DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle

Authors: Cook, Daniel; KOCUREK, BRANDON - Us Food & Drug Administration (FDA); Stonecipher, Clinton; Welch, Kevin; GARDNER, DALE - Retired ARS Employee; MAMMEL, MARK - Us Food & Drug Administration (FDA); REED, ELIZABETH - Us Food & Drug Administration (FDA); RAMACHANDRAN, PADMINI - Us Food & Drug Administration (FDA); ERICKSON, DAVID - Us Food & Drug Administration (FDA); COMMICHAUX, SETH - Us Food & Drug Administration (FDA); OTTESEN, ANDREA - Us Food & Drug Administration (FDA)

Submitted to: Toxicon
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/5/2025
Publication Date: 2/5/2025
Citation: Cook, D., Kocurek, B., Stonecipher, C.A., Welch, K.D., Gardner, D.R., Mammel, M., Reed, E., Ramachandran, P., Erickson, D., Commichaux, S., Ottesen, A. 2025. DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle. Toxicon. 256. Article 108285. https://doi.org/10.1016/j.toxicon.2025.108285.
DOI: https://doi.org/10.1016/j.toxicon.2025.108285

Interpretive Summary: Prepared and stored feeds, fodder, silage, and hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous plants have played significant roles in livestock deaths from forage consumption in recent years in the Western United States including Salvia reflexa. Metagenomic data, genome skims, and metabarcodes have been used for identification and characterization of plants in complex matrices including diet composition of animals, mixed forages, and herbal products. Here, metagenomic profiling, genome skims, and metabarcoding were used to retrospectively describe the composition of contaminated alfalfa hay from a case of Salvia reflexa poisoning that killed 165 cattle. Both methods provided similar estimates of Salvia to chemical methods. Additionally, both methods provided similar estimates of species composition in the contaminated hay and rumen contents of poisoned animals. The data demonstrate that genome skims and DNA barcoding may provide useful tools for plant poisoning investigations.

Technical Abstract: Prepared and stored feeds, fodder, silage, and hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous plants have played significant roles in livestock deaths from forage consumption in recent years in the Western United States including Salvia reflexa. Metagenomic data, genome skims, and metabarcodes have been used for identification and characterization of plants in complex matrices including diet composition of animals, mixed forages, and herbal products. Here, metagenomic profiling, genome skims, and metabarcoding were used to retrospectively describe the composition of contaminated alfalfa hay from a case of Salvia reflexa poisoning that killed 165 cattle. Both methods provided similar estimates of Salvia to chemical methods. Additionally, both methods provided similar estimates of species composition in the contaminated hay and rumen contents of poisoned animals. The data demonstrate that genome skims and DNA barcoding may provide useful tools for plant poisoning investigations.