Aptamer-Functionalized Magnetic Nanoparticles for Rapid Isolation of Environmental Escherichia coli

Access to safe water remains a vital public health challenge, especially in low- and middle-income countries like Colombia, where untreated sources lead to severe diarrheal diseases in children under five. Escherichia coli (E. coli), a key indicator of fecal contamination, is often detected using culture-based methods that are time-consuming and rely on specialized infrastructure. To overcome these limitations, we developed an aptamer-based isolation system targeting environmental E. coli. Aptamers were obtained using a Cell-SELEX protocol, and after six enrichment rounds, two candidates—APT-EC-1 and its truncated version APT-EC-MUT—were synthesized and attached to carboxyl-functionalized magnetic nanoparticles (MNP-COOH). Both complexes demonstrated a strong binding affinity and high specificity, successfully isolating E. coli from environmental and ATCC reference strains in the laboratory. Sensitivity tests detected E. coli at dilutions up to 1:10,000, showing reliable performance. In early in-field testing with environmental water samples, APT-EC-1 consistently identified E. coli colonies, while APT-EC-MUT struggled with low bacterial levels, illustrating performance differences. These findings demonstrate the promise of aptamer-functionalized MNPs as the basis for quick, affordable, and portable biosensors for water quality testing, especially in resource-scarce areas. Future efforts will add colorimetric or electrochemical readouts to allow real-time, on-site detection of fecal contamination.