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“All of your answers are approximate, you might as well live with it…”

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Andrew Rau-Chaplin, 1½ hours ago

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(Integrated(Rapid(Infec6ous(Disease(Analysis(

www.irida.ca(

Rob Beiko Faculty of Computer Science Dalhousie University June 12

Microbial genomics for rapid investigation of infectious disease

Image © Kenneth Todar(

2009 and Influenza A

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Influenza A RNA genome (14,000 nucleotides) Eight segments (Image: Tao and Zheng, Science 2012)

S. Typhi CT18 DNA genome (~5,100,000 nucleotides) One chromosome + two plasmids Science (2001)

VIRUS BACTERIUM

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Outbreak investigation

Similari6es:(place,(6me,(gene$cs'

fda.gov(

2014(

2010%2013(

Inns(et(al.((2015)(

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Outbreak investigation in Canada

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NATIONAL(MICROBIOLOGY(LABORATORY(

PROVINCIAL'PUBLIC'HEALTH'LABORATORIES'

CLINICAL(ISOLATES(

SENTINEL'SURVEILLANCE'(FoodNet(Canada)(

CLINICAL,(FOOD,(ENVIRONMENTAL(

CANADIAN'FOOD'INSPECTION'AGENCY'

(Regulatory)'

FOOD(ISOLATES(

LISTERIA()(E.(COLI(O157:H7(%(SALMONELLA(%(SHIGELLA(

PFGE/MLVA(

PUBLIC'HEALTH'ACTION!

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Pulsed Field Gel Electrophoresis Serratia - NICU

Jang(et(al.,(J(Hosp(Infect((2001)(

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15 gigabases per run $1000 - $1500 / run, 1 day

Tinier pieces (150 – 400 bases)

< 1 kilobase per run $2 / run, 1-3 hours (96 in parallel)

Tiny pieces (600 – 1000 bases)

2011: Illumina MiSeq 1977: Sanger sequencing ( )

DNA Sequencing

10/10/2013( VanBUG( 12(

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MiSeq projects at Dalhousie • Bedford(Basin(microbial(monitoring(• Pediatric(Crohn’s(disease(samples(• Global(microbial(air(sampling(• Mink(genomes(•  Sequencing(Lactobacillus(genomes(from(the(poop(of(old(mice(

• Wastewater(diversity(and(func6on(in(the(Arc6c(• Verifying(ingredients(in(dog(food((((((((((()(•  Exercise(and(the(Microbiome(

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(Integrated(Rapid(Infec6ous(Disease(Analysis(

www.irida.ca(

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!  1.56M,(3%year(Genome(Canada(Large%Scale(Applied(Placorm(Grant((

!  SFU(/(BCCDC(/(PHAC%NML(/(Dalhousie(!  DNA(sequencing(and(downstream(applica6ons(

•  data(management(/(federa6on(•  analysis(workflows(•  ontologies(•  APIs(•  3rd%party(applica6ons(

!  Implementa6on(in(provincial(public(health(labs(!  Training(

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Five Pillars of IRIDA

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! Ontologies(and(data(standards(! NCBI,(MiXS,(vegetables(

! Metadata(! Data(provenance(! Data(quality(!  Environmental(informa6on(

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Data sharing!

• BIG challenges – different jurisdictions, “ownership” of epi data. Privacy!

• Health service providers – concerns about privacy and data breach

• Technology outstrips policy •  What digital records could we get TODAY?

• Canada lagging in data sharing

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! Calling(isolates(based(on(gene6c(varia6on(

! Tradi6onal:(! Pulsed%field(! Mul6%locus((standards!(mlst.net)(

! Whole(genomes:(! Lots(of(informa6on!(! Too(much(informa6on!(! Lots(of(filtering(and(quality(control(required(

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! Workflow(management(

! REST%like(API((3rd(–(party(applica6ons)(

! Security:(authen6ca6on(/(authoriza6on(

! Data(models(&(implementa6on(

Local Storage

Remote APIs

IRIDA’s Federated Design

List(Samples(

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! Each(pipeline(is(implemented(as(a(Galaxy(workflow(

!  Internal(analysis(pipelines(! Assembly(and(annota6on(! Phylogene6cs(! “Line(list”(management(

! 3rd%party(applica6ons(

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Sampled(genomes( Quality(control( Tree(genera6on(/(visualiza6on(

Single-Nucleotide Variant Phylogenetic Pipeline (SNVPhyl)

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GenGIS

Data(from(Hai6(cholera(outbreak,(2010(hnp://kiwi.cs.dal.ca/GenGIS(

IslandViewer

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!  Interfaces(/(environment(

! Personas(!  Researchers(!  Epidemiologists(!  Clinical(microbiologists(/(lab(technicians(

! Workflow(design(and(execu6on(

Full Privileges

Cluster' Line'List'ID'

Pa$ent'Name'

Prov.'Health'No.'

Age' Sex' Loca$on' Sample'ID'

Collec$on'Date'

Culture'Result'

A( 1( John(Smith( 4513253244( 26( M( Vancouver( F14231( 14/03/21( Salmonella(

sp.(

A( 2( Sally(Smith( 4519567458( 24( F( Vancouver( F14235( 14/03/21( Salmonella(

sp.(

B( 3( Tom(Jones( 4517543216( 35( M( Vancouver( M6542( 14/03/24( Salmonella(

sp.(

B( 4( Helen(Jones( 9856321124( 35( F( Vancouver( S1245( 14/03/22( Salmonella(

sp.(

C( 5( Jennifer(Lee( 4516853122( 29( F( Vancouver( S5642( 14/03/22( Salmonella(

sp.(

C( 6( Michael(Brown( 9456534561( 45( M( Victoria( T68954( 14/03/25( Salmonella(

sp.(

Phylogene$c'Tree'

Gene$c'Distance'

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Limited Privileges

Cluster' Line'List'ID'

Pa$ent'Name'

Prov.'Health'No.'

