Video transcript
EPA Environmental Science Series: Antimicrobial resistance
Seminar 21st May 2019 transcript

Andrea Hinwood: So welcome to our fifth environmental science seminar series today on antimicrobial resistance outside the hospital walls, understanding environmental hot spots drivers and risks. And we have a special guest today Associate Professor Erica Donner and I’m sure you're going to find her talk very interesting. She comes to us from the University Of South Australia and it's an honour to have her share her knowledge and insights with us today.

I'd also like to acknowledge the traditional custodians of the land on which we meet today and pay my respects to Elders past and present. And I extend my respect to the Aboriginal Torres Strait Islander people, colleagues, staff and students who are present here today. And a big welcome to those joining us by the livestream audience. We know that there are many of you out there, it's often very hard to interact with you, so I hope that you're able to see the slides and hear the presentations and get what you need from this particular presentation. I'd also like to welcome a VIP guest, Chairman of the EPA board Cheryl Batagol who's joining us today. And she chairs the heads of EPA as well. So it's terrific that she can come along and learn about, and talk with us, about this emerging issue. A few housekeeping notes please keep your phone on silent for the duration of the event and in case of an emergency the tones will go off and follow the instructions of staff out the doors and down the stairs.

So, we're going to talk today about antimicrobial resistance and importantly what this has to do with the environment sector. We all know that when anti-microbial medicines were developed - it's pretty amazing, and I think for those of us that have been around - we know that they change human health. And I know personally what a great relief it is when you're ill and you take some antibiotics, and you feel well again. We know that these medicines changed human health by helping the body's natural immune system fight infections from bacteria, viruses and fungi. 

They've enhanced our ability to prevent and control infection and we've seen an incredible reduction in mortality from infectious disease. If you look at the graph with the red line, we had a spike in 1920 at the time of the Spanish flu pandemic. Since the 1940s antibiotics the most common form of antimicrobial medicine has saved millions of lives and they've also saved lives during many medical procedures like organ transplantations. Often we don't think about that side of things but if you think about it, when you go into hospital and have an operation antibiotics really help. However, the more we use these products the less effective they're becoming. Antibiotic resistance develops naturally and our actions, which is why we're here talking about the environment, can actually enhance this. So, when human and animal health professionals over prescribe antibiotics, when people don't take antibiotics as directed, when we combine that with poor hygiene and a lack of infection prevention and control i.e. not washing hands properly, and with people traveling around the world, we spread resistant bacteria. So, penicillin was usefully introduced in 1942 and a few years later 2.3 million doses were distributed en masse for allied troops. By 1945 resistance of bacteria to penicillin was already observed. So, we're already seeing the impacts some considerable period of time ago. If AMR resistance continues at current rates antimicrobials will lose their effectiveness. 

This means when we talked before about operations and surgical procedures etc., treatments that that that we might use - chemotherapy for cancer - could become very difficult for us to use. While this is very gloom and doom, I think we do need to present the current state of knowledge. It's estimated that 700,000 people die of resistant infections each year. This is more than the number of people that die from cancer. So, this is not a minor issue. By 2050, 10 million lives a year, and a cumulative 100.2 trillion US dollars of economic output, are at risk due to the rise of drug resistant infections. 

Exacerbating this is the over-counter sales of antibiotics. In parts of Asia 20 to 30 per cent of antibiotics are believed to be consumed without prescription and in some parts of Africa the figure is a hundred per cent. In Australia we're monitoring AMR and Australians are being provided more than 30 million prescriptions for antibiotics. Observations to date have observed resistance in different microbes, such as E Coli. 

Until recently AMR has been seen as a problem for human health, it's also noted in the animal health sector as well, but predominantly in human health. We hear the language of superbugs and how we have problems in our hospitals. But in our environment AMR can spread through activities such as aquaculture, wastewater treatment, livestock production, poor antibiotic regulations, poor waste management practices, including poor sanitation, and other chemical stresses in the environment can exacerbate AMR. In addition, environmental factors and pollution such as biocides and metals can influence microbial ecology and resistance and further spread AMR. 

So for this reason, it's seen as an environmental emerging contaminant, for want of a better language. As an EPA we need some tools to actually understand this particular phenomenon, we need to look at surveillance, and we need to understand what the contributors are to AMR and whether the environment sector is a significant contribution to this particular phenomenon. 

At EPA work is underway to build on our understanding of the connection between environment animals, by investigating the diversity and abundance of AMR in Victoria. Our focus is currently on agricultural effluents as run-off inputs into water bodies, because AMR is an area that presents a significant challenge to all of us. And we're here today because we can actually do something about it. This is not something that we don't have the tools - there are many unanswered questions - but we do phenomenally have the tools to actually deal with it. 

So it gives me great pleasure today to introduce our guest speaker Associate Professor Erica Donner. She's an environmental scientist specialising in environmental chemistry and microbiology. Her research spans a range of interdisciplinary research topics with a current focus on the environmental dimensions of AMR and the approach to AMR surveillance and management. She's leading critical work to understand the effects of environmental stresses on microbial ecology and resistance and particularly in relation to the processes associated with wastewater treatment and reuse, and the role of environmental pollution in promoting the development and spread of antimicrobial resistance. She leads an international collaboration project on AMR in wastewater treatment plants and downstream environments. She's a member of the European cost action working group on the microbe and mobile antibiotic resistance in treated wastewater and downstream environments, and she's deputy chair of the wastewater and water environments working group for the international network, wildlife agricultural soils, water environments and anti-microbial resistance. What is known needed and feasible for global environmental surveillance. So it's my great, great pleasure today to introduce associate Professor Donner and please join me in welcoming her. Thank you.

