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arxiv: 2606.23148 · v1 · pith:XQ3XN5SHnew · submitted 2026-06-22 · 🧬 q-bio.PE

Bayesian modelling of herd-level infection dynamics in cattle: Local spread as the primary driver of Salmonella Dublin persistence on \"Oland

Stefan Widgren , Ivana Ewerl\"of , Arianna Comin , Robert Johansson , Stefan Engblom This is my paper

Pith reviewed 2026-06-26 06:10 UTC · model grok-4.3

classification 🧬 q-bio.PE
keywords Salmonella Dublincattle herdsBayesian inferencereproduction numberlocal spreadstate-space modelinfection dynamicsÖland
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The pith

Restricting cattle movements alone cannot bring the effective reproduction number of Salmonella Dublin below 1 on Öland, as local spread and within-herd transmission each contribute half the force of infection.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper formulates herd-level S. Dublin infection as a dynamic state-space model and applies particle Markov-chain Monte Carlo to infer dynamics from bulk tank milk samples across Öland holdings. It establishes that most herds have basic reproduction number below 1 so infection dies out after introduction, yet average effective reproduction number sits at 1, producing stable endemic presence. The central result is that local spread and within-herd transmission each drive roughly 50 percent of new infections, rendering movement restrictions on infected cattle insufficient to achieve Rt below 1. A sympathetic reader cares because the decomposition directly identifies which transmission routes must be targeted for eradication programs in Swedish cattle.

Core claim

Using Bayesian simulation-based inference on bulk tank milk results, the infection process is formulated as a dynamic state-space model and particle Markov-chain Monte Carlo methods infer the underlying dynamics and estimate R0 and Rt. Most holdings have R0 less than 1, indicating infection is expected to die out after introduction, but a subset has R0 greater than 1 with higher spread risk. On average Rt is approximately 1, suggesting stable endemic presence unless effective interventions are implemented. Local spread and within-herd transmission contribute equally, approximately 50 percent each, to the force of infection, demonstrating that restricting movements of infected cattle is insuf

What carries the argument

Dynamic state-space model of herd infection status, inferred via particle Markov-chain Monte Carlo from bulk tank milk samples, used to estimate R0 and Rt while decomposing force of infection into local-spread and movement components.

If this is right

  • Infection is expected to die out after introduction in most holdings where R0 is less than 1.
  • A subset of holdings with R0 greater than 1 carries elevated risk for sustained spread.
  • Average Rt near 1 implies stable endemic presence unless targeted interventions are added.
  • Any control program must address both local spread and within-herd transmission to reduce prevalence.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Control programs will need measures such as improved local biosecurity or environmental hygiene in addition to movement rules.
  • The same state-space approach could test whether similar transmission balances exist in other regions with persistent S. Dublin.
  • If the equal-contribution finding holds, prioritizing herd-level hygiene alongside movement controls would be the logical next intervention to evaluate.

Load-bearing premise

The bulk tank milk sample results accurately reflect the underlying herd infection status in the state-space model formulation.

What would settle it

A controlled field trial that implements only movement restrictions on infected cattle and directly measures whether Rt falls below 1, or an independent measurement of local transmission rates that differs substantially from the model's 50 percent attribution.

Figures

Figures reproduced from arXiv: 2606.23148 by Arianna Comin, Ivana Ewerl\"of, Robert Johansson, Stefan Engblom, Stefan Widgren.

Figure 1
Figure 1. Figure 1: A schematic representation of the stochastic compartment model for [PITH_FULL_IMAGE:figures/full_fig_p008_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: Schematic overview of the state-space model for [PITH_FULL_IMAGE:figures/full_fig_p012_2.png] view at source ↗
Figure 3
Figure 3. Figure 3: Approximate posterior distribution of the compartment model parameters for [PITH_FULL_IMAGE:figures/full_fig_p016_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Distribution of the estimated transmission kernel for [PITH_FULL_IMAGE:figures/full_fig_p021_4.png] view at source ↗
Figure 5
Figure 5. Figure 5: Histogram of the average basic reproduction number [PITH_FULL_IMAGE:figures/full_fig_p022_5.png] view at source ↗
Figure 6
Figure 6. Figure 6: Probabilistic model of OD value as a function of the prevalence of antibody [PITH_FULL_IMAGE:figures/full_fig_p023_6.png] view at source ↗
Figure 7
Figure 7. Figure 7: False positive/negative trade-off of the proposed OD value model under different [PITH_FULL_IMAGE:figures/full_fig_p023_7.png] view at source ↗
Figure 8
Figure 8. Figure 8: Classification of bulk tank milk (BTM) samples as seropositive against [PITH_FULL_IMAGE:figures/full_fig_p024_8.png] view at source ↗
Figure 9
Figure 9. Figure 9: Simulated effective reproduction number ( [PITH_FULL_IMAGE:figures/full_fig_p027_9.png] view at source ↗
read the original abstract

