Detection and diagnosis of bloodborne pathogens are critical for patients and for preventing outbreaks, yet challenging due to these diseases’ nonspecific initial symptoms. We advanced CRISPR-based Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN) technology for simultaneous detection of pathogens on numerous samples. We developed three specialized panels that target viral hemorrhagic fevers, mosquito-borne viruses, and sexually transmitted infections, collectively identifying 23 pathogens. We used deep learning to design CARMEN assays with enhanced sensitivity and specificity, validating them and evaluating their performance on synthetic targets, spiked healthy normal serum samples, and patient samples for Neisseria gonorrhoeae in the United States and for Lassa and mpox virus in Nigeria. Our results show multiplexed CARMEN assays match or outperform individual assay RT-PCR in sensitivity, with matched specificity. These findings underscore CARMEN’s potential as a highly effective tool for rapid, accurate pathogen detection for clinical diagnosis and public health surveillance.

N.L.W., and P.C.S. are coinventors on a patent related to this work. P.C.S. is a cofounder of and consultant to Sherlock Biosciences, and a board member of the Danaher Corporation, and holds equity in the companies. The other authors declare no competing interests.

This work is made possible by support from Flu Lab and a cohort of generous donors through TEDs Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation, and Open Philanthropy. P.C.S. was supported by the Howard Hughes Medical Institute and Merck KGaA Future Insight Prize.

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Ethics committee/IRB of Broad Institute/Sabeti Lab gave ethical approval for this work

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

All requests for raw and analyzed data and materials will be reviewed by the Broad Institute of Harvard and MIT to verify if the request is subject to any intellectual property or confidentiality obligations. Data and materials that can be shared will be released via a material transfer agreement.