Professor Amy Pruden, of Virginia Tech, USA, shares her insights on the latest advances to tackle the ‘slow pandemic’ of antimicrobial resistance.
For her keynote presentation at the IWA World Water Congress & Exhibition in Toronto, Canada, in August, Professor Amy Pruden, of Virginia Tech, USA, chose a title of ‘The Water Sector and the Slow Pandemic of Antimicrobial Resistance’. It is a title capturing an issue that stems from a natural ability of microbes that brings with it dire warnings.
Pruden sums up antimicrobial resistance, or AMR, as “the ability of microbes to survive antimicrobial treatments”. So, this includes resistance to antibiotics – “one very precious class of antimicrobials that treat bacterial infections”.
“How do they do this? Simply put, it’s in their DNA – their antibiotic resistance genes, or ARGs. These encode the ability of bacteria to do things like pump the antibiotic out of the cell, to break the antibiotic down, or to modify the cell target so that the antibiotic is no longer effective,” explains Pruden.
“Microbes are a lot smarter than we often give them credit for,” she continues. “They are very adept at evolution on very rapid time scales. They can also do something that we humans can’t do – they can physically share their DNA through horizontal gene transfer.” This latter point is relevant for water treatment – killing microbes may not be enough. “We also have to think about their DNA.”
A global health concern
Then come the warnings. One hundred years ago, a simple cut or bout of pneumonia was deadly, and this is not a place to which we would wish to return, comments Pruden. Noting a report in The Lancet and the 2016 UK ‘O’Neill Report’, sponsored by the Wellcome Trust and the UK Department of Health, she says: “They issue a dire warning that the slow pandemic of AMR is here. And if we don’t coordinate globally to do something about it, deaths due to AMR will surpass those due to cancer.
“On a hopeful note, there is global action taking root,” Pruden continues. One key example here is the World Health Organization’s (WHO’s) Global Action Plan on Antimicrobial Resistance, with WHO advocating for a ‘One Health’ approach. This requires all Member States to develop a national action plan for combating antimicrobial resistance. “To date, 164 of these national action plans have been published,” says Pruden.
Other examples she gives include the G7 Health Ministries. “When they met in 2022, they identified three top global public health threats: the COVID-19 pandemic, the slow pandemic of AMR, and climate change,” notes Pruden. The response, supported as part of the G7 Pact for Pandemic Readiness, included “development of integrated, interoperable and interdisciplinary surveillance”, including antimicrobial resistance. Here, Pruden points out: “They specifically call out non-invasive national wastewater surveillance systems.”
The water sector contribution
The global ‘One Health’ response to AMR requires action on multiple fronts and, on this note, Pruden highlights the UN Environment Programme (UNEP) report ‘Bracing for superbugs’. This covers the state of the science, the role of antimicrobial resistance in the environment, and what can be done about it. “I’m proud to be one of the co-authors of this report,” says Pruden.
“One of the take-home consensus messages was that AMR challenges cannot be understood or addressed separately from the triple planetary crisis of climate change, biodiversity, and pollution and waste.
“The report elaborates on the role of antimicrobial resistance in the environment, particularly the water environment. So, water environments are key recipients, conduits and sources of exposure for AMR,” she adds, noting prime examples given as agricultural runoff, industrial inputs, and wastewater inputs.
“It also highlights how, if we are going to use this ‘One Health’ framework – people, animals, environment – that has been adopted by the World Health Organization, we need to get a handle on the understanding of the environmental dimensions of AMR.”
Here, Pruden highlights the relevance of wastewater. For a start, pharmaceuticals are not broken down fully in the body, so pharmaceuticals such as antibiotics are excreted into sewage. Wastewater also contains antibiotic resistant pathogens, antibiotic resistant genes (ARGs), and mobile genetic elements (MGEs) – “pieces of DNA that help ARGs move across bacterial populations”. Meanwhile, treatment processes such as activated sludge – perfected over the past 100 years – select for a particular microbial ecology. “We are concerned that this could be inadvertently creating an environment that’s ideal for selecting for antibiotic resistance, so some refer to this as a possible hot spot for the evolution of AMR.” This is a point Pruden returns to later.
Pruden highlights that the UNEP report also provides a framework for taking action around the environment and AMR, especially around the sectors that produce and use antimicrobials and the wastes they produce. “We need to think about their waste management in terms of AMR. So, do we need to focus on source control? Do we need to focus on requiring that there be pretreatment before discharge to the sewage works?” asks Pruden.
The need for monitoring
“One of the things that the water sector can do right now is help support monitoring of AMR. There are a lot of knowledge gaps in terms of the rates of resistance and where it’s coming from,” she says.
This need was noted in the 2019 launch of the Water Research Foundation (WRF) ‘Project 5052’, the findings of which were summarised in a 2022 Environmental Science & Technology paper, covering research in Switzerland, Hong Kong, India, the Philippines, Sweden, and the USA.
“We spent a good portion of the pandemic wrapping our heads around what we need to do in terms of AMR monitoring in water environments,” says Pruden. “A key takeaway is that where to monitor and what to monitor really depends on the objective of your monitoring programme.”
She points to four aspects around monitoring: monitoring antimicrobial resistant bacteria and genes circulating in human populations; quantifying what is evading treatment; quantifying removal efficiencies; and assessing evolution of new resistance pathogens and mobile ARGs.
