Progress 07/01/18 to 03/31/23
Outputs
Target Audience:The target audiences during this reporting period included: 1. Laboratory-based training: scientists focusing on bioinformatic and laboratory approaches to analyze and validate multi-omics datasets were trained during this period. 2. Informal outreach: This work was discussed extensively with members of the MN poultry industry and allied industry. This includes primarily broiler and turkey companies in MN, and several agricultural feed additive companies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work supported research by two PhD students in the Comparative Molecular Biosciences graduate program at the University of Minnesota. One graduated in 2021 and the second will graduate in 2023. How have the results been disseminated to communities of interest?Results have been shared with the scientific community and with members of the poultry industry via local meetings (Minnesota Turkey Growers Association), national meetings (Poultry Science Association, Conference for Research Workers in Animal Diseases), and industry member meetings (National Chicken Council). What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Objective 1. We have develoiped a CRISPR/Cas system in E. coli and Salmonella. Using CRISPR-Cas9 technology, we have successfully developed a system that targets avian pathogenic E. coli (APEC) multidrug resistance-encoding plasmids. Interestingly, we determined that the target sequences of these plasmids have varying levels of efficacy in vitro against APEC plasmids. The most efficacious target identified was targeting the hlyF hemolysin gene of APEC plasmids. With this target, we are able to eliminate the plasmid following electroporation at rates of 90%, both when the plasmid is in laboratory strains and wild type APEC strains. We have next developed plasmid-based delivery systems utilizing IncP and IncX plasmid backbones. These plasmids were tested to deliver the CRISPR-Cas9 systems against wild type APEC in a simulated poultry litter environment. Thisdemonstrates its ability to target a highly relevent poultry pathogen (APEC) habroring MDR phenotypes. Objective 2. Two vaccine ecology studies were conducted. First, we partnered with a commercial turkey company to collect samples from 16 different farms with matched control/vaccinated barns. These farms were receiving a commercial E. coli vaccine for the first time ever. Flocks were followed for 2 cycles. Weekly samples were collected, including litter samples, boot sock samples, cloacal swabs, and tracheal swabs. Samples were cultured in enterobacterial enrichment broth and stored. More than 12,000 samples were collected. We screened over 1,000 of these samples using a top-down approach (PCR through whole genome sequencing) to determine if application of a commercial E. coli vaccine shifts on-farm ecology of commensal and clinical E. coli populations. We found that two rounds of E. coli vaccination with an O78-based APEC vaccine do shift the populations of E. coli in the gut and respiratory tract of birds, with shifts away from Clermont phylogenetic groups haboring the O78 serogroup. A second was done as a part of a PhD thesis with a student funded through a separate USDA National Needs Fellowship. She partnered with a commercial turkey company to follow flocks with histories of no Ornithobacterium rhinotracheale (ORT) vaccination versus those with histories of continuous ORT vaccination. She developed an ORT culturing method where she can isolate ORT from a mixed community. Samples were collected for this project in 2020. This workillustratedthe lack of efficacy of "controlled exposure" of live, non-attenuated Ornithobacterium rhinotracheale (ORT) to prevent subsequent infection with ORT. Our analyses indicate that this practice has little to no impact on preventing the same strains from causing disease later in the turkey's life. We have collected clinical E. coli, ORT, and Pasteruella from turkey producers. To date we have collected nearly 4,000 total isolates, and the majority of these have been whole genome sequenced. These data form the basis for online tools and research tools for the poultry industry to track bacterial pathogens through production systems. As a result of this work, we published a paperwhich redefines the avian pathogenic E. coli pathotype. Objective 3. A systematic review has been completed by scientists in our laboratory studying the impact of probiotic use on poultry performance. This is pending publication. We have published multiple papers describing lactobacilli-based and phytogenic interventions which successfully reduce Salmonella load within the bird and/or during processing. We have established a cell adhesion/invasion model to study lactobacilli/Salmonella interactions, and have screened lactobacilli from ten different species for their adhesion and/or invasion