• Research

Air-seq: using DNA sequencing to provide early warning of airborne pathogens

Highly sensitive, real-time, in-field detection of airborne pathogens

Project summary.

Led by: Richard Leggett

Start date: 2015

Funding: 

BBSRC 

DARPA SIGMA+ Sensors Program - DNA sequencing for biological threat monitoring

UK Defence Science and Technology Laboratory

Home Office

Department of Transport

Kromek

Air-seq technology has been in development at the Earlham Institute since 2015, combining the latest DNA sequencing technologies with rapid and sensitive custom bioinformatics analysis software. 

Originally conceived as a tool for in-field surveillance of agricultural pathogens (particularly fungal pathogens that threaten some of our most crucial crops), we have carried out a number of proof-of-concept trials to validate the Air-seq technology. We have expanded our focus to include the detection of bacterial and viral human pathogens in urban environments, working with Kromek Plc - a UK-based engineering company specialising in the development of sensors - as part of a project funded by DARPA, the US Defense Advanced Research Projects Agency. 

Air-seq represents a truly unbiased technology capable of detecting any biological agent. The future applications of this technology are far-reaching.

Details.

The Air-seq pipeline begins with the capture of an air sample, typically at a rate of hundreds of litres of air each minute.

The sampler captures biological material into a small volume of liquid and a process of enrichment and DNA extraction follows. This is sometimes, though not always, followed by amplification, prior to sequencing. 

Researchers at the Earlham Institute have created bespoke software that can analyse data in real-time, as sequencing progresses, and highlight the presence of specific pathogens. In the case of bacterial threats, live information on antimicrobial resistance and virulence conferring genes is also provided.

Tools.

MARTi

MARTi is a software package designed for performing real-time analysis of metagenomic samples using nanopore sequencing. If you’re not working in real-time, MARTi may still be a quick and easy analysis soultion for you. And if you’re not using nanopore sequencing, you may still benefit from using MARTi to analyse your data. 

https://www.earlham.ac.uk/marti

Collaborators.

Natural History Museum

Matt Clark and Raju Misra - Development of molecular biological and computational pipeline for Air-seq

John Innes Centre

Paul Nicholson - Applying Air-seq to monitor emerging crop pathogens.

Kromek Plc

Kromek are a worldwide supplier of detection technology focusing on the medical, security screening, and nuclear markets. Kromek is developing a prototype device for automated air collection and detection, and will be commercialising this product.

Impact statement.

Within the agricultural sector, early detection and quantification of crop pathogens has the potential to reduce the use of pesticides, reduce crop losses due to the damage by pathogens, and, based on exact knowledge of pathogen levels and strain, improve crop spraying results thanks to better selection of agrochemicals. The technology can also help to identify novel pathogens, new strains of known pathogens, and help develop better modelling of disease epidemiology.

For homeland security and public health monitoring, the project is developing an automated system for detection and geolocation of airborne biological threats. This would enable the detection of minute traces of pathogenic agents circulating in the air. We have been able to demonstrate extremely high sensitivity and specificity rates for the technology, and significantly reduced the time from air sampling to the detection, compared with conventional lab-based diagnostics that can take days and are generally species-specific.

The outbreak of COVID-19 demonstrated the significant impact of biological threats on public health and the global economy. The ongoing project with Kromek has the potential to demonstrate the positive impact of a mobile bio-surveillance system which is enabled through sequencing and bioinformatics tools developed at the Earlham Institute. This technology could be installed in high-footfall areas such as hospitals, mass-transportation hubs, and even entertainment venues.