Erica Donner: Okay thank you very much Andrea for the excellent introduction and the background. I have to say I’m really grateful for the invitation from EPA to speak today on this topic, because it is very much an emerging topic on the Australian environmental research agenda. We still need to do a lot of work to get the message out about how important it is and what a role environmental regulators and managers do have to play in dealing with this issue. It's great to see that EPA has really championed it and is working to get that message out. 

So I’m going to start with a little bit more background on AMR in general and then I'll move into more specifics on how we understand what our environmental hot spots drivers and risks and where we are in moving forward with that. So, it's the type of topic where you end up working together with a really wide range of people, and a lot of people, because it's not something anyone can tackle on their own. It really requires a collaborative and interdisciplinary research effort. I will acknowledge a lot more people later, but I'd really like to give a special acknowledgement to the key members of the research group I work with at UniSA who have been working together with me to start to look at AMR signatures in different environments and we've really been working over the past few years to start comparing and contrasting the antimicrobial signatures. It's often referred to as the resistor. Right from hospital sewers through to wastewater treatment plants, various treatment stages, and through into the products themselves that come from that such as recycled water, coastal effluents; and then the produce that has grown with recycled water, biosolids to land, and back into wildlife habitats and coastal environments, and the animals that live there. So as you've already heard antimicrobial resistance is really occurring when microorganisms adapt to resist stress and so it is a natural process that's been happening for as long as they've been around. But the impact of this is that it can be driven to evolve in different ways and towards multi-drug resistance when we don't handle antibiotics with good stewardship and we're seeing the implications of this all around the world. Basically what it results in is we most often see it in that medications used to cure infections are becoming ineffective so it's really becoming evident in a clinical setting. But multi-drug resistant pathogens are really increasingly common worldwide and we hear more and more about the rise of superbugs. This is what it looks like to a microbiologist. This is a typical plate where you've got a bacterial colony growing there and these discs have different antibiotics in them, and you can see that where the colony is growing right up to the disc it means that antibiotic is not effective against that bacteria, whereas when you have a nice clearance like this depending on the width of the clearance you can say whether the bacteria is susceptible to that antibiotic or not. 

So Andrea mentioned but really one of the big drivers has been that there's been a lack of incentive in the drug development pipeline to create, or find and discover, new antibiotics. From the introduction of penicillin which was first used therapeutically during the Second World War and was remarkably successful in lowering death rates in soldiers, we had the golden age of antibiotics, through here where these are all different classes of antibiotics. So within each one there may be dozens of different drugs that are developed, but they have different modes of action against the microbes. 

So basically since this period here we stopped having new classes of antibiotics discovered and it's largely driven by economic reasons, because if we, I mean we're at the point where we really need new classes because we're having pan resistant outbreaks where you really can't treat those bacteria at all when people die, but it's not really a very good incentive to drug discovery companies, because if they develop one the international community will want them to not use it very widely, but to restrict it and save it for those people that really need it. So that's not a very good proposition to a drug development company. So the effects of selective pressure really what drives this and this occurs in all different environments. So you can imagine that if this is someone's gut and you have a population of a bacteria that is causing an infection, most of them are susceptible to the antibacterial you're going to apply but there are a couple of resistant bacteria there. Once you take the antibiotics the proportion of the resistant bacteria will gradually increase and if you stop taking the antibiotics that if there was a cost associated with carrying that resistance. you may go back towards the susceptible population but generally what we see is that you know this doesn't always happen and it depends what combination of therapies are used and how often. And this holds true in any environment so it could be you know in an animal gut, it could be in the environment where we have these stresses present acting on our microbial communities. So that's really the basis of it. And there are several different ways in which bacteria can acquire and transmit resistance. So we have vertical transmission where basically a bacterium might mutate to be resistant to a stress and over time just with normal cell division more and more of the population carry that as long as it doesn't have a fitness cost which causes them to not survive. 

But what we're really worried about with multi-drug resistance is horizontal transmission and what's scary about this is that bacteria can basically share DNA pass it one to the other. So if you put a stress in place it's very easy for a resistance to spread through populations quite rapidly by sharing bits of DNA. So in the case of a plasmid they can transfer it directly one to the other and plasmids are circular pieces of DNA that tend to carry lots of different types of resistance. So it's separate to the chromosome it's carrying auxiliary genes that aren't needed for the cell to survive but if there's a stress there that makes it useful to have that they will they will share and carry these plasmids and what we tend to see is that they not only have antibiotic resistance on them, and often to several different classes of antibiotics, but also metal resistances and other types of genes you know that might degrade different types of organic pollutants, so that effectively if one of those stresses is there you select for resistance to all of the things that are carried on that plasmid. So that's quite a major thing that we need to look at in AMR. 

What's particularly scary is that these horizontal transfer mechanisms work across species boundaries. You might have one type of organism carrying it but doesn't mean it can't pass it to another type of pathogen. That goes as well for the difference between a commensal organism that's not causing disease, but it's in your gut. It doesn't mean that it can't pick up a plasma that's making it resistant and hyper virulent. So yeah we have other mechanisms phase transfer where a virus that infects a bacteria actually picks up bits of that bacteria's genetic material and transfers it to other bacteria infects. And also if we have a process such as chlorination for example that breaks open the cell bits of that DNA that aren't degraded can actually transfer into other bacteria that have survived the process. So this is a snapshot of what it looked like in Europe in 2015 to an infectious diseases physician. This really shows the resistance to last line antibiotics in key nosocomial infections. These are actual organisms causing hospital healthcare associated infections. So people often contract a resistant infection in hospital. Because they're usually in a vulnerable state. So you can see here that these third generation cephalosporins and carbopenems are some of our last sign antibiotics that we try to reserve for sicker patients. But increasingly doctors will go to use them and find that in fact that bacteria is resistant to those. So this great cause for concern particularly when you think that some of them can transmit between speed across species boundaries. This is why we talk about approaching a post-antibiotic era. There are cases where it's quite often that people might not get the treatment they need because they're in a developing country and the drugs not there unable for them to take it, or they may get prescribed the wrong drug, but now we also see these cases where there's literally no available drug left to give that patient and they die. This is happening you know in the US and in highly developed countries. 

