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The Impact Aerobic and Anaerobic Incubations of Poultry Litter Have on Class 1 Integron Resistome and Microbiome

Author

Listed:
  • John J. Maurer

    (School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA)

  • Alexa Hoke

    (School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA)

  • Keshav C. Das

    (College of Engineering, University of Georgia, Athens, GA 30602, USA)

  • Jian Wu

    (College of Engineering, University of Georgia, Athens, GA 30602, USA)

  • Mark A. Williams

    (School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA)

  • Sydney Kinstler

    (School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA)

  • Casey Ritz

    (Department of Poultry Science, University of Georgia, Athens, GA 30602, USA)

  • Gregory P. Pittman

    (Cooperative Extension Service, University of Georgia, Athens, GA 30602, USA)

  • Roy Berghaus

    (Department of Population Health, University of Georgia, Athens, GA 30602, USA)

  • Margie D. Lee

    (Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA)

Abstract

Animal manure is a desirable fertilizer because of its rich nitrogen, but it also contains a large and diverse reservoir of antimicrobial resistance (AMR) genes (ARGs). To reduce this AMR reservoir, five treatments (passive aeration, forced aeration, static or anaerobic incubations, autoclaving) were assessed for their impact on the poultry litter resistome. Bacterial DNA was extracted from the litter and the qPCR-estimated copy number of 16S rrs , class1 integrons ( intI1 ) and associated resistance genes ( aadA , sul1 ). Then, 16S amplicon metagenomic sequencing was used to determine community diversity and composition. Depending on incubation conditions, class 1 integrons and their associated ARGs were reduced by 0.5 to 1.0 Log 10 /g poultry litter. Only autoclaving reduced integrons and associated AMR genes by three Log 10 . Changes in AMR abundance reflected fluctuations in litter bacteriome composition at the family, genus, and sequence variant level. There was a negative correlation between class 1 integron and AMR genes, with genera belonging to Actinobacteria, Firmicutes, and Proteobacteria phyla. While these poultry litter treatments failed to reduce AMR abundance, aerobic and anaerobic treatments reduced taxons that contained pathogenic species. The approach to remediating resistance in poultry litter may be more effective if is focused on reducing bacterial pathogens.

Suggested Citation

  • John J. Maurer & Alexa Hoke & Keshav C. Das & Jian Wu & Mark A. Williams & Sydney Kinstler & Casey Ritz & Gregory P. Pittman & Roy Berghaus & Margie D. Lee, 2025. "The Impact Aerobic and Anaerobic Incubations of Poultry Litter Have on Class 1 Integron Resistome and Microbiome," Agriculture, MDPI, vol. 15(4), pages 1-19, February.
    • Handle: RePEc:gam:jagris:v:15:y:2025:i:4:p:398-:d:1590768
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