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Paper of the Month

Uncovering the Spread of Superbugs in the Environment – a Snapshot of Ontario Water Sources

By Clara Wong


“Catastrophic”, “disastrous impacts”, “no time to wait” – just a sampling of the fear-inspiring verbiage contained in a recent UN report that outlines the looming spectre of drug-resistant infections. Indeed, UN Deputy Secretary-General Amina Mohammed calls antimicrobial resistance (AMR) “one of the greatest threats we face as a global community.”

How abundant are antibiotic resistant bacteria (ARB)? How widespread are the antibiotic resistant genes (ARG) they develop after escaping antimicrobial agents designed to kill them?

The questions have fascinated Ryerson University Molecular Science master’s candidate Farhan Yusuf since he joined the Gilbride Lab in 2013 – not long after the research group began a four-year study on the subject.

ARB in the Environment – an Urgent Area of Study

The danger of AMR is not new within clinical settings, but awareness is much lower in another context – one that risks eventual worldwide movement of ARB: aquatic environments.

Recognizing the need, Yusuf and his colleagues Rosha Pashang, Simon Zhao and Shadi Deljoomanesh investigated this latter context under the supervision of Dr. Kimberley A. Gilbride. Their findings were recently published in the Canadian Journal of Microbiology.

Levels “Far Higher” Than Anticipated

Specifically, the researchers examined the prevalence and dissemination of tetracycline-resistant bacteria at four aquatic sites in Southern Ontario: a wastewater treatment plant and a selection of rural and urban waters.

Samples were divided into two different microbial populations:

  • Tetrr, taken from the environment and tested on a plate supplemented with tetracycline
  • Tets, tested without pressure – no added tetracycline

Antimicrobial susceptibility testing revealed that 83% of Tetr isolates exhibited multiple antibiotic resistance (MAR) – currently defined by resistance to three or more antibiotics – compared to only 43% of Tets isolates under no selection pressure.

“We did expect to find tetracycline resistance since it’s an antibiotic naturally found in the environment,” says Yusuf, “but the overall abundance was far higher than we had thought.”

Yusuf elaborates: “Our data demonstrates possible co-occurrence of certain antibiotics which can be transferred to other members in the community. For example, if isolates were resistant to chloramphenicol and ciprofloxacin, they were likely to be resistant to tetracycline also.”

Another interesting observation: The rural lake site had lower levels of ARB than the urban beach waters – not surprising. Yet, when comparing antibiotic profiles, no specific site had a majority amount of MAR. Urban or rural, all had similar MAR scores – indicating that MAR is widespread. However, when the data between the Tetrr and Tets populations was grouped together, they displayed significant differences in MAR scores, suggesting that isolates that carry one ARG it can likely carry multiple resistance genes.

Benefits of a Culture-Based Approach

A notable feature of the study was choice of methodology. Up to the present, ARG research has faced a key challenge. “Many researchers look into metagenomics for dissemination patterns,” explains Yusuf. “While this can provide more overall data from an entire community, it’s impossible to link the data points to any specific bacteria.”  

Yusuf’s group chose culture-based techniques instead. Although more labour intensive, isolating the bacteria made it possible to draw definite causal links – not just assumptions – between ARGs and the ARB that carry them.

“Connecting the ‘who’ to the ‘what’ is exactly what we wanted to achieve in linking bacteria taxa to functional genes and resistances,” says Yusuf.

Racing to Avert a Post-Antibiotic Era

Although localized, the team’s findings represent one more slice within the scope of a growing global problem. Their work identifies potential environmental reservoirs of resistant genes – and amplifies the message that managing the proliferation of AMR has become as critical in the environment as in clinical settings. “Water is ever flowing, so you can hope that ARGs stay within their zones,” Yusuf reflects, “but the evidence is not supporting that. They’re traveling. They’re moving a lot. It’s disheartening.”

Still, Yusuf looks ahead. “I’m happy that we got results from the data. We’re doing our part. But there’s still much to do.”

The group’s next projects: studying the spread of ARGs via bacterial conjugation, and investigating ciprofloxacin – a semi-synthetic antibiotic with low exposure outside a clinical setting, but for which several resistances have already been found.

The group’s work contributes to the development of epidemiological frameworks for disease management and preventative measures – noble efforts that may help avert an impending public health crisis and ensure a sustainable future for humanity.

Funding was made possible by the NSERC Discovery Grant, Ryerson Health Care Grant and Faculty of Science Booster Grant.