Microbiome analysis using metagenomics next-generation sequencing (mNGS) is rarely performed in patients receiving extracorporeal membrane oxygenation (ECMO). Patient body sites were swabbed within 72 hours of ECMO cannulation and weekly during ECMO course. Specimens underwent 16S sequencing to identify the microbiome along with mNGS to determine antimicrobial resistance genes. Fifty-two year old male who suffered polytraumatic injuries and developed acute respiratory syndrome was placed on veno-venous (VV) ECMO to treat severe respiratory failure. On ECMO day 1, the patient was undergoing treatment for urinary tract infection due to susceptible Pseudomonas aeruginosa (PsA). On ECMO day 22, the patient developed fulminant septic shock and tracheal aspirate and blood cultures both grew MDR PsA and Enterobacter cloacae complex (ECC) and ultimately died on day 23. There were significant microbiome and antimicrobial resistance changes that preceded sepsis on day 22, as evidenced by the increase in oral PsA colonization and expansion of resistance genes, such as KPC and OXA-50, which suggest several possible reservoirs for infection outside of the circuit. Further application of these methods is needed to understand microbiome changes in ECMO and ultimately guide infection prevention efforts.