March 12 2010 at 125PM 240PM 1150 Snee Hall Optimizing Intervention Strategies in Food Animal Systems modeling production health and food safety Elva Cha DVM PhD candidate Rebecca Smith DVM PhD candidate Zhao Lu PhD Research Associate and Cristina Lanzas DVM PhD Resea ID: 688463
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Computational Sustainability March 12, 2010 at 1:25PM – 2:40PM 1150 Snee Hall Optimizing Intervention Strategies in Food Animal Systems: modeling production, health and food safety
Elva Cha, DVM, PhD candidate, Rebecca Smith, DVM, PhD candidate, Zhao Lu, PhD, Research Associate and Cristina Lanzas, DVM, PhD, Research Associate and
Yrj
ö
T. Gröhn, DVM, MPVM, MS, PhD
Department of Population Medicine and Diagnostic Sciences,
College of Veterinary Medicine, Cornell UniversitySlide2
Perhaps I should start with “ a disclaimer”… If I understood correctly, your approach is to assume the model is 'correct', then optimize the system. As veterinarians, our responsibility is to build a model based on subject matter representing reality.Of course, our goal is to find the optimal way to control disease (not necessarily eradication). And sometimes we need to learn the economically optimal way to coexist with them.Slide3
Food Supply Veterinary Medicine….all aspects of veterinary medicine's involvement in food supply systems, from traditional agricultural production to consumption.
Modeling production, health and food safety
:
1. Optimizing health and management decisions
2.
Mathematical modeling of
zoonotic
infectious diseases
(such as
L.
monozytogenes
, E. coli, MDR salmonella and
paratuberculosis
).Slide4
Three examples …Modeling production and health:Project 1. “Optimal Clinical Mastitis Management in Dairy cows.” Elva
Cha’s
PhD research
Project 2.
“
Cost Effective Control Strategies for The Reduction of
Johne’s
Disease on Dairy Farms.” Zhao Lu, Research Associate and Becky
Smith’s PhD
research
2. Modeling Food Safety:
Project 3.
“Food Animal Systems-Based Mathematical Models of Antibiotic Resistance among
Commensal
Bacteria.” Cristina Lanzas, Research AssociateSlide5
Let’s start with…1. Modeling production and health: Our overall goal is to develop a comprehensive economic model, dynamic model (DP), to assist farmers in making treatment and culling decisions.
Our 1
st
example:
Elva
Cha’s
PhD research: “Optimal Clinical Mastitis Management in Dairy cows”Slide6
Mastitis (inflammation in mammary gland)Common, costly disease (major losses: milk yield, conception rates, and culling). The question we address is whether it is better to treat animals at the time CM is first observed or whether it is worthwhile collecting more information related to the nature of the pathogen involved (Gram-positive or Gram-negative, or even the actual pathogen), and then make a treatment decision.
More information would seem to be of benefit
when deciding what to do with diseased cows,
but
unless the additional tests provide a different recommended outcome,
they are only an extra cost.
Slide7
Objective:We will build upon our existing Dynamic Programming model. This work requires us to determine the risk and consequences of CM (milk loss, delayed conception, mortality) as functions of cow characteristics, including the disease history and disease prognosis of the cow.
