Sampling strategy and assessment options for environmental antimicrobial resistance in airborne microorganisms

Skjøth, C. ORCID: https://orcid.org/0000-0001-5992-9568 and Petch, Geoffrey (2022) Sampling strategy and assessment options for environmental antimicrobial resistance in airborne microorganisms. Project Report. Environment Agency, Bristol.

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Abstract

Executive summary
The appearance and spread of antimicrobial resistant (AMR) microorganisms and their
genes in the environment are a major concern. While little is known about these
microorganisms within the atmosphere, recent studies report of their presence in the air
covering the UK. This report aims at summarizing sampling options for airborne
microorganisms including assessing their potential for containing antimicrobial resistance
genes and whether the microorganisms possess the capability for transmission through the
atmosphere to other parts of the environment.
The review extends previous works on antimicrobial resistant microorganisms in the
atmosphere by
• Assessing the composition of the atmospheric microbiome, where AMR organisms
occur.
• Determining the specification for bioaerosol samples suitable for analysis for AMR.
• Reviewing methods available for bioaerosol sampling and compare them with the
sample specification.
The work was used to identify the most suitable approach for identifying antimicrobial
resistant microorganisms in the UK atmosphere and finds the following:
• Airborne fungal spores and bacteria with the potential to contain antimicrobial
resistant genes may be present all year round, but the highest concentrations should
be expected in the summer and autumn.
• Sources of antimicrobial resistant microorganisms are expected to be mainly
anthropogenic. Some sources (e.g., crop fields) will peak in summer or early autumn,
while other sources (e.g., agricultural buildings or waste sites) will be linked to
activities and can be more or less constant throughout the year.
• It is not known if antimicrobial resistant microorganisms have spread to the wider
environment and if the atmosphere contains a non-trivial, expectedly low,
concentration of these harmful microorganisms.
• There are two main analytical approaches to quantify biodiversity and antimicrobial
resistant microorganisms. One approach is based on culturing and a second is based
on molecular methods. Both have advantages and disadvantages, and it is
recommended to use both approaches in campaigns and long-term monitoring.
• There is no superior device for the collection of antimicrobial resistant
microorganisms and the type of device depends on the objectives of the study. Many
available instruments have been developed for one specific purpose. The best
sampling strategy is often to combine at least two types of instruments: One type that
samples directly onto growing media such as a cascade impactor and a second type
that uses a set of filters such as a high-volume cascade sampler. In some cases, a
cost-effective solution for long term campaigns or monitoring can be the application
of semi-automatic mini cyclones.
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• Guidelines for storing and processing of fungal spores and bacteria have been
produced based on general knowledge on fungal spores, bacteria and how to handle
genetic material. It is important to apply a common set of protocols, partly to allow for
robust intercomparison of studies and partly to protect the samples against loss of
material during transport, storage, or handling.
• A decision tree and a set of questions that typically need addressing for developing
a campaign has been produced, where the aim is the detection of airborne
microorganisms, suspected to contain antimicrobial resistant genes. This is
supported by two practical examples on how to develop a campaign at several
locations addressing fungal spores or a single site campaign addressing both fungal
spores and bacteria.
• A number of data sets as well as models are needed for further understanding and
potential mitigation. Basic atmospheric models from air quality studies are already
available, while more advanced models handling viability and potential transmission
have not yet been developed. The most import data sets are meteorological data
supported by specific vegetation variables with land cover and land use data. Activity
data around anthropogenic activities such as harvesting, handling of waste sites or
animal productivity may also be important.
Until now, it has not been possible to identify studies on antimicrobial resistant
microorganisms covering the UK atmosphere. Consequently, it is not possible to assess the
extent of the problem and whether this causes a significant risk to humans, animals, or the
environment. Neither is it known if there is a trend such as increased concentrations of
specific harmful microorganisms or if there is an overall increase in biodiversity of
microorganisms with antimicrobial resistant genes.

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