Invasion of bacteria swimming upstream into microstructured devices

Bacteria have the remarkable ability to swim upstream, called positive rheotaxis. This motion against flow can cause not only respiratory, gastrointestinal, and urinary tract infections but also the contamination of medical devices and hospital equipment. However, it remains unknown how bacteria navigate upstream through these microstructured environments with narrow channels and wide cavities. Here, combining microbiology experiments and nanofabrication with mathematical modeling and computational fluid dynamics, we reveal how Escherichia coli invade such environments in four stages: stage I, breakout from colonized cavities against the current; stage II, propagation upstream in narrow channels; stage III, infiltration of new cavities; and stage IV, colonization with biofilms under flow. Surprisingly, we find that wider channels with faster counterflows are more prone to invasion, but this can be inhibited effectively with sharp corner designs. Next, we explore the serial invasion of multiple cavities in a row. Rather than slowly colonizing the cavities sequentially from the downstream end, bacteria rapidly swim all the way upstream and form streamer-like bioaggregates, enabling them to take possession of the entire channel three times faster. These results shed new light on pathogen motility in host-relevant shear regimes and offer solutions that can be implemented directly in biomedical devices.