Rapid monitoring of bioaerosols in Urban, Agricultural and Industrial Environments

Lead Research Organisation: University of Essex
Department Name: Biological Sciences

Abstract

The impact of emissions from urban, agricultural and industrial areas on local air quality is a growing concern. However, understanding the identities, distribution and abundance of airborne microorganisms remains in its infancy. Deleterious health effects can arise following exposure to infective bacterial and viral organisms. Indeed, the risk to human exposure from bioaerosols and volatile organic compounds are still difficult to quantify in real time. There is also growing concern about the accidental or deliberate release of biological materials in the environment and the associated impacts on human/animal health and the economy. Thus, rapid bioaerosol detection is an urgent civilian and military requirement. In 2012, the Government instigated a "Blackett Review" to address the question "Which technologies or capabilities will enable rapid, wide-area surveillance of a broad spectrum of biological agents in the next 15 years?" As the risk of exposure is directly linked to the concentration and type of microorganisms, much clearer characterisation, quantification and monitoring methods are needed if the temporal and spatial trends of infectious species are to be evaluated in different environments. Current monitoring methods are labour-time intensive, expensive and inefficient at capturing sufficient amounts of biomaterial for bioaerosol characterisation. Furthermore, there is currently no standardised protocol established which often leads to an underestimation of the diversity and quantity of microbial load. Thus, a more in-depth understanding of bioaerosol material is required. Next Generation Sequencing (NGS) has facilitated the characterisation of bioaerosol material at the fine-scale. However, such methods are being used with no guidelines as to the type of filter to be used; sampling flow rate, time period, or extraction methods. Furthermore, simply characterising the aerosol microbiome is only the first step to understanding the microbial processes occurring in bioaerosols in different environments. Metatranscriptomics which provides an understanding of how communities respond to changes in their environment may be more appropriate to analysing complex bioaerosol communities and their interactions with biotic/ abiotic factors in the environment.
The overall aim of this project is to develop a 'bio-toolkit' for high-confidence, wide-area biodetection and biomonitoring of bioaerosols from urban, agricultural and industrial environments. Specifically, the project aims to develop novel techniques for rapid, high-throughput sample capture, concentration and preparation for detecting bioaerosols. The project will utilise a combination of NGS (metagenetic) and chemical marker analysis to characterise the aerosol microbiome across environments. This will provide a robust, cost-effective, sensitive approach to identify, quantify and monitor key pathogens in bioaerosols. We will use metatranscriptomics to identify the functional diversity of the aerosol microbiome and provide insights into the processes supporting bacterial diversity in aerosol samples. We will examine how functional diversity changes across environment type and context and provide additional phylogenetic information on total bacterial diversity. A major project output for end-user beneficiaries will be an optimised network system for the rapid and responsive wide-area real-time monitoring (i.e. detection, characterisation and quantification) of bioaerosols (specifically bacterial pathogens) across urban, agricultural and industrial environments using portable 'in-field' micro-instrumentation. We will produce a database of microbial volatile organic markers for the rapid characterisation of bioaerosols from different sources. The project also provides a better understanding of the impact of bioaerosols from different sources on human exposure which is of direct relevance to the NERC strategy.

Planned Impact

Who will benefit? This project will develop a 'bio-toolkit' for high-confidence, wide-area biodetection and biomonitoring of bioaerosols from urban, agricultural and industrial environments. There are several end-user beneficiaries in both private & public sectors e.g. Environment Agency (EA), Defra, Dstl, Department of Health (DoH), Public Health England, Local Hospital/ Healthcare Authorities, composting/biowaste processing companies, Local Authorities, agricultural & farming sectors. Development of novel techniques for rapid, high-throughput sample capture, concentration and preparation and a robust, cost-effective, sensitive approach to identify, quantify and monitor bioaerosols will enable these organisations to save resources by targeting their actions on specific aspects of bioaerosol exposure (e.g. pathogen mitigation) that have the greatest environmental and human health impact. The project also benefits academics and the public.