So we see that it really is an issue sorry more doom and gloom I'll move on soon. 

Anyway we're on the cusp of this post antibiotic era and we already talked about the fact that it's predicted to cause more deaths than cancer by 2050. This led the World Health Organization to declare a global health emergency and they called on all nations to act and to develop a national action plan. So there's the World Health Organization's global action plan calling for this and Australia responded, this was in 2015, we responded the same year with our first national anti-microbial resistance strategy. I say we but I had nothing to do with it. Basically in this in both accounts the call is for us to take a one health approach to dealing with this issue because it's not just something that affects clinical medicine. Animal industries have a large role to play and it and obviously impacts on animal industry businesses if their animals are coming down with resistant infections that can't be treated. It can have large impacts for business in terms of milk production things like that but also companion animals and again into the environment, and we need to think I’ll show you a lot more examples of that so I won't go on now. 

But since our strategy came out we've increased and improved the surveillance system around medical surveillance in Australia clinical surveillance it's still partial information going in based in you know on different streams of information but we're starting to get a good snapshot of how the situation is across Australia. We've seen that we were high users of antimicrobials that often a lot of the antimicrobial prescriptions given were inappropriate so they're given when a patient isn't actually showing signs of illness or it's the wrong antibiotic being prescribed. So there's a lot of work to be done still on stewardship in Australia. But it's not really the focus today. The focus is where does the environment fit in all of this. 

So I mentioned that I think that it's an ancient ecological phenomenon to develop resistance and indeed the vast majority of antibiotics have been discovered from environmental microbial communities. So right through from penicillin and through the discovery pipeline and even the most recently proposed new class of anti-bacterials was found in soil using this ichip device. So the soil microbial communities are incredibly diverse and that's why we have the potential to probably find many more antibiotics if the money and time is spent to do that.

But on the one health side, So when we talk about antimicro resistance in the environment we have to think in three different types of pollutants. Basically the antibiotics or antimicrobial compounds themselves are environmental contaminants to be considered, but so are the antimicrobial resistant organisms and so are their genes and the genes we can kind of think of if you're used to environmental monitoring in the same way as you'd measure a chemical in the environment, in a matrix you can also measure the quantity of particular genes. So what do we have we have antimicrobials being used in lots of different environments in people in animals in hospitals but also people at home in the community. They are very active compounds but they're not completely metabolized in people. Something like up to 70 can pass through unmetabolized and depending on the compound. And again they're not always removed in conventional wastewater treatment processes so some are getting out into the environment. Some are used directly in aqua farming and straight on in horticulture or in animal husbandry in environments. So of course there's manure pathways to consider and things like that as well. So it's really a one health issue. 

Because people realize that wastewater had a key role to play in this, because a lot of the resistant organisms might be linked to you know enteric pathogens and things like that, wastewater became a real focus for AMR and the environment and you know how effective is our treatment in dealing with this. But we have to always remember that the vast majority of wastewater around the world is not even treated at all so you know we're very lucky in Australia that our wastewater is treated and we might be lowering these things although not as well as we might hope to if we optimize treatment for it, but we still have all those questions to answer. But in other parts of the world you know the waste is going straight into the environment and that as you'll see also impacts on the situation globally. so there's been a lot of interest in looking at treatment plant efficiency but also in different types of environments and you know what are the fate of these bacteria in the genes and so on down the train. So we are interested in the next part of that which is recycled water, because where I work in south Australia we recycle a lot of water and we move more and more towards that. It underpins a lot of our industry sector and horticulture viticulture agriculture through those water supplies. So it's very important that we stay on top of the risks but we use it in a very wide you know we use recycled water for urban greening and ovals for food production to make good habitat areas for birds and so on. So it's very important, as our biosolids which we also reuse 100 of our biosolids in agriculture in South Australia which is obviously another product coming from the wastewater treatment process. So wastewater contains a really wide variety of chemical stresses, not just antibiotics because of course we have all these different sources coming in, and we need to think about what's happening to those in the plant and where they're ending up. But it's not just the chemicals that's very diverse. One of the focuses of a lot of research has been on the treatment process and that's because it's a biological treatment stage. 

In case you're not familiar, for example in conventional activated sludge we basically have big reactors where we maintain these really robust microbial communities. And their job is to improve the water quality and part of that is in degrading organic compounds. So what we are inadvertently selecting for is bacteria that carry resistance there. And it may be that with them carrying resistance to metals but doesn't mean it's not selecting for resistance to antibiotics. 

So the reason for this is that if they if they're not resistant to pollutant pulses and an industry release something above their permit or what have you then basically the process breaks down and we can't settle the sludge in that system and decant off the clean water. This is what happens when the community gets stressed and we lose the whole treatment process. But there's other stresses as well such as the disinfection stages at the end of the treatment process. So it is a very diverse community that lives in a wastewater treatment plant and I guess I just want to show you how complex it is because we need to think about all of these different - this is at the genus level - but different bacteria going in are carrying different combinations of resistance. They're interacting in these environments and they have the potential to transfer genes so here in these networks we basically, see for example in red, these are genera that are most characteristic of the influent coming in and they're being removed through the treatment process, which is why they're all red and not a mixture of red and blue and these are basically transient communities. They're coming in they're often the things like e coli and the entire pathogens that we want to remove and that's what the treatments may have been originally designed to do. So we have other things that are characteristic of our effluent communities though and we need to look a bit more carefully at what exactly that is and go beyond our indicator organisms to understand it better

On the other side with the sludge communities, you have also characteristic communities that contain similar or different organisms but you have some that are also present in all of this. And then what this shows here is that for example alcobacter are most closely related to the influent community they're not really coming out in effluents. But they're being partitioned out into the sludge side of the treatment process. So we have very powerful techniques now to start to really pick apart this. So the point is it's very complicated on the microbial side but of course the chemical side is just as complicated. 

