Progress 10/01/19 to 09/30/20
Outputs
Target Audience:scientists, policy makers, general public, animal producers Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has allowed for the training on one postdoctoral researcher, one graduate student and one undergraduate student. They have presented their research at professional meetings in posters and oral presentations. How have the results been disseminated to communities of interest?Results have been disseminated to the communities of interest by presentations at scientific professional meetings, peer-reviewed publications What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, weplan to submit the following manuscripts: Muurinen J, Cairns J, Ekakoro E, Ruple A, Johnson TA. Antibiotic resistance units and strategies for their removal from production animal microbiomes Wickware CL, Chastain C, Schinckel AP, Richert BT, Radcliffe JS, Johnson TA. Dextrin soluble fiber aters the piglet microbiome and gut health Duttlinger AW,Martinez REC, McConn BR, Kpodo KR,Lay, Jr. DC, Richert BT, Johnson TA, Johnson JS. Replacing dietary antibiotics with 0.20% L-glutamine in swine nursery diets: impact on intestinal physiology and microbiome following weaning and transport
Impacts
What was accomplished under these goals?
Due to increasing antimicrobial drug resistance of pathogenic bacteria, international health organizations are advising livestock and poultry industries to limit the use of antimicrobials in growth promotion. Together with growing consumer concerns regarding antimicrobial use in animal agriculture, markets are favorable to alternative growth promoters. Since the interest towards enhancing animal productivity and health through microbiome approaches is also increasing, it is important to study the linkages between the resistome and bacterial community structure to avoid enriching ARGs in animal microbiomes. Our Muurinen et al. study explores the influences of different growth promoters on the bacterial community and resistome compositions and we show that replacing the use of antibiotics with alternative growth promoters is probably an insufficient antibiotic resistance mitigation strategy and that resistance gene mobility might be an underestimated factor in the emergence of antimicrobial resistance through animal agriculture. OurVenkateswarlu et al. study describes a novel approach to the discovery of new antibiotic molecules and demonstrates the activity of phenelfamycin againstgonorrhoeae, a sexually transmitted infection in humans. Additionally, we described the putative biosynthetic pathway by which bacteria produce this antibiotic. This is an interesting study because we were able to purify this anitbiotic from previously known bacteria, but their ability to produce this antibiotic was previously unknown. Additionally we are currently working on a review article that describes how antibiotic resistance genes are organized in the bacterial chromosome and approaches (in addition to reduced antibiotic use)that can be employed to reduce antimicrobial resistance. This is a novel and interesting approach to consider how to reduce antimicrobial resistance.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2020
Citation:
Muurinen J!, Richert J, Wickware CL , Richert B, Johnson TA. 2020. Swine Growth Promotion with Antibiotics or Alternatives can Increase Antibiotic Resistance Gene Mobility Potential, Scientific Reports
- Type:
Journal Articles
Status:
Accepted
Year Published:
2020
Citation:
Venkateswarlu Y, Medina R, Johnson TA, Koteva K, Cox G, Thaker M, Wright G. 2020. Resistance-guided discovery of elfamycin antibiotic producers with antigonococcal activity. ACS Infectious Diseases
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wickware CL , Johnson TA, Koziol JH. 2020. Composition and diversity of the preputial microbiota in healthy bulls. Theriogen, 145:231-237.
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:Target Audiences: animal producers, microbiologists, policy makers Efforts: 1)Enhance surveillance and monitoring of antibiotic resistance and develop improved diagnostic tests. In collaboration with Purdue engineers, veterinarians and animal diagnostic lab we are working on developing a rapid diagnostic test to diagnose and recommend treatment for bovine respiratory disease. Developed assays for the four most common bovine respiratory disease (BRD) pathogens Worked to improve the agreement between BRD pathogen resistance genotypes and phenotypes by identifying additional resistance marker genes IMPACT:Will provide veterinarians a rapid test to aid in the antibiotic prescription decision-making process and will increase antibiotic stewardship and hopefully decrease resistance 2)Determine the ecology and mechanisms involved in resistance and transmission of resistance. *Project 1:Environmental fate of antibiotic resistance genes in the bovine and swine agroecosystems (*collaboration with Bo Norby) Sampled dairy and swine manure, stored manure, as well as corn field prior to, and immediately, 3 weeks and 6 weeks after manure application at the Purdue University farm Established partnerships to sample farms in Finland, Michigan, and New York Began use of epicPCR, a molecular technique to link a taxonomic marker (16S) and a resistance gene to allow culture independent identification of bacteria that encode resistance genes. IMPACT:Improve understanding of the impact of soil manuring and the environmental fate of antibiotic resistance genes Project 2:Effect of carbadox and Zn Cu additives on antibiotic resistance gene profiles Used a highly parallel qPCR array (WaferGen) to determine the abundance of hundreds of antibiotic resistance genes (ARGs) in feces from pigs fed Zn and Cu, Carbadox or