abilities. This work is currently under review for publication. We studied host specificity of L. johnsonii in detail using high-resolution genomics, in vitro phenotypic assays, and live bird trials. We determined that evidence of host specificity exists even between different avian species (chickens versus turkeys), and host-specific strains demonstrate superior ability to influence performance compared to non-host-specific counterparts. Objective 4. Blog articles have been written with focus on vaccination and its impacts on poultry bacterial pathogen populations. We have utilized the data from this study to develop a course at the University of Minnesota on poultry food safety (POUL 5102) which is a component of a newly developed Poultry Health Certificate Program.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Delago J, Miller EA, Flores-Figueroa C, Munoz Aguayo J, Cardona C, Smith AH, Johnson TJ. Survey of clinical and commensal Escherichia coli from commercial broilers and turkeys, with emphasis on high-risk clones using APECTyper. Poultry Science, Jul;102(7):102712.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Johnson TJ, Miller EA, Flores-Figeuroa C, Munoz-Aguayo J, Cardona C, Fransen K, Lighty M, Gonder E, Nezworski J, Haag A, Behl M, Kromm M, Wileman B, Studniski M, Singer RS. Refining the definition of the avian pathogenic Escherichia coli (APEC) pathotype through inclusion of high-risk clonal groups. Poultry Science 101:102009.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Johnson A, Miller EA, Weber B, Flores-Figueroa C, Munoz Aguayo J, Kollanoor Johny A, Noll S, Brannon J, Kozlowicz B, Johnson TJ. Evidence of host specificity in Lactobacillus johnsonii genomes and its influence on probiotic potential in poultry. Poultry Science 102:102858.
|
Progress 07/01/22 to 03/31/23
Outputs
Target Audience:The target audiences during this reporting period included: 1. Laboratory-based training: scientists focusing on bioinformatic and laboratory approaches to analyze and validate multi-omics datasets were trained during this period. 2. Informal outreach: This work was discussed extensively with members of the MN poultry industry and allied industry. This includes primarily broiler and turkey companies in MN, and several agricultural feed additive companies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work supported research by two PhD students in the Comparative Molecular Biosciences graduate program at the University of Minnesota. One graduated in 2021 and the second will graduate in 2022. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Live poultry trials and poultry litter experiments will be conducted to determine if CRISPR/Cas9 can be delivered via conjugative plasmids to eliminate APEC plasmids. Objective 2. E. coli field trial samples will be further processed in the laboratory using PCR and whole genome sequencing. Objective 3. Systematic review will be completed. In vitro adhesion and invasion assays will be utilized to study lactobacilli/Salmonella interactions. Objective 4. A symposium will be organized to deliver information about vaccination on bacterial populations to producers and stakeholders.
Impacts
What was accomplished under these goals?
Objective 1. We have been working on the CRISPR/Cas system in E. coli and Salmonella. Using CRISPR-Cas9 technology, we have successfully developed a system that targets avian pathogenic E. coli (APEC) multidrug resistance-encoding plasmids. Interestingly, we determined that the target sequences of these plasmids have varying levels of efficacy in vitro against APEC plasmids. The most efficacious target identified was targeting the hlyF hemolysin gene of APEC plasmids. With this target, we are able to eliminate the plasmid following electroporation at rates of 90%, both when the plasmid is in laboratory strains and wild type APEC strains. We have next developed plasmid-based delivery systems utilizing IncP and IncX plasmid backbones. These plasmids will be tested to deliver the CRISPR-Cas9 systems against wild type APEC in a simulated poultry litter environment. Finally, this system will be tested in live birds via oral gavage to confirm the ability to target APEC plasmids. The successful validation of this system will demonstrate its ability to target a highly relevent poultry pathogen (APEC) habroring MDR phenotypes. This work is in preparation for publication. Objective 2. Two vaccine ecology studies are being conducted. First, we partnered with a commercial turkey company to collect samples from 16 different farms with matched control/vaccinated barns. These farms were receiving a commercial E. coli vaccine for the first time ever. Flocks were followed for 2 cycles. Weekly samples were collected, including litter samples, boot sock samples, cloacal swabs, and tracheal swabs. Samples were cultured in enterobacterial enrichment broth and