Alderliesten, J. B., Zwart, M. P., de Visser, J. A. G. M., Stegeman, A., & Fischer, E. A. J. (2026). The effects of ecological interactions and distinct conjugation rates on the invasion of a conjugative plasmid in bacterial communities. Ecological Modelling, 512, Article 111418. [DOI] [Portal]

Tubay, J. M., Fischer, E. A. J., Meester, M., Tobias, T., & Stegeman, A. (2025). HogDSim - A within-farm modeling framework for infectious diseases of swine. Smart Agricultural Technology, 12, Article 101652. [DOI] [Portal]

Meester, M., Valenzuela Agüí, C., Tobias, T. J., Hakze-van der Honing, R. W., Guinat, C., Bouwknegt, M., du Plessis, L., Fischer, E. A. J., Spaninks, M., Stadler, T., van der Poel, W. H. M., & Stegeman, A. (2025). Zoonotic hepatitis E virus spreads through environmental routes in pig herds-A phylodynamic analysis. PLoS Pathogens, 21(11 November), Article e1013710. [DOI] [Portal]

Van Der Roest, B., Fischer, E. A. J., Klinkenberg, D., Bootsma, M. C. J., Maticic, M., Resman-Rus, K., Korva, M., Avsic-Zupanc, T., & Kretzschmar, M. (2025). Phylodynamic inference suggests introductions as main driver of Mpox Clade II outbreak in 2022 in Slovenia. Epidemiology and Infection, 153. [DOI] [Portal]

Antonopoulos, A., Ciria, N., Regan, Á., Tubay, J., Ciaravino, G., Hayes, B., Lambert, S., Vergne, T., Velkers, F., Biebaut, E., Viltrop, A., Dewulf, J., Charlier, J., Fischer, E., & Palau, A. A. (2025). PARAMETRA: A transmission modelling database for livestock diseases. Preventive Veterinary Medicine, 245, Article 106668. [DOI] [Portal]

Van der Roest, B. R., Bootsma, M. C. J., Fischer, E. A. J., Gröschel, M. I., Anthony, R. M., de Zwaan, R., Kretzschmar, M. E. E., & Klinkenberg, D. (2025). Phylodynamic assessment of SNP distances from whole genome sequencing for determining Mycobacterium tuberculosis transmission. Scientific Reports, 15(1), Article 10694. [DOI] [Portal]

Dórea, F. C., Correia-Gomes, C., Carmo, L. P., Fischer, E. A. J., Messam, L. L. M. V., Schulz, K., Vergne, T., & Brodbelt, D. C. (2025). SVEPM 2024, the annual conference of the Society for Veterinary Epidemiology and Preventive Medicine, Uppsala, Sweden. Preventive Veterinary Medicine, Article 106458. [DOI] [Portal]

Brimer, S. K., Fischer, E. A. J., Beckstead, R., White, J., Cazaban, C., Tatár-Kis, T., Velkers, F. C., Elattrache, J., & Stegeman, A. (2025). A vaccine programme comprising GA08 (GI-27) and Mass (GI-1) strains prevents DMV1639 (GI-17) infectious bronchitis virus transmission among broiler chickens. Avian Pathology, 54(1), 83-95. [DOI] [Portal]

Dankittipong, N., Stegeman, J. A., de Vos, C. J., Wagenaar, J. A., & Fischer, E. A. J. (2024). Investigating a propagation of emerging carbapenemase-producing Enterobacteriaceae in Dutch broiler production pyramid through stochastic simulation. One Health, 19, Article 100945. [DOI] [Portal]

Chanchaidechachai, T., Fischer, E. A. J., Saatkamp, H. W., de Jong, M. C. M., & Hogeveen, H. (2024). One-size measures do not fit all areas: Evaluation of area-specific control of foot and mouth disease in Thailand using bioeconomic modelling. Preventive Veterinary Medicine, 233, Article 106359. [DOI] [Portal]

Swinkels, A. F., Fischer, E. A. J., Korving, L., Kusters, N. E., Wagenaar, J. A., & Zomer, A. L. (2024). Selection for amoxicillin-, doxycycline-, and enrofloxacin-resistant Escherichia coli at concentrations lower than the ECOFF in broiler-derived cecal fermentations. Microbiology spectrum, 12(10), Article e0097024. [DOI] [Portal]

Swinkels, A. F., Berendsen, B. J. A., Fischer, E. A. J., Zomer, A. L., & Wagenaar, J. A. (2024). Extended period of selection for antimicrobial resistance due to recirculation of persistent antimicrobials in broilers. Journal of Antimicrobial Chemotherapy, 79(9), 2186-2193. Article dkae213. [DOI] [Portal]