no additive Each of these treatments resulted in unique ARG profiles and some enriched ARGs IMPACT:Zn and Cu are already available and used as antibiotic alternatives, but may co-select for all the resistance genes that prompted the Veterinary Feed Directive rules. We are investigating their impact on the animal microbiome and resistome. *Project 3:Plasmid-mediated transfer of antibiotic resistance genes toEnterococcus faecalisJH2-2 in poultry litter (*collaboration with Torey Looft) Enterococcus faecalisJH2-2 usually acquires two resistance gene at a time. The same genetic element with the same resistance genes were found with different flanking elements in different plasmids. IMPACT:Quantifying and understanding the horizontal transfer of resistance plasmids will allow us to judge the impact of animal management practices. This is also a fairly novel method to study the ecology of antibiotic resistance genes. 3)Develop and evaluate interventions (including alternatives to antibiotics) that reduce antimicrobial resistance in food production systems.? Determination of resistance gene profiles when alternatives to antibiotics are included in animal diets. Swine experiments were completed with treatment groups that received the normal diet amended with Zn and Cu, beta glucan, wheat bran, glutamine, dextrin, and other complex oligosaccharides. High throughput qPCR arrays (WaferGen) were used to determine the resistance gene profile and 16S rRNA gene sequencing was also completed. Analysis is still underway. IMPACT:We are testing marketed alternatives to antibiotics for their selective pressure for antibiotic resistance genes. This will aid companies and producers to increase their antimicrobial stewardship. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? In the Johnson lab we are training a doctoral student in 16S gene amplicon sequencing and high-throughput qPCR array technologies. In addition, we are a part of multidisciplinary teams to provide well rounded training to students. How have the results been disseminated to communities of interest? Results have been desiminated atinternational and nationalsymposium and to other local and regional talks to peer researcher, industry partners and in peer-reviewed publication. What do you plan to do during the next reporting period to accomplish the goals?Our goals center around publishing the work we have undertaken. 1. Complete and publish our metagenomic analysis of the impacts of bacitracin methylene disalicylate on the turkey intestinal microbial community, 2. Publish our findings on the effects of ZnCu and mushroom feed additives to the intestinal microbial community. 3. Publish our findings on the impact of glutamine as an antibiotic alternative. 4. Publish our results on the use of loop-mediated isolthermal amplification (LAMP) to target bovine respiratory pathogens. 5. Complete the laboratory work associated with the fate of antibiotic resistance genes in Finnish and American swine and dairy systems. 6. Publish a review article on antibiotic resistance units of concern.
Impacts
What was accomplished under these goals?
1)Enhance surveillance and monitoring of antibiotic resistance and develop improved diagnostic tests. In collaboration with Purdue engineers, veterinarians and animal diagnostic lab we are working on developing a rapid diagnostic test to diagnose and recommend treatment for bovine respiratory disease. Developed assays for the four most common bovine respiratory disease (BRD) pathogens Worked to improve the agreement between BRD pathogen resistance genotypes and phenotypes by identifying additional resistance marker genes IMPACT:Will provide veterinarians a rapid test to aid in the antibiotic prescription decision-making process and will increase antibiotic stewardship and hopefully decrease resistance 2)Determine the ecology and mechanisms involved in resistance and transmission of resistance. *Project 1:Environmental fate of antibiotic resistance genes in the bovine and swine agroecosystems (*collaboration with Bo Norby) Sampled dairy and swine manure, stored manure, as well as corn field prior to, and immediately, 3 weeks and 6 weeks after manure application at the Purdue University farm Established partnerships to sample farms in Finland, Michigan, and New York Began use of epicPCR, a molecular technique to link a taxonomic marker (16S) and a resistance gene to allow culture independent identification of bacteria that encode resistance genes. IMPACT:Improve understanding of the impact of soil manuring and the environmental fate of antibiotic resistance genes Project 2:Effect of carbadox and Zn Cu additives on antibiotic resistance gene profiles Used a highly parallel qPCR array (WaferGen) to determine the abundance of hundreds of antibiotic resistance genes (ARGs) in feces from pigs fed Zn and Cu, Carbadox or no additive Each of these treatments resulted in unique ARG profiles and some enriched ARGs IMPACT:Zn and Cu are already available and used as antibiotic alternatives, but may co-select for all the resistance genes that prompted the Veterinary Feed Directive rules. We are investigating their impact on the animal microbiome and resistome. *Project 3:Plasmid-mediated transfer of antibiotic resistance genes toEnterococcus faecalisJH2-2 in poultry litter (*collaboration with Torey Looft) Enterococcus faecalisJH2-2 usually acquires two resistance gene at a time. The same genetic element with the same resistance genes were found with different flanking elements in different plasmids. IMPACT:Quantifying and understanding the horizontal transfer of resistance plasmids will allow us to judge the impact of animal management practices. This is also a fairly novel method to study the ecology of antibiotic resistance genes. 