benefit.

• Detect coagulase-negative

staphylococci

• Detect atypical

mycobacteria

• Minor calls improve VME

in 2nd line tuberculosis

drugs.

Sequence data has additional benefits

Sequencing based solutions will

• Help us better understand within

patient diversity

• Fit in with a global

surveillance system

The Future: A sequencer in your USB stick?

Silicon Revolution (Moore’s Law)

Sequencing Technology

The Future: A sequencer in your USB stick?

PEN R

ERY R

CIP R

METH R

FUS S

CLIN R

TET S

RIF S

GEN R

MUP S

TRIM R

VAN S

Mykrobe is ready for field trips…

Tablet Smart Phone

Raspberry Pi

Model B

- CHEAP!!

• Mykrobe predictor is ready for :

• Windows

• Mac

• Linux

• Basespace (submitted)

• Will be tested in 3 UK hospitals in 2015

Mykrobe predictor

Try it out! - you can

download it now.

mykrobe.com

Acknowledgments

PI - Zam Iqbal

• Simon Heys, Bill Huang• Claire Gordon, Tim Walker, Tim Peto, Sarah Walker,

Louise Pankhurst, Antonina Votintseva, Derrick Crook• Mariateresa deCesare, David Buck, Gil McVean.• Stefan Niemann, E Grace Smith, Nazir Ismail, Roland Diel,

Shaheed Omar

phelimb@well.ox.ac.uk zam@well.ox.ac.uk

@phelimb @ZaminIqbal

Thanks for listening.

http://mykrobe.com

Mykrobe replaces post culture DST with whole genome sequencing + software analysis.

Mykrobe predictor fits into clinical workflow.

M. tuberculosis

Mykrobe replaces post culture DST with whole genome sequencing + software analysis.

Mykrobe predictor fits into clinical workflow.

S. aureus

Future advances may decrease required

culture times

Can we also make it robust to decreased culture times?

S. aureus

M. Predictor can accurately determine target

species.

• Speciation was tuned to be as sensitive and specific to

target species.

• Sensitivity and specificity to detect S. Aureus -100%, 98.5%

• Sensitivity and specificity to detect MTBC - 100%,100%

Mykrobe and SeqSphere

Mykrobe and KvarQ

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