real-5me veterinary surveillance in companion animals · real-5me veterinary surveillance in...

S A V S N E T TheSmallAnimalVeterinarySurveillanceNetwork

PhilJones

MiningdatafromveterinaryrecordsReal-5meveterinarysurveillanceincompanionanimals

1 S A V S N E T TheSmallAnimalVeterinarySurveillanceNetwork

1

University of Liverpool, Department of Epidemiology and Population Health, Institute of Infection and Global Health, Leahurst Campus, Neston, Cheshire, CH64 7TE.

United Kingdom.

“TheBrief”•  HowSAVSNETsurveillancesystemworks.•  Whatdataiscollected.•  Howitiscollected,especiallytheextracConfrompracCceandlaboratoryinformaCon.

•  Howthedatacanbeusedanditsvalue.•  Applyingtothepigindustry.•  LimitaConsandhowtheyhavebeenaddressedforthefollowingchallenges:– DataConfidenCality,–  StandardisaCon,– Goodcoverage,–  Cost,–  Real-CmereporCngin/out.


•  HowSAVSNETsurveillancesystemworks.•  Whatdataiscollected.•  Howitiscollected,especiallytheextracConfrom

pracCceandlaboratoryinformaCon.

Collec5ngdata

Project1

CommerciallaboratorydiagnosCcdata

Project2Real-CmeelectronichealthrecorddatafromveterinarypracCces

Research-readydatamadeavailablethroughDataAccessandPublicaConsPanel(DAPP)

(seewww.savsnet.co.ukformoredetails)

DatacollecCon,collaConandanalysis

SAVSNETstructure

VeterinarypracCcedataProject2

Real-time electronic health record data from veterinary practices

•  Every participating veterinary practice has been actively recruited •  Signed agreement

Ethical&professionalapproval

Research Ethics Committee :

Aims supported by :

ALL University research projects (including undergraduate projects) must have ethical approval.

VeterinarypracCcedataInthewaiCngroom…

Approved by the University of Liverpool’s Research Ethics Committee. Supported by RCVS.

Consent by opt-out

Assumes owners have an opportunity to view poster. See later…

VeterinarypracCcedataIntheconsultaConroom…

VeterinarypracCcedataAttheendoftheconsultaCon…

100% 10%

GI QUESTIONNAIRE Questions)asked)if)Vet)selects)Gastroenteric)signs)option)on)first)screen.)Definition(in(the(box:(“Signs(including(but(not(limited(to:(diarrhoea,(vomiting,(weight(loss,(poor(appetite.” 1. Please indicate the clinical signs present* • Diarrhoea • Small intestinal diarrhoea • Large intestinal diarrhoea/colitis • Haemorrhagic diarrhoea • Melaena • Vomiting – without blood • Vomiting – with blood • Weight loss/failure to gain weight • Poor appetite • Other

2. Please indicate disease severity • Mild illness i.e. normal apart from GI disease • Moderately ill • Severely ill/debilitated 3. How does this consultation relate to this episode of illness • First presentation • Revisit/check-up • Don’t know 4. How long approximately has the pet had this episode of illness? • Less than 1 week • Between 1 week − less than 1 month • 1 month and over • Don’t know 5. What diagnostic options will be used today for this episode of illness? * • None • Faecal parasitology/bacteriology • Faecal virology • Virus serology • Diagnostic Imaging • Haematology/biochemistry • Serum B12/Folate and/or serum TLI • Canine/feline specific pancreatic lipase • Urinalysis • Other 6. What advice did you give today? * • Change of diet • Fasting • Admit patient for treatment • Refer patient • Check-up in near future • Other *indicates multiple options may be chosen

Average time to complete = 6-7 seconds

“The SAVSNET window”

VeterinarypracCcedataThetwo-wayinformaConhighway

PMS provides modal empty iFrame at end of consultation

SAVSNET servers provide content

essential software for veterinary professionals

CASENOTESTHE VET SOLUTIONS NEWSLETTER : SPRING 2011 : ISSUE 17

!!

Connectivity is a buzz word in all walks

of life today. We want to be connected

to our friends – old and new – through

Facebook, Linkedin and Friends

Reunited. Equally we want our phone

connected to our car, our PC and

to the email server at work.

The same principle applies to our lives in practice.

