Authors: Subbiah Murugan, Thirumalapura Nagaraja, Thompson David, Kuchipudi Suresh V, Jayarao Bhushan, Tewari Deepanker
Journal: Frontiers in veterinary science
Summary
# Editorial Summary Next-generation sequencing (NGS) offers a potentially transformative diagnostic tool for equine practitioners dealing with tick-borne diseases, enabling unbiased detection of multiple pathogens simultaneously in blood samples without prior assumptions about which agents might be present. Researchers applied metagenomic analysis to blood from 10 horses with suspected tick-borne infections and 5 healthy controls, extracting microbial DNA and performing shotgun sequencing on an Illumina MiSeq platform, generating 0.4–0.6 million reads per sample for taxonomic classification. The technique successfully identified *Anaplasma phagocytophilum* in 5 of the 10 suspect horses (10–42.5% of Alphaproteobacterial reads), with 4 of these 5 cases subsequently confirmed by conventional PCR, though notably 2 PCR-positive animals yielded no detectable tick-borne microbial sequences via metagenomic analysis. Whilst the method demonstrated utility in detecting blood-borne pathogens and has clear potential for investigating polymicrobial infections and emerging diseases in equine populations, practitioners should recognise that incomplete concordance between NGS and traditional testing means metagenomic analysis works best as a complementary rather than replacement diagnostic approach. For equine clinicians, this research validates NGS as a valuable investigative tool when conventional diagnostics prove inconclusive or when surveying populations for multiple concurrent tick-borne infections.
Read the full abstract on PubMed
Practical Takeaways
- •NGS metagenomic analysis offers an unbiased, culture-independent method for detecting tick-borne pathogens in equine blood samples that may complement or serve as an alternative to PCR when pathogen identification is needed
- •A. phagocytophilum should be considered in horses presenting with signs of tick-borne disease; metagenomic screening can rapidly identify this pathogen without prior clinical suspicion of a specific agent
- •PCR and metagenomic approaches show variable agreement (80% in this study), so confirmatory testing or combined approaches may be warranted for clinical diagnosis
Key Findings
- •Metagenomic NGS analysis identified Anaplasma phagocytophilum in 5 of 10 horses with suspected tick-borne infection (50% detection rate), with 10-42.5% of Alphaproteobacterial reads from positive animals
- •Four of five horses positive for A. phagocytophilum by metagenomic analysis were confirmed positive by PCR validation
- •Bacterial genomes comprised 0.5-1% of total microbial reads, with dominant phyla being Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria and Tenericutes
- •Two horses tested positive by PCR but negative by metagenomic analysis, demonstrating both the strengths and limitations of the NGS approach