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Livestock Waste and Treated Wastewater Can Be Reservoirs for Antimicrobial Resistance

14 March 2023by Barış Özdinç

Antimicrobial resistance (AMR) is a growing public health concern, with the potential to render many of our current antibiotics ineffective. 


A recent study draws conclusions on the potential role of livestock waste and treated wastewater as reservoirs for AMR. The study investigated the presence and abundance of AMR genes in livestock waste and treated wastewater samples collected from different locations in California, USA. 


The researchers used metagenomic sequencing to analyze the samples, which enabled them to identify and quantify the different AMR genes present. The genetic content in the samples was extracted and sequenced by paired-end shotgun sequencing by CosmosID (Germantown, MD, USA). 


Bacterial taxonomic, antimicrobial resistance and virulence factor compositions were elucidated using CosmosID-HUB Microbiome, which matched genetic sequences to those from a defined genomic database.


In this article, we’ll take a closer look at this study, its findings, and the wider impact these results have on the livestock industry. Read on to learn more.

What were the findings?

The study discovered that there were no significant differences in the alpha diversity of bacterial taxa among the various microbiomes based on the inverse Simpson’s Index of Diversity. However, differences in AMR mechanisms were observed between swine manure and other sources. 


The study also identified four resistance classes for antibiotic resistance genes in microbiome samples, with a high percentage of the virulence factor genes associated with Bacteroidetes fragilis and Enterobacter aerogenes. The network analysis revealed co-occurrence patterns between various genes and bacterial taxa. 


The metabolic reconstruction analysis indicated that carbapenem resistance, multidrug resistance, and efflux pumps were the most prevalent drug resistance mechanisms. 


Bacteroidales was identified as the primary taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. Overall, the study suggests that spreading waste from these sources can lead to the dissemination of antimicrobial resistance and virulence factors, which can negatively impact both soil and human health on agricultural lands.

How does this research support the livestock sector?

This recent study adds to the growing body of evidence demonstrating the potential for livestock waste to contribute to the spread of antimicrobial resistance. 


Additionally, the study underscores the importance of effective management strategies to reduce the spread of AMR, such as improved wastewater treatment and the implementation of best practices for livestock waste management. 


By addressing the issue of AMR in these environmental compartments, we can help to protect both human and animal health and preserve the effectiveness of our current antibiotics.


The study found that both livestock waste and treated wastewater samples contained a wide range of AMR genes, including those that confer resistance to clinically important antibiotics. 


The researchers also found that the abundance of AMR genes was higher in the livestock waste samples compared to the treated wastewater samples, indicating that livestock may be an important source of AMR. 

In summary

The study highlights the need for better management of livestock waste and treated wastewater to reduce the spread of AMR. It also underscores the importance of continued surveillance and monitoring of AMR in different environmental compartments, including agricultural land, to better understand the extent of the problem and inform effective mitigation strategies.


Overall, the study provides important insights into the potential role of livestock waste and treated wastewater as reservoirs for AMR and underscores the urgent need for action to address this growing public health threat.

How did Cosmos-ID support this research? 

CosmosID’s comprehensive, genomics-based platform enabled researchers to rapidly and accurately identify AMR genes and VFGs in a wide range of environmental samples. Using the CosmosID-HUB Microbiome, the research team was able to rapidly analyze thousands of microbial genomes from various microbial sources with high accuracy.


The results were displayed in interactive visualizations, which allowed the researchers to explore the data from various angles to gain new insights and identify patterns. The team was also able to quickly filter for relevant genes of interest and generate detailed reports for rapid evaluation.


Overall, CosmosID’s platform enabled the research team to quickly analyze and interpret their data with unprecedented speed and accuracy. The results of this study demonstrate the power of advanced genomics-based platforms such as CosmosID HUB Microbiome to provide the complete picture needed to tackle complex public health challenges.

Looking for state-of-the-art microbiome sequencing to further your own research?

At CosmosID, we provide cutting-edge microbiome sequencing services and functional metagenomic analysis services to accelerate your research. Our platform is designed to help you quickly and accurately analyze complex microbial data and generate insights that are actionable and scientifically sound.


With our suite of analysis tools, you’ll have everything you need to gain deeper insights into the microbial composition of any sample. We’re dedicated to providing our customers with the highest quality data and insights.

Contact us today and power your research.


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Barış Özdinç

Barış Özdinç analyzes microbiome research with his educational background in genetics and evolution. As a research analyst for CosmosID, he combines metagenomics and data analyses to identify microbial biomarkers in disease cohorts and evaluate microbiome research tools. His work involves curating microbiome data and creating interesting microbiome content for newsletters and blog posts. Barış Özdinç received his bachelor’s degree in genetics and master’s degree in biodiversity, evolution, and conservation from University College London (UCL). Currently, he lives in Istanbul, Turkey, where he lives with his cat, Delight, and mentors female students in their STEM career pursuits.