PowerPoint Presentation

Mykrobe predictor A desktop application identifying species and antibiotic resistance from S. aureus and M. tuberculosis raw genome sequence data.

Phelim Bradley phelimb@well.ox.ac.ukZamin Iqbal zam@well.ox.ac.uk

Wellcome Trust Centre for Human Genetics

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Mykrobe predictor:WGS to perform susceptibility testing

Implemented:Developed general framework for AMR resistance prediction from WGSSpecific implementations for S. aureus and M. tuberculosis.

Bradley et al (in press.)

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Drag and drop demo

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Drag and drop demo

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Mykrobe predictor is as sensitive and specific as Disc and Phoenix for S. aureus DST .

We achieved an overall sensitivity 99.1% and 99.6% specificity across 12 antibiotics in S. aureus.

FN predict S truth R

FP predict R truth S

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WGS could increase speed of DST

S. aureus timeline

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WGS could increase speed of DSTM. tuberculosis timeline

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Future advances may decrease required culture timesCan we also be robust to decreased culture times?

SequencingCulture

Mykrobe

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Future advances may decrease required culture timesCan we also be robust to decreased culture times?

SequencingCulture

Mykrobe

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"Staphylococcus aureus": "169","Coagulase-Negative Staphylococcus": "4

"mecA" : "median_cov": 6,"tetL" : "median_cov": 149" METH -> S TET -> RResistotyping in the context of contaminates can reduce false positives.

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Minor calls improve sensitivity to 2nd line TB drugs

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The Future: A sequencer in your USB stick?

PENRERYRCIPRMETHRFUSSCLINR

TETSRIFSGENRMUPSTRIMRVANS

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Mykrobe predictor is ready for :WindowsMacLinux

Will be tested in 3 UK hospitals in 2015/2016

Mykrobe predictor

Try it out! - you can download it now. mykrobe.com

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AcknowledgmentsZam Iqbal

Simon Heys, Bill HuangClaire Gordon, Tim Walker, Tim Peto, Sarah Walker, Louise Pankhurst, Antonina Votintseva, Derrick CrookMariateresa deCesare, David Buck, Gil McVean.Stefan Niemann, E Grace Smith, Nazir Ismail, Roland Diel, Shaheed Omar

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phelimb@well.ox.ac.uk zam@well.ox.ac.uk @phelimb @ZaminIqbal Thanks for listening.

http://mykrobe.com

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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

Mykrobe (Sa)SeqSphere (Sa)Mykrobe (Mtb)KvarQ (Mtb)

RAM100Mb8Gb100Mb30Mb

Time/sample on laptop1.5 mins -2.75 mins40 mins

Time/sample on server44 sec19 mins47s23 mins

CPU time (Mtb validation set)--1 day30 days

CPU time (Sa validation set)5.8 hours6.2 days--

Speciation of clinical samplesYesNoYesNo (MTBC only)