Field-based, real-time metagenomics and phylogenomics for responsive pathogen detection: lessons from nanopore analyses of Acute Oak Decline (AOD) sites in the UK.

Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018


In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear.

This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented.

Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort.