A data-driven within-host model reveals that different antibiotics are associated with divergent effects on antibiotic resistance carriage and abundance in hospitalised patients, with important implications for antibiotic stewardship.

Bats' uniquely robust innate antiviral immune defenses select for faster transmitting viruses likely to generate extreme virulence upon spillover to secondary hosts with immune systems divergent from those of bat.

With a data-driven mathematical modelling approach, within-host ecological information alone can provide clues on the mechanistic basis of diverse malaria infection outcomes.

Mathematical models of the build-up and depletion of the hypnozoite reservoir in the liver can inform the design of treatment strategies for preventing Plasmodium vivax relapse infections.

An individual-based model estimates exogenous boosting of immunity following re-exposure to chickenpox is limited to 2 years after re-exposure, but an increase in herpes zoster incidence is still expected to occur following universal varicella vaccination.

A novel mathematical modeling framework for antibiotic-resistant bacteria combining within-host microbiome-pathogen interactions with population-level pathogen epidemiology, demonstrating how antibiotic consumption and ecological competition come together to drive the spread of resistance.

The use of within-host pathogen genomic sequence data can be used to improve phylogenetic and transmission estimates.

An analysis of influenza viruses from naturally infected people suggests a tight transmission bottleneck and little positive selection within hosts.

Despite the virus' error prone polymerase, influenza virus antigenic evolution is rare, even in previously immune hosts, virus replication occurs before producing new antibodies.

Specialized fungal pathogen populations infect rice varieties with contrasting immune systems co-cultivated in a traditional agro-system, indicating the relevance of crop diversity to restricting epidemics in the landscape.