Age' Sex' Loca$on' Sample'ID'

Collec$on'Date'

Culture'Result'

A( 1( John(Smith( 4513253244( 26( M( Vancouver( F14231( 14/03/21( Salmonella(

sp.(

A( 2( Sally(Smith( 4519567458( 24( F( Vancouver( F14235( 14/03/21( Salmonella(

sp.(

B( 3( Tom(Jones( 4517543216( 35( M( Vancouver( M6542( 14/03/24( Salmonella(

sp.(

B( 4( Helen(Jones( 9856321124( 35( F( Vancouver( S1245( 14/03/22( Salmonella(

sp.(

C( 5( Jennifer(Lee( 4516853122( 29( F( Vancouver( S5642( 14/03/22( Salmonella(

sp.(

C( 6( Michael(Brown( 9456534561( 45( M( Victoria( T68954( 14/03/25( Salmonella(

sp.(

Phylogene$c'Tree'

Gene$c'Distance'

Large-scale sequencing initiatives

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FDA GenomeTrakr

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Public Health England project (>10,000 Salmonella so far)

• As(of(2015,(sequencing(every(sampled(Salmonella(isolate(collected(in(England(

• Over(10,000(sequenced(to(date(•  8000(already(available(for(download(in(the(public(databases(

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Gary(van(Domselaar,(NML(31(

The Global Microbial Identifier

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What’s next?

??? per run $900 / run, 6 hours

Huge pieces (max so far – 200-300 kilobases) Can stop / restart using same disposable flowcell

2015: Oxford Nanopore MinION

15 cm (-ish)

thehightechsociety.com(

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Quick(et(al.((2015)(

“Using(a(novel(streaming(phylogene6c(placement(method(samples(can(be((assigned(to(a(serotype(in(40(minutes(and(determined(to(be(part(of(the(outbreak(in(less(than(2(h.”(

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Ebola monitoring

34(blogs.biomedcentral.com Joshua Quick, Nick Loman

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Example workflow

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6 hrs

Change(flowcell(

Samples evaluated against reference in real time

Posi6ve(ID(/((placement(

Load(DNA(

"( "( "("( "( "("("("(

confidence(

Challenges

•  Sample(extrac6on:(geong(DNA(from(stuff(• Clinical%grade(evalua6on(

•  Training(•  Equipment(reliability(•  Sequencing(errors(•  Quality(of(reference(data(/(anribu6on(algorithms(

• Database(updates(in(real(6me(•  Ethics(/(privacy((Genomes(Sequenced(While(U(Wait)(

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The Point

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Comprehensive monitoring Accurate typing Rapid identification Real-time decision making

Acknowledgements PIs'

Fiona(Brinkman(–(SFU(Will(Hsiao(–(PHMRL(Gary(Van(Domselaar(–(NML(Morag(Graham(%(NML(Rob(Beiko(–(Dalhousie((University'of'Lisbon'Joᾶo(Carriҫo((Na$onal'Microbiology'Laboratory'(NML)'Franklin(Bristow(Aaron(Petkau(Thomas(Manhews(Josh(Adam(Adam(Olsen(Tara(Lynch(Shaun(Tyler(Philip(Mabon(Philip(Au(Celine(Nadon(Manhew(Stuart%Edwards(Chrystal(Berry(Lorelee(Tschener((Laboratory'for'Foodborne'Zoonoses'(LFZ)'Eduardo(Taboada(Peter(Kruczkiewicz(Chad(Laing(Vic(Gannon(Manhew(Whiteside(Ross(Duncan(Steven(Mutschall(

Simon'Fraser'University'(SFU)'Melanie(Courtot(Emma(Griffiths(Geoff(Winsor(Julie(Shay(Manhew(Laird(Bhav(Dhillon(Raymond(Lo((BC'Public'Health'Microbiology'&''Reference'Laboratory'(PHMRL)'and'BC''Centre'for'Disease'Control'(BCCDC)'Judy(Isaac%Renton(Patrick(Tang(Natalie(Prystajecky(Jennifer(Gardy(Damion(Dooley(Linda(Hoang(Kim(MacDonald(Yin(Chang(Eleni(Galanis(Marsha(Taylor(Cletus(D’Souza(Ana(Paccagnella((University'of'Maryland'Lynn(Schriml((Canadian'Food'Inspec$on'Agency'(CFIA)'Burton(Blais(Catherine(Carrillo(Dominic(Lambert((Dalhousie'University'Alex(Keddy( 38(

McMaster'University'Andrew(McArthur(Daim(Sardar((European'Nucleo$de'Archive'Guy(Cochrane(Petra(ten(Hoopen(Clara(Amid((European'Food'Safety'Agency'Leibana(Criado(Ernesto(Vernazza(Francesco(Rizzi(Valen6na((((

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Seminar from the Will Hsiao, BC Centres for Disease Control

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Materials to be available on http://bioinformatics.ca/

June 24-26, 2015

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The Bioinformatics Exam of the Future

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tagc.com.au(commons.wikimedia.org/wiki/File:DNA_ahelatest_moodustunud_niit_katsu6_korgil..JPG(hnp://omicfron6ers.com/2014/06/11/diaryofaminion_part2/(

2009 was a long time ago

42(J.(Craig(Venter(Ins6tute(

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43(Photo credit: Emma Allen-Vercoe Some slides courtesy of Gary Van Domselaar, NML