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. Advance online publication. https://doi.org/10.1016/j.prevetmed.2024.106121
https://dspace.library.uu.nl/bitstream/handle/1874/435930/1-s2.0-S0167587724000072-main.pdf?sequence=1

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. https://doi.org/10.1371/journal.pcbi.1010928
https://dspace.library.uu.nl/bitstream/handle/1874/435929/journal.pcbi.1010928_1_.pdf?sequence=1

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. https://doi.org/10.1016/j.prevetmed.2023.106045
https://dspace.library.uu.nl/bitstream/handle/1874/435928/1-s2.0-S016758772300209X-main.pdf?sequence=1

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. https://doi.org/10.1016/j.prevetmed.2023.105998

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. https://doi.org/10.3389/fvets.2023.1151772

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. https://doi.org/10.1016/j.prevetmed.2023.105927
https://dspace.library.uu.nl/bitstream/handle/1874/428657/1_s2.0_S0167587723000910_main.pdf?sequence=1

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. https://doi.org/10.1016/j.plasmid.2022.102627

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. https://doi.org/10.1093/femsec/fiac090

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. https://doi.org/10.3390/antibiotics11020281

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. https://doi.org/10.1016/j.jtbi.2021.110937

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. https://doi.org/10.1111/tbed.14173

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. https://doi.org/10.1016/j.prevetmed.2021.105468

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. https://doi.org/10.1371/journal.pone.0259466

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. https://doi.org/10.1038/s41467-021-27096-9

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. https://doi.org/10.1098/rspb.2021.2027

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. https://doi.org/10.1016/j.prevetmed.2021.105384

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. https://doi.org/10.3389/fmicb.2020.566619

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. https://doi.org/10.3390/vaccines8040614

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. https://doi.org/10.1002/mbo3.1114

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. https://doi.org/10.1186/s12866-020-01825-4

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. https://doi.org/10.1016/j.psj.2020.04.025

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/

Sok, J., & Fischer, E. A. J. (2019). Farmers’ heterogeneous motives, voluntary vaccination and disease spread: an agent-based model. European Review of Agricultural Economics. https://doi.org/10.1093/erae/jbz041

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). https://doi.org/10.3390/microorganisms7100431

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. https://doi.org/10.1016/j.vetmic.2019.108446

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. https://doi.org/10.1128/AEM.00892-19
https://dspace.library.uu.nl/bitstream/handle/1874/386571/Applied_and_Environmental_Microbiology_2019_Fischer_e00892_19.full.pdf?sequence=1

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. https://doi.org/10.1186/s42523-019-0009-z

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. https://doi.org/10.1093/jac/dkz035

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. https://doi.org/10.1016/j.prevetmed.2018.12.002
https://dspace.library.uu.nl/bitstream/handle/1874/377898/1_s2.0_S0167587718304720_main.pdf?sequence=1

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. https://doi.org/10.3389/fmicb.2018.00235

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). https://doi.org/10.1128/AEM.03439-16

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. https://doi.org/10.1016/j.vetmic.2017.03.024

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. https://doi.org/10.1111/tbed.12577

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. https://doi.org/10.1371/journal.pone.0157816

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. https://doi.org/10.1016/j.prevetmed.2016.07.005

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. https://doi.org/10.1016/j.prevetmed.2015.06.006

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. https://doi.org/10.1186/s12917-015-0435-4

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. https://doi.org/10.1016/bs.apar.2014.12.002

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. https://doi.org/10.1186/1471-2180-14-77

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. https://doi.org/10.1186/1297-9716-44-58

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. https://doi.org/10.1016/j.prevetmed.2011.08.007

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. https://doi.org/10.1007/s10441-012-9162-4

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. https://doi.org/10.1371/journal.pntd.0001330

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. https://doi.org/10.1371/journal.pone.0014061

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. https://doi.org/10.1186/1471-2334-8-126

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. https://doi.org/10.1016/j.cmpb.2008.04.004

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. https://doi.org/10.1017/S0950268808000381

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. https://doi.org/10.1186/1471-2334-8-125

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. https://doi.org/10.1016/j.prevetmed.2005.01.012

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. https://doi.org/10.1016/j.prevetmed.2004.12.002