We want all our in practice gadgets connected to

each other so that the data and information from

the in-house laboratory can be joined up with the

images from the x-ray equipment or ultrasound.

Similarly, we want to connect up our insurance

claims with the insurance company, the microchip

registrations with the microchip database and lab

results with the external labs.

Of course, the central glue for this connectivity is

the practice management system. Much of this

‘glue’ already exists within Vet solutions’ practice

management systems, PremVet and RoboVet.

For example, lablink can feed results from most

in-house lab machines, such as QCR’s Vetscan

range, to PremVet or RoboVet. Similarly, images

can be linked to clinical records, and with the

appropriate viewing software, can be presented

to clients in the consulting room as required or

sent to a third party referral centre.

A new initiative along this same connectivity

theme is emerging in reception. Fewer and fewer

businesses take cheques and increasingly we rely

on our plastic card as a means of payment.

Typically practices are receiving payments of

between £60,000 to £80,000 per month via credit

or debit cards. To date there has been no

integration between the practice management

system and the chip and PIN card reader. This

means that there is currently a need for double

entering the bill amount into the card reader, the

potential for miss keying the amount, and

ultimately a lot of hassle at the end of the day to

unravel and reconcile.

Technology now exists to integrate the practice

management system with the chip and PIN

reader, much like the process applied at most

multiple retail stores.

This has a number of advantages to the practice:

No double entry of transaction amount –

saving time and eliminating errors

Faster verification when passed securely across

the internet as opposed to a telephone line

No call charges for transaction verification

No longer a need for a dedicated analogue

phone line

No longer a clash between analogue phone

line and inbound fax!

Potentially quicker transfer of cleared funds

into bank account improving cash flow

Completely safe and secure transactions

and banking industry compliant.

This new functionality is being introduced

to RoboVet users this spring in the form of a

new module called the iCAP reader (integrated

chip and PIN reader) and only requires a swap

of chip and PIN reading machines to those

of our banking partner.

SPRINGUSER DAYS 2011

SEE PAGE 03

COME TO SEE US AT BSAVA CONGRESS 2011

SEE PAGE 03

EDINBURGH10 MAY

MANCHESTER11 MAY

SPRINGUSER DAYS

2011

BSAVA CONGRESS31 MARCH –3 APRIL

STAND 414

Want to improve cash flow and save time in reception? Call 0131 556 0555 option 4 or email [email protected]

Are you well connected?

SAVSNET works closely with practice management system (PMS) providers:

Content within SAVSNET window is not hard-coded.

WhereisSAVSNET?

Distribution of SAVSNET practices (14 Sept 2016)

SurveyallocaCon

Surveyalloca5on

Howmuchdata?

VeterinarypracCcesurveillanceWhatdatadowecollect?

IdenCficaCon DateofconsultaCon

PracCceID

AnimalID

Geography Owner’sfullpostcode

Signalment Species

Breed

Dateofbirth

Gender

Neuteringstatus

Historical VaccinaConhistory

Weighthistory

Miscellaneous Insurancestatus

Microchipstatusandnumber(ifpresent)

Treatments Prescribeddrugsandothertreatments

Freetext Clinicalnotes

TheSAVSNETwindow Q1

QuesConnaire(ifadministered)

Financial data

Veterinary surgeon ID

Owner name and address

✘

✘

✘

LaboratorydiagnosCcdataProject1

Commercial laboratory diagnostic data

•  Laboratories are recruited as data providers •  SAVSNET accepts data in most convenient format for the laboratory

LaboratorydiagnosCcsurveillanceOverview

•  MinimalimposiCon

•  Whatdatadowerequest?–  SampleID

–  Species–  Breed–  FullpostcodeofveterinarypracCce–  Sampletype

–  Assaytypeandmethod

–  Result–  InterpretaCon(ifneeded)

•  Currentlysubmi?ngdata?

