Swine Health Monitoring Project

December 3, 2016

Bob Morrison, P.I.

The SHMP teamFaculty• R. Morrison• A. Perez• M. Torremorell• M. Alkhamis• K. VanderWaal• J. Alvarez and• D. Linhares• D. Holtkamp

Students & postdocs• Andreia Arruda• Carles Vilalta• Emily Geary• Paulo Fioravante• Kaushi Kanankege• Gustavo Machado• Pablo Valdes• Gustavo De-Sousa-E-Silva

Current participation

• Currently 29 systems with 1,022 sow farms & 2.63 m sows– 21 production companies– 4 veterinary practices– 4 regional projects

• 22 and 4 projects share logo stating intentions

• 300 non participants receive weekly report

SHMP Objectives

• Long term – to develop capacity to support industry response to emerging pathogens.

& • Short term – deliver value to encourage

participation:– monitor disease incidence & prevalence.– supplement outbreak investigation.– understand implications of pig movement.

Our process

Weekly report• Page 1 – Participants

• Page 2 – PRRS summary

• Page 3 – PED summary

• Page 4 – Senecavirus A etc.

• Page 5 – Science page

• Page 6 – Others receiving dated report

• Page 7–xx – System reports

Publications• Tousignant et al. Temporal and spatial dynamics of porcine reproductive and respiratory

syndrome virus infection in the United States. Am J Vet Res. January 2015, Vol. 76, No. 1, Pages 70-76.

• Tousignant et al. Comparison between the 2013–2014 and 2009–2012 annual porcine reproductive and respiratory syndrome virus epidemics in a cohort of sow herds in the United States. Can Vet J 2015; 56:1087–1089.

• Alvarez et al. Impact of PEDv on Performance of Growing Pigs. PLOS One. March 13, 2015 http://dx.doi.org/10.1371/journal.pone.0120532

• Goede et al. Production impact & time to stability in sow herds infected with porcine epidemic diarrhea virus (PEDV). Preventive Veterinary Medicine. Volume 123, 1 January 2016, Pages 202–207.

• Alvarez et al. Spatial and temporal epidemiology of porcine epidemic diarrhea (PED) in the Midwest and Southeast regions of the United States. Prev Vet Med. Vol 123, 1 January 2016, Pages 155–160

• Valdes et al. Measuring Progress on the Control of Porcine Reproductive and Respiratory Syndrome (PRRS) at a Regional Level: The Minnesota N212 Regional Control Project (Rcp) as a Working Example. PLOS One. Feb 19, 2016 http://dx.doi.org/10.1371/journal.pone.0149498

• Alkhamis et al. Applications of Bayesian Phylodynamic Methods in a Recent U.S. Porcine Reproductive and Respiratory Syndrome Virus Outbreak. Front. Microbiol., 02 February 2016 http://dx.doi.org/10.3389/fmicb.2016.00067

Weekly science page receives positive feedback

PRRS Incidence

PED Incidence

Tableau

VDLs: (UMN – 6 systems)

SQL db:PINs w/location

Sequences

ARC GISGoogle Earth

Visualization

Alteryx:data

cleaning

Vet reports

Today

Excel

Advanced Analytics&

Visualization

Tableau

VDLs: (UMN, ISU, SDSU etc)

SQL db:PINs w/location

Movement

Sequences

Feed deliveries

ARC GISGoogle Earth

Visualization

Alteryx:data

cleaning

Vet reports

Eventually

Performance

Data visualizationSense-Making

Communication

SHMP • Prevalence• Incidence• EWMA• TTS• Heat maps

• ORF5 sequences• Susceptibility

VDL

State IL State MN

System 1 System 3

EWMA

Time To Stability (TTS)

Considerable difference in trend of TTS across

SHMP systems

1

1

Shedding farms: Status 1, 2vx &2fvi

SimilarityStrainAll

SimilarityStrainD15-001988

SimilarityStrainD15-030196

Penicillin

IsolatePasteurella multocida

AntimicrobialMultiple values

Enrofloxacin

Enrofloxacin

IsolateStreptococcus suis

AntimicrobialMultiple values

Florfenicol

Related Studies

Should I build at top or bottom of hill. And do surrounding trees matter?

• Objective:– Investigate whether land elevation and

coverage are associated with PRRS breaks• While accounting for other important factors

Vehicles• Network analysis

People• log

Fomites

Airborne• Weather & location

Other• Manure removalFeed• Swab bins

Outbreak Investigation - supplement

Potential sources after ruling out pigs & semen

Outbreak investigation - supplement• 3 regions• What will we learn?– Proportion breaks associated with neighboring pig sites– Develop capacity and analytical approach to supplement

current veterinarian’s investigation

• What tools will we use?– Sequence similarity over time and space– Weather analysis– Was transport associated?– Transmission chain analysis

Can we detect new strains of PRRSv?

PRRS Management

• 174 TTS & TTBP – Carl Betlach & Daniel Linhares• TTS at farrowing – Hunter Baldrey• TTS with wean down – Carles Vilalta

and with ISU:• Using SHMP data to estimate cost (Derald)• Biosecurity assessment (Derald & Daniel)• SPC for early detection of PRRS break (Daniel)

Wean-down study

• Where biosecurity is sufficient, PRRS virus dies out of sow herds (stability).

• TTS at weaning is a function of litter status at birth and spread in lactation– TTS median at weaning is ~28 wks (Linhares et al,

Betlach et al)– TTS median at farrowing is 13 weeks (Baldrey et al)

• Ho: Decreasing prevalence by wean-down will decrease TTS if biosecurity is sufficient.

• Enroll 30 farms with matched controls• Protocol– Starting at 8 weeks post break, monitor prevalence of

litters at 1-3 days– Vaccinate at processing at __ wks or __ prevalence– Max biosecurity 1-2 wk before wean-down (e.g. 0 foster)– Wean down to 10-14 days (younger is better)

• Start monitoring at weaning• $1,000 credit / herd at achieving stability (BI)

SHMP – update summary

• Critical issues:– Data security and confidentiality– Create value through data analysis and

interpretation

• Value for all can be gained from sharing data.