To do this
To determine the economically optimal amount of information needed to make mastitis treatment decisionsSlide8
How do we address our objective?We will compare 2 modelsModel 1 which will identify cows based on generic (non-specific) mastitisAnd Model 2, whereby if a cow has mastitis, it will be specified as gram-positive, gram-negative or other types of mastitisWe will then compare the profit of each modelWhat is this model?Slide9
The modelsThe models will calculate the optimal policy for each individual cowThis can be done by ‘dynamic programming’Slide10
Dynamic programmingNumerical method for solving sequential decision problemsBased on the ‘Bellman principal of optimality’In our case, the ‘system’ is dairy cows, observed over an infinite time horizon split into ‘stages’ i.e. months of a cow’s lifeSlide11
Dynamic programming At each stage, the state of the system is observedE.g. pregnancy status, disease status, milk yieldAnd a decision is madeReplace, keep (treat and inseminate) or sellThis decision influences stochastically the state to be observed at the next stage
Depending on the state and decision, a reward is gainedSlide12
Dynamic programmingValue function is the expected total rewards from the current stage until the end of the horizonOptimal decisions depending on stage and state are determined backwards step by stepSlide13
Structure of the hierarchic Markov process optimization modelSlide14
Parameters in our modelFor each type of mastitisRisk of mastitisRepeated risk of mastitisEffect on milk yieldEffect on conceptionEffect on mortality and cullingSlide15
LimitationsNow we can only study 3 different types of mastitis, although we have data for very specific types of mastitis! (i.e. >3!)Why is this a limitation? Can’t we simply expand the model?Slide16
Implications of a larger modelBy expanding the model, we will encounter the ‘curse of dimensionality’An opportunity cost of including another disease, and hence the parameters associated with itThe model increases as a power function, not by a factor of 1, 2 or 3…This makes computations even more challenging and time consumingSlide17
The curse of dimensionalityexample: Houben et al. 1994 State variables:
Age (monthly intervals, 204 levels)
Milk yield, present lactation (15 levels)
Milk yield, previous lactation (15 levels)
Length of calving interval (8 levels)
Mastitis, present lactation (4 levels)
Mastitis, previous lactation (4 levels)
Clinical mastitis (yes/no)
Total state space 6,821,724 statesSlide18
The curse of dimensionalityexample: Gröhn et al. 2003 State variables: Parity
(12 levels)
Conception in month
(10 levels)
Stage of lactation (20 levels)
Milk yield (5 levels)
Month of
calving (12 levels)
Disease index
(212 levels)
Total state space 144,000 x 212= 30,528,000Slide19
Structure of the hierarchic Markov process optimization model: First level: 5 milk yield levelsSecond level: 8 possible lactations and 2 carry-over mastitis states from previous lactation (yes/no).Third level: 20 lactation
stages (max calving interval of 20 months).
5 temporary milk yield levels
(relative to permanent milk yield),
9 pregnancy status levels
(0=open, 1-7 months pregnant, and 8=to be dried off), one involuntary culled state
13 mastitis states:
0=no mastitis
1 = 1
st
occurrence of CM (observed at the end of the stage),
2, 3, 4 = 1, 2, 3 and more months after 1
st
CM,
5 = 2
nd
CM,
6, 7, 8 = 1, 2, 3 and more months after 2
nd
CM,
9 = 3
rd
CM,
10, 11, 12 = 1, 2, 3 and more months after 3
rd
CM,
CM events > 3 assigned same penalties as if they were 3
rd
occurrence.
After deleting impossible stage-state combinations, the model described 560,725 stage-state combinations.Slide20
If we were able to overcome the curse of dimensionality … No longer only generic guidelines for the generic cow. The DP recommendations could be tailored to the individual cow in real time according to her cow characteristics and economics of the herd.Slide21
Project 2: “Cost Effective Control Strategies for The Reduction of Johne’s Disease on Dairy Farms”Zhao Lu, PhD, Research Associate, and Becky Smith, DVM, PhD studentSlide22
Johne’s disease (paratuberculosis)Johne’s disease is a chronic, infectious, intestinal disease caused by infection with Mycobacterium avium subspecies paratuberculosis (
MAP
).
Infection process of
paratuberculosis
on a dairy cow:
Transient shedding
Latency
Low shedding
High shedding
Infection status
Disease status
No clinical signs
Sub-clinical
Clinical
InfectionSlide23
Issues of Johne’s diseaseEconomic loss: > 200 million $ per year (Ott, 1999) due to the reduced milk production, lower slaughter value, etc.Public health: a potential association between Johne’s disease and human Crohn’s disease has been debated. Control of
Johne’s
disease:
Test and cull strategies, i.e., to cull/remove infectious animals form herd by test-positive results using diagnostic testing methods, such as culture and ELISA tests.
Improved hygiene management;
Vaccination.
However, it is difficult to control JD spread:
Long incubation period;
Low diagnostic test sensitivity for animals shedding low levels of MAP;
Cross reactivity of
Johne’s
disease vaccines with tuberculosis (TB).Slide24
Modeling of MAP transmission on a dairy herdA deterministic compartmental model (Mitchell et al., 2008). The test-based culling rates of low and high shedders are denoted by δ1 and δ2, respectively.
