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Foot wounds are the most common diabetes-related cause of hospitalization and frequently result in amputation. Although generally diagnosed clinically based on signs and symptoms of inflammation, empirical antibiotic treatment should be based on tissue cultures until resolution of infection. Advances in molecular detection over the past decade, including rapid chromogenic agar and real-time polymerase chain reaction, have improved diagnostic capabilities. However, chronic wounds may host biofilm bacteria not adequately detected by current microbiological testing. Enhanced DNA testing is required to identify these pathogens as well as evolving and previously underdiagnosed bacteria. Two options, nucleic acid fluorescent in situ hybridization and rDNA sequencing, are on the horizon for clinical use. Wound biofilms also necessitate more complex clinical management including debridement, augmenting host defenses, suppression of biofilms, and wound closure. Adopting these advances in diagnosis and treatment may help with overall prognosis and reduce health care costs.