We have pretty much every chemical we use in society ends up in wastewater and we expect to have it taken out which is quite a big ask. Particularly when you think that any of those compounds going in can go down biotransformation pathways, can become lots of daughter products which have their own pathway, and it's an impossible task at this point to know what are the effects of all of those compounds that we're putting into these systems. 

On the spatial scale it varies as well. This is a map of some different metals in a biosolid sample of the micro scale. And you can see that a bacteria living just here for example is going to have a high copper stress but one over here isn't seeing any copper at all. So the complexity of it and trying to understand the selective pressures in this system is really quite difficult. 

We use a whole range of different methods to get to the bottom of this now. We're very lucky because the methodologies and the approaches have moved on a lot in recent years. So we can use different molecular biology techniques to detect and quantify genes. We can also use omics based approaches where we take DNA or RNA and sequence it in order to find out who is in the community and what exactly can they do what resistances are they carrying what function do they have - what positive functions because bacteria have a lot of positive functions for us in society as well. And then we have classical microbiology which still plays a really key role because without an isolate we can't sequence that particular bacteria's DNA and move towards genomic epidemiology approaches, which is what we're doing more and more to track outbreaks and stresses. So I mentioned the possibility for different stresses to still select for antimicrobial resistance. This is an example where we have a metal pulse stress on a wastewater influent community. And you see very clearly that here's the control community. This is just the main taxer at the genus level, but you see with an increasing levels of silver or of copper or zinc,

when we put that pulse of metal in you very quickly change the community structure. And that can persist at the high metal concentrations even a week later and where they've reverted whether the stress was less they don't they haven't gone back to the original community. So we have to just bear in mind you know how much of that is going on is a big task to try and understand this and how it fits with risk assessment. If we can use some gene screening approaches using things like APCR array to look at specific resistance genes and how if there's a bit of a signature about which ones are present. For example here we look at whether they're more there's more presence of these genes in the influent compared to the effluent and you see that we do remove through the process quite a lot of those but what we have to consider is do we remove them completely are they in something that can regrow, are they just below detection limit for example and I’ll show some more information like that later. 

We also see again that the sludges contain a wide variety of resistances and when we move through into the biosolids we see this strong signature of that remaining into the fresh biosolids. But as a result of the aging process a lot of those genes are disappearing as the bacteria dying off during the aging process and also the DNA is getting degraded, so that's a positive thing. We need to think about how we manage those processes to optimize this as well. I was going to show some data where you can really see the depth of how you can probe these communities and this was taxonomic information and this is resistance gene information. 

There are literally thousands of genes we can screen for that were known or putative resistance genes and that's growing all the time as we find more out. But you can you can start to see when you delve down into that that there are you know rarer genes that are in emerging outbreaks that unless we spend a lot of money on sequencing we won't pick up, but there are characteristic genes they're very common in the environment now. A lot of things like tetracycline and sophonomide resistance genes we use so widely as growth promoters around the world in animal husbandry that they're literally present now in every environment and it just goes to show how important it is to manage properly, because there are other things that have been withheld from animal use in Australia which we don't see so widely like that. 

So when we take that kind of data we can start to visualize it in different ways, there's literally you know these are huge data sets but we can take a snapshot here. This is a coastal water transect down a coast. And you can see that some resistances are much more characteristic in this part of the transect and others are here. We can start to use machine learning approaches and other types of modelling and methods to interrogate the data and see if there's characteristic signatures of different environments and how that links up with the organisms that are present there and this is all the information that we need to somehow put together to come up with a strong risk assessment of which genes are important, which ones are we're seeing where there's greater pollution, which ones are linked to hospital outbreaks, you know if we're going to pick something to focus on to do risk assessment which one is it and which approach do we take. That's about where we are at globally with how to deal with AMR and the environment 

Over here you can see as well though it's pretty characteristic. This is just a range of vancomycin resistance genes in some different sludges and biosolids. You see immediately that there's these two samples that have the greater diversity of those genes. These are fresh sludge samples and these are the biosolid samples. So you can see that our treatment processes and stockpiling and so on are effective in reducing these gene burdens, but we need to work out you know to what level do we need to reduce them to and which ones do we really need to be concerned about. 

We can take all this kind of data and start to make comparisons. Again this is at the genus level. But for example we can compare the communities in a wastewater influent and effluent. We can see let's go beyond indicator organisms which ones are being really effectively removed as a result of our treatment processes which ones tend to make it through but they're being removed but not quite so effectively. And then what is the composition of the of the community that's really coming through and not being removed. Is it containing organisms we need to worry about, or you know we're selecting for super resistant organisms in our in our water at the end we need to know this kind of information. And again we can do things like compare a surface water and a sediment see if particular organisms and genes are more likely to build up in the sediment might be a problem over time, or a good target for surveillance

Now we use different approaches to really understand this on a specific level uh this is unpublished data so I couldn't say which genes they are. But this is effluent recycled water effluents and we're basically focused on really key emerging risks that are popping up in clinical outbreaks around Australia and we've lined up our assays to exactly match those clinical assays so we can say that you know this has epidemiological significance, because these are things that are either just popping up in outbreaks or not here yet and we want to see if we detect them in environmental systems. When we use DNA we would also pick them up even if they're actually you know just present and the bacteria has already been killed so we do the RNA as well to see if these genes are actually being expressed are they in an organism that's metabolically active.