3)Develop and evaluate interventions (including alternatives to antibiotics) that reduce antimicrobial resistance in food production systems. Determination of resistance gene profiles when alternatives to antibiotics are included in animal diets. Swine experiments were completed with treatment groups that received the normal diet amended with Zn and Cu, beta glucan, wheat bran, glutamine, dextrin, and other complex oligosaccharides. High throughput qPCR arrays (WaferGen) were used to determine the resistance gene profile and 16S rRNA gene sequencing was also completed. Analysis is still underway. IMPACT:We are testing marketed alternatives to antibiotics for their selective pressure for antibiotic resistance genes. This will aid companies and producers to increase their antimicrobial stewardship.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Johnson, T. A., Sylte, M. J., & Looft, T. (2019). In-feed bacitracin methylene disalicylate modulates the turkey microbiota and metabolome in a dose-dependent manner. Scientific Reports, 9(1), 8212. http://doi.org/10.1038/s41598-019-44338-5
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Johnson, T.A. (2019). Antibiotic resistance gene ecology in the pig and turkey microbiomes. Microbiome Movement Animal Health and Nutrition. St. Louis, MO. October 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Muurinen J., Richert J., Richert B. & Timothy Johnson T.A. (2019). Will antibiotic-alternative growth promoters reduce antibiotic resistance in the microbiome? 5th Symposium on the Environmental Dimension of Antibiotic Resistance. Hong Kong, China
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Progress 04/03/18 to 09/30/18
Outputs
Target Audience: Veterinarians Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?In the Johnson lab we are training a doctoral student in 16S gene amplicon sequencing and high-throughput qPCR array technologies. How have the results been disseminated to communities of interest?Results have been desiminated at an international symposium and to other local and regional talks to peer researcher, industry partners and in peer-reviewed publication. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete our analysis on the impact of alternatives to antibiotic feed additives, as well as launch a broader study on the ecology of resistance genes in the agroecosystem, including manure application, resistance genes in animal feed, and strategies to select against antibiotic resistance in microbial communities.
Impacts
What was accomplished under these goals?
Objective 1: Purdue researchers, in collaboration with USDA scientists in Iowa and Georgia, are characterizing tetracycline resistant plasmids that were horizontally acquired by Enterococcus faecalis JH2-2 in poultry litter from commercial, organic and backyard layer flocks. Horizontal gene transfer is an important mechanism by which bacteria can become resistant to one or more antibiotics be acquiring the needed genes from their bacterial neighbors. We found that Enterococcus faecalis JH2-2,acquired, on averagetwo resistance genes. These genes encode resistance to tetracycline, chloramphenicol, aminoglycosides and erythromycin. Purdue researchers, in collaboration with USDA scientists at the National Animal Disease Center in Ames, Iowa have characterized the impacts of an antibiotic containing feed additive bacitracin methylene disalicylate. Beginning in 2017, the subtherapeutic use of most antibiotic compounds for growth promotion in food producing animals in the US was prohibited, highlighting the need discover alternativegrowth promotants. Identifying the mechanism of action of growth promoting antibiotics mayaid in the discovery of antibiotic alternatives. We describe the effects of feeding a subtherapeutic (50g/ton of feed) and therapeutic (200g/ton) concentration of bacitracin methylene disalicylate(BMD) to commercial turkeys for 14 weeks, and its effect on turkey microbial communities and cecal metabolomes. Both BMD concentrations had an immediate and lasting impact on the microbiota structure, and reduced bacterial richness through the end of the study (12 weeks).Metabolomic analysis identified 712 biochemicals, and 69% of metabolites were differentially present in BMD treated turkeys for at least one time point (q<0.1). Amino acids, carbohydrates, nucleotides, peptides, and lipids were decreased in the turkey cecum early after BMD administration. Long-term metabolome alterations continued even after withdrawal of BMD. The microbial composition, determined by 16S rRNA gene sequencing, was predictive of the metabolome, indicating a connection between the microbiome and metabolome. In-feed BMD may cause bacterial metabolic shifts, leading to beneficial traits that can be targeted to improve animal health and production. This work has been submitted for peer-reviewed publication. Objective 3: Researchers at Purdue are investigating the impacts of alternative to antibiotic feed additives for their impact on animal performance, microbiome composition and antibiotic resistance gene burden. We are investigating compound, including soluble fiber, beta glycan, supplemental zinc and copper, and complex oligosaccharides. These feed additives may result in an increase of decrease in animal health status, antibiotic resistance gene burden or an altered microbiome composition.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
T. A. Johnson, M. J. Sylte, T. Looft. The in-feed antibiotic bacitracin modulates microbiome structure, metabolome, and host responses in a dose-dependent manner. International Symposium on Microbial Ecology. Leipzig, Germany. August 2018.
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