Diagnosis of bacteraemia in neonatal foals using 16S rRNA sequencing

Diagnosis of bacteraemia in neonatal foals using 16S rRNA high-throughput sequencing
Equine Vet J. 2026 Jul 1. doi: 10.1002/evj.70222. Online ahead of print.
Authors
Flavie Payette 1 , Alicia E Long 1 , Weiming Hu 2 , Kyle Bittinger 2 , Ahmed M Moustafa 2 , Darko Stefanovski 1 , Michelle Abraham 1 , Maia R Aitken 1
Affiliations

1 Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, Pennsylvania, USA.
2 Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.

PMID: 42381558
DOI: 10.1002/evj.70222

Abstract

Background: Sepsis is an important cause of morbidity and mortality in foals. Early diagnosis can improve outcome but is complicated by non-specific clinical signs and delayed confirmation of infection via blood culture. Molecular assays represent a rapid and more sensitive alternative.

Objectives: To evaluate and compare bacterial load and composition in blood and blood culture media (BCM) of sick and healthy foals using molecular assays and to compare results with traditional bacterial culture.

Study design: Cross-sectional observational clinical study.

Methods: Thirteen septic foals, 10 sick non-septic and 8 healthy foals were included. Bacterial load and composition from whole blood (WB), pre-enriched BCM and contamination controls were analysed by quantitative PCR and sequencing of the universal bacterial 16S rRNA marker gene.

Results: WB sequencing yielded more positive samples (25/31) than BCM (6/62; p < 0.01). Positive blood culture and WB sequencing were comparable in only 3/12 foals. Sequencing samples were at high potential for contamination, with most samples having high relative abundances (RAs) of Paucibacter and Ralstonia. High RAs of Actinobacillus and Staphylococcus in septic foals may, however, suggest true pathogen detection. No significant differences in bacterial RAs, 16S rRNA gene load (qPCR), or other sequencing-based metrics were found between foal groups and between WB and contamination controls. Main limitations: Inherent inaccuracies of classification schemes for septic and sick non-septic foals and the impact of contamination when sequencing low biomass samples. Conclusions: High-throughput sequencing represents a possible avenue for the diagnosis of bacteraemia in foals but has high potential for environmental and extraction-related contamination and cannot replace blood culture at this time. Further research to optimise detection yield and sensitivity on WB samples is warranted. Keywords: SIRS; bloodstream infection; foal; horse; neonate; sepsis. © 2026 The Author(s). Equine Veterinary Journal published by John Wiley & Sons Ltd on behalf of EVJ Ltd.