And what do we see well a lot of them we didn't pick up. We don't pick up in the influents we don't pick up in the effluents and that's very good. Others we do see are already in wastewater but they might not be causing clinical outbreaks. Now that might depend on what organisms carrying them and we at the moment we're at the technical limits with how we combine that kind of data and that's a real key thing that people are working on around the world is coming up with methods to work out which genes are in which bacteria but using big data sets.

And then we see with the RNA you know we see that actually a big part of that, we're seeing the same pattern, but they're definitely in organisms that are metabolically active but then if we hold that water for seven days incubation and see what happens then with the RNA suddenly we see this one pop up which is one that we wouldn't like to see there. But it's actually in so what has happened either it's an organism that made it through the disinfection process but below detection level by this method, and then after regrowth we can detect it or it was in an organism that died during the disinfection process but the DNA has been taken up by an organism that survived and that's grown. We don't know so these are the kind of things that we need to clarify but we do see that we see you know. Here again this one was not present over here but it's there's regrowth here. This one's decreased so that's probably linked to the fact that that's an organism that hasn't grown well in the incubation. So it's a really dynamic thing to try and do risk assessment on. 

But if that just in case that's uh concerning I'll just point out that, you know all environments are containing these things that we need to take into account in risk assessment, so we really have to have baselines and benchmarking comparisons across environments. These are carbopenem-resistant enterobacteriaceae which is a particularly concerning group of organisms because these are causing some of the worst outbreaks and predicted to cause an increasing number of or a large proportion of the deaths that predicted for AMR and these are isolated each plate is from one mil of water from a dam on my property. And it's fenced so there's no livestock in there it's literally rainwater going into an open dam. This is from a recycled water in an urban environment it's a mixture of storm water and runoff and mixed with some recycled wastewater. You can see uh that the organisms that are living there are different I suspect both are linked to the birds that live there. And what do we see with the recycled water uh from nine liters so these were from one mil from nine litres we couldn't we couldn't get one single colony. So we have to really compare between environments because often we think of something in the environment as being cleaner but it isn't necessarily and what happens with farmers growing salads and things if they're with recycled water, they often do things like shandy their recycled water with an on-site water supply which might be an open dam and what they might do is actually increase their risk so these are the kinds of things that in terms of food chain security and protecting industries, we need to get to the bottom of these kind of things and optimize our on-farm water management. Same thing with managed aquifer recharge often we think people are happier to see recycled water go back through a natural system or an aquifer, but it doesn't mean that the water coming out the other end is necessarily better than what went in. 

So aside from looking at all the impacts from those processes and from what we're releasing from society, we can also use wastewater in a really positive way which is to see if we can use it to detect emerging risks and to help clinicians know what emerging risks are coming as well. So we already have wastewater monitoring done for public health benefit through the national wastewater drug monitoring program. But this is all focused on illicit drugs. And there is potential to extend that to antimicrobials particularly because the information we have is partial. Because if you base it on what's prescribed most a lot of people are getting antibiotics that they don't take the whole course or they actually don't take them at all they just got it because they were going to go overseas, or we don't know, but that makes it very difficult to really link up parts of the stewardship and work out exactly what's happening. So there's potential to use wastewater in a really positive way like that and in this paper we've also explained how it could be we can use it for more and more pathogen monitoring and looking at microbial related risks.

We see emerging reports of how people traffic these things around the world and we can pick up the indications of that even on airplane waste water and airport wastewater and we can potentially use these things to monitor what's coming into the country as well. I just put this I was looking for a airport plane picture and I discovered that there's a hotel chain called AMR hotels which I thought was rather unfortunate. 

This is actually a bit of an issue for health workers. There's plenty of reports coming out now showing students that go on working in an anti-microbial hot spot in some countries will return actually with positive carriage of of ESPL's (this is extended spectrum beta lactamase resistant Enterobacteriaceae). These are really a key emerging risk, but in this case for example this is looking at this is the largest study in The Lancet that looked at how many of people coming back from overseas were positive for ESPL's after travel that hadn't been beforehand. It's over a third of the people and then what's very interesting is how long does it take for those people to clear it from their system. Remembering that it's going into our wastewater at that time. How long does it take for it to establish in the community. And what we saw was here that yeah so 65 of 577 of the travellers with persistent carriage were still colonized at 12 months and that the probability of transmitting that to another household member was 12 per cent. So this is why it's such a global issue because it doesn't in a way I mean we can make things better by having good stewardship and good environmental management here but it's only by acting as a global community that we can really address it everywhere. And so we see this as we use genomic epidemiology methods more and more you can start to see the same - you can basically track clonal outbreaks -  so you get sort of different strains of bacteria and so you might have some that are not really very virulent or don't cause disease, but others become super successful and established in a particular hospital or environment and then transmit to another environment and again take off there. We can track that now and it's really interesting people have looked at you know pathways of travel and so on it can be used to track even you know the transmission and establishment within hospital facilities and so on. But here these are all different countries. It's looking at the emergence of methicillin resistant strains here and then some at some point there's picked up the fluoroquinolone resistance and then you can see you know specific patterns of successful clones linked to different countries, but also that sometimes they may pop up something very similar to that might pop up in a hospital somewhere else in the globe and so on. 

So we're starting to do global collaborative work to try and look at things like for example compare influent wastewater and effluents to see if it links up with what we see in clinical outbreaks around the world. In this case we were looking at kef kefir taxon resistant fecal coliform so they're it's an important antibiotic for reserve treatment and we're just we're the only Australian partner in this but in our recycled water we wouldn't pick up any but we certainly have them in our influents. In other parts of the world they're picking them up very much in the effluents as well. So we can see that environmental management is going to play a big role. 

