biostudies-literatureUnknown7(9)Lees JAEMBL | European Bioinformatics InstituteIn this review, we assess the status of computational modelling of pathogens. We focus on three disparate but interlinked research areas that produce models with very different spatial and temporal scope. First, we examine antimicrobial resistance (AMR). Many mechanisms of AMR are not well understood. As a result, it is hard to measure the current incidence of AMR, predict the future incidence, and design strategies to preserve existing antibiotic effectiveness. Next, we look at how to choose the finite number of bacterial strains that can be included in a vaccine. To do this, we need to understand what happens to vaccine and non-vaccine strains after vaccination programmes. Finally, we look at within-host modelling of antibody dynamics. The SARS-CoV-2 pandemic produced huge amounts of antLife science alliancee202402666https://www.ebi.ac.uk/biostudies/studies/S-EPMC11192964biostudies-literatureRecent approaches in computational modelling for controlling pathogen threats.PMC11192964Hellewell JShaw LPLees JARussell TWfalseRecent approaches in computational modelling for controlling pathogen threats.In this review, we assess the status of computational modelling of pathogens. We focus on three disparate but interlinked research areas that produce models with very different spatial and temporal scope. First, we examine antimicrobial resistance (AMR). Many mechanisms of AMR are not well understood. As a result, it is hard to measure the current incidence of AMR, predict the future incidence, and design strategies to preserve existing antibiotic effectiveness. Next, we look at how to choose the finite number of bacterial strains that can be included in a vaccine. To do this, we need to understand what happens to vaccine and non-vaccine strains after vaccination programmes. Finally, we look at within-host modelling of antibody dynamics. The SARS-CoV-2 pandemic produced huge amounts of ant2024-01-01T00:00:00Z2024 Sep2025-04-04T12:47:49.641Z2025-04-04T12:47:49.641ZS-EPMC111929643890667610.26508/lsa.202402666