Elongation suppresses rheotaxis and enables microfluidic enrichment of β-lactam-resistant bacteria.

Antimicrobial resistance (AMR) complicates the treatment of diseases including lung and urinary tract infections (UTIs), which are among the most common bacterial infections worldwide. Motile pathogens can use rheotaxis to swim upstream against fluid flows, potentially promoting access to upper regions of anatomical tracts. However, it remains unclear how antibiotic exposure and resistance influence this transport process. Here, using single-cell tracking microscopy, we investigate how elongation induced by β-lactam antibiotics affects the rheotactic migration of E. coli in confined microfluidic channels. Remarkably, we find that rheotaxis can be inhibited 100-fold by antibiotics, even if the susceptible elongated cells remain fully motile. However, resistant bacteria remain short and retain upstream migration under the same conditions. Using genetically engineered bacteria with tunable cell length, we show that the underlying mechanism that governs rheotaxis is the coupling between cell morphology and flow vorticity, where elongated cells are rapidly rotated downstream. Finally, we exploit this length-dependent transport difference to separate short and elongated cells under flow and enrich ampicillin-resistant cells from mixed populations. Together, these results establish bacterial elongation as a key control parameter for rheotactic transport, and provide a proof-of-concept strategy for enriching β-lactam-resistant bacteria for potential use in rapid AMR detection.