I mentioned we go in the sewers under the hospitals, so in this study we were looking at a time series across different wards. This is oncology specific wastewater, long-term care and we do other wards like Emergency. What you see here is that again I couldn't say which genes they are but we see some that you know routinely there. These are ones that we know are linked to current clinical outbreaks. These are ones that are emerging around the world as really key resistances that we don't want to see and in some cases we're picking them up in a few clinical outbreaks around Australia. Not very often in the hospital wastewater but they're there. And you know that might just be linked to one patient going to the toilet. But what we see with some of them is that they're routinely there in our influent wastewater at all our major treatment plants, which means that they're already in the community and it does indicate that we can use this for wastewater based epidemiology. And it's not just humans that are trafficking drugs resistance around the world, it's birds as well and other migratory animals. There are report increasing reports of you know whales carrying drug resistant pneumonia or dying from other marine mammals fish carry a lot of AMR, so but there are key pathways so you know flyways for birds.

In this case for example this is the East Asian Australasian flyway is quite a key pathway influencing us and what's really important is it goes through known hot spots of antimicrobial resistance that have developed especially where environmental pollution control has been very poor and where these countries now are really trying to deal with the fact that you know they had great industrial transformation without very strong environmental controls and they now have the signature of that that they need to deal with. But we're linked through our water bird environments and other environments. Not only that but here's a treatment plant for example and this is a key part of the Adelaide International Bird Sanctuary. So there's a lot of connectivity between different environments. This is a local example from some researchers that compared AMR carriage in birds. There's a wastewater treatment plant in Melbourne down here and these are in Antarctica and they certainly pick up that - it depends on the species as well, so I’ll just mention that it was that my dam that I showed is full of wild ducks and here again we see the greater diversity of carriage of resistance genes, but also a greater burden overall in the ducks in the urban environment but what we have to start to understand is how much of this is from the wastewater for example in the lagoons and how much is coming from the docks bringing it in with them through those pathways, because I think what you see from looking at different environments is that it goes both ways and we need to understand that because if we want to produce good quality water, we need to understand the risks of different species and what they might be transferring to other vulnerable species that are using those environments. 

We certainly see a high prevalence of really nasty resistant strains of bacteria in goals for example, but we know they also forage in a lot of uh waste facilities. So zeranoses and AMR this transmission between animals and humans is very key a lot of the transmissible between and we see there's a lot of interesting work done on companion animal to human transmission but also between wild birds moving things in and also that humans can also transmit back to animals, so what's the impact of our health also on wildlife and other environments so I put in the buruli also because it's a good local example which seems to have an environmental transmission component still a bit up in the air but is it possums and a mosquito vector, it could be, but as you see you know there's one of the problems that reasons it's such a issue is because it doesn't respond very well to normal antibiotic regimes. So I’m nearly finished I just point out there's some really interesting studies coming out starting to link what's in the environment to epidemiological outcomes. This beach bum survey is one where they sampled faeces from the different from surfers and non-surfers and started to come up with the numbers of how much greater their carriage of antibiotic-resistant organisms was compared to non-surfers and put some numbers on the risk because these are the kind of things we need to complete our risk assessments. 

And as I mentioned you know it's very much linked to invite to contamination. Some countries produce antibiotics but may have very poor environmental controls on their effluents. In some places there's certainly reports that you know the concentration of antibiotics in their rivers is higher than the therapeutic levels, and that's acting on fish and all the other organisms there, the birds feeding on them and so on so it's very much a one health issue you can see that hopefully clearly now and I've just put this slide from Ausgem there which shows how some of the things fit together and what we need to consider in doing the risk assessments. Ausgem is the Australian center for genomic epidemiological microbiology and we're working with them more and more to look at how you know how do things transmit between in different environments and how can we use these approaches that we've been developing to line up human animal and clinical surveillance and start to really understand the risks and hopefully be able to predict and make software that that can help organizations manage their particular risk, because obviously it's different for a water treatment company compared to animal industries, but in terms of protecting supply lines it's really important that people understand and use these approaches to detect where contamination might be, where key transmission points are and so on. 

So, a little couple of slides just to show how it links to environmental regulation. I won't say much but this this is a useful reference from 2016. It's written by people in the UK environment agency and they just point out that environmental regulators monitor and control many of the pathways that are responsible for resistance driving chemicals and also for the bacteria and that it needs to be a key part of our action plans but that there's still poor fundamental understanding of many of the key issues and there's a lot of work to do. But here they've put in red for example places at which regulation is relevant to their organization and obviously to other environmental regulators as well. So just to conclude I think it's clear that AMR is a one health issue and that we need multi-sectoral action to manage it. It's not just antimicrobial chemicals but it's also the resistance genes and the organisms that are contaminants of emerging concern. We are a very small way along the path to being able to do proper risk assessment and management but we have certain things that are being identified as hot spots but we have very partial information about what environmental signatures of AMR look like and how a pristine environment differs to a polluted environment. It's not just the effects of animals and wildlife on global AMR dissemination but also the impacts of anthropogenic induced AMR on animals and wildlife that we need to consider and how are we going to do the risk assessment, that's a really active area of international collaboration and research and how do we line up surveillance systems so that we can really make the most of our resources and do the best mitigation possible. 

So and there's some more people to thank.


Andrea Hinwood: I know there's a reason why I prefer chemicals in the environment for microbes. This is very complex. So I think what's interesting for me is about as an environmental regulator we should we should actually be putting our efforts, because we can under we already undertake surveillance on chemicals and to some extent we have a look at anti-microbial chemicals, but we're certainly not looking at resistance genes or resistant organisms. 

From a starting point where do you recommend we should be starting to put our effort in this space? 

