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

John J. Maurer (), Alexa Hoke, Keshav C. Das, Jian Wu, Mark A. Williams, Sydney Kinstler, Casey Ritz, Gregory P. Pittman, Roy Berghaus and Margie D. Lee
Additional contact information
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

Agriculture, 2025, vol. 15, issue 4, 1-19

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.

Keywords: poultry litter; resistome; class 1 integron (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.mdpi.com/2077-0472/15/4/398/pdf (application/pdf)
https://www.mdpi.com/2077-0472/15/4/398/ (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:gam:jagris:v:15:y:2025:i:4:p:398-:d:1590768

Access Statistics for this article

Agriculture is currently edited by Ms. Leda Xuan

More articles in Agriculture from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager ().