Archer, Simon C. (2013) Influence of somatic cell count in heifers on lifetime milk yield and disease

197 Pages·2017·1.73 MB·English

by  Christine Middleton

Influence of somatic cell count in heifers on
lifetime milk yield and disease management
Simon C.ArcherBVMS MSc Cert CHP MRCVS
Thesis submitted to The University of Nottingham for the degree
of Doctor of Philosophy
November2013
Abstract
Theaim was toassess theimpact ofmilksomaticcell count (SCC)
duringthe first lactation onthelifetimemilkproductionofcows, andtherefore
estimatepotential savings throughheifermastitis control.Cowlevel SCC over
thefirst lactationwas summarisedas SCC between5 and30days inmilk
(SCC1),andthegeometricmeanandvarianceoffirst lactationSCC.The
impact ofSCC1oncumulativemilk yieldoverdifferent timeperiods was
assessedfor cows in Irish, English, andWelsh dairyherds. Theimpact of
SCC1andthegeometric meanandvarianceoffirst lactationSCC onlifetime
milk yield,andtheassociationbetweenSCC1and disposal risk were assessed
forcows in Irish dairyherds. IncreaseinSCC throughout thefirst lactationwas
associatedwithlargereductions inthemilk yield ofcows, andincreased
disposal risk. Bayesianmicro-simulationwas used to demonstratetheimpact in
different herdscenarios. This was extendedtosynthesiseevidenceonpotential
savings usingprevious research,to estimatetheeconomicimpact ofspecific
interventions toreducetheprevalenceofcows withhighSCC1.Therewas
considerablevariationbetweenherds inthe apparent impact ofSCC1onSCC
throughout thefirst lactation,indicatingtheimportanceof aherdspecific
approachto control.‘Cost effectiveness’ofinterventions toreducethe
prevalenceof cows with highSCC1,was foundtobehighlydependent onthe
willingness ofdecisionmakers topayforcontrol measures. Increaseinherd
sizewas associatedwith increaseincowSCC,highlightinganeed for
improvedmanagement ofmastitis whenexpansionis planned.Animportant
component ofthis shouldbethroughmonitoringandcontrol ofmastitis in
heifers, especiallythoseinspring-calvingIrish dairyherds.
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Publications
Chapter 2
Archer,S.C.,F.McCoy,W.Wapenaar,andM. J.Green.2013. Associationof
season andherdsizewithsomaticcell count for cows in Irish, English, and
Welsh dairyherds. Vet.J.196:515-521.
Chapter 3
Archer,S.C.,F.McCoy,W.Wapenaar,andM. J.Green.2013. Association
betweensomatic cell count earlyinthefirst lactationandthelifetimemilk
yieldof cows in Irish dairyherds. J.DairySci.96:2951-2959.
Chapter 4
Archer,S.C.,F.McCoy,W.Wapenaar,andM. J.Green.2013. Association
betweensomatic cell count afterfirst parturitionandcumulativemilk yield in
dairycows. Vet.Rec.doi: 10.1136/vr.101558.
Chapter 5
Archer,S.C.,F.McCoy,W.Wapenaar,andM. J.Green.2013. Association
betweensomatic cell count earlyinthefirst lactationandthelongevityof Irish
dairycows. J.DairySci.96:2939-2950.
Chapter 6
Archer,S.C.,F.McCoy,W.Wapenaar,andM. J.Green.2013. Association
betweensomatic cell count duringthefirst lactationandthecumulativemilk
yieldof cows in Irish dairyherds. J.DairySci.Submitted.
Chapter 7
Archer,S.C.,F.McCoy,W.Wapenaar,andM. J.Green.2013. Bayesian
evaluationofbudgets for endemicdiseasecontrol; anexampleusing
management changes toreducemilksomaticcell count earlyinthefirst
lactationof Irish dairycows. Prev.Vet.Med.Accepted.
iii
Acknowledgments
Iam grateful forthesupport andencouragement ofmycolleagues,
friends, andfamilythroughout thepreparationofthis thesis. Inparticular I
wouldliketothankmyprimarysupervisorProf. MartinGreen forhis
invaluable guidance,and enthusiasm forthesubject.FinolaMcCoyhadthe
initial inspirationbehindtheproject,securedthe Walsh fellowshipfunding
throughTeagasc,andhas remainedsupportive and constructivethroughout. Dr.
WendelaWapenaarhas also providedawealthofinsightful suggestions. Ihave
beenluckyenoughtohaveworkedinthe companyofsupportivecolleagues
andfriends. Finally, Iwish toacknowledgemyclosefamily; Mum,Dad, Tom,
andRosieforalways beingthere.
“All models arewrong,but someareuseful”Box,GeorgeE.P.
