GenomeTrakr: A Pathogen Database - ICMSF · GenomeTrakr: A Pathogen Database. Marc W. Allard, PhD. Senior Biomedical Research . Services Officer. Division of Microbiology. FAO Expert

GenomeTrakr: A Pathogen Database

Marc W. Allard, PhDSenior Biomedical Research Services OfficerDivision of Microbiology

FAO Expert workshop to develop case studies on the use of Whole Genome Sequencing (WGS) on food safety managment. Nov. 12, 2015

Eric W. Brown, PhDDirector Division of Microbiology

Outline

• Technology shift

• GenomeTrakr: Reference database and pathogen detection pipeline

• Benefits to industry, growers, and distributers.

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Outline

• Technology shift

• GenomeTrakr: Reference database and pathogen detection pipeline

• Benefits to industry, growers, and distributers.

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Current method for pathogen identification

1. antigens are screened to identify serovar2. PFGE: genome is cut into pieces. Sizes of these pieces and

the banding patterns they determine discrimination within serovar.

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PulseNethttp://www.cdc.gov/pulsenet/

• WGS is high resolution 3-5 million data points are collected for each isolate

• WGS analyses are statistically robust Unlike PFGE patterns, WGS data can be analyzed in its

evolutionary context. Accurate and stable genetic changes within pathogen genomes enable us to pin point specific common sources of outbreak strains (farms, processing plants, food types, and geographic regions).

Source Tracking is Key Application

PFGE v/s WGS

PFGE identical in red

NGS distinguishes geographical structure among closely related Salmonella Bareilly strains

Same PFGEbut not part of the outbreak

Outbreak Isolates2-5 SNPs

SNP phylogeny for S. Bareilly strains

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S. Braenderup

Outline

• Technology shift

• GenomeTrakr: reference database and pathogen detection pipeline

• Benefits to industry, growers, and distributers.

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• Bases of DNA (ATGC) are sequentially identified from a DNA template strand

• Next Generation Sequencing (NGS) extends this process across millions of reactions in a massive parallel fashion

• NGS involves rapid sequencing of large DNA stretches spanning entire genomes

– Technology shift– 3-5 million data points for each isolate

• Increasing availability and affordability of NGS is rapidly changing the face of microbiology

DNA Sequencing

$0

$500

$1,000

$1,500

$2,000

$2,500

$3,000

$3,500

2007 2008 2009 2010 2011 2012 2013

Cost per bacterial genome

Desk-top

FDA 1st

$70/genomein 2014

$40/genomein 2015 w/

Higher througputTechnology

GenomeTrakr Fast Facts• First distributed network of labs to utilize WGS

for pathogen identification

• GenomeTrakr network has sequenced more than 40,000 isolates, and closed more than 100 genomes through November 12, 2015.

• Currently sequencing more than 1,000 isolates a month

• The need for increased number of well characterized environmental (food, water, facility, etc.) sequences may outweigh the need for extensive clinical samples

GenomeTrakr Labs• 14 federal labs

• 14 state and university labs

• 1 U.S. hospital lab

• 5 labs outside of the U.S.

• Collaborations with independent academic researchers

• More GenomeTrakr labs coming on-line

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Num

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f Seq

uenc

es(a

s of

the

last

day

of t

he q

uarte

r)

Total Number of Sequences in the GenomeTrakr Database

2013 2014 2015

Average Number of SequencesAdded Per Month in 2013 = 184

Average Number of SequencesAdded Per Month in 2014 = 1,049

First sequences uploaded in Feb 2013

Public Health Englanduploads more than 8,000 Salmonella sequences

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Timeline for Foodborne Illness InvestigationUsing Whole Genome Sequencing

Contaminated food enterscommerce

FDA, CDC, FSIS, and States use WGS in real-time and in parallel on clinical, food,

and environmental samples

Source of contaminationidentified early through WGS combined database queries

Averted Illnesses

Num

ber o

f Cas

es

Days

MINIMAL PATHOGEN METADATA (FOODBORNE OUTBREAKS)

sample_nameorganismstrain/isolate

Category (attribute_package)1a) Clinical/Host-associated

1a1) specific_host1a2) isolation_source1a3) host-diseaseOR

1b) Environmental/Food/Other1b1) isolation_source

Food Industry can hold confidential metadata linked to public records

collection_date

Geographic location

6a) geo_loc_nameOR6b) lat_lon

collected by

Where

When

Who

What

Immediate impacts of WGS to industry, growers, and distributers, countries, states.• Earlier intervention means: 1) Reduced amount of recalled product; 2) fewer sick patients which means fewer lawsuits; 3) less impact overall and minimal damage to

brand recognition.

