Fig 1.
Reproduction cycle of Eimeria sp.
A chicken becomes contaminated by ingesting a sporulated oocyst. This oocyst contains 8 sporozoites which will be released into the intestinal lumen after digestion of the oocyst shell. The sporozoites attach to epithelial cells and penetrate them. Then there is a schizogony phase, which is a phase of asexual multiplication inside the epithelial cell. There are 4 cycles of schizogony. After these 4 multiplication cycles, tens of thousands of merozoites are released in the intestinal lumen. During the asexual reproduction phase, the animal does not excrete pathogens in the environment. After this first phase that takes between 4 to 7 days, there is a phase of sexual reproduction, with production of female and male gametes which fuse to give an egg. The fertilized product forms a zygote which will be surrounded by a thick wall to protect it from the external environment. This oocyst is then excreted into the external environment. At the moment it is released into the external environment, it is not yet infective to a new host; it will become infective after sporulation or sporogony, 2 to 3 days after excretion into the environment. The oocyst is very resistant and can survive up to several months in the environment.
Fig 2.
Compartmental model of disease dynamics and growth impacts in animals.
The compartments are represented by circles: for susceptible animals that can become infected,
for exposed animals that have been infected but are not yet infectious,
for infected animals capable of transmitting the disease, and
for animals that died from the infection. The model includes an environmental component showing pathogen concentration in the environment
and a growth G component representing animal growth trajectories affected by infection. The host traits impacting the different rates are represented in blue: susceptibility, infectivity, recoverability, tolerance and compensatory growth.
Table 1.
Differential model equations.
Table 2.
Definition of model’s variables and initial values.
Table 3.
Parameter names, values and descriptions.
Table 4.
Maximum weight deviation compared with non-infected animals across several articles after experimental ingestion of Eimeria oocysts.
Table 5.
Results of transmission rate, decay rate, shedding rate Parameters Estimation.
Fig 3.
100 epidemics are simulated among 20 chickens in a shared environment.
At time = 0 (5 days of age), one chicken got infected. The figures display the infection status of each animal over time, the infectious load in environment, individual weight curves and weight loss (percentage compared to theoretical weight) from day 0 to day 74 after the beginning of the epidemic.
Fig 4.
Predicted incidence rates for new Cases vs. Observed incidence rates across Experiments I-IV in [22]. The plot compares predicted new cases (dashed lines) and observed new cases (solid lines) across experiments I-IV (Panel A-D).
Fig 5.
Comparison of Observed Oocyst Counts and Predicted Environmental Infectious Loads L(t) across Experiments.
This Fig compares the dynamics of the environmental infectious load derived from our model (L(t), a dimensionless measure of transmission potential) with previously published results [35]. Panels A to D show the experiments I-IV. The black (left) and blue (right) lines both represent inoculated chicken, while grey (left) and yellow (right) lines both represent contact chicken. Error bars indicate variability between different pairs in each experiment. The x-axis shows time after inoculation (days), and the y-axis represents oocyst counts (left) and L(t) (right).
Fig 6.
Impact of host traits on disease dynamics and flock performance.
Comparison between baseline scenario and scenarios with modified traits: reduced infectivity (Inf), reduced susceptibility (Sus), increased recoverability (Rec), increased compensatory growth (CompG) and increased tolerance (Tol). For each scenario the corresponding parameter was increased or decreased of 1 ln unit compared with baseline. Grey lines represent individual simulation trajectories, colored lines show mean trajectories per scenario. Panels show from top left to bottom: infected chickens over time, infectious load in environment, weight growth curves, weight deviation percentage over age, and weight deviation percentage against infectious load.
Fig 7.
Comparison of population average performances between baseline scenario and alternative scenarios.
Inf: decreased infectivity, Sus: decreased susceptibility, Rec: increased recoverability, CompG: increased compensatory growth, Tol: increased tolerance. The color of the boxplot corresponds to the associated p-values from t-tests comparing each scenario to baseline (grey: p > 0.05, green: p < 0.05 and favorable effect, red: p < 0.05 and deleterious effect). Simulations were performed with 500 replicates of 20 birds for each scenario.
Table 6.
Comparative impact of host trait improvements on epidemiological and production outcomes. Percentage change relative to baseline for one-unit improvement in each trait. Green: favorable changes; Red: unfavorable changes. Statistical significance from Bonferroni-corrected t-tests: *** p < 0.001, ** p < 0.01, * p < 0.05, ns = not significant.
Fig 8.
Comparison of one animal performance between baseline scenario and alternative scenarios.
Inf: decreased infectivity, Sus: decreased susceptibility, Rec: increased recoverability, CompG: increased compensatory growth, Tol: increased tolerance. The direct effect of the trait is calculated by considering an individual with a favorable trait value (reducing/increasing average trait by one ln unit) among individuals with baseline trait values. The indirect effect is calculated by considering an individual with baseline trait values among individuals with favorable trait values. The color of the boxplots and bar charts corresponds to the associated p-values comparing each scenario to baseline (grey: p > 0.05, green: p < 0.05 and favorable effect, red: p < 0.05 and deleterious effect). Simulations were performed with 500 replicates of 20 birds for each scenario.