Invasion of Bacteria Swimming Upstream in Structured Microchannels*

Bacteria can swim upstream in narrow channels, causing the contamination of biomedical devices and urinary tract infections (UTIs). Despite these implications for human health, this reorientation against flows remains underexplored in structured environments. Here, we investigate experimentally and theoretically how E. coli bacteria invade microfluidic channels with different architectures. By tracking single cells under different flow conditions, we reveal the three-stage dynamics of bacterial invasion: entering microchannels, propagating upstream, and escaping to enter the next one. Our results show how the channel size and shape significantly influence each of these contamination stages. Additionally, we explore how these processes affect bacterial collective motion and biofilm formation upstream. Our research guides the design of anti-invasion strategies for biomedical devices and sets the foundation for understanding microbial navigation in environmental flow networks.