Impacts to industry, growers, and distributers (continued).•Regular testing throughout network: 1) identifies specific suppliers that are introducing contaminants; 2) identifies whether contaminant is resident to a facility or

transient; 3) knowledge of where contaminant is coming from allows industry

to fix the problem based on scientific evidence.–Shift costs to the supplier who has introduced the contaminant.–How often is the root cause of the problem left unresolved

to occur again at a later date?

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Background: CFSAN SNP PipelineDocumentation: http://snp-

pipeline.rtfd.org

Source Code: https://github.com/CFSAN-Biostatistics/snp-pipeline

PyPI Distribution: https://pypi.python.org/pypi/snp-

pipelinePettengill JB, Luo Y, Davis S, Chen Y, Gonzalez-Escalona N, Ottesen A, Rand H, Allard MW, Strain E. (2014) An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella. PeerJ 2:e620 http://dx.doi.org/10.7717/peerj.620

Intended for use by bioinformaticists (Linux)

Molecular Epidemiology and Ecology of Multi-drug Resistance (MDR) Salmonella

in Tanzania

•Julius Medardus•Sokoine University of agriculture

•Wondwossen A. Gebreyes•[email protected]

ICOPHAI GenomeTrakr partnership

Salmonella lose or gain resistance depending on the ecosystem.

Environment- SSu(Gebreyes and Altier, 2002Gebreyes et al., 2004, 2009)

GIT- ACSSuT (Briggs and Fratamico, 1999)

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?

What triggers the recombination?Interaction between bacterial factors and and

chemical intervention in pig production

ImportantElementIn MDR

CommonIn the

EnvironmentQAC

Quaternary ammonium compoundsqacE on integrons and Quats are commonly used as

disinfectants.

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Co-selection: Heavy metal v. MDR

• Heavy metals in the ecosystem- Cu and Zn;• Assoc. b/n AMR-type and HM- MIC;• Co-selection with MDR; • Association with Invasive NTS strains?;• Efflux pump genes- pcoA and czcD;

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Association- Heavy Metal tolerance and MDRSalmonella

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Odds ratio between copper tolerance (<20mM) and MDR AmStTeKm was 4.6 (Chi-square=17.9; P<0.05)

The odds of having a high Zn MIC (>8mM) were 14.66 times higher in isolates with R-type AmClStSuTe than in those with R-type AmStTeKm(P<0.05).

[Medardus et al., 2014]

FDA GenomeTrakr partnership

924 isolates submittedto FDA-CFSAN • Brazil (4)• Ethiopia (401)• Kenya (86)• Mexico (63)• Tanzania (64)• Thailand (60)• U.S. –OSU (247)

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Tanzania

• WGS- 45 food animal isolates completed • All Unknown STs• Plasmid types- ColRNAI, IncI1, IncI2, IncFII, ColpV2

(total 10)- Others?• Kentucky (16/ 45) and Not conforming with any

known type (n=8)• Pending- HM and biocide tolerance genes/ efflux

system…• Comparison with isolates of human origin?

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COMPARE is a large EU project with the intention to speed up the detection of and response to disease outbreaks among humans and animals worldwide through the use of new genome technology.The above figure represents genomic information as the pathogen-independent language across locations, sectors and time.

http://www.compare-europe.eu/

CoordinatorFrank M. AarestrupTechnical University of DenmarkNational Food [email protected]: +45 35 88 62 81

Co-CoordinatorMarion KoopmansErasmus Medical CentreDepartment of [email protected]: +31 10 70 44 066

Whole Genome Sequencing Program (WGS)

http://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgramWGS/default.htm#trakr

GenomeTrakr• State and Federal laboratory network

collecting and sharing genomic data from foodborne pathogens

• Distributed sequencing based network• Partner with NIH • Open-access genomic reference

database• http://www.ncbi.nlm.nih.gov/bioproject/183844

• Can be used to find the contamination sources of current and future outbreaks

For more information:• For information about joining the

GenomeTrakr network as a sequencing lab, providing isolates to a current member lab for sequencing, or using the GenomeTrakr database as a research tool, please contact FDA at [email protected]

