Agriculture

Overview

Since the 1940s, antimicrobials have been widely used in agriculture to treat infections and promote growth in livestock. This practice has only intensified over time, leading to the contamination of soil with antibiotic residues. This further contributes to the global issue of antimicrobial resistance (AMR) – the process by which microorganisms evolve to withstand the effects of the antibiotics they encounter. Nations worldwide are increasingly recognizing the urgent challenges posed by agricultural antimicrobial resistance (AMR), prompting recent policy interventions to control antibiotic usage in the field. The World Health Organization (WHO), the U.S. Food and Drug Administration (FDA), and the Center for Disease Control and Prevention (CDC), have all implemented several key measures to control the use of antimicrobials in agriculture, which include:

• The National Antimicrobial Resistance Monitoring System (NARM), established in 1996, monitors changes in antibiotic resistance in bacteria in meats, animals, and humans (Karp et al., 2017). The NARMS does not regulate usage but rather provides insight into trends that can be used to make regulatory decisions.

• The National Action Plan for Combating Antibiotic-Resistant Bacteria (CARB) is an initiative aimed to address the growing problem of antibiotic resistance. The plan was first released in 2015, with an update published in 2020. CARB aims to reduce resistant bacteria in both humans and animals by advocating for the responsible usage of antibiotics (“National Action Plan for Combating Antibiotic-Resistant Bacteria, 2020-2025”).

• The Veterinary Feed Directive initiative, introduced in 2017, required veterinary prescriptions for drug usage in animal feed and water, significantly reducing the usage of antibiotics in animal feed (Center for Veterinary Medicine).

Despite efforts to regulate and monitor antibiotic usage, enforcement gaps and over-reliance on voluntary compliance in the agricultural sector have limited the effectiveness of these policies (Office of the Commissioner, 2019). Georgia has one of the largest poultry industries in the country, generating an annual economic impact of $25.5 billion USD and accounting for 47% of the state’s agricultural output (University of Georgia, 2017). Intensive poultry farming practices create conditions that accelerate the development and spread of AMR. Farms act as “animal reservoirs”, further amplifying AMR’s impact across the agricultural sector (Hedman et al., 2020). Through conversations with researchers, we identified there to be a significant lack of information on antimicrobial resistance levels in our local community.

Mrs. Janet Standeven

Figure 1. Janet Standeven

To address this deficiency, Mrs. Janet Standeven – director of the Frugal Science Academy program at Georgia Institute of Technology and a previous advisor of Lambert iGEM – proposed investigating soil samples for resistant genes due to soil’s status as a significant AMR reservoir see Soil Testing page. She also suggested using MiniPCR’s Testing Soil Samples for Antibiotic Resistance. Consequently, we set out to create a map plotting the prevalence of AMR throughout the state of Georgia. By doing so, we aim to help track environmental reservoirs of resistance genes, facilitating better land management practices and targeted antibiotic stewardship programs. Ultimately, this information can guide policy and public health efforts to contain AMR in both agricultural and human health sectors, helping to prevent the further spread of resistant pathogens in the environment.

Dr. Kevin Forsberg

Figure 2. Discussion with Dr. Kevin Forseberg

Initially, we planned to collect soil samples from various farms in the region. However, Dr. Kevin Forsberg – a soil AMR researcher and professor at UT Southwestern – advised us to focus on analyzing samples near waterways due to their role as AMR reservoirs. We decided to focus on the local Chattahoochee River, which is downstream to several farms and supplies over 70% of Georgia’s drinking water (Georgia River Network, 2018). Forsberg informed us that testing soil from waterways would give us a more comprehensive picture of AMR prevalence, as the river naturally collects runoff from multiple agricultural sources. Additionally, Dr. Forsberg introduced us to the concept of integrons – genetic elements that encode multiple AMR genes. He suggested that we find and use integron primers to test for several resistance genes at once, rather than only scanning for TetM and TetB, giving us a more comprehensive map of AMR prevalence.

Shakerag Wastewater Treatment Plant

After our conversations with Dr. Forsberg and further literature review, our team recognized the contamination of soil near waterways as a significant issue. To learn more about protocols addressing antibiotic residues in the water supply, we conducted an interview with our local water treatment facility’s chief engineer, John Marshall. Mr. Marshall informed us that the Environmental Protection Agency (EPA) lacked specific protocols for treating water contaminated with residual antibiotics. He also stated that the contaminated water gets discharged into the Chattahoochee River, raising significant concerns about the potential for AMR spread, emphasizing the need for soil testing from river samples.

Buford Fish Hatchery

To learn more about how antibiotic residue can contaminate waterways, we spoke to Travis Taylor, the manager of the Buford Fish Hatchery. He informed us that at the facility, fish infected with parasites are treated with antibiotics, and then either released back into the Chattahoochee River or buried. Once buried, bacteria resistant to antibiotics are selected and can spread throughout the soil through horizontal gene transfer. This emphasizes the need for regulation regarding the disposal of animals treated with antibiotics. Taking this into consideration, we collected soil samples from the mort bin and the fish hatchery in general.

Citizens in Science

Our team wanted to engage the local community by educating the youth. By holding a biotech bootcamp, we aimed to involve younger participants in hands-on science. We encourage kids to bring in soil samples from different locations for testing. This not only helped them learn wet lab skills but also understand the effects and urgency of AMR (see Education).

Frugal Science Academy

Over the summer, Lambert iGEM took their experiments to Georgia Tech in collaboration with the Frugal Science Academy. We educated our mentors on our initiatives, and with guidance from the Bhamla Lab, the teachers, mentors, and postdocs offered us with experimental feedback on our tests. Their input allowed us to gather more soil samples from various locations across the state, expanding on our dataset and providing a broader range of insights. Many of the teachers lived on farms and were familiar with the impact of antibiotics in livestock and agriculture. They directly testified to the severity of the issue, and shared their experiences of moving away from traditional antibiotics. Additionally, we were given the opportunity to mentor high school students from the state of Georgia, teaching them synthetic biology skills such as PCR, Gel Electrophoresis, and DNA extraction, while also educating them on the prevalence of AMR in agriculture (see Education).

Dr. Carol Bascom-Slack from PARE

Figure 3. Dr. Carol Bascom-Slack

The initial MiniPCR kit Lambert iGEM utilized collaborated with the PARE database– a global research project documenting the prevalence of tetracycline resistance across the world. After testing all of our samples, we spoke to Dr. Carol Bascom-Slack – one of the developers of PARE – who guided us through the database. She explained how antibiotic contamination in soil contributes to the rise of AMR by selecting bacteria with resistance mutations. Resistant organisms are able to survive and reproduce, while non-resistant bacteria are susceptible to antibiotics, therefore leading to the proliferation of resistant bacteria in soil. With the guidance of Dr. Bascom-Slack, we submitted our soil testing results to the database. With this data publicly available, we will be able to directly help scientists develop targeted solutions for AMR in our local community.

Map

After collecting samples across the state of Georgia and testing them for AMR presence, we made a map to display our results (see Fig. 4). This map serves as a powerful educational tool for our local community by providing a visual representation of AMR prevalence. For scientists, our map can also be used to develop tailored solutions to combat the spread of AMR in various locations. The map can be also used in conjunction with other data sets, which include population density, agricultural activities, or healthcare facility locations, allowing scientists to determine causal relationships between these factors and AMR spread. Our team will continue to use and add to the PARE database in the future.

Figure 4. Map showing tetracycline resistance

References