Erica: Yeah so I think it's a good question. It's probably we're at the point where we need to really do wider benchmarking particularly across our own environments because we know that the resistance signatures differ in different environments different countries and you know without doing benchmarking and understanding what a clean environment looks like or a good quality effluent we really can't we can't manage it properly but we don't have that data across a broad range of environments or at this point and what's most important is, for me as a researcher, I’m quite passionate about the fact that we should be working collaboratively and we should be trying to align our methods as soon as possible, because through the sequencing technologies, for example if people sequence to different depths they'll have different you know they may or may not pick up key resistances, but that all depends on yeah aligning techniques in order to be able to compare across environments properly and make the most of the resources. So I think that's very important and I would like to see a lot more collaboration and networking on that front towards having some standardized approaches. 

Andrea: I‚Äôm sure there are lots of questions please we have Erica now ask your questions while you have her. 

Audience member: It's the follow-up question from your question and answer that here now. So is there a national program in Australia I‚Äôm speaking about in relation to one health and antimicrobial resistance now. I guess I asked that question because I’m in another meeting now down the road on antimicrobial resistance that's in the hospital environment. Steve George is speaking there and you mentioned the paper and he was speaking at this minute on that problem. So I guess what I what I'd like to ask is, is there a national program that that brings together, as you described we need to have consistent methods, consistent approaches and communication across those multi-disciplines that are involved in AMR in that one health program, can you just think a little bit about. 

Erica: Sure I’m very happy to actually because Steve is a key collaborator of us, and I mentioned Ausgem, so we've just been successful in getting a medical research futures proposal fund, but it's stage one funding to try and set up exactly that. A system that can feed in all these different data streams and start to really have a strong basis to do risk assessment and management, and across the environment, agriculture and animal and human health sectors. 

So it's just been announced last week. We basically have one year to come up with proof of concept and show how that could work together. It's a lot around software development and merging very different data streams. We hope to move towards having an Australian surveillance method.

Audience member: What did you call it? I spoke briefly with Steve this morning apologizing I couldn't be in his talk, because it was on when I was coming here. I’m heading back to that meeting. What is the name of it and who's involved in it and how are you going to go out to the world of persons who would the world in Australia should I say interested in this topic? 

Erica: so at the moment it's so it's called the outbreak consortium and it's moving towards being able to have surveillance and prediction and management of outbreaks but also on a smaller level supporting industries that need to understand their particular focus. The consortium has 14 different organizations included so it's led by UTS, Ausgen we're leading the environmental and wildlife and water component and then there are various other universities, but also key enemies like microbe who monitor the gut human gut microbiome there's a SACS institute who have the 45 and up study so they track patients or cohorts over a long time. 
So what we don't have at the moment is this kind of data to say if you go into hospital and you're carrying a particular resistant organism that you picked up, what's the difference between your expected health outcome and someone else who is not carrying it. If you go into this combination therapy or this chemotherapy, if you become immunocompromised and so on. So we're moving towards being able to combine these kind of data streams which really it's very powerful, but it's a big exercise in data security and in how to line these things up. So other organizations that are involved CSIRO, health and biosecurity New South Wales. DPI, they’re a major funding partner of Ausgem, and I’ve been spending a lot of time understanding AMR and how to manage an animal husbandry. 

There's a whole group of us, but we are having our kickoff meeting next month and we'll be we'll be using the Illawarra region in New South Wales as a pilot area because it's one health area, one organizational health unit, so it's easier to look at in that context. We have a lot of data going in and then the idea is to look at how we can roll it out Australia-wide. Along the way we're trying to engage with lots of different partners, but I would like to have an environmental platform so that we really have a strong communication and networking on the environmental side. That's always, in every country, it's the weakest point of the one health triad basically. 

Andrea: Okay question here. 

Audience member: My name is Eric, so originally from the Netherlands, I've been privileged to specialise at the world's best hospital in Dubai 20 years ago it doesn't have the issues that we have in every Australian hospital.

Unfortunately, it doesn't get researched, has been made with off-the-shelf components from Sweden from the Netherlands and from Germany. It doesn't use air as a distribution medium for energy. For distribution of energy we use air. There they use water. Why are you not focusing on that? Because it kills millions of people. 

Andrea: So for the people who are online, the question is from a hospital in Dubai, you don't experience these outbreaks, because you're using different technology for heating and cooling etc. So why aren't we using that in the Australian context. Is that right? 

Audience member: the research is not focusing on that. 

Andrea: Can you comment on that? 

Erica: So are you talking about specific organisms though, or specific infections.

Audience member: I nearly died from one of those, golden staph was one of the major ones .Yeah we have in every hospital, but that hospital in Dubai doesn't have it at all. Most Swedish hospitals don't have them at all because they use hydronic heating, hydronic cooling, and the air conditioning inducted systems are growth paradise for these specific bacterial groups, but it doesn't get addressed. I get vilified, I get pushed off the stage by our neighbours. IRA. I've been eliminated out of a committee to fix these massive problems with hospitals.

Andrea: So the question is about golden staph and being present in some hospitals, but not in the ones that you've experienced and whether anyone's actually looking at that.

Erica: Yeah I think yeah it's a key issue in Australia obviously. It's one of the major superbugs that we see coming up commonly. But I think one of the problems with MRSA is that most of it is contracted in the community. So it's not just something we can solve by hospitals. I mean if you go in for a hip operation now, and you're vulnerable because you're an older person, they screen you first to see if you're carrying staph aureus, because a large proportion of population will be carrying it in their nose, or on their skin, and they're vulnerable to infections. 

So I think there's a lot being done specifically focusing on MRSA. We do have some yes special clones in Australia that have been really successful. It's not my specific area but I know there's yeah a lot being done. But certainly I think you're right, the hospital environment there's also a lot to understand about how to optimize surfaces and you know they've realized by starting to do surveillance that the backs of chairs in hospitals are a key point where you know can be a transmission point. People stand like that. So we have to do a lot about understanding you know which key surfaces to clean. I think it's a resource limitation issue though, because we can't just go and build a new hospital everywhere. 