Unifieddatabasewithconsistentterms

THECHALLENGE…differenttermsusedbydifferentlabs

LAB2:A342/dog/WHWT/CH/faecalsample/PCRCPV/-

LAB1:237886/canine/wes5e/CH/faeces/parvoPCR/nega5ve

VetXMLschema–someCmes!Allergy Testing

Updated Small Animal Allergy Tests January 2012

C a r m i c h a e l T o r r a n c e D i a g n o s t i c S e r v i c e s

CTDS Ltd. Blacksmiths Forge, Brookfield Farm, Selby Road, Garforth. W. Yorks. LS25 1NB Tel: 0113 287 0175 / 6259 Fax: 0113 286 5127 Email: [email protected] www.ctdslab.co.uk

Name:

PTDS Code:

Ordered By:

Date Ordered:

Practice Supplies

General: 01582 881368 Pathology: 01582 882634 Email: [email protected] Website: www.ptdslab.co.ukUnit 2a, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR

PRACTICE SUPPLIES ORDER

PLEASE FAX, EMAIL OR RETURN VIA COURIER

Supplied by PTDS:

--/--/--Delivered by courier: Consumables:

Consumable Quantity £

Blood Culture Bottles per bottle 3.00

Boric Acid (7ml) per tube 0.40

Charcoal Swabs per swab 0.20

Charcoal Swab Mini Tip per swab 0.60

Citrate (1.3ml) per tube 0.25

EDTA (1.3ml) 100 7.00

(0.5ml) 100 16.00

Eppendorfs 100 3.00

Faecal Pots with Spoon per tube 0.10

Fluoride-Glucose (0.5ml) 100 15.00

(1.3ml) 100 8.00

Heparin (1.3ml) 100 8.00

Histo Pots (20ml) per tray (25) 4.00

(120ml) per tray (20) 7.00

Pasteur Pipettes 500 5.00

Plain (PCR) Swabs per swab 0.20

Plain Serum (1.3ml) 250 21.00

Serum Gel (1.3ml) 100 15.00

Universals (7ml) per tube 0.06

(25ml) per tube 0.06

Urine Acidification Kit per kit 10.00

Viral Swabs per swab 0.50

Stationery (Free of charge)

Price Lists

Submission Forms

Pre Paid Postage Labels

Urgent Labels

Rabies Forms

Special Delivery 100g

500g

Pre-used (Free of charge)

Bio Hazard Bags

Slide Holders: (2)

(5)

Other – Please Specify:

PTDSPOWELL TORRANCEDIAGNOSTIC SERVICES

Recentfigures

Lab-basedprojectTotalnumberofenrolledlaboratories 11(signed-up)NumberoflabscontribuCngdata 8Numberoftestresults 42M+Numberofsamples 4.5M+

Prac5ce-basedprojectTotalnumberofcontribuCngveterinarypracCces 223Numberofindividualpremises/clinics 489TotalnumberofconsultaCons 1.5M+CurrentconsultaConsperday(Mon–Fri) 5,500–6,000


•  Howthedatacanbeusedanditsvalue.

Howdoweusethedata?

Usingthedata

1.  Datasummariesandbenchmarkingincontextfordatacontributors(laboratoriesandveterinarypracCces)

–  “Wedon’tpayfordatabutwebenchmarkforfree”

–  Secureportallogin

2.  Quarterlysurveillancereportsinveterinaryliterature

3.  ‘Research-ready’dataavailabletoresearchersthroughaneasyapplicaConprocess.

4.  Generalpublic–onlineaccesstodatasummaries

Benchmarkingforproviders

• CompleCngthecircle(s)• Providingvalue• Dataquality• Engagement•  Informclinicaldecisions•  Impact

SAVSNET

labs

vets

owners

benchmarking

www

SAVSNET

Maps showing consult location Coloured areas are published deprivation

MADE UP DATA

PRACTICE VALUE

BOX & WHISKER OF ANONYMISED PEERS

INTERACTIVE CHARTS TO ANALYSE SPECIES, BREED,

GENDER, AGE, NEUTER, INSURANCE AND

MICROCHIP DAILY BREAKDOWN OF

EACH SYNDROME / CONSULTATION TYPE

Wedon’tpayfordatabut…Securereal-CmeanonymisedpracCceportal

Where samples

come from Where TESTS

come from Breakdown by

species

Cats Dogs

Test result by day

day positive

negative

What tests are done in

combination

toxo

plas

ma

Eg proportion of toxoplasma negative results

from male neutered cats

male

entire

cat

toxoplasma

LaboratorydiagnosCcsurveillanceInteracCvebenchmarkingreport

Aresourceforresearch•  Dataaccessand

publicaConpanel(DAPP)–  BSAVA/UoL/

Independent

•  Securedatatransfertools

•  AgreementsSAVSNET

labs

vets

owners

benchmarking

www

DAPP Research

SAVSNET

EXTERNAL DATABASES

Geographical Census Financial Climatic

Agricultural

Academia UoL, UoB

Commercial Pharma

OUTPUTS

Surveillance Veterinary Record

Government VMD

Fees for data access used for sustainability and further development only.