stored. More than 12,000 samples were collected. We have screened over 1,000 of these samples using a top-down approach (PCR through whole genome sequencing) to determine if application of a commercial E. coli vaccine shifts on-farm ecology of commensal and clinical E. coli populations. We found that two rounds of E. coli vaccination with an O78-based APEC vaccine do shift the populations of E. coli in the gut and respiratory tract of birds, with shifts away from Clermont phylogenetic groups haboring the O78 serogroup. WGS will be further used to determine the phylogenetic reach of the vaccine against strains and ST types within this phylotype. This work in in preparation for publication. A second was done as a part of a PhD thesis with a student funded through a separate USDA National Needs Fellowship. She partnered with a commercial turkey company to follow flocks with histories of no Ornithobacterium rhinotracheale (ORT) vaccination versus those with histories of continuous ORT vaccination. She developed an ORT culturing method where she can isolate ORT from a mixed community. Samples were collected for this project in 2020. We have published a manuscript on this work, illustrating the lack of efficacy of "controlled exposure" of live, non-attenuated Ornithobacterium rhinotracheale (ORT) to prevent subsequent infection with ORT. Our analyses indicate that this practice has little to no impact on preventing the same strains from causing disease later in the turkey's life. We have collected clinical E. coli, ORT, and Pasteruella from turkey producers. To date we have collected nearly 4,000 total isolates, and the majority of these have been whole genome sequenced. Analyses of these isolates are in progress. These data will form the basis for online tools and research tools for the poultry industry to track bacterial pathogens through production systems. As a result of this work, we have submitted an articloe for publication which redefines the avian pathogenic E. coli pathotype. Objective 3. A systematic review has been completed by scientists in our laboratory studying the impact of probiotic use on poultry performance. Laboratory work is being conducted on Lactobacillus-based interventions, and good progress has been made examining alternative products plus vaccines combined with lactobacilli for their ability to control Salmonella. We have published multiple papers describing these interventions. We have established a cell adhesion/invasion model to study lactobacilli/Salmonella interactions, and have screened lactobacilli from ten different species for their adhesion and/or invasion abilities. This work is currently under review for publication. Objective 4. Blog articles have been written with focus on vaccination and its impacts on poultry bacterial pathogen populations.
Publications
|
Progress 07/01/21 to 06/30/22
Outputs
Target Audience:The target audiences during this reporting period included: 1. Laboratory-based training: scientists focusing on bioinformatic and laboratory approaches to analyze and validate multi-omics datasets were trained during this period. 2. Informal outreach: This work was discussed extensively with members of the MN poultry industry and allied industry. This includes primarily broiler and turkey companies in MN, and several agricultural feed additive companies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work supported research by two PhD students in the Comparative Molecular Biosciences graduate program at the University of Minnesota. One graduated in 2021 and the second will graduate in 2023. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?We plan to complete and publish the systematic review in Objective 3. We also plan to complete live bird trials to assess host specificity of L. johnsonii in Objective 3.
Impacts
What was accomplished under these goals?
Objective 1. We have been working on the CRISPR/Cas system in E. coli and Salmonella. Using CRISPR-Cas9 technology, we have successfully developed a system that targets avian pathogenic E. coli (APEC) multidrug resistance-encoding plasmids. Interestingly, we determined that the target sequences of these plasmids have varying levels of efficacy in vitro against APEC plasmids. The most efficacious target identified was targeting the hlyF hemolysin gene of APEC plasmids. With this target, we are able to eliminate the plasmid following electroporation at rates of 90%, both when the plasmid is in laboratory strains and wild type APEC strains. We have next developed plasmid-based delivery systems utilizing IncP and IncX plasmid backbones. These plasmids will be tested to deliver the CRISPR-Cas9 systems against wild type APEC in a simulated poultry litter environment. Finally, this system will be tested in live birds via oral gavage to confirm the ability to target APEC plasmids. The successful validation of this system will