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Tableofcontents
Abbreviations.............................................................................................................1
Chapter1: Introduction...........................................................................................2
1.1 Importanceofmastitisindairycows.............................................................2
1.1.1 Pathogensassociatedwithmastitis.......................................................3
1.1.2 Milksomaticcellcountdata..................................................................4
1.2 Mastitisinheifers..........................................................................................5
1.2.1 Importanceofheifers............................................................................6
1.2.2 Economicimpactofmastitisinheifers..................................................6
1.2.3 Epidemiologyofheifermastitis.............................................................7
1.2.4 Controlofmastitisinheifers.................................................................8
1.3 Studypopulationsusedinthisresearch......................................................13
1.3.1 Background..........................................................................................13
1.3.2 DairyfarminginIreland,EnglandandWales......................................13
1.3.3 ImportanceofheifermastitisinIreland..............................................14
1.4 Statisticalmethodsusedinthethesis.........................................................15
1.4.1 Limitationsofobservationalstudies....................................................16
1.4.2 Modeloutcomesandfit......................................................................17
1.4.3 Classicalapproach................................................................................18
1.4.4 Bayesianapproach...............................................................................18
1.4.5 MarkovchainMonteCarlo..................................................................19
1.4.6 Micro-simulation..................................................................................20
1.5 Aimsofthethesis........................................................................................21
1.5.1 Summary..............................................................................................21
1.5.2 Descriptivedata(chapter2)................................................................21
1.5.3 Somaticcellcountearlyinthefirstlactationandthelifetimemilkyield
ofcowsinIrishdairyherds(chapter3)...............................................................21
1.5.4 Somaticcellcountearlyinthefirstlactationandthecumulativemilk
yieldofcowsinEnglishandWelshdairyherds(chapter4)................................22
1.5.5 Somaticcellcountearlyinthefirstlactationandlongevityofcowsin
Irishdairyherds(chapter5)................................................................................22
1.5.6 Somaticcellcountduringthefirstlactationandthelifetimemilkyield
ofcowsinIrishdairyherds(chapter6)...............................................................22
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1.5.7 Bayesianevaluationofbudgetsforendemicdiseasecontrol;an
exampleusingmanagementchangestoreducesomaticcellcountearlyinthe
firstlactationofcowsinIrishdairyherds(chapter7).........................................22
Chapter2: Associationofseasonandherdsizewithsomaticcellcountforcowsin
Irish,English,andWelshdairyherds...........................................................................23
2.1 Introduction.................................................................................................23
2.2 Materialsandmethods................................................................................25
2.2.1 Dataselection......................................................................................25
2.2.2 Descriptivestatistics............................................................................26
2.2.3 Modeldevelopment............................................................................27
2.2.4 Assessmentofmodelfit......................................................................29
2.3 Results..........................................................................................................30
2.3.1 Descriptivestatistics............................................................................30
2.3.2 Modelresults.......................................................................................36
2.3.3 Modelfit..............................................................................................45
2.4 Discussion....................................................................................................45
2.4.1 Associationbetweenseasonandsomaticcellcount..........................45
2.4.2 Associationbetweenherdsizeandsomaticcellcount.......................46
2.5 Conclusion....................................................................................................47
Chapter3: Associationbetweensomaticcellcountearlyinthefirstlactationand
thelifetimemilkyieldofcowsinIrishdairyherds......................................................48
3.1 Introduction.................................................................................................48
3.2 Materialsandmethods................................................................................50
3.2.1 Dataselection......................................................................................50
3.2.2 Statisticalanalysis................................................................................51
3.2.3 Modelchecking....................................................................................52
3.2.4 Micro-simulation..................................................................................53
3.2.5 Changeinrevenue...............................................................................54
3.3 Results..........................................................................................................55
3.3.1 Descriptiveresults...............................................................................55
3.3.2 Modelresults.......................................................................................56
3.3.3 Modelchecking....................................................................................58
3.3.4 Micro-simulationresults......................................................................60
3.4 Discussion....................................................................................................61
3.5 Conclusions..................................................................................................65
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Chapter4: Associationbetweensomaticcellcountearlyinthefirstlactationand
thecumulativemilkyieldofcowsinEnglishandWelshdairyherds..........................66
4.1 Introduction.................................................................................................66
4.2 Materialsandmethods................................................................................67
4.2.1 Dataselection......................................................................................67
4.2.2 Dataanalysis........................................................................................67
4.2.3 Modeldevelopment............................................................................67
4.2.4 Modelchecking....................................................................................69
4.2.5 Micro-simulation..................................................................................70
4.2.6 Changeinrevenuefromcumulativemilkyield...................................71
4.3 Results..........................................................................................................72
4.3.1 Descriptiveresults...............................................................................72
4.3.2 Modelresults.......................................................................................74
4.3.3 Modelchecking....................................................................................75
4.3.4 Micro-simulationresults......................................................................76
