Joining the fight against antibiotic resistance

The World Health Organization has beautifully summarized the threat that antibiotic resistance poses to human health:

"Key facts

• Antibiotic resistance is one of the biggest threats to global health, food security, and development today
• Antibiotic resistance can affect anyone, of any age, in any country
• Antibiotic resistance occurs naturally, but the misuse of antibiotics in humans and animals is accelerating the process
• A growing number of infections—such as pneumonia, tuberculosis, gonorrhea, and salmonellosis—are becoming harder to treat as the antibiotics used to treat them become less effective
• Antibiotic resistance leads to longer hospital stays, higher medical costs, and increased mortality"

Monitoring antibiotic resistance in biological and environmental samples is essential for defining the scope of the problem, developing interventions, and decreasing resistance selection pressure.

At Takara Bio, we find inspiration from our customers who take such challenges head-on. We recently had the opportunity to talk to one of these customers, Dr. Windi Muziasari, founder and CEO of Resistomap. Resistomap is a company based in Finland with a mission to mitigate the spread of antibiotic resistance in the environment by providing robust tools for monitoring. Windi told us what led her to become a scientist and fight antibiotic resistance.

How did you become interested in antibiotic resistance?

When I moved to Finland in March 2010, I worked as a research assistant in Prof. Marko Virta's group. I was performing DNA extraction from sediment samples from Finnish fish farms and using qPCR for the detection and quantification of tetracycline-resistance genes, tetH and tetA.

This was when I discovered AMR (antibiotic multi-resistance) and the threat it represents for human health, including in the aquaculture world. I have always thrived on doing research that can be directly used in real life, and studying AMR in Finnish farms fit well with my passion. I pursued my PhD research based on my project in the Virta group to study the impact of fish farms on the sediment resistomes (collections of antibiotic resistance genes [ARGs]).

I continued my research on AMR during my postdoc within the Antibiotic Resistance in Indonesia Project. The more I learned, the more I realized that AMR is a global problem, especially in developing countries. People were dying without realizing that it was because they were infected with bacterial pathogens resistant to antibiotics, such as tuberculosis. My uncle's wife and his two daughters passed away due to tuberculosis, which was caused by a bacterial strain that is resistant to all antibiotics available in Indonesia. They couldn't afford to buy the antibiotics still effective on this bacterial strain, which had to be imported from the US. This situation is happening every day in Indonesia and other countries. I think it is essential that we all work together to solve this problem before it's too late. Since my expertise is focusing on AMR in the environment, I am contributing to the fight from this angle. Founding and running Resistomap is the result of my commitment to contribute to fighting AMR.

Windi Muziasari, PhD, CEO at Resistomap

Why is it important to study the presence of antibiotic-resistance genes in the environment?

Most bacteria in the environment are not easy to culture or isolate with current methods. To understand the bigger picture of resistant bacteria in whole bacterial communities, we study the genes that encode their resistance to antibiotics. Of course, studying the presence of ARGs alone will not solve the problem, as it represents only one part of other complementary research that provides a better and more complete understanding of this issue.

Many studies have shown the importance of studying the presence of ARGs in the environments from which ARGs originate and disperse:

• The source of clinically important ARGs can originate from environmental bacteria (natural resistomes) since most antibiotics are found in nature.
• Environmental bacteria can act as an intermediate to disseminate clinically important ARGs. Bacterial ARGs can spread from humans or animals to nature and then back to humans or animals, especially ARGs carried by mobile genetic elements.
• Any polluted environments, including wastewater and manure, can act as reservoirs of ARGs. From these environments, ARGs are then acquired by human or animal flora and eventually transfer to pathogens. For example, in the case of "farm to fork," ARGs can be acquired by our normal flora via food. For more details, you can read this highly informative report from the AMR Alliance.

What questions are your customers looking to address, and how can you help them?