Salmonella Dublin (S. Dublin), a zoonotic serotype adapted to cattle, causes animal welfare issues and economic losses. The disease has proven particularly challenging to control in \"Oland, Sweden. This study uses Bayesian simulation-based inference of bulk tank milk sample results to analyse the S. Dublin infection dynamics in \"Oland cattle. The infection process was formulated as a dynamic state-space model and particle Markov-chain Monte Carlo methods were applied to infer the underlying infection dynamics and estimate the basic reproduction number ($R_0$) as well as the effective reproduction number ($R_t$). These metrics provide insight into transmission dynamics, enabling assessment of the effectiveness of the current S. Dublin control in Swedish cattle and identification of interventions that may reduce the prevalence. The results show that most holdings on \"Oland have $R_0 < 1$, indicating that infection is expected to die out after introduction. However, in a subset of holdings $R_0 > 1$, and there the risk for spread of S. Dublin is higher. Furthermore, the analysis reveals that on average, $R_t \approx 1$, suggesting a stable endemic presence unless effective interventions are implemented. In addition, the results show that it is insufficient to restrict the movements of infected cattle on \"Oland to bring $R_t < 1$, as local spread and within-herd transmission contribute equally to the force of infection (approximately 50% each). These findings demonstrate how Bayesian data-driven analysis can support evidence-based decision making for the control and eradication of S. Dublin in cattle.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 2 minor

Summary. The manuscript develops a Bayesian dynamic state-space model for Salmonella Dublin herd-level infection dynamics on Öland, Sweden, fitted via particle MCMC to bulk tank milk sample data. It estimates herd-specific basic reproduction numbers R0 (most <1, some >1) and effective reproduction numbers Rt (average ≈1), and decomposes the force of infection to conclude that local spread and within-herd transmission each contribute ~50%, implying that cattle movement restrictions alone cannot bring Rt below 1.

Significance. If the central transmission-route attribution holds, the work supplies quantitative, data-driven evidence on control strategies for an economically important zoonosis, showing that endemic stability requires interventions beyond movement bans. The use of particle MCMC to infer latent states and route-specific parameters from imperfect observations is a clear methodological strength.

major comments (2)
  1. [§3.2 (state-space model, observation process)] §3.2 (state-space model, observation process): The headline 50/50 force-of-infection split is obtained by attributing transmission routes after mapping bulk tank milk results to latent infection states. No sensitivity analyses are reported for test sensitivity, intermittent shedding, or within-herd prevalence heterogeneity; if the observation model is misspecified, the posterior on the route-specific parameters is biased and the equal-contribution claim does not follow.
  2. [§4.2–4.3 (Rt and force-of-infection decomposition)] §4.2–4.3 (Rt and force-of-infection decomposition): The reproduction numbers and transmission proportions are computed from parameters estimated on the identical dataset used to fit the model. Without out-of-sample validation, alternative observation models, or explicit robustness checks to priors, the finding that local spread and within-herd transmission contribute equally (and that movement restrictions are therefore insufficient) remains sensitive to modeling choices.
minor comments (2)
  1. [Abstract] Abstract: the description of the inference method could briefly note the priors or any model-validation steps performed.
  2. [Methods] Notation: herd-specific R0 and the components of the force of infection should be defined with explicit equations before the results section.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their constructive comments, which highlight important aspects of model robustness. We respond point-by-point below and will incorporate revisions where appropriate.

read point-by-point responses

  1. Referee: §3.2 (state-space model, observation process): The headline 50/50 force-of-infection split is obtained by attributing transmission routes after mapping bulk tank milk results to latent infection states. No sensitivity analyses are reported for test sensitivity, intermittent shedding, or within-herd prevalence heterogeneity; if the observation model is misspecified, the posterior on the route-specific parameters is biased and the equal-contribution claim does not follow.

    Authors: We agree that dedicated sensitivity analyses would strengthen confidence in the observation model and the resulting force-of-infection attribution. The current model uses literature-derived values for test characteristics, but we will add explicit sensitivity analyses varying test sensitivity, incorporating intermittent shedding, and allowing for within-herd prevalence heterogeneity. These will be reported in a revised §3.2 and supplementary material. revision: yes

  2. Referee: §4.2–4.3 (Rt and force-of-infection decomposition): The reproduction numbers and transmission proportions are computed from parameters estimated on the identical dataset used to fit the model. Without out-of-sample validation, alternative observation models, or explicit robustness checks to priors, the finding that local spread and within-herd transmission contribute equally (and that movement restrictions are therefore insufficient) remains sensitive to modeling choices.

