Surveillance Readiness Audit: Completeness of Surveillance-Critical Metadata in U.S. Clinical Pathogen Genomes, 2015 to 2026

A pathogen genome supports early outbreak detection only when it is deposited with basic context: when and where the sample was collected, its source and host, whether it came from a patient, and, for resistance surveillance, its antimicrobial susceptibility. NCBI Pathogen Detection integrates the national public record of bacterial and fungal pathogen genomes, but the completeness of this context has not been measured routinely across organisms. This paper describes the Surveillance Readiness Audit v1.0.0, an open, reproducible audit of six surveillance-critical metadata fields (collection date precision, state geography, isolation source, host, epi type and antimicrobial susceptibility testing (AST) availability) for every U.S. isolate in 107 organism groups, stratified by organism, year added and submitter type. The v1.0.0 build, from NCBI data retrieved on 14 October 2026, covers 1,239,575 U.S. isolates added from 2015 to 2026, of which 911,265 (73.5%) are clinical. Only 13.4% of clinical isolates record a state, compared with 84.8% of environmental isolates, and only 6.1% carry all five core fields; 0.8% carry AST results. Year-only collection dates rose from 17.0% of clinical isolates added in 2022 to 69.2% of those added in 2024. Submissions owned by federal agencies account for 83.8% of clinical isolates, and 2.7% of them record a state. The gaps that most limit early detection from the public record are therefore geography and date precision in a small number of high-volume network programs, and susceptibility data everywhere.