How will they benefit? The project enhances quality of life, health & environment as follows:
1. Data on a high throughput air sampling methods and equipment for wide-area biodetection will inform EA, Defra, Dstl and Public Health England on bioaerosol exposure and monitoring.
2. Data on the composition and dynamics of bioaerosols (including pathogens) from different environmental sources will inform composting/biowaste processing industry and agriculture on operational best-practice for the management of biowaste and human exposures.
3. Data from the project will inform how climate change affects pathogens in air (e.g. through extreme weather conditions) in different environments.
4. Data from the project will produce a network integration system for use with portable micro-instrumentation to monitor and track bioaerosols in real time across urban, agricultural and industrial environments. This will benefit Dstl's policy on wide-area surveillance of broad spectrum of biological agents for civilian and military benefit.

The project increases the effectiveness of public services & policy as follows:
1. The project will generate a comprehensive dataset on sources, emission rates, source apportionment methodologies, mechanisms and concentration characteristics of bioaerosols from different environmental sources. This will provide a better understanding of the impact of bioaerosols from different environments on human exposure (especially on agricultural scenarios) enabling improved mitigation strategies to be developed for reducing bioaerosol emissions and improve environmental air quality (EU Air Quality Directive).
2. Characterization of aerosolised material of biological origin (including pathogens) from different environmental sources will inform Local Healthcare Authorities and DoH's policy for pathogen mitigation.
3. Data on how climate change affects the pathogens in air can be used by Defra and Public Health England to more accurately predict potential bioaerosol exposures under future climate scenarios, helping Local Health Authorities adapt to climate change.
4. Data obtained will inform EA policy of the regulation of composting/biowaste sites and inform Environmental Permitting (England and Wales) Regulations.
5. Data will help to meet the Government's goals for management of UK's recycling strategies.
 
Description Overall project Aims and objectives

A rapid monitoring system for bioaerosols in urban, agricultural, and industrial sites via:
? High-throughput sampling
? Next generation sequencing technologies
? Chemical marker analysis
? Statistical design
? Network systems

Four work packages (1,2, and 3 at Essex University)

Work package 1
Aims:
1. Optimise techniques for bioaerosol sample collection
2. Optimise DNA/RNA extraction methods

Key findings: We have optimised methods for collection and isolation of DNA and RNA from microbial bioaerosols. We have tested three bioaerosol sampling methods: filtration, impingement, and impaction. Key findings include that filters out-perform liquid impingement systems in terms of total material collected; however, as a longer sampling time are required with filters, impingement systems are recommended when a large number of samples are needed. For example, when fine temporal data is desired.

Key Outputs: Our results are a key resource for bioaerosol sampling, useful to both scientists carrying out pure research and those developing regulatory monitoring for bioaerosols. A manuscript with our findings is going to be submitted to "Molecular Ecology Resources" in the next month. We have also published a book chapter in "Springer Protocols Handbooks" detailing best practice for analysis of high-throughput DNA sequencing data 1 (https://doi.org/10.1007/8623_2016_228) and contributed to a review in "Wiley Interdisciplinary Reviews" of the current state and future prospects of in-field metagenomics 2 (https://doi.org/10.1002/wat2.1280).

To ensure that the scientific field is aware of our results we have presented our results at international conferences and a manuscript with our findings is going to be submitted to Molecular Ecology Resources in the next month. We have disseminated our findings to key government agencies, DSTL and PHE via program meetings which they have attended; and also with joint sampling with DSTL.

Work Package 2
Aims:
1. Characterise bioaerosol microbiome using NGS
2. Quantify key pathogens using Q-PCR

Key findings: We have undertaken a sampling campaign at 10 sights (3 x urban and agricultural, and 4 x industrial) in winter and summer.

Microbial bioaerosols are more abundant in winter but this varies between types of site.

The composition and abundance of bioaerosols varies in different size fractions at all sites. This has implications for dispersal and pathogen risk. (Manuscript in prep for submission to Microbial Ecology)

We have developed a method (based on LAMP-PCR) which can indicate the presence < 4 copy numbers of a target pathogen in a sample in less than 30 mins. The result can be indicated by a colour change and requires no complex equipment.

Key Outputs: We have presented our results at a number of international conferences and manuscripts are in preparation for submission to peer reviewed journals.

A dataset comprising 720 samples is the most detailed metagenetic sampling survey of bioaerosols in the UK to date. The dataset is comprised of three types of data:
• broad scale temporal data (2 hrs per sample)
• fine scale temporal data (20 mins per sample)
• fine scale spatial data (grid of 50-56 samples per site)

In addition, this data can be put into context with chemical biomarker data from work package 3 and data from the spectral intensity bioaerosol sensor (SIBS) collected in collaboration with the NERC ENDOTOX project.