FDASteven Musser Patrick McDermott Ruth TimmeMarc Allard Peter Evans Eric BrownJustin Payne Charlie Wang Rebecca BellChristine Keys Errol Strain Yan LuoJames Pettengill Hugh Rand Darcy Hanes Gopal Gopinathrao Chis Grim Palmer OrlandiDavid Melka Cary Pirone Davies Justin PayneMaria Hoffman Eric Stevens Andrea OttesenTim McGrath Don Burr Jie ZhengCong Li George Kastanis Tim MuravundaShaohua Zhao

National Institutes of health (NCBI)David Lipman Jim Ostell William KlimkeMartin Shumway Richa Agarwala

State Health LabsBill Wolfgang (NY) Dave Boxrud (MN) Anita Wright (FL)Elizabeth Driebe (AZ) Angela Fritzinger (VA)Ailyn Perez-Osorio (WA) More to come…….

USDADavid Goldman Kristin Holt

IlluminaSusan Knowles Omayma Al-Awar Kelly Hoon

With Additional Thanks….

And a Growing Cast of Colleagues….

ORA OCC OFS OC OAO OFVM/SRSC CFSAN CDERCBER CDRH CVM NCTR FDA CHIEF SCIENTIST OIP OARSASCIENCE BOARD IAS FFC FERN JIFSAN ADVISORY COMMITTEE IFSHMOFFETT CENTER CIO DAUPHIN ISLAND CFSAN-OCD CORE WESTERN CENTER

INTERNAL FDA STAKEHOLDERS

FDLIGMAVaFSTFCDCFBIPULSENET-LATIN AM.AM. ACAD MICROBIOLASMFSISARSUNIV VERMONTMINN DOHAZ DOHUNIV FLVA DOHWA DOHTX DOHNY AG LABIRISH FSANOVA SE UNIVIGS BALTIMOREINFORM MEETINGHONGKONG POLYT U

NISTITALIAN FSAEFSAWHO-FOOD SAFETT DIR.WHO-GFNCDC-EUEMERGING INFECTIOUS DIS CONFDANISH TECH UNIVNM STATE UNIV/ NM DOHCARLOS MALBRAN INST/ARGST COULD UNIV/FOOD MICROSENASICAGMINY DOH/WADSWORTH CENTUNIV HAMBURGCHINA CDCNESTLEFERA-UKMD DOHIAFPAPHLAFDOBELGIUM

VaTechUS ARMYUS NAVYMELBOURNE FSA (AUS)UNIV NEBRASKAPUBLIC HEALTH ENGLANDDHSDELMARVA TASKFORCEPENN STATE FOOD SCIENCEPROD MAN ASSOCILLUMINAUNIV IRELAND/DUBLIN COLLEGENCBI/NIHGSRS GLOBAL SUMMITFAO/OIEPUBLIC HEALTH CANADACFIAHEALTH CANADAINTL VTEC MEETINGCPS-GAAOACUNITED FRESHCOLUMBIA

HAWAII DOHCA DOHALASKA DOHSOUTH DAK UNIVUNIV GAUNIV IOWA/DOHUNIV CHILEBRAZILOSU VETNETTURKEYMEXICOIEHSILLAKERNEW ENG BIOLABPACIFIC BIOCLC-BIO/QIAGENCON-AGRADUPONTAGILENTUC-DAVISHARVARD MEDINFORM MEETINGTHAILAND

FDA\CFSAN Validation Efforts1. Technical Performance

Accuracy: Salmonella LT2 and Agona SL4832. Intralaboratory variation, sequencing platform

Salmonella Montevideo (180+ runs)3. Interlaboratory variation

Salmonella Braenderup BAA-664 (PFGE control), ISO/CEN4. Bioinformatics Pipeline

Software ValidationCollaborations w/ Canada, CDC, NIH/NCBI

Salmonella BraenderupInterlaboratory Study

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Salmonella Braenderup

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Salmonella BraenderupEnvironmental Samples from Florida

Contract Lab → FDA\CFSAN

FDA\CFSAN (454)