• Dataaccessavailableforallresearchers• DataAccessandPublicaConsPanel

– BSAVA– UniversityofLiverpool– Externalreviewers

• SimpleapplicaConprocess

Dataaccess

Application for the use of SAVSNET data

Page 1

SAVSNET Reference Number Please refer to guidance notes in completing this form. We recommend that you have an informal discussion

with one of the SAVSNET team before making your application.

Details of applicant(s) Lead applicant’s name

Names of other people who will

have access to SAVSNET data Affiliation (Company / University /

Organization or other)

Purpose for requesting data Purpose for requesting data

Question being asked

Access period

Data required Type of data

Number of consultations / laboratory reports Date range for data

Species

Breed

Age range

Any other requirements


•  DataConfidenCality,•  StandardisaCon,•  Goodcoverage,•  Cost,•  Real-CmereporCngin/out.

Dealingwithchallenges

Challenges

1.   Dataconfiden5ality(needtoinspireconfidence)–  Ethicalapproval&supportfromRCVS–  Ownerconsent–  Signedagreements(e.g.commercially-sensiCvedatanotdisclosed)

–  UoLsecureservers–  De-idenCficaConsooware–  DAPPanddatachaperone–  Secureportalsfordataproviders–  AvoidingcombinaConsofidenCfiers(“the19yowidowinManchester”)–  IndependenceofUniversity–  CloselinkswithFarrInsCtuteofHealthInformaCcsResearch

Challenges

2.   Standardisa5on–  Developmentof‘API’(applicaConprogramminginterface)

–  IntegratedatafrommulCplePMSsooware

3.   Goodcoverage–  IniCallyworkedwithmarket-leadingPMSproviders–  UserexperienceofSAVSNETwindowparamount–  Intenserecruitmentdrives–  WorkwithmulCplePMSproviders

Challenges

4.   Cost–  MajorityofiniCalfundingfromlargegrants–  AddiConalfundingfromcommercial/academic

researchers–  Allfundsusedforsustainability–  “Wedon’tpayfordatabutwebenchmarkforfree”

5.   Real-5merepor5ngin/out–  Team

•  Academicstaff•  3.5FTEcoreteam(inc.soowaredeveloperandepidemiologist)


•  Applyingtothepigindustry.

Beyondthecuteandcuddly…Poten5altoapplySAVSNETtechnologyto

otherveterinarysectors

Valueandavailabilityofdata

• SAVSNEThasshownthat:•  Labdatacanbecollected•  Vetdataaccessiblethroughsooware

• ProducCondatacouldprovideimportantinsights• Dataalreadyexistsbutunder-uClised

• Enhancecurrentsurveillance• Economical• Technicallyfeasible

Labs

Vets

Producers

Volume of data Q

ualit

y of

dat

a

“Pyramid of scrutiny” (Meah and Lewis, 1999)

BuildingonSAVSNETexperience

•  ApplicaConforethicalapproval•  Contractsandagreements–UoLlegal

•  RecruiCngveterinarypracCces•  Pre-exisCngrelaConshipswithPMSproviders

•  LaboratorydatacollecCon–  Specificrulesneedtobedevelopedbuttechnicalprinciplesestablished

•  Real-Cmebenchmarkingfordatacontributors•  Securedata-handlinganddataconfidenCality•  DAPPapplicaConprocessfordataaccess•  StaCsCcalanalyses•  NaturallanguageprocessingofEHRs•  Financialmodelsforlong-termsustainability

Challenges1.Ethicsandownerconsent

•  Consent-by-opt-out– AssumesownershaveopportunitytoreadposterbeforeconsultaCon– Geographicalmarkers(e.g.postcode)maybeuniqueidenCfiersinruralseqng

– Agriculturaldatamaybe“moresensiCve”

–  Therefore,consent-by-opt-outisNOTappropriateforfarmvets

•  Needtodevelopnewmodelforconsent– WorkableandmeetsRECapproval– RecruitveterinarypracCces–  ?Recruitfarmers(consent-by-opt-in)

Challenges2.Mobileelectronichealthrecords

•  Collaboratewithcommercialthirdparty

•  PilotstudiesatUoLsuggestachangeinveterinaryculturemayberequiredtoobtainfarm-animalEHRs

•  BUTmanycommercialcompaniesaredevelopingmobileapps

•  SAVSNETethosregardingnotpayingfordata,freebenchmarkingandaccessibilitytodatamustbeobserved

Mobile device

UoL secure servers Veterinary practice PMS

•  Dealingwithgroupsratherthanindividuals

Challenges3.Ownerdata

•  Incompanionanimals,EHRsheldalmostexclusivelybyveterinarypracCces– BUTthatislikelytochange!

