Tackling antibiotic resistance, one piece of possum poo at a time
Antibiotic resistance is the phrase on everyone’s lips these days, with scientists searching far and wide for solutions to this growing problem. Now, a citizen science project led by Macquarie University is seeking answers in one of the most unlikely places you could imagine — possum poo.
As explained by Dr Koa Webster, Project Coordinator on the ‘Scoop a Poop’ project, evidence of antibiotic resistance has been found in gut and faecal bacteria from numerous wildlife species in both terrestrial and marine environments — so it’s not just an issue that affects humans.
“Resistance doesn’t exist in isolation in human-associated bacteria, but rather there are connections between humans, agricultural and domestic animals, and wildlife — which means that we need to consider all three groups when we study antibiotic resistance,” she said.
“Possums are common throughout Australia, particularly in urban areas. They are an ideal species to look at to see how prevalent antibiotic resistance is in the bacteria hosted by Australian wildlife. In addition, their poo is easy to identify.”
Scoop a Poop was the brainchild of Associate Professor Michelle Power, who had an ongoing research interest in antibiotic-resistant bacteria and their presence in wildlife. According to Dr Webster, Associate Professor Power conceived Scoop a Poop “as a way to investigate antibiotic resistance in a common wildlife species, and also as a science outreach program to teach school students about antibiotic resistance”.
After obtaining a $402,000 Citizen Science Grant from Inspiring Australia in May 2017, it was time for Associate Professor Power and her colleagues to commence their investigation into antibiotic resistance in native animals — an investigation that would not be possible without the assistance of students from participating schools, their parents and Youth at the Zoo.
“Because the project investigates the occurrence of antibiotic resistance genes in wildlife populations, we want samples from as broad a geographical area as possible,” Dr Webster explained. “We could go on multiple field trips to gather our own samples, but we would never be able to get the broad range that can be covered by citizen scientists.
“In addition, involving citizen scientists give us an opportunity to provide a science outreach lesson to the schools and community groups involved in the project. We can educate about the risks of antibiotic resistance, how it is affecting our wildlife and what members of the public can do to help reduce the development of resistance in the community.”
It certainly helps that the collection kits are easy to use, comprising gloves, a jar, a swab (only for older students and adults) and an instruction card. Then, it’s a simple matter of locating some possum poo, putting on the gloves and scooping a few pellets into the jar using the lid’s built-in scoop.
“You [then] open the swab packet and stick the swab into one of the poo pellets, then place the swab in its special tube,” Dr Webster said. Barcodes are provided to stick on to the jar and the swab tube, while a sample information card helps users record the date and location of the collection.
The project will also soon be supported by a new app, free to download from the App Store and Google Play, which allows participants to log their collection location using their phone’s GPS — the information will then be sent straight to the project database. Users will also be able to view a map of collection locations as they are verified; a feature known as ‘Scatlas’.
Once the samples have been picked up from participants’ schools and take back to the lab, Associate Professor Power’s undergraduate students log the sample ID and collection information. Dr Webster said, “If the kit includes a swab, we freeze the media from the swab tube at -80°C for later culturing. The scat samples are kept in a cool room until we have enough samples to run a DNA extraction protocol.
“For DNA extraction, we use a FastPrep machine (to lyse the cells) and a specialist faecal DNA extraction kit. Once we have enough samples to run an analysis, we run a series of PCR reactions, followed by gel electrophoresis and visualisation on a gel imaging machine (GelDoc).
“Our PCRs test for Class 1 integrons, which are a type of mobile DNA that are associated with antibiotic resistance. Not all resistance is controlled by Class 1 integrons, but this is the specific mechanism that we are interested in for this project.”
Now one year into the project, Dr Webster can reveal that, according to the preliminary results, ~25% of the possum samples tested so far have been positive for Class 1 integrons. “In future, we will be doing further PCRs and gene sequencing to identify the particular antibiotics that the genes carried on the integrons confer resistance to,” she said.
“The prevalence of ~25% is a high proportion compared to our previous studies in other wildlife species, and it will be interesting to see if we see similar results across the whole Sydney basin and in more rural and regional areas.”
Although the project is currently aimed towards school and community groups, members of the public can pick up collection kits of their own at special events such as the upcoming Macquarie University Open Day on 18 August. You can also follow the project on Facebook and Twitter, or get involved by emailing Dr Webster at firstname.lastname@example.org.
“The project has started in Sydney but we are expanding to regional NSW shortly and then to at least two other states over the course of the project,” Dr Webster said. “Ideally, we would like to get samples from across Australia!”
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