Dórea, F. C., Vergne, T., Correia-Gomes, C., Carmo, L. P., Fischer, E. A. J., Messam, L. L. M. V., Brodbelt, D. C., & Robinson, P. A. (2024). SVEPM 2023, the annual conference of the Society for Veterinary Epidemiology and Preventive Medicine: Toulouse finally welcomes us in person. Preventive Veterinary Medicine, 226, Article 106174. [DOI] [Repository]

Dankittipong, N., Broek, J. V. D., de Vos, C. J., Wagenaar, J. A., Stegeman, J. A., & Fischer, E. A. J. (2024). Transmission rates of veterinary and clinically important antibiotic resistant Escherichia coli: A meta- ANALYSIS. Preventive Veterinary Medicine, 225, Article 106156. [DOI] [Repository]

Furusawa, M., Widgren, S., Evers, E. G., & Fischer, E. A. J. (2024). Quantifying health risks from ESBL-producing Escherichia coli in Dutch broiler production chains and potential interventions using compartmental models. Preventive Veterinary Medicine, 224, Article 106121. [DOI] [Repository]

Van der Roest, B. R., Bootsma, M. C. J., Fischer, E. A. J., Klinkenberg, D., & Kretzschmar, M. E. E. (2023). A Bayesian inference method to estimate transmission trees with multiple introductions: applied to SARS-CoV-2 in Dutch mink farms. PLoS Computational Biology, 19(11), Article e1010928. [DOI] [Repository]

Chanchaidechachai, T., Saatkamp, H. W., Hogeveen, H., de Jong, M. C. M., & Fischer, E. A. J. (2023). Evaluation of foot and mouth disease control measures: Simulating two endemic areas of Thailand. Preventive Veterinary Medicine, 220, Article 106045. [DOI] [Repository]

Dankittipong, N., Alderliesten, J. B., Van den Broek, J., Dame-Korevaar, M. A., Brouwer, M. S. M., Velkers, F. C., Bossers, A., de Vos, C. J., Wagenaar, J. A., Stegeman, J. A., & Fischer, E. A. J. (2023). Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens. Preventive Veterinary Medicine, 219, 1-13. Article 105998. [DOI] [Repository]

Fischer, E. A. J., Broens, E. M., Kooistra, H. S., De Rooij, M. M. T., Stegeman, J. A., & De Jong, M. C. M. (2023). Contribution of cats and dogs to SARS-CoV-2 transmission in households. Frontiers in Veterinary Science, 10, Article 1151772. [DOI] [Repository]

Dórea, F. C., Vergne, T., Correia-Gomes, C., Carmo, L. P., Fischer, E. A. J., Brodbelt, D. C., Robinson, P. A., & van Schaik, G. (2023). SVEPM 2022, the annual conference of the Society for Veterinary Epidemiology and Preventive Medicine: A joyful hybrid meeting after two years online. Preventive Veterinary Medicine, 215, Article 105927. [DOI] [Repository]

Huisman, J. S., Benz, F., Duxbury, S. J. N., de Visser, J. A. G. M., Hall, A. R., Fischer, E. A. J., & Bonhoeffer, S. (2022). Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods. Plasmid, 121, 1-12. Article 102627. [DOI] [Repository]

Kers, J. G., Velkers, F. C., Fischer, E. A. J., Stegeman, J. A., Smidt, H., & Hermes, G. D. A. (2022). Conserved developmental trajectories of the cecal microbiota of broiler chickens in a field study. FEMS Microbiology Ecology, 98(9), 1-11. Article fiac090. [DOI] [Repository]

Dankittipong, N., Fischer, E. A. J., Swanenburg, M., Wagenaar, J. A., Stegeman, A. J., & De Vos, C. J. (2022). Quantitative Risk Assessment for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms. Antibiotics, 11(2), 1-29. Article 281. [DOI] [Repository]

Alderliesten, J. B., Zwart, M. P., de Visser, J. A. G. M., Stegeman, A., & Fischer, E. A. J. (2022). Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut. Journal of Theoretical Biology, 533, 1-11. Article 110937. [DOI] [Repository]

van Aart, A. E., Velkers, F. C., Fischer, E. A. J., Broens, E. M., Egberink, H., Zhao, S., Engelsma, M., Hakze-van der Honing, R. W., Harders, F., de Rooij, M. M. T., Radstake, C., Meijer, P. A., Munnink, B. B. O., de Rond, J., Sikkema, R. S., van der Spek, A. N., Spierenburg, M., Wolters, W. J., Molenaar, R.-J., ... Smit, L. A. M. (2022). SARS-CoV-2 infection in cats and dogs in infected mink farms. Transboundary and emerging diseases, 69(5), 3001-3007. [DOI] [Repository]