• VastamountsofproducCondataisrouCnelycollectedformanagementpurposes

• Canownerdatabeintegrated?

Challenges3.Ownerdata

9

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets

Number of piglets2006

2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date

Farrowing dateFarm EA01

Farm EA01

Farm EA019

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA02

Farm EA029

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA03

Farm EA039

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA04

Farm EA049

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA05

Farm EA059

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA06

Farm EA069

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA07

Farm EA079

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA08

Farm EA089

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA09

Farm EA099

9

910

10

1011

11

1112

12

1213

13

13Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date


Farm EA10

Farm EA10(Moving averages)

(Moving averages)

(Moving averages)Piglets born live per litter on 10 farmsPiglets born live per litter on 10 farms

Piglets born live per litter on 10 farms

0

0

05

5

510

10

1015

15

15mean of liveborn

mea

n of

live

born

mean of livebornea01

ea01

ea01ea02

ea02

ea02ea03

ea03

ea03ea04

ea04

ea04ea05

ea05

ea05ea06

ea06

ea06ea07

ea07

ea07ea08

ea08

ea08ea09

ea09

ea09ea10

ea10

ea10Mean number of piglets born live per litterMean number of piglets born live per litter

Mean number of piglets born live per litterby parity category on each farm

by parity category on each farm

by parity category on each farm1

1

12 to 3

2 to 3

2 to 34 to 6

4 to 6

4 to 67 & over

7 & over

7 & overParity number

Parity number

Parity number

10.4

10.4

10.410.6

10.6

10.610.8

10.8

10.811.0

11.0

11.011.2

11.2

11.2Number of piglets

Num

ber o

f pig

lets


2006

20062007

2007

20072008

2008

20082009

2009

20092010

2010

20102011

2011

2011Farrowing date

Farrowing date

Farrowing dateMoving average for all farms

Moving average for all farms

Moving average for all farmsNumber of live piglets born per litterNumber of live piglets born per litter

Number of live piglets born per litter

Preliminary farm-based data

Harriet Bell, (undergraduate vet student)

Challenges4.IniCalfundingduringdevelopmentphase

• CompeCConforfundingisintense!

• Teamofpeoplecanbeexpensive–  Databasedeveloper–  Soowaredeveloper–  Epidemiologist–  Projectco-ordinator–  Adminsupport

• BUTcanpickthebarlesandgrowincrementally

Challenges5.TrustandcompeCConfordata

• Commercially-sensiCvedata• Needtoinspireconfidenceinprocess•  Ifdatahasavalue,whygiveittous?

– Trackrecord– Transferrabletechnologiesavailable– IndependentdatacuraConBUT– Fullvalueofdataisonlyrealisedwhencombinedwithdatafromacrossthewholesector

Conclusions

• DataminingofveterinaryERHforsurveillanceandresearchisfeasible.

• Manyofthemethods,experiencesandtechnologiesdevelopedforSAVSNETaretransferrabletootherveterinarysectors.

• BUTcollaCngfarmdata(veterinarypracCce/producerdata)presentssomeunique(butnotinsurmountable)challenges.


WhokeepsSAVSNETrunning?Meetthecoreteam

Core team

Bethany Heayns Project co-ordinator

Fernando Sanchez-Vizcaino Veterinary epidemiologist

Susan Bolan Administrator

SAVSNET Board of Directors

Michael Day

Susan Dawson

P-J Noble Alan Radford

Ros Gaskell

Phil Jones

Tarek Menacere The software developer

Sally Everitt Jenny Newman

Maya Wardeh

TheSAVSNETTeam

David Singleton

Post-graduate research students

Katie McConnell

CAPITAL


real-5me veterinary surveillance in companion animals · real-5me veterinary surveillance in...

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