We have developed a custom bioinformatics pipeline for identifying pathogens in high-throughput DNA sequencing datasets. This can be used to detect pathogens in any 16S rRNA high-throughput DNA sequencing dataset, not just bioaerosols.

Our LAMP assay for detection of pathogens can form the basis of a portable micro-instrumentation for real-time wide-area bioaerosol quantification. Further development and field testing is required. We hope to test this with a commercially available product (OptiGene) for real-time quantification in the field as so far we are limited to presence or absence.

Samples for metagenomic and metatranscriptome sequencing are yet to be sent, yields or DNA are low for bioaerosol sampling and we are still finalising the best strategy.

Work Package 4
Aims: to improve statistical design and develop network systems for rapid bio monitoring to understand:
1. The ecological drivers of pathogenic bioaerosol communities
2. The spatial distributions of pathogenic bioaerosols
3. Predict pathogenic bioaerosol distributions

Key findings: All samples are collected but the modelling for this data will take place over the coming year.
Exploitation Route We have developed a custom bioinformatics pipeline for identifying pathogens in high-throughput DNA sequencing datasets. This can be used to detect pathogens in any 16S rRNA high-throughput DNA sequencing dataset, not just bioaerosols.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Environment,Pharmaceuticals and Medical Biotechnology

 
Description Undergraduate Research Bursary
Amount £1,200 (GBP)
Organisation The Aerosol Society 
Sector Charity/Non Profit
Country United Kingdom
Start 06/2016 
End 08/2016
 
Description small research grants
Amount £3,000 (GBP)
Organisation The Aerosol Society 
Sector Charity/Non Profit
Country United Kingdom
Start 06/2017 
End 12/2017
 
Title OpenChrom® - The open source alternative 
Description OpenChrom® is an open source software for chromatography and mass spectrometry based on the Eclipse Rich Client Platform (RCP). Its focus is on handling mass spectrometry data files natively. Hence, mass spectrometric data generated, for example, by GC/MS, LC/MS, HPLC-MS, ICP-MS or MALDI-MS may be imported directly, without prior conversion, for subsequent visualization and evaluation. Aside from the support of various vendor data formats, data may also be imported in common formats such as NetCDF, csv or mzXML. All data format converters are provided as separate plug-ins which are not open source but free to use. Moreover, OpenChrom® offers a nicely adaptable graphical user interface and is available for various operating systems, e.g. Windows, Linux, Solaris and Mac OS X. 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact OpenChrom® is tailored for data analysis purposes including processing, visualization and reporting. The implemented batch-processing features allow high-throughput evaluation of data acquired across our different gas chromatography systems in one unique environment - it further allows us to undertake multivariate analysis and chemical fingerprint comparison using the same platform. We are actively collaborating with the Dr. Philip Wenig the Founder, to expand the database and filter analysis for volatile organic compounds and hydrocarbons. 
URL https://www.openchrom.net/
 
Description Dstl 
Organisation Defence Science & Technology Laboratory (DSTL)
Country United Kingdom 
Sector Public 
PI Contribution Meeting at Dstl to discuss project and finalise secondment. Second meeting with Dstl to discuss progress to date
Collaborator Contribution Information on pathogen levels and sampling techniques
Impact None
Start Year 2015
 
Description Environmental Agency 
Organisation Environment Agency
Country United Kingdom 
Sector Public 
PI Contribution Sampling methodology
Collaborator Contribution pathogen levels
Impact No
Start Year 2015
 
Description Public Health 
Organisation Public Health England
Country United Kingdom 
Sector Public 
PI Contribution Discuss on pathogens
Collaborator Contribution Discussion about pathogens
Impact None
Start Year 2015
 
Description UCL 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Generation of aerosols
Collaborator Contribution Use of environmental chamber at the Healthy Infrastructure Research Group
Impact None
Start Year 2015
 
Description European Aerosol Conference, Zurich 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk entitled "he bioaerosol bacterial microbiome at urban, agricultural, and industrial sites: Exposure, size fraction and composition"
Year(s) Of Engagement Activity 2017
URL http://www.gaef.de/EAC2017/EAC2017abstracts/T402/T402N06f.pdf
 
Description NERC Environmental Microbiology and Human Health Programme, Third Annual Programme Conference 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Overveiw of Rambie findings
Year(s) Of Engagement Activity 2018
 