    Authors: We acknowledge that all estimates derive from the same dataset. We will add prior sensitivity analyses and alternative observation-model specifications to §4 and the supplement. Full out-of-sample validation is constrained by the exhaustive nature of the Öland dataset; we will discuss this limitation and implement temporal hold-out checks where feasible. revision: partial

Circularity Check

0 steps flagged

No significant circularity; model outputs are data-informed inferences, not reductions by construction

full rationale

The paper formulates a state-space model for infection dynamics, applies particle MCMC to infer parameters and latent states from bulk tank milk observations, then computes R0, Rt, and route-specific force-of-infection contributions as posterior-derived quantities. These steps follow standard Bayesian inference without self-definitional loops, fitted-input-as-prediction, or load-bearing self-citations that collapse the central claims. The 50/50 split emerges from the fitted transmission parameters rather than being imposed by definition or renaming. The derivation chain remains self-contained against external data.

Axiom & Free-Parameter Ledger

2 free parameters · 2 axioms · 0 invented entities

Based on abstract only; the model relies on fitted transmission rates and the state-space assumption to derive the force of infection contributions.

free parameters (2)
  • herd-specific R0
    Inferred per holding to determine if >1 or <1
  • force of infection components = 50% local, 50% within-herd
    Derived from the model fit to data leading to 50% local and 50% within-herd
axioms (2)
  • domain assumption Bulk tank milk samples provide reliable indicators of herd-level infection status
    Basis for the inference of infection dynamics
  • domain assumption The infection process follows a dynamic state-space model
    Formulation used for particle MCMC inference

pith-pipeline@v0.9.1-grok · 5843 in / 1454 out tokens · 45232 ms · 2026-06-26T06:10:00.279794+00:00 · methodology

discussion (0)

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Reference graph

Works this paper leans on

59 extracted references · 44 canonical work pages

  1. [1]

    , year 2008

    author Allen, L.J.S. , year 2008 . title An introduction to stochastic epidemic models , in: editor Brauer, F. , editor van den Driessche, P. , editor Wu, J. (Eds.), booktitle Mathematical Epidemiology . publisher Springer Berlin Heidelberg , address Berlin, Heidelberg , pp. pages 81--130 . :10.1007/978-3-540-78911-6_3

    work page doi:10.1007/978-3-540-78911-6_3 2008

  2. [2]

    Particle

    author Andrieu, C. , author Doucet, A. , author Holenstein, R. , year 2010 . title Particle M arkov chain M onte C arlo methods . journal Journal of the Royal Statistical Society Series B: Statistical Methodology volume 72 , pages 269--342 . :10.1111/j.1467-9868.2009.00736.x

    work page doi:10.1111/j.1467-9868.2009.00736.x 2010

  3. [3]

    , author Roberts, G.O

    author Andrieu, C. , author Roberts, G.O. , year 2009 . title The pseudo-marginal approach for efficient M onte C arlo computations . journal The Annals of Statistics volume 37 , pages 697--725 . :10.1214/07-AOS574

    work page doi:10.1214/07-aos574 2009

  4. [4]

    , author Engblom, S

    author Bauer, P. , author Engblom, S. , author Widgren, S. , year 2016 . title Fast event-based epidemiological simulations on national scales . journal Int. J. High Perf. Comput. Appl. volume 30 , pages 438--453 . :10.1177/1094342016635723

    work page doi:10.1177/1094342016635723 2016

  5. [5]

    , author Hagenaars, T

    author Benincà, E. , author Hagenaars, T. , author Boender, G.J. , author van de Kassteele, J. , author van Boven, M. , year 2020 . title Trade-off between local transmission and long-range dispersal drives infectious disease outbreak size in spatially structured populations . journal PLOS Computational Biology volume 16 , pages 1--18 . :10.1371/journal.p...

    work page doi:10.1371/journal.pcbi.1008009 2020

  6. [6]

    , author van Schaik , G

    author Bergevoet, R. , author van Schaik , G. , author Veling, J. , author Backus, G. , author Franken, P. , year 2009 . title Economic and epidemiological evaluation of Salmonella control in D utch dairy herds . journal Preventive Veterinary Medicine volume 89 , pages 1--7 . :10.1016/j.prevetmed.2008.12.007

    work page doi:10.1016/j.prevetmed.2008.12.007 2009

  7. [7]