“The first one is wastewater-based epidemiology – testing the sewage itself to get a sense of the carriage of AMR organisms in the population served. The second is to look at the effluents coming out of these plants and to see if there are any AMR constituents of clinical concern. The third is to look at the treatment processes, quantify removal rates and identify which are the most effective at attenuating AMR. Finally, the fourth is the issue of hot spots: are there places in the environment where there’s a convergence of factors, where there’s an elevated probability of resistant pathogens evolving?”
Techniques for testing
In terms of testing techniques, Pruden says: “AMR is tricky… It is a multi-headed beast. So, there’s really hundreds of strains of bacteria that can be resistant, and thousands of ARGs, so we concluded that really all the methods have value. Again, it depends on what your objectives are.”
She notes that use of cultures is always going to be of value: “It’s the one method that can confirm a viable organism.” Here, she refers to WHO’s Tricycle Protocol. Non-culture-based techniques include those built around polymerase chain reaction (PCR). “Then, most recently, a real game changer has been DNA sequencing… We can use non-targeted DNA sequencing to profile everything that’s in there and just compare with databases to see what we’re interested in.”
“Recently, we were able to demonstrate the potential of this metagenomic DNA sequencing approach. We sent students around the world and sampled sewage from representative wastewater treatment plants. It was really remarkable how we could distinguish these sewages based on their ARG content,” says Pruden.
“What we saw was that the wastewater from Sweden had the lowest abundances of ARGs of anywhere that we tested. This makes sense because they’ve been one of the most proactive countries in terms of adopting policy to combat the spread of AMR, including banning antibiotic use in livestock since the late 1990s.
“We also saw that the highest levels of ARGs in sewage were in parts of the world that have very high population densities and that don’t require a prescription from a doctor to use antibiotics,” she adds.
“There’s a lot of potential here, not only to fill the gap in terms of clinical testing and understanding the rates of antibiotic resistance carried in human populations, but also to inform effective global policy – what works in terms of stemming the spread of antimicrobial resistance.”
Here, Pruden returns to the question of whether wastewater treatment plants are hot spots for AMR. “We went to those same wastewater treatment plants, and we sequenced the metagenomes of the activated sludge. The ARGs were sharply depleted in the activated sludge. This is quite encouraging, that wastewater treatment plants can be a barrier to the proliferation of ARGs.”
This was explored further using long-read DNA sequencing. “We concluded that the microbial ecology of activated sludge is a natural barrier to the proliferation of ARGs.”
“That’s not the full story,” adds Pruden, who says that current work is looking at which ARGs escape treatment and which are transferred horizontally. Bench-scale testing involved using blends of municipal sewage and hospital sewage, and it was possible to track increases in ARGs that related to the same classes of antibiotics increasing in the sewage. This work was published recently in Nature Communications.
The benefits of monitoring
There is a wider dimension to this wastewater monitoring. “We talk about the need for a One Health framework to combat the spread of AMR globally, but the environmental dimension of that One Health framework is really not up to speed with the level of knowledge of the others. This kind of monitoring can also help us to identify epidemiological links between the environment, humans and animals; then we can focus on those areas of transmission. We really need these large, comparable, longitudinal datasets to identify the drivers of AMR.”
Other areas include the need to inform risk assessment around regulatory limits, and to identify hot spots for the evolution and spread of AMR. “That way, we can focus our resources there, and we can identify treatment technologies that most effectively mitigate AMR,” says Pruden. There is also the potential to inform human and animal medicines regulation about which antibiotics will be most effective at population scales. Imagining doctors being able to check in real time on a mobile phone app, Pruden comments: “This last one is kind of a dream of mine.”
Picking up on the UNEP report, Pruden highlights areas where the water sector can contribute to progress, including continuing to design and operate treatment processes that produce excellent water quality. “These will surely also benefit AMR,” she says. Another is to work to identify which processes are most effective at removing antimicrobials, resistant bacteria, ARGs and mobile genetic elements (MGEs), and ones that do not increase these constituents. Another is the potential for source control, including at locations such as hospitals and pharmaceutical manufacturing facilities. Another is to look at the needs of locations currently without appropriate waste treatment. “Sadly, it is often the low- and middle-income countries that bear the burden of AMR,” adds Pruden.
She emphasises that there is a global, coordinated effort under way around AMR, so the sector is not alone. There are also wider opportunities to seek partners and co-benefits in relation to other contaminants of emerging concern.
Addressing the audience in Toronto, Pruden was also pleased to highlight that she is part of a team selected for a new US Environmental Protection Agency National Priorities grant focused on AMR. This was launched on 1 August, to be led by Lola Olabode, at the WRF. “Our focus is really going to be on filling many of these data gaps, and especially how we can inform risk assessment and move towards policy development that’s effective for combating AMR – and hopefully provide you all in the water sector with the information and tools you need to help the cause.”
More information
The ‘O’Neill Report’ – amr-review.org
UNEP report ‘Bracing for superbugs’ – www.unep.org/resources/superbugs/environmental-action
The Lancet report: ‘Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis’
2022 Environmental Science & Technology paper title: ‘Demonstrating a comprehensive wastewater-based surveillance approach that differentiates globally sourced resistomes’
Nature Communications report title: ‘Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment’
US EPA National Priorities project: ‘Quantifying wastewater sources of antibiotic resistance to aquatic and soil environments and associated health risks’
2022 Microbiome paper ‘Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge’,
doi.org/10.1186/s40168-021-01216-5