Chanchaidechachai, T., de Jong, M. C. M., & Fischer, E. A. J. (2021). Spatial model of foot-and-mouth disease outbreak in an endemic area of Thailand. Preventive Veterinary Medicine, 195, 1-10. Article 105468. [DOI] [Repository]

de Vos, C. J., Hennen, W. H. G. J., van Roermund, H. J. W., Dhollander, S., Fischer, E. A. J., & de Koeijer, A. A. (2021). Assessing the introduction risk of vector-borne animal diseases for the Netherlands using MINTRISK: A Model for INTegrated RISK assessment. PLoS One, 16(November), Article e0259466. [DOI]

Lu, L., Sikkema, R. S., Velkers, F. C., Nieuwenhuijse, D. F., Fischer, E. A. J., Meijer, P. A., Bouwmeester-Vincken, N., Rietveld, A., Wegdam-Blans, M. C. A., Tolsma, P., Koppelman, M., Smit, L. A. M., Hakze-van der Honing, R. W., van der Poel, W. H. M., van der Spek, A. N., Spierenburg, M. A. H., Molenaar, R. J., Rond, J. D., Augustijn, M., ... Koopmans, M. P. G. (2021). Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands. Nature Communications, 12(1), 1-12. Article 6802. [DOI] [Repository]

Duxbury, S. J. N., Alderliesten, J. B., Zwart, M. P., Stegeman, A., Fischer, E. A. J., & de Visser, J. A. G. M. (2021). Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli. Proceedings. Biological sciences, 288(1962), 1-8. Article 20212027. [DOI] [Repository]

Deng, Z., Koop, G., Hogeveen, H., Fischer, E. A. J., van den Borne, B. H. P., van der Tol, R., & Lam, T. J. G. M. (2021). Transmission dynamics of Staphylococcus aureus and Streptococcus agalactiae in a Dutch dairy herd using an automatic milking system. Preventive Veterinary Medicine, 192, Article 105384. [DOI] [Repository]

Dame-Korevaar, A., Kers, J. G., van der Goot, J., Velkers, F. C., Ceccarelli, D., Mevius, D. J., Stegeman, A., & Fischer, E. A. J. (2020). Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers. Frontiers in Microbiology, 11, Article 566619. [DOI] [Repository]

Tatár-Kis, T., Fischer, E. A. J., Cazaban, C., Walkó-Kovács, E., Homonnay, Z. G., Velkers, F. C., Palya, V., & Stegeman, J. A. (2020). A herpesvirus of Turkey-based vector vaccine reduces transmission of newcastle disease virus in commercial broiler chickens with maternally derived antibodies. Vaccines, 8(4), Article 614. [DOI] [Repository]

Kers, J. G., Fischer, E. A. J., de Oliveira , J., Tersteeg - Zijderveld, M., Kostanti, P., Stegeman, J. A., Smidt, H., & Velkers, F. C. (2020). Associations between phenotypic characteristics and clinical parameters of broilers and intestinal microbial development throughout a production cycle: a field study. MicrobiologyOpen, 9(11), Article e1114. [DOI] [Portal]

Alderliesten, J. B., Duxbury, S. J. N., Zwart, M. P., de Visser, J. A. G. M., Stegeman, A., & Fischer, E. A. J. (2020). Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis. BMC Microbiology, 20(1), Article 135. [DOI] [Repository]

Korevaar, M. A., Fischer, E. A. J., van der Goot, J., Velkers, F. C., Ceccarelli, D., Mevius, D. J., & Stegeman, J. A. (2020). Early life supply of competitive exclusion products reduces colonization of Extended Spectrum Beta-Lactamase producing Escherichia coli in broilers. Poultry Science, 99(8), 4052-4064. [DOI] [Repository]

Sok, J., & Fischer, E. A. J. (2020). Farmers’ heterogeneous motives, voluntary vaccination and disease spread: an agent-based model. European Review of Agricultural Economics, 47(3), 1201-1222. [DOI] [Portal]