    , author Hagenaars, T.J

    author Boender, G.J. , author Hagenaars, T.J. , year 2023 . title Common features in spatial livestock disease transmission parameters . journal Scientific Reports volume 13 , pages 3550 . :10.1038/s41598-023-30230-w

    work page doi:10.1038/s41598-023-30230-w 2023

  8. [8]

    , author Hagenaars, T.J

    author Boender, G.J. , author Hagenaars, T.J. , author Bouma, A. , author Nodelijk, G. , author Elbers, A.R.W. , author de Jong, M.C.M. , author Van Boven, M. , year 2007 . title Risk maps for the spread of highly pathogenic avian influenza in poultry . journal PLoS computational biology volume 3 , pages e71 . :10.1371/journal.pcbi.0030071

    work page doi:10.1371/journal.pcbi.0030071 2007

  9. [9]

    , author Engblom, S

    author Bronstein, S. , author Engblom, S. , author Marin, R. , year 2023 . title Bayesian inference in E pidemics: linear noise analysis . journal Mathematical Biosciences and Engineering volume 20 , pages 4128--4152 . :10.3934/mbe.2023193

    work page doi:10.3934/mbe.2023193 2023

  10. [10]

    , author Dervic, E

    author Conrady, B. , author Dervic, E. , author Klimek, P. , author Pedersen, L. , author Reimert, M.M. , author Rasmussen, P. , author Apenteng, O. , author Nielsen, L. , year 2024 . title Social network analysis reveals the failure of between-farm movement restrictions to reduce Salmonella transmission . journal Journal of Dairy Science volume 107 , pag...

    work page doi:10.3168/jds.2023-24554 2024

  11. [11]

    P., Laird, N

    author Dempster, A.P. , author Laird, N.M. , author Rubin, D.B. , year 1977 . title Maximum likelihood from incomplete data via the em algorithm . journal Journal of the royal statistical society: series B (methodological) volume 39 , pages 1--22 . :10.1111/j.2517-6161.1977.tb01600.x

    work page doi:10.1111/j.2517-6161.1977.tb01600.x 1977

  12. [12]

    The construction of next-generation matrices for compartmental epidemic models

    author Diekmann, O. , author Heesterbeek, J.A.P. , author Roberts, M.G. , year 2010 . title The construction of next-generation matrices for compartmental epidemic models . journal Journal of the royal society interface volume 7 , pages 873--885 . :10.1098/rsif.2009.0386

    work page doi:10.1098/rsif.2009.0386 2010

  13. [13]

    , author Van Leeuwen, E

    author Endo, A. , author Van Leeuwen, E. , author Baguelin, M. , year 2019 . title Introduction to particle M arkov-chain M onte C arlo for disease dynamics modellers . journal Epidemics volume 29 , pages 100363 . :10.1016/j.epidem.2019.100363

    work page doi:10.1016/j.epidem.2019.100363 2019

  14. [14]

    , author Eriksson, R

    author Engblom, S. , author Eriksson, R. , author Widgren, S. , year 2020 . title Bayesian epidemiological modeling over high-resolution network data . journal Epidemics volume 32 , pages 100399 . :10.1016/j.epidem.2020.100399

    work page doi:10.1016/j.epidem.2020.100399 2020

  15. [15]

    , author Nielsen, L.R

    author Ersb ll, A.K. , author Nielsen, L.R. , year 2011 . title Spatial patterns in surveillance data during control of Salmonella D ublin in bovine dairy herds in J utland, D enmark 2003--2009 . journal Spatial and Spatio-temporal Epidemiology volume 2 , pages 195--204 . :10.1016/j.sste.2011.07.003

    work page doi:10.1016/j.sste.2011.07.003 2011

  16. [16]

    o f, I.R. , author Fr \

    author Ewerl \"o f, I.R. , author Fr \"o ssling, J. , author Tr ven, M. , author Gunnarsson, S. , author Steng \"a rde, L. , author Hurri, E. , author Widgren, S. , year 2025 . title Exploring structural changes in the S wedish cattle population and between-holding movements . journal Preventive Veterinary Medicine , pages 106608 :10.1016/j.prevetmed.2025.106608

    work page doi:10.1016/j.prevetmed.2025.106608 2025

  17. [17]