demonstrate its ability to target a highly relevent poultry pathogen (APEC) habroring MDR phenotypes. This work is in preparation for publication. Objective 2. Two vaccine ecology studies are being conducted. First, we partnered with a commercial turkey company to collect samples from 16 different farms with matched control/vaccinated barns. These farms were receiving a commercial E. coli vaccine for the first time ever. Flocks were followed for 2 cycles. Weekly samples were collected, including litter samples, boot sock samples, cloacal swabs, and tracheal swabs. Samples were cultured in enterobacterial enrichment broth and stored. More than 12,000 samples were collected. We have screened over 1,000 of these samples using a top-down approach (PCR through whole genome sequencing) to determine if application of a commercial E. coli vaccine shifts on-farm ecology of commensal and clinical E. coli populations. We found that two rounds of E. coli vaccination with an O78-based APEC vaccine do shift the populations of E. coli in the gut and respiratory tract of birds, with shifts away from Clermont phylogenetic groups haboring the O78 serogroup. WGS will be further used to determine the phylogenetic reach of the vaccine against strains and ST types within this phylotype. This work in in preparation for publication. A second was done as a part of a PhD thesis with a student funded through a separate USDA National Needs Fellowship. She partnered with a commercial turkey company to follow flocks with histories of no Ornithobacterium rhinotracheale (ORT) vaccination versus those with histories of continuous ORT vaccination. She developed an ORT culturing method where she can isolate ORT from a mixed community. Samples were collected for this project in 2020. We have published a manuscript on this work, illustrating the lack of efficacy of "controlled exposure" of live, non-attenuated Ornithobacterium rhinotracheale (ORT) to prevent subsequent infection with ORT. Our analyses indicate that this practice has little to no impact on preventing the same strains from causing disease later in the turkey's life. We have collected clinical E. coli, ORT, and Pasteruella from turkey producers. To date we have collected nearly 4,000 total isolates, and the majority of these have been whole genome sequenced. Analyses of these isolates are in progress. These data will form the basis for online tools and research tools for the poultry industry to track bacterial pathogens through production systems. As a result of this work, we have submitted an articloe for publication which redefines the avian pathogenic E. coli pathotype. Objective 3. A systematic review has been completed by scientists in our laboratory studying the impact of probiotic use on poultry performance. Laboratory work is being conducted on Lactobacillus-based interventions, and good progress has been made examining alternative products plus vaccines combined with lactobacilli for their ability to control Salmonella. We have published multiple papers describing these interventions. We have established a cell adhesion/invasion model to study lactobacilli/Salmonella interactions, and have screened lactobacilli from ten different species for their adhesion and/or invasion abilities. This work is currently under review for publication. Objective 4. Blog articles have been written with focus on vaccination and its impacts on poultry bacterial pathogen populations.
Publications
|
Progress 07/01/20 to 06/30/21
Outputs
Target Audience:The target audiences during this reporting period included: 1. Laboratory-based training: scientists focusing on bioinformatic and laboratory approaches to analyze and validate multi-omics datasets were trained during this period. 2. Informal outreach: This work was discussed extensively with members of the MN poultry industry and allied industry. This includes primarily broiler and turkey companies in MN, and several agricultural feed additive companies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work supported research by two PhD students in the Comparative Molecular Biosciences graduate program at the University of Minnesota. One graduated in 2021 and the second will graduate in 2022. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Live poultry trials and poultry litter experiments will be conducted to determine if CRISPR/Cas9 can be delivered via conjugative plasmids to eliminate APEC plasmids. Objective 2. E. coli field trial samples will be further processed in the laboratory using PCR and whole genome sequencing. Objective 3. Systematic review will be completed. In vitro adhesion and invasion assays will be utilized to study lactobacilli/Salmonella interactions. Objective 4. A symposium will be organized to deliver information about vaccination on bacterial populations to producers and stakeholders.
Impacts
What was accomplished under these goals?
