World AMR Awareness Week 2024 - Day 2

Why AMR in the environment matters

As mentioned, antimicrobial resistance extends far beyond clinical settings. In fact, the environment plays a crucial role in the complex web of factors contributing to the spread. Various pathways allow for the introduction of antibiotic residues, resistant bacteria, ARGs, and other antimicrobials into the environment, including:

• Human Wastewater: Effluents from hospitals and communities frequently contain antibiotic residues and resistant bacteria, which can potentially enter natural water bodies if they are not properly treated.
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• Agricultural Activities: The use of antibiotics in livestock farming and aquaculture can also facilitate the spread of resistant bacteria and antimicrobial residues through excrement, manure, and runoff.

• Industrial Effluents: Discharges from a variety of industries, even those not directly involved in pharmaceuticals, can contain antimicrobial agents and heavy metals, both of which may contribute to co-selective pressure.

Through these and many other pathways, resistant bacteria and ARGs can accumulate in the environment over time, forming hotspots. These hotspots can become points of exposure where resistance genes may spread to humans, animals, and other ecosystems, amplifying the risk of broader impacts.

Comprehending environmental antimicrobial resistance and monitoring crucial pathways is essential for early detection to intercept and mitigate our impact before it becomes a widespread issue.

How can we use this information

Awareness and knowledge are the foundations for action. Only by understanding the microbiological state of the environment can we begin to mitigate our impact, and the place to start is through continuous analysis and surveillance using environmental samples.

Environmental samples include any material collected from ecosystems, such as water, soil, sediments, and even faeces or manure, as gut microbiomes could be among the most significant ecosystems in the context of AMR. These types of samples are crucial for identifying where resistance genes are concentrated and tracking their spread over time.

What does sampling look like?

With initiatives like the EU Wastewater Treatment Directive (EU-WWTD) and advancements in wastewater-based epidemiology, water environments—particularly wastewater, urban water bodies, and rivers—are among the most prime examples for targeted sampling efforts. These environments provide critical insights into pollution, antimicrobial resistance (AMR), and public health risks.

When sampling wastewater treatment plants (WWTPs), key stages are typically targeted: influent (incoming water), effluent (treated water), and specific points within the treatment process. Influent and effluent samples are often collected using automated sampling stations that provide representative samples at set intervals. In cases where more precise evaluations of individual treatment processes are needed, or where sampling stations are unavailable, mobile sampling units can be connected directly to the pipes or water source. These units can be programmed to collect composite samples, providing targeted data for specific treatment stages or compensating for the absence of permanent sampling stations.

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In rivers downstream of urban areas or WWTPs, sampling involves selecting locations both upstream (to establish a baseline) and downstream (to assess the impact of discharges). This comparative approach helps evaluate the effects of urban and treatment plant discharge on water quality. Sampling in these environments can also be conducted with mobile units or manually by researchers, depending on the study's objectives and resources.

Adhering to standardised methods, using sterile equipment, and properly preserving samples are crucial to ensure the accuracy and reliability of data for effective environmental monitoring and analysis.

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‍What Happens After Collection?

The collection is just the beginning. Samples must be filtered and/or frozen as soon as possible to preserve the microbiome's state, then transported to a lab for DNA extraction and subsequently sent to laboratories equipped to analyse AMR markers.

For example, at Resistomap, we utilise the Takara Bio high-throughput Smartchip qPCR technology to detect and quantify hundreds of ARGs across diverse samples. This analysis transforms raw environmental samples into actionable data which could later be used to:

• Identify resistance hotspots to guide interventions.
• Track trends over time to understand AMR dynamics.
• Comparing ARG profiles across regions for global understanding.

Tomorrow, our colleagues from Takara Bio will delve deeper into the different technology behind analysing environmental samples and how it can empower scientists and policymakers to combat AMR effectively.

Conclusion‍

AMR monitoring starts with careful sample collection, a critical step that bridges the environment and science. By collecting the right samples using reliable methods, we can uncover valuable insights into how resistance genes spread—and how we can act to slow their spread.

Stay tuned for more content on AMR throughout this week, where we’ll explore the technologies that analyse these samples and provide the data needed to tackle antimicrobial resistance head-on.

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