    , author Santman-Berends, I

    author Fabri, N. , author Santman-Berends, I. , author Weber, M. , author van Schaik , G. , year 2024 . title Risk factors for the introduction of Salmonella spp. serogroups B and D into D utch dairy herds . journal Preventive Veterinary Medicine volume 232 , pages 106313 . :10.1016/j.prevetmed.2024.106313

    work page doi:10.1016/j.prevetmed.2024.106313 2024

  18. [18]

    , author K \"u nsch, H.R

    author Fearnhead, P. , author K \"u nsch, H.R. , year 2018 . title Particle filters and data assimilation . journal Annual Review of Statistics and Its Application volume 5 , pages 421--449 . :10.1146/annurev-statistics-031017-100232

    work page doi:10.1146/annurev-statistics-031017-100232 2018

  19. [19]

    , author Wells, S

    author Fossler, C. , author Wells, S. , author Kaneene, J. , author Ruegg, P. , author Warnick, L. , author Bender, J. , author Eberly, L. , author Godden, S. , author Halbert, L. , year 2005 a. title Herd-level factors associated with isolation of Salmonella in a multi-state study of conventional and organic dairy farms: I. Salmonella shedding in cows . ...

    work page doi:10.1016/j.prevetmed.2005.04.003 2005

  20. [20]

    , author Wells, S

    author Fossler, C. , author Wells, S. , author Kaneene, J. , author Ruegg, P. , author Warnick, L. , author Bender, J. , author Eberly, L. , author Godden, S. , author Halbert, L. , year 2005 b. title Herd-level factors associated with isolation of Salmonella in a multi-state study of conventional and organic dairy farms: II . Salmonella shedding in calve...

    work page doi:10.1016/j.prevetmed.2005.04.002 2005

  21. [21]

    , author Taskar, B

    author Ganchev, K. , author Taskar, B. , author Gama, J. , year 2007 . title E xpectation M aximization and posterior constraints , in: editor Platt, J. , editor Koller, D. , editor Singer, Y. , editor Roweis, S. (Eds.), booktitle Advances in Neural Information Processing Systems

    2007

  22. [22]

    , author Salmond, D.J

    author Gordon, N.J. , author Salmond, D.J. , author Smith, A.F. , year 1993 . title Novel approach to nonlinear/non-gaussian B ayesian state estimation , in: booktitle IEE proceedings F (radar and signal processing) , pp. pages 107--113 . :10.1049/ip-f-2.1993.0015

    work page doi:10.1049/ip-f-2.1993.0015 1993

  23. [23]

    , author R Core Team , year 2024

    author Hong, Y. , author R Core Team , year 2024 . title poibin: The Poisson Binomial Distribution . https://CRAN.R-project.org/package=poibin. note r package version 1.6

    2024

  24. [24]

    , author Ingram, L.A

    author Jones, T.F. , author Ingram, L.A. , author Cieslak, P.R. , author Vugia, D.J. , author Tobin-D'Angelo, M. , author Hurd, S. , author Medus, C. , author Cronquist, A. , author Angulo, F.J. , year 2008 . title Salmonellosis outcomes differ substantially by serotype . journal The Journal of Infectious Diseases volume 198 , pages 109--114 . :10.1086/588823

    work page doi:10.1086/588823 2008

  25. [25]

    , author Boender, G.J

    author de Koeijer, A.A. , author Boender, G.J. , author Nodelijk, G. , author Staubach, C. , author Meroc, E. , author Elbers, A.R. , year 2011 . title Quantitative analysis of transmission parameters for bluetongue virus serotype 8 in W estern E urope in 2006 . journal Veterinary research volume 42 , pages 1--9 . :10.1186/1297-9716-42-53

    work page doi:10.1186/1297-9716-42-53 2011

  26. [26]

    , author Metcalfe, H.J

    author La Ragione, R. , author Metcalfe, H.J. , author Villarreal-Ramos, B. , author Werling, D. , year 2013 . title Salmonella infections in cattle. , in: booktitle Salmonella in domestic animals . publisher CABI Wallingford UK , pp. pages 233--262 . :10.1079/9781845939021.0233

    work page doi:10.1079/9781845939021.0233 2013

  27. [27]

    , author Bolic, M

    author Li, T. , author Bolic, M. , author Djuric, P.M. , year 2015 . title Resampling methods for particle filtering: classification, implementation, and strategies . journal IEEE Signal processing magazine volume 32 , pages 70--86 . :10.1109/MSP.2014.2330626

    work page doi:10.1109/msp.2014.2330626 2015

  28. [28]