Objective 1. We have been working on the CRISPR/Cas system in E. coli and Salmonella. Using CRISPR-Cas9 technology, we have successfully developed a system that targets avian pathogenic E. coli (APEC) multidrug resistance-encoding plasmids. Interestingly, we determined that the target sequences of these plasmids have varying levels of efficacy in vitro against APEC plasmids. The most efficacious target identified was targeting the hlyF hemolysin gene of APEC plasmids. With this target, we are able to eliminate the plasmid following electroporation at rates of 90%, both when the plasmid is in laboratory strains and wild type APEC strains. We have next developed plasmid-based delivery systems utilizing IncP and IncX plasmid backbones. These plasmids will be tested to deliver the CRISPR-Cas9 systems against wild type APEC in a simulated poultry litter environment. Finally, this system will be tested in live birds via oral gavage to confirm the ability to target APEC plasmids. The successful validation of this system will demonstrate its ability to target a highly relevent poultry pathogen (APEC) habroring MDR phenotypes. This work is in preparation for publication. Objective 2. Two vaccine ecology studies are being conducted. First, we partnered with a commercial turkey company to collect samples from 16 different farms with matched control/vaccinated barns. These farms were receiving a commercial E. coli vaccine for the first time ever. Flocks were followed for 2 cycles. Weekly samples were collected, including litter samples, boot sock samples, cloacal swabs, and tracheal swabs. Samples were cultured in enterobacterial enrichment broth and stored. More than 12,000 samples were collected. We have screened over 1,000 of these samples using a top-down approach (PCR through whole genome sequencing) to determine if application of a commercial E. coli vaccine shifts on-farm ecology of commensal and clinical E. coli populations. We found that two rounds of E. coli vaccination with an O78-based APEC vaccine do shift the populations of E. coli in the gut and respiratory tract of birds, with shifts away from Clermont phylogenetic groups haboring the O78 serogroup. WGS will be further used to determine the phylogenetic reach of the vaccine against strains and ST types within this phylotype. This work in in preparation for publication. A second was done as a part of a PhD thesis with a student funded through a separate USDA National Needs Fellowship. She partnered with a commercial turkey company to follow flocks with histories of no Ornithobacterium rhinotracheale (ORT) vaccination versus those with histories of continuous ORT vaccination. She developed an ORT culturing method where she can isolate ORT from a mixed community. Samples were collected for this project in 2020. We have published a manuscript on this work, illustrating the lack of efficacy of "controlled exposure" of live, non-attenuated Ornithobacterium rhinotracheale (ORT) to prevent subsequent infection with ORT. Our analyses indicate that this practice has little to no impact on preventing the same strains from causing disease later in the turkey's life. We have collected clinical E. coli, ORT, and Pasteruella from turkey producers. To date we have collected nearly 4,000 total isolates, and the majority of these have been whole genome sequenced. Analyses of these isolates are in progress. These data will form the basis for online tools and research tools for the poultry industry to track bacterial pathogens through production systems. As a result of this work, we have submitted an articloe for publication which redefines the avian pathogenic E. coli pathotype. Objective 3. A systematic review has been completedby scientists in our laboratory studying the impact of probiotic use on poultry performance. This will be completed in 2021. Laboratory work is being conducted on Lactobacillus-based interventions, and good progress has been made examining alternative products plus vaccines combined with lactobacilli for their ability to control Salmonella. We have published multiple papers describing these interventions. We have established a cell adhesion/invasion model to study lactobacilli/Salmonella interactions, and have screened lactobacilli from ten different species for their adhesion and/or invasion abilities. This work is currently under review for publication. Objective 4. Blog articles have been written with focus on vaccination and its impacts on poultry bacterial pathogen populations. We are working on formal online extension materials to provide on poultrydiseaseplanning.com that will inform about vaccine use and considerations in poultry production. A symposium is being targeted for 2022 at a national poultry research meeting.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Miller EA, Winfield B, Weber BP, Flores-Figueroa C, Munoz-Aguayo J, Huisinga J, Johnson TJ. 2021. Convergence of the turkey gut microbiota following cohabitation under commercial settings. Journal of Animal Science and Biotechnology 12:1-10.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Nair DVT, Johnson TJ, Noll SL, Johny AK. 2021. Effect of supplementation of a dairy-originated probiotic bacterium, Propionibacterium freudenreichii subsp. freudenreichii, on the cecal microbiome of turkeys challenged with multidrug-resistant Salmonella Heidelberg. Poultry Science 100:283-295.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Nair DVT, Thomas JV, Dewi G, Brannon J, Noll SL, Johnson TJ, Cox RB, Johny AK. 2020. Propionibacterium freudenreichii B3523 reduces cecal colonization and internal organ dissemination of multidrug-resistant Salmonella Heidelberg in finishing turkeys. Journal of Applied Poultry Research 30:100107.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2022
Citation:
Dewi G, Manjankattil S, Peichel C, Jia S, Nair D, Vickers Z, Johnson TJ, Cardona C, Noll S, Johny AK. 2022. Effect of plant-derived antimicrobials against multidrug-resistant Salmonella Heidelberg in ground turkey. Poultry Science, In Press.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Smith E, Miller EA, Munoz-Aguayo J, Flores-Figueroa C, Nezworski J, Studniski M, Wileman B, Johnson TJ. 2021. Genomic diversity and molecular epidemiology of Pasteurella multocida. PLOS ONE 16:e0249138.
