How can resistance genes from livestock manure be contained?

Antibiotics given to farm animals select for resistant bacteria, and the resistance genes end up in manure that is spread on fields. The question is how to stop these genes from spreading through soil, water and crops toward people.

Question

How can we address the challenge of antibiotic resistance genes that arise from antibiotic use in livestock and poultry and spread through manure and organic waste? The question covers how strongly farming practices select for resistance, how well manure treatments such as composting and anaerobic digestion remove resistance genes, how the genes move through soil, water and crops, and which interventions reduce the risk to human health.

Background

The question belongs to the theme "sustaining healthy agroecosystems" in the 100 essential questions for the future of agriculture, selected in 2023 by an editorial panel of the journal Modern Agriculture from 419 questions submitted worldwide, next to a question on reducing or replacing antibiotic use in livestock [1]. It is a One Health problem that links animal, environmental and human health.

What is known

• At three large commercial swine farms in China, 149 resistance genes were detected; the 63 most abundant were enriched 192-fold (median) and up to 28,000-fold compared with antibiotic-free manure or soil, and their abundance correlated closely with transposases ($r^2 = 0.96$), pointing to potential horizontal transfer [2].
• Global antimicrobial use in food animals was estimated at 63,151 tonnes in 2010 and projected to grow by 67% by 2030 [3]. A later estimate put use at 99,502 tonnes in 2020, rising by 8% to 107,472 tonnes by 2030, with 67% of hotspots in Asia [4].
• Conventional livestock-waste treatments do not completely remove resistance genes, which are then released to soil and water, with several possible exposure routes to humans [5].

What would count as progress

No single result settles a question like this; contributions like these would move it forward:

• Monitoring datasets that follow resistance genes from farm to manure to field, crops and water, with standardised quantification, released openly.
• Meta-analyses of how efficiently manure treatments remove specific classes of resistance genes and mobile genetic elements.
• Intervention studies that link reduced antibiotic use or better manure treatment on farms to measurable declines in resistance downstream.

References

1. Hu, Y. et al. (2023). 100 essential questions for the future of agriculture. Modern Agriculture 1(1), 4–12.
2. Zhu, Y.-G. et al. (2013). Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proceedings of the National Academy of Sciences 110(9), 3435–3440.
3. Van Boeckel, T. P. et al. (2015). Global trends in antimicrobial use in food animals. Proceedings of the National Academy of Sciences 112(18), 5649–5654.
4. Mulchandani, R., Wang, Y., Gilbert, M. & Van Boeckel, T. P. (2023). Global trends in antimicrobial use in food-producing animals: 2020 to 2030. PLOS Global Public Health 3(2), e0001305.
5. He, Y. et al. (2020). Antibiotic resistance genes from livestock waste: occurrence, dissemination, and treatment. npj Clean Water 3, 4.

Source

Imported from 100 essential questions for the future of agriculture, question 65, curated by Hu et al. Listed as open in the source (2023) and still an active research question as of 2026-10-20. The statement above is written in our own words; see the source for the original wording, history and discussion.