    , author Mercat, M

    author Madouasse, A. , author Mercat, M. , author Van Roon, A. , author Graham, D. , author Guelbenzu, M. , author Santman Berends, I. , author Van Schaik, G. , author Nielen, M. , author Fr \"o ssling, J. , author gren, E. , et al., year 2022 . title A modelling framework for the prediction of the herd-level probability of infection from longitudinal dat...

    work page doi:10.24072/pcjournal.80 2022

  29. [29]

    , author Nielsen, L

    author Meletis, E. , author Nielsen, L. , author Madouasse, A. , author Conrady, B. , year 2023 . title Application of a B ayesian hidden M arkov model to determine dairy cattle herd status and test characteristics from Salmonella D ublin national surveillance data , in: booktitle Society for Veterinary Epidemiology and Preventive Medicine, Proceedings : ...

    2023

  30. [30]

    , year 2013 a

    author Nielsen, L.R. , year 2013 a. title Salmonella D ublin in cattle: epidemiology, design and evaluation of surveillance and eradication programmes . Ph.D. thesis. Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen. note Available at https://curis.ku.dk/ws/portalfiles/portal/168826927/Liza\_Rosenbaum\_...

    arXiv 2013

  31. [31]

    , year 2013 b

    author Nielsen, L.R. , year 2013 b. title Within-herd prevalence of Salmonella D ublin in endemically infected dairy herds . journal Epidemiology and Infection volume 141 , pages 2074--–2082 . :10.1017/S0950268812003007

    work page doi:10.1017/s0950268812003007 2013

  32. [32]

    , author van den Borne , B

    author Nielsen, L.R. , author van den Borne , B. , author van Schaik , G. , year 2007 a. title Salmonella D ublin infection in young dairy calves: Transmission parameters estimated from field data and an SIR -model . journal Preventive Veterinary Medicine volume 79 , pages 46--58 . :10.1016/j.prevetmed.2006.11.006

    work page doi:10.1016/j.prevetmed.2006.11.006 2007

  33. [33]

    , author Warnick, L

    author Nielsen, L.R. , author Warnick, L. , author Greiner, M. , year 2007 b. title Risk factors for changing test classification in the D anish surveillance program for Salmonella in dairy herds . journal Journal of dairy science volume 90 , pages 2815--2825 . :10.3168/jds.2006-314

    work page doi:10.3168/jds.2006-314 2007

  34. [34]

    , author Green, L

    author Nielsen, T. , author Green, L. , author Kudahl, A. , author Østergaard, S. , author Nielsen, L. , year 2012 . title Evaluation of milk yield losses associated with Salmonella antibodies in bulk tank milk in bovine dairy herds . journal Journal of Dairy Science volume 95 , pages 4873--4885 . :10.3168/jds.2011-4332

    work page doi:10.3168/jds.2011-4332 2012

  35. [35]

    , author Kudahl, A

    author Nielsen, T. , author Kudahl, A. , author Østergaard, S. , author Nielsen, L. , year 2013 . title Gross margin losses due to Salmonella D ublin infection in D anish dairy cattle herds estimated by simulation modelling . journal Preventive Veterinary Medicine volume 111 , pages 51--62 . :10.1016/j.prevetmed.2013.03.011

    work page doi:10.1016/j.prevetmed.2013.03.011 2013

  36. [36]

    , author Chowell, G

    author Nishiura, H. , author Chowell, G. , year 2009 . title The effective reproduction number as a prelude to statistical estimation of time-dependent epidemic trends , in: editor Chowell, G. , editor Hyman, J.M. , editor Bettencourt, L.M.A. , editor Castillo-Chavez, C. (Eds.), booktitle Mathematical and Statistical Estimation Approaches in Epidemiology ...

    work page doi:10.1007/978-90-481-2313-1_5 2009

  37. [37]

    o m, K. , author Wahlstr \

    author Nyman, A.K.J. , author gren, E.C. , author Bergstr \"o m, K. , author Wahlstr \"o m, H. , year 2013 . title Evaluation of the specificity of three enzyme-linked immunosorbent assays for detection of antibodies against Salmonella in bovine bulk milk . journal Acta Veterinaria Scandinavica volume 55 , pages 1--7 . :10.1186/1751-0147-55-5

    work page doi:10.1186/1751-0147-55-5 2013

  38. [38]

    , author Damiaans, B

    author Renault, V. , author Damiaans, B. , author Humblet, M.F. , author Jim \'e nez Ruiz, S. , author Garc \' a Bocanegra, I. , author Brennan, M.L. , author Casal, J. , author Petit, E. , author Pieper, L. , author Simoneit, C. , et al., year 2021 . title Cattle farmers’ perception of biosecurity measures and the main predictors of behaviour change: The...