4.4 Discussion....................................................................................................78
4.5 Conclusion....................................................................................................81
Chapter5: Associationbetweensomaticcellcountearlyinthefirstlactationand
thelongevityofcowsinIrishdairyherds....................................................................82
5.1 Introduction.................................................................................................82
5.2 Materialsandmethods................................................................................84
5.2.1 Dataselection......................................................................................84
5.2.2 Definitionofdisposal...........................................................................84
5.2.3 Modeldevelopment............................................................................85
5.2.4 Modelassessment...............................................................................87
5.2.5 Micro-simulationofherdscenarios.....................................................88
5.2.6 Micro-simulationofbaselinedisposalrisk..........................................91
5.3 Results..........................................................................................................94
5.3.1 Descriptiveresults...............................................................................94
5.3.2 Modelresults.......................................................................................95
5.3.3 Inclusionoftime-varyingcovariates....................................................98
5.3.4 Modelassessment...............................................................................99
5.3.5 Micro-simulationofbaselinedisposalrisks.......................................102
5.3.6 Micro-simulationofherdscenarios...................................................103
5.4 Discussion..................................................................................................106
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5.5 Conclusions................................................................................................109
Chapter6: Associationbetweensomaticcellcountduringthefirstlactationand
thecumulativemilkyieldofcowsinIrishdairyherds..............................................110
6.1 Introduction...............................................................................................110
6.2 Materialsandmethods..............................................................................111
6.2.1 Dataselection....................................................................................111
6.2.2 Firstlactationsomaticcellcountandcumulativemilkyield;statistical
analysis 112
6.2.3 Somaticcellcountlegacyduringthefirstlactation;statisticalanalysis
116
6.3 Results........................................................................................................118
6.3.1 Descriptiveresults.............................................................................118
6.3.2 FirstlactationSomaticcellcountandcumulativemilkyield;model
results 120
6.3.3 Somaticcellcountlegacyduringthefirstlactation;modelresults...128
6.4 Discussion..................................................................................................131
6.5 Conclusions................................................................................................133
Chapter7: Bayesianevaluationofbudgetsforendemicdiseasecontrol;an
exampleusingmanagementchangestoreducemilksomaticcellcountearlyinthe
firstlactationofcowsinIrishdairyherds..................................................................134
7.1 Introduction...............................................................................................134
7.2 Materialsandmethods..............................................................................136
7.2.1 Overview............................................................................................136
7.2.2 Lifetimemilkyieldmodel(Model3.1)...............................................137
7.2.3 Cowdisposalmodel(Model5.1).......................................................138
7.2.4 One-stepmicro-simulation................................................................139
7.2.5 Willingnesstopay..............................................................................143
7.3 Results........................................................................................................145
7.3.1 Potentialsavings................................................................................145
7.3.2 Costeffectivenessofinterventions...................................................148
7.4 Discussion..................................................................................................151
7.5 Conclusions................................................................................................156
Chapter8: Generaldiscussionandconclusions..................................................157
8.1 Dataqualityversusquantity......................................................................157
8.2 Insightsonaetiology..................................................................................158
8.3 Apparentprevalenceofheifermastitis.....................................................159
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8.4 Importanceofmonitoringmastitis............................................................161
8.4.1 Seasonalvariationinmilksomaticcellcount....................................161
8.4.2 Herdexpansion..................................................................................162
8.5 Somaticcellcountearlyinthefirstlactationandlifetimemilkyield.......163
8.5.1 Importanceofheifermastitiscontrol................................................163
8.5.2 Reasonsforchangeinlifetimemilkyield..........................................164
8.6 Somaticcellcountlegacythroughoutthefirstlactation..........................166
8.7 Importanceoflowsomaticcellcountinheifers.......................................166
8.8 Budgetsformastitiscontrolinpreandperi-partumheifers.....................167
8.9 Furtherresearch........................................................................................168
8.10 Conclusions................................................................................................169
8.10.1 Overview............................................................................................169
8.10.2 Chapter2...........................................................................................169
8.10.3 Chapter3...........................................................................................170
8.10.4 Chapter4...........................................................................................170
8.10.5 Chapter5...........................................................................................170
8.10.6 Chapter6...........................................................................................171
8.10.7 Chapter7...........................................................................................171
References.................................................................................................................172
Appendix....................................................................................................................184
Examplecodeforalinearregressionmodelincludingpredictionsandmicro-
simulation..............................................................................................................184
Examplecodeforalogisticregressionmodel.......................................................186
Examiners..............................................................................................................187
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Abbreviations
AFC Ageat first calving
BCI Bayesiancredibleinterval
CNS Coagulase-negativeStaphylococci spp.
DIM Days inmilk
FLMY First lactationmilk yield
LiMY Lifetimemilk yield
IMI Intramammaryinfection
IQR Interquartile range
kg Kilogram(s)
ln Natural logarithm of
mL Millilitre
MCMC MarkovchainMonteCarlo
p Probability
ppp Pre-andperi-partum
SCC Milksomaticcell count inthousands (unless
stated)
SCC1 Milksomaticcell count inthousands (unless
stated)measuredat 5to 30days inmilk
duringthe first lactation
TDY Test daymilk yield
1