Description Aerosol Society Annual Conference 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation on work to date - number of follow up questions
Year(s) Of Engagement Activity 2016
 
Description Bioaerosols from composting research discussion day 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Introduction on RAMBIE and ENDOTOX II projects to EA, PHE, Imperial College and discussion on the research progress made and opportunities on the application of molecular methods, Exposure monitoring, occupational studies and epidemiology; discussion on how to broaden further the two NERC projects and consideration for EU funded project call
Year(s) Of Engagement Activity 2015
 
Description European Aerosol Conference 2016, Tours, France 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Poster entitled "Rapid monitoring of bioaerosols in industrial, agricultural and urban environments" - number of requests for addtional information
Year(s) Of Engagement Activity 2016
URL http://api.mycongressonline.net/api-Congress-agenda.html?record=539cbaf9-939f-9a68-0c81-5540e2221c41...
 
Description Molecular Microbial Ecology Group (MMEG) meeting 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Poster at Molecular Microbial Ecology Group (MMEG) meeting 2018, Swansea
Year(s) Of Engagement Activity 2018
 
Description NERC Environmental Microbiology and Human Health Programme, First Annual Programme Conference 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Update of the 4 projects founded by NERC, 2 in bioaerosols and 2 in water
Year(s) Of Engagement Activity 2016
 
Description NERC Environmental Microbiology and Human Health Programme, Second Annual Programme Conference 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Update of the 4 projects founded by NERC, 2 in bioaerosols and 2 in water
Year(s) Of Engagement Activity 2017
 
Description RAMBIE project update meeting with the Project Management Group 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Overview on the different sampling campaign and regimes tested across urban, rural and industrial sites and challenges in sampling bioaerosols on representative sites - discussion with representatives of the EA, Dstl on what to focus on and how to plan and organise next sampling campaign - All agreed to identify a site for deploying all battery of monitoring and sampling equipment (Coriolis, impeger, SIBS and WIBS)
Year(s) Of Engagement Activity 2016
 
Description Science for the Green Economy - Advanced rapid monitoring of bioaerosols in Urban, Agricultural and Industrial Environments 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The first national debate in Science for the Green Economy explored technology and management issues, including the disruptive innovations and the policy and regulatory environment in which new technologies might thrive. As the world works towards the goals agreed at COP21 in Paris, these discussions are more important than ever.
The debate was chaired by Cranfield University's Professor Paul Leinster CBE (former Environment Agency CEO) and included contributions from Hayden Morgan (UK Green Investment Bank), Ben Ritchie (Aberdeen Asset Management), Alison Carter (ENDS Report), Julian Richardson (Parhelion Underwriting Ltd) as well as experts in law, the circular economy, corporate responsibility, and emissions reducing energy technology.
Year(s) Of Engagement Activity 2016
URL http://www.cranfield.ac.uk/s4ge
 
Description Science to Policy meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Rambie update at Science to Policy meeting in Bristol, 17 October 2018
Year(s) Of Engagement Activity 2018
 
Description Symposium on bioaerosol, microbiome and lung disease, RIVM, The Netherlands 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Symposium organized as part of a mutual interest of PHE and RIVM in bioaerosols. It aims to strengthen the capacity and knowledge to service science based policies and regulations.
Year(s) Of Engagement Activity 2017
URL http://hieh.hpru.nihr.ac.uk/sites/default/files/private/secure/Symposium%2018%20may%20Bioaerosol%20a...
 
Description WP8 -Enhanced understanding of bioaerosol emissions and models 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Update on Rambie at the WP8 PIG meeting on Enhanced understanding of bioaerosol emissions and models
Year(s) Of Engagement Activity 2018
 
Description conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk on "Pathogenic Bioaerosol Detection in Under 60 Minutes" at the International Aerosol Conference, St Louis, September 2018
Year(s) Of Engagement Activity 2018
 
Description one day meeting on bioaerosols, Bristol, June 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The purpose of this meeting is to bring together this mix of researchers to present exciting new work and discuss the challenges that still exist in bioaerosol research. Over 60 attendees
Year(s) Of Engagement Activity 2017
URL https://aerosol-soc.com/events/bioaerosols-focus-meeting-10/
 
Description talk at the one day meeting on bioaerosols 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact talk entitled "Novel insights into the size distribution of bacterial bioaerosols at composting sites"
Year(s) Of Engagement Activity 2017