    work page doi:10.1111/tbed.13935 2021

  39. [39]

    , author Rosenthal, J.S

    author Roberts, G.O. , author Rosenthal, J.S. , year 2009 . title Examples of adaptive mcmc . journal Journal of Computational and Graphical Statistics volume 18 , pages 349--367 . :10.1198/jcgs.2009.06134

    work page doi:10.1198/jcgs.2009.06134 2009

  40. [40]

    , author Madouasse, A

    author van Roon, A.M. , author Madouasse, A. , author Toft, N. , author Santman-Berends, I.M. , author Gethmann, J. , author Eze, J. , author Humphry, R.W. , author Graham, D. , author Guelbenzu-Gonzalo, M. , author Nielen, M. , et al., year 2022 . title Output-based assessment of herd-level freedom from infection in endemic situations: Application of a B...

    work page doi:10.1016/j.prevetmed.2022.105662 2022

  41. [41]

    , author Klinkenberg, D

    author Schaik, G.V. , author Klinkenberg, D. , author Veling, J. , author Stegeman, A. , year 2007 . title Transmission of Salmonella in dairy herds quantified in the endemic situation . journal Veterinary Research volume 38 , pages 861--869 . :10.1051/vetres:2007036

    work page doi:10.1051/vetres:2007036 2007

  42. [42]

    title RStan : the R interface to Stan

    author Stan Development Team , year 2024 . title RStan : the R interface to Stan . https://mc-stan.org/. note R package version 2.32.6

    2024

  43. [43]

    title Surveillance of infectious diseases in animals and humans in S weden 2019

    author SVA , year 2020 . title Surveillance of infectious diseases in animals and humans in S weden 2019 . howpublished Swedish Veterinary Agency (SVA), Uppsala, Sweden . Available at https://www.sva.se/media/nyglg2zq/sva-rapport-64-surveillance-2019.pdf (Online; accessed 09-December-2025)

    2020

  44. [44]

    title Surveillance of infectious diseases in animals and humans in S weden 2020

    author SVA , year 2021 . title Surveillance of infectious diseases in animals and humans in S weden 2020 . howpublished Swedish Veterinary Agency (SVA), Uppsala, Sweden . Available at https://www.sva.se/media/glund5y5/sva-rapport-68-surveillance2020_2022-04-08.pdf (Online; accessed 09-December-2025)

    2021

  45. [45]

    title Surveillance of infectious diseases in animals and humans in S weden 2021

    author SVA , year 2022 . title Surveillance of infectious diseases in animals and humans in S weden 2021 . howpublished Swedish Veterinary Agency (SVA), Uppsala, Sweden . Available at https://www.sva.se/media/acikdklm/sva-rapport-79-surveillance-2021.pdf (Online; accessed 09-December-2025)

    2022

  46. [46]

    title Surveillance of infectious diseases in animals and humans in S weden 2022

    author SVA , year 2023 . title Surveillance of infectious diseases in animals and humans in S weden 2022 . howpublished Swedish Veterinary Agency (SVA), Uppsala, Sweden . Available at https://www.sva.se/media/ptxlmbkl/surveillance-2022-web-2025-04-10.pdf (Online; accessed 09-December-2025)

    2023

  47. [47]

    title Smittläget i S verige för djursjukdomar och zoonoser 2023 [surveillance of infectious diseases in animals and humans in S weden 2023]

    author SVA , year 2024 . title Smittläget i S verige för djursjukdomar och zoonoser 2023 [surveillance of infectious diseases in animals and humans in S weden 2023] . howpublished Swedish Veterinary Agency (SVA), Uppsala, Sweden . Available at https://www.sva.se/media/3xjbzi4a/smittlaget_2023_webb_v20250410.pdf (Online; accessed 09-December-2025)

    2024

  48. [48]

    title Smittläget i S verige för djursjukdomar och zoonoser 2024 [surveillance of infectious diseases in animals and humans in S weden 2024]

    author SVA , year 2025 a. title Smittläget i S verige för djursjukdomar och zoonoser 2024 [surveillance of infectious diseases in animals and humans in S weden 2024] . howpublished Swedish Veterinary Agency (SVA), Uppsala, Sweden . Available at https://www.sva.se/media/ui4btz3d/smittlage_2024_v250616.pdf (Online; accessed 09-December-2025)

    2025

  49. [49]

    title Utveckling av nytt system för att hantera salmonella i nöt- och grisbesättningar

    author SVA , year 2025 b. title Utveckling av nytt system för att hantera salmonella i nöt- och grisbesättningar. R edovisning av myndigheternas arbete under 2024 och början av 2025. SVA :s rapportserie nr 117. SVA , 2025 [ D evelopment of a new system for managing salmonella in cattle and pig herds. R eport on the authorities' work during 2024 and early ...

