Performing Department
Microbiological Sciences
Non Technical Summary
Although antimicrobial resistance genes may have a reservoir in livestock herds receiving antibiotics, and in someenvironments, the processes that lead to the incorporation of those antimicrobial resistance genes into environmentalmicrobiomes are poorly understood. This gap in knowledge means that it is currently difficult to explain whether and under whatconditions the application of manure may lead to persistence and spread of antimicrobial resistance genes through the soil, and possibly crop, microbiomes. Understanding that spread over space and time is essential to devising surveillance and/orintervention strategies in farms.We propose to compare antimicrobial resistance genes and overall microbial composition in minimally treated cowmanure and in soils receiving applications of that manure. We also propose to map the persistence and spread of microbes andtheir antimicrobial resistance genes. Using spatial mathematical models, we will determine the extent to which manureapplication affects the composition of the soil microbiome and its antimicrobial resistance genes.We will use our findings in this project as the subject matter for undergraduate and graduate course activities. The persistenceand spread of soil microbes and their antimicrobial resistance genes is accessible to most microbiology students because oftheir familiarity with hospital-acquired antibiotic resistant infections. By completing our course module, soil science students willgain valuable experience in microbiological thinking just as microbiology students will gain valuable insights into how microbesand their genes spread through outdoor environments.By completing these activities, we will expand our knowledge of the whether manure application to the land changesthe microbiome of the soil environment and how much the soil microbiome can act as a reservoir of resistance genes againstantimicrobial compounds.
Animal Health Component
0%
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Goals / Objectives
Enhance surveillance and monitoring of antibiotic resistance and develop improved diagnostic tests.
Determine the ecology and mechanisms involved in resistance and transmission of resistance.
Create and deliver programs on antibiotic stewardship in food production systems through education and outreach.
Project Methods
Objectives 1 and 2:Sample site and collection. The sample site for study of the persistence and spread of antimicrobial resistance genes will be afarm plot used for the cultivation of soybeans and corn for cattle feed. The participating farm uses all major classes ofantimicrobials to support herd health and production. The field receives applications of minimally treated manure in the latespring, prior to planting. We will collect soil samples from the field and from cattle manure four times yearly. One sample will becollected prior to manure application, and a second 1-2 weeks following manure application. Two subsequent samples will beused to assess how microbial communities, indicator organisms and their associated antimicrobial resistance genes developfollowing manure applications.Indicator organism analysis (E. coli). E. coli will be isolated from surface soil samples using well-establishedmethods. These E. coli isolates will be subject to genome sequencing using short and long read technology; they will also betested for antimicrobial resistance against all major classes of antibiotics. We can compare the genomes of E. coli isolates fromsoil to those obtained from manure on the farm. Using the genome sequences and autocorrelation analysis, we can reconstructhow much new E. coli isolates resemble those from earlier samples, thus understanding the patterns of persistence in the field.We can use similar analyses to map the extent of E. coli in the surface soils of the sampled crop field. That will permit us tounderstand how manure application changes the pattern and how the pattern develops over time. With sufficient sequenceinformation, we will also be able to map the persistence and spread of antimicrobial genes associated with E. coli.Soil metagenome analysis. DNA will be extracted from soil samples from each time point. This can be sequencedusing shotgun metagenomics to detect antimicrobial resistance genes and to catalog their diversity in the soil microbiome. Withsufficient resources, we can map the spatial extent of antimicrobial resistance genes in the soil metagenome and compare thosemaps to those obtained from E. coli isolates. By comparing those patterns of persistence and spread over time using spatialautoregressive modeling techniques, we can begin to draw associations between the application of manure, changes in theantimicrobial resistance genes in E. coli and whether there are concomitant changes in the antimicrobial resistance genes in the soil metagenome.Objective 5Module development - A module about spatial ecology will be developed for deployment in courses on geographic informationsystems (GIS)-enabled soil science and microbial ecology. Students will be provided data and a walkthrough for the analysis ofthat data in a pre-assembled geostatistical analysis environment. A subsequent course meeting will help students plot theirresults in map surfaces in a geographic information system (GIS) workspace. The effectiveness of the activity will be assessed through student responses to pre- and post-completion questions during the module and responses to a survey about themodule.