Currently, our customers are mainly research groups, and a few examples of how we are helping these groups are:

• Studying the impact of antibiotic usage for livestock
• Monitoring the spread of ARGs in wildlife
• Evaluating technology they have developed to reduce the release of ARGs into the environment (for example, a technology that will be applied in wastewater treatment plants)
• Studying the dissemination of ARGs from animal farms → manure → soil
• Examining the dissemination of ARGs from human waste (blackwater/sewer/sewage) → agriculture soil → runoff water
• Studying the prevalence of ARGs in zoo animals
• Examining the prevalence of clinical ARGs in isolated pathogens

Takara Bio's SmartChip qPCR system gives us the ability to study up to 384 genes at once, allowing us to provide the ARG data in a comprehensive format within two weeks. We offer the flexibility to choose any ARGs of interest. For example, if the customer only focuses on studying beta lactam resistance genes, we can customize the SmartChip assays to fit their needs by using the following configuration: 144 assays (beta lactam resistance genes) for 12 samples, with three technical replicates for each sample.

Currently, we are running a pilot study with a dairy company in order to evaluate the quality of their dairy farms by investigating the ARG sources at the farms and assess the impact of antibiotic use on the farms. We're also working with wastewater treatment plants and hospitals to evaluate the need for routine monitoring of ARGs in wastewater.

What methods can be used to monitor antibiotic resistance genes? What are their pros and cons?

This was the subject of my PhD thesis! You will find more information on Page 13 (Table 4) of my thesis about the pros and cons of using qPCR, qPCR arrays, or metagenomics for monitoring ARGs (input requirements, limit of detection, cost per sample, throughput, equipment requirements, etc.)

In recent years, both SmartChip qPCR technology (qPCR array) and metagenomics have gained sensitivity, and the amount of input DNA needed has gone down to as low as 0.2 µg.

Why did Resistomap choose the SmartChip Real-Time PCR system as the core technology for their services?

I am constantly reviewing available technologies enabling the study of ARGs in the environment. As of now, the SmartChip qPCR is the most popular and affordable system, providing the best price:quality ratio to our customers; the cost per sample of SmartChip qPCR is less than any other available method.

As the founder of Resistomap, I decided to work with a system I'm familiar with to jump-start our project. I have been successfully using the SmartChip system for ARG research since 2014. My own experience with the technology, combined with the features of the SmartChip system, helps in convincing our customers that it is the right tool for the job.

Furthermore, we are now developing our own software analysis tool to automate the raw data from the SmartChip qPCR system and send it directly to customers in a digital format. Thus, we can provide an even faster service to our customers, especially for routine monitoring of ARGs.

The COVID-19 pandemic has impacted everybody around the world. How is Resistomap responding to the crisis?

We are eager to contribute to fighting the COVID-19 pandemic. With our partner Nordic Laboratories, we are developing a service to monitor the presence of SARS-CoV-2 in wastewater for wastewater-based epidemiology (WBE). WBE is crucial for monitoring the spread of SARS-CoV-2 due to the nature of the virus; as most infected individuals develop mild or no symptoms, many were not tested and thus remain undetected. Furthermore, as extensive testing is challenging in terms of sample collection and detection methods (especially in countries with limited facilities for molecular laboratory testing), wastewater testing is beneficial as it provides comprehensive data for a larger population at a significantly lower cost. Wastewater monitoring for SARS-CoV-2 can also serve as an early warning system for future outbreaks of the virus, and the data obtained can help policymakers to take preventive measures that limit the potential health and economic damage to the society. In addition, the data obtained from wastewater monitoring of SARS-CoV-2 can be used to evaluate the effectiveness of interventions (e.g., social distancing and vaccination).

Thanks for telling us about the important work Resistomap is doing, Windi. To hear more from Windi about her current projects, view her webinar. We look forward to seeing what Resistomap does next!

References

World Health Organization website newsroom >>

Muziasari, W.I., Impact of Fish Farming on Antibiotic Resistome and Mobile Elements in Baltic Sea Sediment. dissertationesscholadoctoralisscientiaecircumiectalis, alimentariae, biologicae. University of Helsinki, (2016).