Time-resolved bottleneck analysis in bacterial infection dynamics

Within-host pathogen dynamics can be difficult to track, involving pathogen expansions and restrictions by host barriers bottlenecks, ultimately determining the outcome of the infection. We use a neutral barcoding approach to monitor the root entry bottleneck during infections of tomato plants Solanum lycopersicum by the bacterial phytopathogen Ralstonia pseudosolanacearum . In our context, classical bottleneck analyses frameworks showed to be poorly accurate. By investigating data with novel bottleneck models, we conclude that the overlooked time dimension is crucial to understand root colonisation but also allows the resolution of previously inaccessible infection metrics. We define a new type of “time-resolved” bottlenecks describing infection scenarios where entry of pathogen occurs continuously with growth of pathogen in the host. Application of the “time-resolved” bottleneck framework to two published animal infection datasets confirms that it is not host-specific but may provide new conceptual understanding to many experimental studies that assumed bottlenecks to be instantaneous.