X
1
Susceptible
-
d
X
2
Resistant
d
Tr
Transient
d
()
H
Latent
d
Y
1
Low
d
Y
2
High
d
1
2
Slide25
Evaluation of effectiveness of test-based culling in Johne’s disease controlThe reproduction ratio R0 was derived and a global parameter uncertainty analysis was performed to determine the effectiveness of test-based culling intervention (Lu et al., 2008)Slide26
A stochastic multi-group model(Evaluation of effectiveness of test-based culling)
Calves
Heifers
Cows
Slide27
Optimal control of Johne’s disease:economic modelObjective function (cost function): Profit: selling milk, culling cows (meat);Cost: raising first and second-year calves/heifers; diagnostic testing; Lost: false-positive testing results. Control: various scenarios of test-based culling rates and management
Constraints: a system of dynamic equations.
Compartment model providing numbers of calves, heifers, and cows in each compartment, which are needed in the objective functional (cost function).
A deterministic, discrete time economic model has been developed to find optimal test-based culling rates with large (6 and 12 month) time steps. Slide28
What do we want?(Optimal control of test-based culling rates)A deterministic, continuous time economic model. Analytical studies of linear controls (test-based culling rates);Numerical search of optimal test-based culling rates.
A stochastic economic model.
Reasons: more realistic (variable prevalence and fadeout due to random events)
Optimal culling rates using stochastic differential equations;
Numerical simulations of optimal culling rates for the mean of cost function.
Economic analysis of
Johne’s
disease vaccines.
Mathematical modeling of imperfect
Johne’s
vaccines is in progress.
Slide29
Modeling the efficacy of an imperfect vaccine with multiple effectsVaccines are often imperfect They may not prevent all infectionsThey may have effects other than decreasing susceptibilityEfficacy can be considered as the proportional effect on a rate or probability parameter in a compartmental model5 vaccine effects:Vertical transmission
Horizontal transmission
Susceptibility
Infectiousness
Duration of latency
Duration of low-infectious period
Progression of clinical symptomsSlide30
Modeling vaccine efficacy against JD
X
1
(1-p)(
-)
(1-p)
d
X
2
Resistant
d
Tr
Transient
d
()
H
Latent
d
Y
1
Low
d
Y
2
High
d
Susceptible
VX
1
Susceptible
p
(-)
p
d
VX
2
Resistant
d
VTr
Transient
d
e
20
()
VH
Latent
d
e
3
VY
1
Low
d
e
4
VY
2
High
d
e
5
Slide31
Estimating vaccine efficacy against JD with field dataKnown information:birth datedeath date annual test dates and resultsvaccination statusMissing information:Date of infectionOnset of low-sheddingOnset of high-sheddingTrue infection status (if all tests results were negative)
To estimate vaccine efficacy,
missing information must also be estimatedSlide32
Estimating vaccine efficacy with Markov Chain Monte Carlo modelsMCMC models are Bayesian statistical models, useful for disease modeling because theyCan account for nonlinear systemsparameters may be inter-relatedCan account for time-dependence i.e. infectious pressureHave a mechanism for missing-data problems:Missing information can be estimated probabilistically, given a set of parameters drawn from a prior distributionThe full dataset can then be used to determine the relative likelihood of a different set of parameters drawn from the prior
The new set of parameters may be accepted or rejected, based on its relative likelihood
This process is iterated until it converges on a posterior distribution for all parametersSlide33
Validating MCMC modelsIn order to test that an MCMC model predicts the true parameter distribution, we feed it data simulated with known parametersIn the case of the JD model, the full model requires individual animal data:Infection statusVaccination statusDates of birth, compartment transitions, deathWe need an individual-animal stochastic modelSlide34
Optimal control of Johne’s disease using an individual-based (agent-based) modeling approachControls: test-based culling, farm management, JD vaccinesAdvantages of individual-based modeling (IBM)Providing a general framework to model infectious disease transmission in a dairy herd;Integrating all individual information together to predict the dynamics on farms;Adding controls on farm level and/or individual animals easily.
Economic analysis based on IBM would be more accurate.
Disadvantages of IBM
Individual information collection: a detailed profile for each animal in a herd.