Andrea: Okay another question over here, yes?


Andrea: the question for those online, any food standards bodies looking at this area at the moment. 
Erica: Yeah I’m just starting to look more into that, but as an example the Centers for Disease Control in the US, which monitor and are involved whenever there's a foodborne outbreak in the US, they collect isolates now from anyone that they think is linked. 

You see how complex the supply chains are, because you know when you have an outbreak it might be across 20 states, but there might be three people in that state, 11 people in that state, but they'll link it back to the same source. They're doing that through genomic epidemiological approaches. It's not you know a surefire method. They can't always do it quickly. That's why you see that they may withdraw the whole you know product from sale until they work out where it's coming from. But certainly with lettuce outbreaks that that's proving very successful and each isolate is now screened for antimicrobial resistance as well.

Andrea: Question up the back, yes? 

Audience member: Hi thank you very much for your presentation and I’m from Safety here Victoria and part of our work is to try to improve antimicrobial stewardship in the hospital setting. And just you referenced Australia's national antimicrobial resistance strategy, which was released in 2015 and expires this year. The biggest gap I think in the strategy is that while it acknowledges the one health aspect of AMR there's no mention of the seven key objectives of what is happening with the environment. Environment wasn't involved in that. Is that going to change the next strategy? 

Erica: So I’m not directly involved but I’ve been asking that same question last week.

Andrea: It is a question about the strategy in 2015 and that it was absent in terms of the environment and the role that environment plays in terms of AMR.

Erica: Yes so in that strategy you're right it says one health which is what's in the World Health Organization global action plan. But one health really did emerge from aligning animal and human health and so that's why globally environment has been playing a less active role. But we're realizing how much it is left out. When that action plan for Australia was released, it was a joint press release by the minister of agriculture and minister health. No mention of environment. And when you look at the plan you're exactly right, there's nothing really about how the environment fits in. 

I think it's becoming more that you know people are becoming more aware of it but there's a lot of work to be done because it's such a new topic still to the environmental sector as well. 

I think, and as far as I know, it's going to get a mention again in the next one but I don't think we've moved much beyond that and part of that is why I think we need to have a platform where we clearly come together as a sector and, you know, show that we're on board and managing it in a unified way.

Andrea: Now I've endorsed that from the environment sector from a state-based agency is it is something that we have recognised that that has numerous touch points and I think it's something we need to evaluate the contribution that it's making and of course undertake relevant surveillance that helps us actually determine how significant this is so that's something that we hope to work on. Are there any other quick questions before we finish up.

We've got Erica for another five minutes that's it.

That's right if there are any follow-up questions, and I’m happy to take them on and provide them to Erica. 

Okay on that note I’m going to thank you all very much for coming this afternoon, for spending your time listening to this important topic. I’m sure that we'll meet again to talk about this please join me in thanking Erica very much for her time and effort today.

And we certainly wish you well on trying to sort out this very complex but important area and of course the science is quite amazing, and it's just as well we've got these new techniques because we probably wouldn't have been able to do a lot of this 10 15 years ago. 

Our next environmental science seminar series is in August. Please keep an eye out for that and we'll relate release details in the next couple of months. Thanks again, see ya.

Event date: 21 May 2019

Bacteria, viruses and parasites – microorganisms – can be found everywhere, in our environments and inside our bodies. Many are harmless and beneficial for our health, but some can cause disease. Antimicrobial drugs such as antibiotics and antiviral agents have been very effective in controlling spread of disease, and saving lives. However, the frequent use and misuse of antimicrobial drugs has led to some pathogens becoming resistant to several types of drugs. These pathogens are commonly called superbugs.

Superbugs are becoming increasingly common worldwide, and are causing a range of illnesses that are extremely difficult to treat. The World Health Organization has declared antimicrobial resistance (AMR) a global health emergency, and has called upon nations worldwide to urgently address and manage this issue.

While AMR is most commonly discussed in the context of hospitals and animal health, it is also considered an environmental contamination issue. Antimicrobial agents, antimicrobial resistant organisms, and antimicrobial resistance genes are all considered to be environmental contaminants.

For this Environmental Science Series event, Associate Professor Erica Donner shared her research on this topic, providing information about health effects, the current state of knowledge in key environments, and insights into what we can do to assist in preventing the further development and spread of AMR.

Speaker bio: Associate Professor Erica Donner

Associate Professor Erica Donner is an environmental scientist who specialises in environmental chemistry and microbiology. Her research provides a fundamental basis for environmental risk assessment and management, and she works across a range of interdisciplinary research topics ranging from the transport, fate and effects of environmental contaminants, to wastewater treatment and reuse, and the beneficial use and optimisation of treated waste products.

Associate Professor Donner leads an international collaboration project on antimicrobial resistance in wastewater treatment plans and downstream environments. She is a member of the European COST Action ES1403 Working Group on the ‘Microbiome and mobile antibiotic resistome in treated wastewater and downstream environments’ and is Deputy Chair of the Wastewater and Water Environments Working Group for the international JPI AMR ‘WAWES’ network: “Wildlife, Agricultural soils, Water environments and antimicrobial resistance - what is known, needed and feasible for global Environmental Surveillance”.

Speaker bio: Dr Andrea Hinwood

Dr Andrea Hinwood was appointed as Victoria's first Chief Environmental Scientist in 2017.

Dr Hinwood is an accomplished environmental scientist with specialist expertise in environmental exposures and human health.

Dr Hinwood was previously an Associate Professor at Edith Cowan University and held appointments as a member and Deputy Chair of the Environmental Protection Authority of Western Australia and a sessional member of the State Administrative Tribunal of Western Australia. 

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Reviewed 5 May 2021