    2025

  50. [50]

    , author Veling, J

    author Vaessen, M. , author Veling, J. , author Frankena, K. , author Graat, E. , author Klunder, T. , year 1998 . title Risk factors for Salmonella D ublin infection on dairy farms . journal Veterinary Quarterly volume 20 , pages 97--99 . :10.1080/01652176.1998.9694848

    work page doi:10.1080/01652176.1998.9694848 1998

  51. [51]

    , author Schukken, Y

    author Van Schaik, G. , author Schukken, Y. , author Nielen, M. , author Dijkhuizen, A. , author Barkema, H. , author Benedictus, G. , year 2002 . title Probability of and risk factors for introduction of infectious diseases into dutch spf dairy farms: a cohort study . journal Preventive veterinary medicine volume 54 , pages 279--289 . :10.1016/S0167-5877...

    work page doi:10.1016/s0167-5877(02)00004-1 2002

  52. [52]

    Bayesian Analysis , author =

    author Vehtari, A. , author Gelman, A. , author Simpson, D. , author Carpenter, B. , author Burkner, P.C. , year 2021 . title Rank-normalization, folding, and localization: An improved R for assessing convergence of MCMC . journal Bayesian analysis volume 16 , pages 667--718 . :10.1214/20-BA1221

    work page doi:10.1214/20-ba1221 2021

  53. [53]

    , author Viske, D

    author Vågsholm, I. , author Viske, D. , year 2007 . title Översyn av salmonellakontrollprogrammet - färdplan [ S almonella control program review - R oadmap], 2007:10 . howpublished Swedish Board of Agriculture, Jönköping, Sweden . Available at https://www2.jordbruksverket.se/webdav/files/SJV/trycksaker/Pdf_rapporter/ra07_10.pdf, (Online; accessed 10-Oct...

    2007

  54. [54]

    , author Str ger, U

    author Wedderkopp, A. , author Str ger, U. , author Bitsch, V. , author Lind, P. , year 2001 . title Testing of bulk tank milk for Salmonella D ublin infection in D anish dairy herds . journal Canadian Journal of Veterinary Research volume 65 , pages 15

    2001

  55. [55]

    , author Bauer, P

    author Widgren, S. , author Bauer, P. , author Eriksson, R. , author Engblom, S. , year 2019 . title SimInf : An R package for data-driven stochastic disease spread simulations . journal Journal of Statistical Software volume 91 , pages 1--42 . :10.18637/jss.v091.i12

    work page doi:10.18637/jss.v091.i12 2019

  56. [56]

    , author Bowers, R.G

    author Xiao, Y. , author Bowers, R.G. , author Clancy, D. , author French, N.P. , year 2005 . title Understanding the dynamics of Salmonella infections in dairy herds: a modelling approach . journal Journal of Theoretical Biology volume 233 , pages 159--175 . :10.1016/j.jtbi.2004.09.015

    work page doi:10.1016/j.jtbi.2004.09.015 2005

  57. [57]

    , year 2017

    author Ågren, E.C. , year 2017 . title Salmonella in S wedish cattle: epidemiology and aspects on control . Ph.D. thesis. Department of Biomedical Sciences and Veterinary Public Health, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala. note Available at https://pub.epsilon.slu.se/14155/17/agren_e_1703...

    2017

  58. [58]

    , author Johansson, J

    author Ågren, E.C. , author Johansson, J. , author Frössling, J. , author Wahlström, H. , author Emanuelson, U. , author Sternberg-Lewerin, S. , year 2015 . title Factors affecting costs for on-farm control of Salmonella in S wedish dairy herds . journal Acta Veterinaria Scandinavica volume 57 , pages 28 . :10.1186/s13028-015-0118-y

    work page doi:10.1186/s13028-015-0118-y 2015

  59. [59]

    , author Sternberg Lewerin , S

    author Ågren, E.C. , author Sternberg Lewerin , S. , author Wahlström, H. , author Emanuelson, U. , author Frössling, J. , year 2016 . title Low prevalence of Salmonella in S wedish dairy herds highlight differences between serotypes . journal Preventive Veterinary Medicine volume 125 , pages 38--45 . :10.1016/j.prevetmed.2015.12.015

    work page doi:10.1016/j.prevetmed.2015.12.015 2016