Fischer, E. A., Dierikx, C., van Essen-Zandbergen, A., Mevius, D., Stegeman, A., Velkers, F., & Klinkenberg, D. (2019). Competition between Escherichia coli with and without Extended-Spectrum-Beta-Lactamase-carrying plasmids in the broiler chicken gut. Applied and Environmental Microbiology, 85(17), e00892. https://www.mendeley.com/catalogue/8408e9b7-1dfc-3451-93af-57322bd283eb/

Kers, J. G., Fischer, E. A. J., Stegeman, J. A., Smidt, H., & Velkers, F. C. (2019). Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens. Microorganisms, 7(10). [DOI] [Repository]

Dame-Korevaar, A., Fischer, E. A. J., van der Goot, J., Velkers, F., van den Broek, J., Veldman, K., Ceccarelli, D., Mevius, D., & Stegeman, A. (2019). Effect of challenge dose of plasmid-mediated extended-spectrum β-lactamase and AmpC β-lactamase producing Escherichia coli on time-until-colonization and level of excretion in young broilers. Veterinary Microbiology, 239, Article 108446. [DOI] [Repository]

Fischer, E. A. J., Dierikx, C. M., van Essen-Zandbergen, A., Mevius, D., Stegeman, A., Velkers, F. C., & Klinkenberg, D. (2019). Competition between Escherichia coli populations with and without plasmids carrying a gene encoding extendedspectrum beta-lactamase in the broiler chicken gut. Applied and Environmental Microbiology, 85(17), Article e00892. [DOI] [Repository]

Kers, J. G., Velkers, F. C., Fischer, E. A. J., Hermes, G. D. A., Lamot, D. M., Stegeman, J. A., & Smidt, H. (2019). Take care of the environment: housing conditions affect the interplay of nutritional interventions and intestinal microbiota in broiler chickens. Animal Microbiome, 1(1), Article 10. [DOI] [Repository]

Hordijk, J., Fischer, E. A. J., van Werven, T., Sietsma, S., Van Gompel, L., Timmerman, A. J., Spaninks, M. P., Heederik, D. J. J., Nielen, M., Wagenaar, J. A., & Stegeman, A. (2019). Dynamics of faecal shedding of ESBL- or AmpC-producing Escherichia coli on dairy farms. Journal of Antimicrobial Chemotherapy, 74(6), 1531-1538. [DOI] [Repository]

Dame-Korevaar, A., Fischer, E. A. J., van der Goot, J., Stegeman, A., & Mevius, D. (2019). Transmission routes of ESBL/pAmpC producing bacteria in the broiler production pyramid, a literature review. Preventive Veterinary Medicine, 162, 136-150. [DOI] [Repository]

Kers, J. G., Velkers, F. C., Fischer, E. A. J., Hermes, G., Stegeman, J. A., & Smidt, H. (2018). Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens. Frontiers in Microbiology, 9, Article 235. [DOI] [Repository]

Ceccarelli, D., van Essen-Zandbergen, A., Smid, B., Veldman, K. T., Boender, G. J., Fischer, E. A. J., Mevius, D. J., & van der Goot, J. A. (2017). Competitive Exclusion Reduces Transmission and Excretion of Extended-Spectrum-β-Lactamase-Producing Escherichia coli in Broilers. Applied and Environmental Microbiology, 83(11). [DOI] [Portal]

Dame-Korevaar, A., Fischer, E. A. J., Stegeman, A., Mevius, D., van Essen-Zandbergen, A., Velkers, F., & van der Goot, J. (2017). Dynamics of CMY-2 producing E. coli in a broiler parent flock. Veterinary Microbiology, 203, 211-214. [DOI] [Repository]

Faverjon, C., Leblond, A., Lecollinet, S., Bødker, R., de Koeijer, A. A., & Fischer, E. A. J. (2017). Comparative Risk Analysis of Two Culicoides-Borne Diseases in Horses: Equine Encephalosis More Likely to Enter France than African Horse Sickness. Transboundary and Emerging Diseases, 64(6), 1825-1836. [DOI] [Portal]

Hagenaars, T. J., Fischer, E. A. J., Jansen, C. A., Rebel, J. M. J., Spekreijse, D., Vervelde, L., Backer, J. A., de Jong, M. C. M., & Koets, A. P. (2016). Modelling the Innate Immune Response against Avian Influenza Virus in Chicken. PLoS One, 11(6), Article e0157816. [DOI] [Repository]

Fischer, E. A. J., Martínez López, E. P., De Vos, C., & Faverjon, C. (2016). Quantitative analysis of the probability of introducing equine encephalosis virus (EEV) into The Netherlands. Preventive Veterinary Medicine, 131, 48-59. [DOI] [Repository]

