Antimicrobial resistance associated with the poultry production environment

Authors: Cook, Kimberly - Kim

Submitted to: UJNR Food & Agricultural Panel Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 10/15/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary: Livestock and poultry production environments are highly variable; on-farm practices, the size and nature of production, regional weather and regulations, integrator requirements, water source and bedding material all vary considerably. Due to these complexities, knowledge gaps remain in understanding the relationship between management practices, environmental factors, antibiotic use and antimicrobial resistant bacteria in agroecosystems. Research is needed to characterize resistance across multiple points in the production environment, to determine the persistence and contributing factors for resistance and to better understand the ecology of microbial communities with resistance. Poultry litter (PL) is a mixture of manure, bedding, feathers and spilled feed. PL is periodically removed from poultry production facilities and applied to soil where it serves as a valuable nutrient source and soil conditioner. Different PL management methods are used in areas of concentrated poultry production to maximize the fertilizer value of PL and reduce runoff of nutrients. However, the effect of these practices on microbial populations with genes for antibiotic resistance (AR) is unknown. The objectives of studies conducted as part of this research are to better understand (1) the effect of PL application and PL management on AR populations and (2) determine how AR is persisting and moving between environments and populations. A two year field scale study was conducted to evaluate AR populations present in soils managed by conventional or no-till application. In addition lab studies were conducted to evaluate which genes were moving from the PL community to other bacteria. Results and discussion: In soils with applied PL, concentrations of AR genes for sulfonamide and tetracycline resistance increased significantly (up to 3.0 orders of magnitude) following PL application but were near background by the end of the season. These results suggest that the concentration of bacteria with AR genes significantly increase in soils where PL is deposited but levels are mitigated by time and landscape management. Few differences were observed in soils under conventional till (CT) or no till (NT) management. In the second year of the study peak concentrations of antibiotic resistance genes (ARG) were reached sooner, were significantly lower and had fewer days above background. Results suggest that AR bacteria present in PL transferred mobile genetic elements (MGE) with antibiotic resistance genes to recipients. The recipients gained resistance to multiple antimicrobials; including those for resistance to lincomycin, tetracycline, chloramphenicol, erythromycin and gentamicin. On-going research is being conducted to determine the nature of the resistances and more importantly the MGE that are carrying resistance genes from one bacterium to another under agriculturally relevant conditions.

Technical Abstract: Introduction National and international organizations have stressed the seriousness of the current global antimicrobial resistance (AMR) challenge. These reports have emphasized the need for research to bridge gaps in understanding how AMR emerges and spreads through agricultural production ecosystems. Livestock and poultry production environments are highly variable; on-farm practices, the size and nature of production, regional weather and regulations, integrator requirements, water source and bedding material all vary considerably. Due to these complexities, knowledge gaps remain in understanding the relationship between management practices, environmental factors, antibiotic use and antimicrobial resistant bacteria in agroecosystems. Research is needed to characterize resistance across multiple points in the production environment, to determine the persistence and contributing factors for resistance and to better understand the ecology of microbial communities with resistance. Poultry litter (PL) is a mixture of manure, bedding, feathers and spilled feed. PL is periodically removed from poultry production facilities and applied to soil where it serves as a valuable nutrient source and soil conditioner. However, the high volume of PL produced and applied in some regions raises concerns about contamination from nutrients, bacteria and runoff. Different PL management methods are used in areas of concentrated poultry production to maximize the fertilizer value of PL and reduce runoff of nutrients. However, the effect of these practices on microbial populations with genes for antibiotic resistance (AR) is unknown. The objectives of studies conducted as part of this research are to better understand (1) the effect of PL application and PL management on AR populations and (2) determine how AR is persisting and moving between environments and populations. Materials and Methods Field scale study to evaluate antibiotic resistance (AR) populations present in soils managed by conventional or no-tell application. The two year field study was conducted to determine the fate of naturally occurring pathogens, fecal indicator bacteria (FIB) and bacteria containing antibiotic resistance genes (ARG) following application of poultry litter (PL) to soils under conventional till (CT) or no (NT) till management. Microbial populations were quantified in soils with applied PL using a combination of culture and quantitative, real-time (qPCR) analysis as previously described (Cook et al, 2014). Plasmid capture studies offer a means to evaluate the subset of plasmids with antimicrobial resistance (AMR) which are mobilized between complex, mixed microbial communities from environmental systems (i.e. PL) and recipient strains containing traceable markers (i.e. fluorescent markers). Recipients (transconjugants) carrying the mobilized plasmids with resistance genes (and associated determinants) can then be recovered from the complex community and plasmids captured in these organisms can be further characterized. In this research plasmid capture studies were conducted as previously described for swine slurry and biosolids. Poultry litter microbial populations served as donors while Gram-positive or Gram-negative isolates served as recipients. Recipients were captured from the mixed flora and characterized for antibiotic susceptibility. Results and Discussion Effect of poultry litter (PL) and soil management on bacteria with antibiotic resistance genes (ARG): Microbial populations with genes conferring resistance to tetracycline (tetQ and tetW), erythromycin (ermB and ermF) or sulfonamides (sulI), were quantified using quantitative, real-time (qPCR) analysis. In soils with applied PL, concentrations of ARG for sulfonamide and tetracycline resistance increased up to 3.0 orders of magnitude (OM; mean concentrations 2.6 to 6.9 x 108 copies g-1) following