Carbapenemase-producing Gram-negative bacteria are among the most urgent antimicrobial resistance threats in the United States, and public health lab-oratories increasingly characterize them by whole-genome sequencing. The NCBI Pathogen Detection project screens every public genome in its scope with AMRFinderPlus, but its outputs are organized by organism group and release rather than by place and time, and sample metadata are free text. This paper describes the US Carbapenemase Genomic Panel v1.0.0, an open, versioned ta-ble of five carbapenemase families (KPC, NDM, OXA-48-like, VIM and IMP) in public U.S. genomes of Klebsiella, Escherichia coli, Enterobacter, Acinetobacter and Pseudomonas aeruginosa, tabulated by state, collection year, organism and harmonized isolation source (clinical, screening, environmental, unknown). Fam-ily membership follows the AMRFinderPlus Reference Gene Hierarchy, and every harmonization decision is published with the data. The v1.0.0 build, from NCBI data retrieved on 12 October 2026, covers 257,965 genomes, of which 38,511 (14.9%) carry at least one of the five families. NDM-carrying genomes (17,736) now outnumber KPC-carrying genomes (16,911), and NDM has exceeded KPC in every complete collection year since 2021. A state could be assigned to only 34.3% of carbapenemase-positive genomes; 90.2% of the remainder come from a single CDC BioProject (HAI-Seq Gram-negative bacteria) that records country only. The panel therefore supports national trend description and state-level description of the located public record, but not comparison of burden between states. The scripted pipeline is designed for annual refresh, with each version archived under a stable concept DOI.

In 1928, Alexander Fleming accidentally discovered penicillin, which was followed by the subsequent work of Sir Howard Florey and Ernst Chain in the early 1940s. The golden age of infectious disease management had just begun, or so it was taught. However, this triumph was short-lived; within a few years, the first resistant organism was isolated. That initial resistance has snowballed, leading to an annual record of 35,000 deaths in the USA and a global death toll of 1.27 million in 2019. By 2050, the world may face an additional US$1 trillion in healthcare costs. Microbial organisms seem to be outpacing researchers; their intrinsic and acquired ability to evade drugs that once killed or inactivated them is alarming, placing global health institutions and scientists under immense pressure. The way forward requires a shift in approach. Timely and accurate diagnosis of AMR organisms is a critical component. Developing rapid diagnostic test kits will enable real-time infection control decisions to prevent community spread, while the continuous advancement of vaccines will foster herd immunity. Stricter policies to eliminate over-the-counter and unauthorized purchases of antimicrobial agents are necessary to mitigate this “unfolding pandemic.” Furthermore, as antimicrobial use in agriculture rises globally, concerted efforts must be made to control this practice, as AMR organisms are evidently transferred from animals to humans. In conclusion, combining the social determinants of health with a biomedical approach is the best path forward; until all nations are protected, no nation is truly safe. Sustained advocacy regarding the dangers of antimicrobial abuse, alongside research into rapid diagnostic kits and vaccines, is essential to mitigate these growing threats.

Public genomic and wastewater surveillance data for highly pathogenic avian influenza A(H5N1) in the United States are open, large, and held in systems that do not speak to one another. We describe H5N1 Marker Watch, an open dataset that tabulates published antiviral-resistance and mammalian-adaptation marker positions in publicly deposited U.S. A(H5N1) protein sequences by state, collection year and host group, and places those counts alongside CDC National Wastewater Surveillance System H5 detections for the same state and year. Version 1.0.0 covers 95,582 protein sequences from 18,378 distinct isolates collected between 2022 and 2026 across 52 states and territories, screened at 36 marker positions drawn from WHO and CDC sources, producing 688,287 individual calls, joined to 124,427 wastewater results from 49 states of which 3,010 detected H5. Markers associated with reduced susceptibility to clinically used antivirals are rare: the neuraminidase substitution H275Y, the one substitution WHO identifies as a known clinical resistance marker, appears in 7 of 19,141 covering sequences (0.037%). The mammalian-adaptation picture differs: PB2 E627K rises across the period, from 0.126% of covering sequences in 2022 to 5.18% in the partial year 2026, while two further markers sit at frequencies better read as fixed features of the circulating clade. We report a methodological finding of general relevance: published marker positions arrive in several numbering conventions and some sources list the same site twice under two of them, so every position is validated against a named reference before it is counted. 11 of 36 markers required a numbering translation and 3 proved to be duplicates. Marker status throughout is genotype, not confirmed phenotype; no susceptibility testing was performed or is implied. Data, code and documentation are released openly and the pipeline is built for annual refresh.

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.