Infectious disease surveillance and monitoring is critical in settings where disease outbreaks and antibiotic resistance can dramatically impact human health. Rapid and accurate detection of human pathogens between closely related strains and across phylogenetic kingdoms is paramount to mitigate disease outbreaks and to diagnose affected individuals.  Here, we use demonstrate cross-kingdom species detection by simultaneously sequencing DNA from 8 bacteria and 2 fungi in the ZymoBIOMICS control.  We test this on long-read (PacBio, oxford nanopore), short read (Illumina), and linked, long-read (10x Genomics) platforms.  We also show that these standard aliquots can be used for benchmarking a variety of tools and also characterize their epigenetic changes (base modifications).  These standards are now being used internationally as part of a large-scale effort and improving metagenomics use in the clinic, or “precision metagenomics,” as well as for city-scale monitoring of the dynamics of anti-microbial resistance (AMR) with the Metagenomics of Subways and Urban Biomes (MetaSUB) project. 

 

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