(also an advantage)
Simulations: efficient algorithm and powerful computers are necessary.Slide35
Project 3: “Develop, evaluate and improve food animal systems-based mathematical models of antimicrobial resistance among commensal bacteria”Cristina Lanzas, DVM, PhD, Research AssociateSlide36
Bergstrom and Feldgarden, 2008 At least 200,000 people suffer from hospital acquired infection every year, and at least 90,000 die in US. Economical burden of antimicrobial resistance in clinical settings in US is estimated to be as high as $ 80 billion annually.
Pathogens outside the hospital are also becoming progressively resistant to common antimicrobials.
Antimicrobial resistance is also considered a food safety issue because infections with drug resistant foodborne pathogens (e.g.
Salmonella
) can be particularly serious.
Slide37Slide38
Reservoirs of resistant genes are found in commensal bacteria in the human and animal gastrointestinal tracts (small intestine supports ~ 1010 bacterial cells/g) . Commensal bacteria can transfer mobile genes coding antimicrobial resistance among themselves and to pathogen bacteria (e.g. plasmid transfer between Salmonella and E. coli)
Molecular mechanisms involved in the spread of antimicrobial resistance. Inter-cellular movement (horizontal spread) is the main cause of acquisition of resistance genes.
Boerlin, 2008
Salyers et al., 2004Slide39
WITHIN HOST
R
S
Population dynamics of antibiotic-sensitive and –resistant bacteria
Linked to antibiotic exposure
Emergence of resistance during antibiotic treatment
Fitness cost linked to microbial growth
BETWEEN HOSTS
Transmission of resistant clones
Individuals colonized with either susceptible or resistant strains
The host population is divided according its epidemiological status (e.g. susceptible, infectious)
“Binary response”: Animal carries the bacteria carrying the resistance or not
S
I
-
+Slide40
Within host dynamics of antimicrobial resistance disseminationMicrobial growth for sensitive and resistant strains with horizontal gene transfer
Logistic Growth
Antibiotic effect
Plasmid loss during segregation
Plasmid transfer
Percentage of resistant bacteria 24 h after the end of the antimicrobial treatmentSlide41
Between host dynamics of antimicrobial resistance dissemination
S
I
S
I
R
I
SR
S
susceptible
I
infectious
W
environment
γ
πη
λSlide42
Integrating within and between host antimicrobial resistance dynamics Interventions to minimize the dissemination of antimicrobial resistance can be applied at different organizational levels (e.g. within host/between hosts and environment):Optimize antimicrobial dosage regimes to mitigate the dissemination of antimicrobial resistance within enteric commensal bacteria.Reduce the exposure of animals to antimicrobial resistant bacteria. Mathematical approaches that integrate within and between host dynamics are necessary to optimize mitigation strategies acting at different hierarchical scales:
Agent-based/Individual-based models
Dynamic nested models
Slide43
Modeling On-farm Escherichia coli O157:H7 population dynamics Metapopulation models has allowed us to investigate the potential role of non-bovine habitats (i.e., water troughs, feedbunks, and the surrounding pen environment) on the persistence and loads of E. coli O157:H7 in feedlots.O157:H7 survive and reproduce in water troughs, feed, slurry, pen floors.
Ayscue et al.,
Foodborne
Pathog
Dis
, 6:461-470 (2009)Slide44
Monogastric calfGrowing ruminant heifer
Lactating cow
Bred ruminant heifer
Dry cow
Cull cow
Dairy beef
S, R
S, R
S, R
S, R
Animal patches
Selective
pressures
Environment
(S, R)
Water
(S,R)
This metapopulation approach is suitable for modeling the dynamics of antimicrobial resistance dissemination. Pharmacokinetics and pharmacodynamics and biological fitness of antimicrobial resistance can be integrated.Slide45
Assuming three types of ecological patches (water, environment and n animals) and assuming indirect transmission (bacteria are transmitted to animals through water and environment):
For the
j
animal:
Water patch:
Environmental patch:Slide46
Potential students projects Application of optimal control to evaluate strategies in metapopulation models Development of agent based models to address antimicrobial resistance dissemination. Optimization in agent based models Optimization in hierarchical models