Integrating microbial sequencing data into electronic health records, while presenting privacy concerns, will improve patient care and population health and will expand the secondary uses of such data.

The growing availability of microbial genomes sequenced for health care rather than research raises the question of whether such data should be included in an individual’s electronic health records (EHR). While integrating human genome data into EHR has been widely discussed1, microbial genomic data bring unique and important challenges. One challenge is that the ownership of microbial genomic data remains ambiguous. Genomics service providers, public health agencies that fund such services, and patients consider themselves as stakeholders in genomic data governance. While human DNA defines our identity, this cannot be said about the genomes of coronaviruses, Salmonella or other microorganisms. These pathogens are temporary residents, and their genomes remain the same when sampled from different humans, especially those within a transmission chain2.

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