|
Progress 07/01/19 to 06/30/20
Outputs
Target Audience:The target audiences during this reporting period included: 1. Laboratory-based training:scientists focusing on bioinformatic and laboratory approaches to analyze and validate multi-omics datasets weretrained during this period. 2. Informal outreach: This work was discussed extensively with members of the MN poultry industry and allied industry. This includes primarily broiler and turkey companies in MN, and several agricultural feed additive companies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This work supported research by twoPhD students in the Comparative Molecular Biosciences graduate program at the University of Minnesota. One graduated in 2021and the second will graduate in 2022. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Live poultry trials and poultry litter experiments will be conducted to determine if CRISPR/Cas9 can be delivered via conjugative plasmids to eliminate APEC plasmids. Objective 2. E. coli field trial samples will be further processed in the laboratory using PCR and whole genome sequencing. Objective 3. Systematic review will be completed. In vitro adhesion and invasion assays will be utilized to study lactobacilli/Salmonella interactions. Objective 4. A symposium will be organized to deliver information about vaccination on bacterial populations to producers and stakeholders.
Impacts
What was accomplished under these goals?
Objective 1. We have been working on the CRISPR/Cas system in E. coli and Salmonella. Using CRISPR-Cas9 technology, we have successfully developed a system that targets avian pathogenic E. coli (APEC) multidrug resistance-encoding plasmids. Interestingly, we determined that the target sequences of these plasmids have varying levels of efficacy in vitro against APEC plasmids. The most efficacious target identified was targeting the hlyF hemolysin gene of APEC plasmids. With this target, we are able to eliminate the plasmid following electroporation at rates of 90%, both when the plasmid is in laboratory strains and wild type APEC strains. We have next developedplasmid-based delivery systems utilizing IncP and IncX plasmid backbones. These plasmids will be tested to deliver the CRISPR-Cas9 systems against wild type APEC in a simulated poultry litter environment. Finally, this system will be tested in live birds via oral gavage to confirm the ability to target APEC plasmids. The successful validation of this system will demonstrate its ability to target a highly relevent poultry pathogen (APEC) habroring MDR phenotypes. This work is in preparation for publication. Objective 2.Two vaccine ecology studies are being conducted. First, we partnered with a commercial turkey companyto collect samples from 16 different farms with matched control/vaccinated barns. These farms were receiving a commercial E. colivaccine for the first time ever. Flocks were followed for 2cycles. Weekly samples were collected, includinglitter samples, boot sock samples, cloacal swabs, and tracheal swabs. Samples were cultured in enterobacterial enrichment broth and stored. More than 12,000 samples were collected. We have screened over 1,000 of these samples using a top-down approach (PCR through whole genome sequencing) to determine if application of a commercial E. coli vaccine shifts on-farm ecology of commensal and clinical E. coli populations. We found that two rounds of E. coli vaccination with an O78-based APEC vaccine do shift the populations of E. coli in the gut and respiratory tract of birds, with shifts away from Clermont phylogenetic groups haboring the O78 serogroup. WGS will be further used to determine the phylogenetic reach of the vaccine against strains and ST types within this phylotype. This work in in preparation for publication. A second wasdoneas a part of a PhD thesis with a student funded through a separate USDA National Needs Fellowship. Shepartneredwith a commercial turkey company to follow flocks with histories of no Ornithobacterium rhinotracheale (ORT) vaccination versus those with histories of continuous ORT vaccination. She developed an ORT culturing method where she can isolate ORT from a mixed community. Samples were collected for this project in 2020.We have published a manuscript on this work, illustrating the lack of efficacy of "controlled exposure" of live, non-attenuated Ornithobacterium rhinotracheale (ORT) to prevent subsequent infection