Increasing antimicrobial resistance (AMR) poses a challenge for treatment of bacterial diseases. In real life, bacterial infections are typically embedded within complex multispecies communities and influenced by the environment, which can shape costs and benefits of AMR. However, knowledge of such interactions and their implications for AMR in vivo is limited. To address this knowledge gap, we investigated fitness-related traits of a pathogenic bacterium (Flavobacterium columnare) in its fish host, capturing the effects of bacterial antibiotic resistance, multispecies coinfections (metazoan fluke Diplostomum pseudospathaceum), and antibiotic exposure. We quantified real-time replication and virulence of sensitive and resistant bacteria and demonstrate that both bacteria can benefit from coinfection in terms of persistence and replication, depending on the coinfecting partner and antibiotic presence. We also show that antibiotics can benefit resistant bacteria by increasing bacterial replication under coinfection with flukes. These results emphasize the importance of diverse, inter-kingdom coinfection interactions and antibiotic exposure in shaping costs and benefits of AMR, supporting their role as significant contributors to the spread and long-term persistence of resistance.

This dataset comprises bacterial growth data and fish survival data.

Bacterial growth data comprises qPCR data and high-resolution melting assays (HRM) data. For qPCR data, Cq values were estimated from qPCR runs and exported as tabular files by the machine manufacturer's software (BioRad, CFX Manager Version 3.1.1517.0823). For HRM data, relative fluorescence values were measured for each plate well at different temperatures and exported as tabular files using the machine manufacturer's software (same software as for the qPCR data).

For fish survival data, fish (kept in individual tanks) were monitored for disease symptoms and morbidity at one-hour intervals. Moribund fish that had lost their natural swimming buoyancy and/or did not react to external stimuli were euthanized. The fish surviving until the end of the experiment were also euthanized. Time of death and survival until the end of the experiment (yes/no event) were recorded for each fish.

The data is provided as plain text, tab-separated tabular files. This format ensures that the data files can be read easily by most programs, for example with R.