Backer, J. A., van Roermund, H. J. W., Fischer, E., van Asseldonk, M. A. P. M., & Bergevoet, R. H. M. (2015). Controlling highly pathogenic avian influenza outbreaks: An epidemiological and economic model analysis. Preventive Veterinary Medicine, 142-150. [DOI] [Repository]

Faverjon, C., Leblond, A., Hendrikx, P., Balenghien, T., de Vos, C., Fischer, E., & de Koeijer, A. A. (2015). A spatiotemporal model to assess the introduction risk of African horse sickness by import of animals and vectors in France. BMC Veterinary Research, 11(1), Article 127. [DOI]

Blok, D. J., de Vlas, S. J., Fischer, E. A. J., & Richardus, J. H. (2015). Mathematical Modelling of Leprosy and Its Control. Advances in Parasitology, 87, 33-51. [DOI]

Fischer, E. A. J., Dierikx, C. M., Van Essen-Zandbergen, A., Van Roermund, H. J. W., Mevius, D. J., Stegeman, A., & Klinkenberg, D. (2014). The IncI1 plasmid carrying the bla _CTX-M-1 gene persists in in vitro culture of a Escherichia coli strain from broilers. BMC Microbiology [E], 14(1), Article 14:77. [DOI]

Fischer, E. A., Boender, G. J., Nodelijk, G., De Koeijer, A. A., & Van Roermund, H. J. (2013). The transmission potential of Rift Valley fever virus among livestock in the Netherlands: A modelling study. Veterinary Research, 44(1), Article 58. [DOI]

Döpfer, D., Geue, L., Schares, S., Mintel, B., Hoffmann, B., & Fischer, E. A. J. (2012). Dynamics of shiga-toxin producing Escherichia coli (STEC) and their virulence factors in cattle. Preventive Veterinary Medicine, 103(1), 22-30. [DOI]

Boender, G. J., de Koeijer, A. A., & Fischer, E. A. J. (2012). Derivation of a Floquet Formalism within a Natural Framework. Acta Biotheoretica, 60(3), 303-317. [DOI]

Fischer, E. A. J., de Vlas, S. J., Habbema, J. D. F., & Richardus, J. H. (2011). The long term effect of current and new interventions on the new case detection of leprosy: A modeling study. PLoS Neglected Tropical Diseases, 5(9), Article e1330. [DOI]

Fischer, E., Vlas, D. S., Meima, A., Habbema, D., & Richardus, J. (2010). Different mechanisms for heterogeneity in leprosy susceptibility can explain disease clustering within households. PLoS One, 5(11), Article e14061. [DOI]

Fischer, E. A. J., Pahan, D., Chowdhury, S. K., & Richardus, J. H. (2008). The spatial distribution of leprosy cases during 15 years of a leprosy control program in Bangladesh: An observational study. BMC Infectious Diseases, 8, Article 126. [DOI]

Fischer, E. A. J., De Vlas, S. J., Richardus, J. H., & Habbema, J. D. F. (2008). MUSIDH, multiple use of simulated demographic histories, a novel method to reduce computation time in microsimulation models of infectious diseases. Computer Methods and Programs in Biomedicine, 91(3), 185-190. [DOI]

Hoeven, T. A., Fischer, E. A. J., Pahan, D., & Richardus, J. H. (2008). Social distance and spatial distance are not the same, observations on the use of GIS in leprosy epidemiology. Epidemiology and Infection, 136(12), 1624-1627. [DOI]

Fischer, E. A. J., Pahan, D., Chowdhury, S. K., Oskam, L., & Richardus, J. H. (2008). The spatial distribution of leprosy in four villages in Bangladesh: An observational study. BMC Infectious Diseases, 8, Article 125. [DOI]

Van Asseldonk, M. A. P. M., Van Roermund, H. J. W., Fischer, E. A. J., De Jong, M. C. M., & Huirne, R. B. M. (2005). Stochastic efficiency analysis of bovine tuberculosis-surveillance programs in the Netherlands. Preventive Veterinary Medicine, 69(1-2), 39-52. [DOI]

Fischer, E. A. J., Van Roermund, H. J. W., Hemerik, L., Van Asseldonk, M. A. P. M., & De Jong, M. C. M. (2005). Evaluation of surveillance strategies for bovine tuberculosis (Mycobacterium bovis) using an individual based epidemiological model. Preventive Veterinary Medicine, 67(4), 283-301. [DOI]