with ORT. Our analyses indicate that this practice has little to no impact on preventing the same strains from causing disease later in the turkey's life. We havecollectedclinical E. coli, ORT, and Pasteruella from turkey producers. To date we have collected nearly 4,000 total isolates, and the majority of these have been whole genome sequenced.Analyses of these isolates are in progress. These data will form the basis for online tools and research tools for the poultry industry to track bacterial pathogens through production systems. Objective 3.A systematic review is being coordinated by scientists in our laboratorystudying the impact of probiotic use on poultry performance. This will be completed in 2021.Laboratory work is being conducted on Lactobacillus-based interventions, andgood progress has been made examining alternative products plus vaccines combined with lactobacilli for their ability to control Salmonella. We have published multiple papers describing these interventions.We have established a cell adhesion/invasion model to study lactobacilli/Salmonella interactions, and have screened lactobacilli from ten different species for their adhesion and/or invasion abilities. This work is currently under review for publication. Objective 4. Blog articles have been written with focus on vaccination and its impacts on poultry bacterial pathogen populations. We are working on formal online extension materials to provide on poultrydiseaseplanning.com that will inform about vaccine use and considerations in poultry production. A symposium is being targeted for 2022at a national poultry research meeting.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Smith E, Miller EA, Munoz-Aguayo J, Flores-Figueroa C, Nezworski J, Studniski M, Wileman B, Johnson TJ. Genomic diversity and molecular epidemiology of Pasteurella multocida. PLOS ONE 16:e0249138.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Miller EA, Winfield B, Weber BP, Flores-Figueroa C, Munoz-Aguayo J, Huisinga J, Johnson TJ. Convergence of the turkey gut microbiota following cohabitation under commercial settings. Journal of Animal Science and Biotechnology 12:1-10.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Azam M, Mohsin M, Johnson TJ, Smith EA, Johnson A, Umair M, Saleemi MK, Rahman S. Genomic landscape of multi-drug resistant avian pathogenic Escherichia coli recovered from broilers. Veterinary Microbiology 247.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Smith E, Miller E, Weber B, Munoz-Aguayo J, Flores-Figueroa C, Huisinga J, Nezworski J, Kromm M, Wileman B, Johnson TJ. Genomic landscape of Ornithobacterium rhinotracheale in commercial turkey production in the United States. Applied and Environmental Microbiology 86:e02874-19.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Ward TL, Weber BP, Mendoza KM, Danzeisen JL, Llop K, Lang K, Clayton JB, Grace E, Brannon J, Radovic I, Beauclaire M, Heisel TJ, Knights D, Cardona C, Kogut M, Johnson C, Noll SL, Arsenault R, Reed KM, Johnson TJ. Antibiotics and host-tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expression. mBio 10: e02171-19.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Smith E, Johnson TJ, et al. Genomic landscape of Ornithobacterium rhinotracheale in commercial turkey production in the United States. American Association of Avian Pathologists Annual Meeting, July 2020, Virtual.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Stumvoll K, Kromm M, Gerken E, Tourville J, Lighty M, Johnson TJ. Impact of E. coli vaccination on production performance of turkeys and the phylogenetics of E. coli population over time. American Association of Avian Pathologists Annual Meeting, July 2020, Virtual.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Johnson T, Weber B, Reed K, Noll S, Knights D, Ward T, Cardona C, Kogut M, Arsenault R. Antibiotic-free alternatives to improve health and performance in commercial turkeys: genomic insights. Conference for Research Workers in Animal Diseases, Chicago, IL, December 2019.
|
Progress 07/01/18 to 06/30/19
Outputs
Target Audience:The target audiences during this reporting period included: 1. Laboratory-based training: twopostdoctoral scientists focusing on bioinformatic and laboratory approaches to mitigate antimicrobial resistance weretrained during this period. 2. Scientific symposia: The knowledge generated from this project was disseminated to poultry producers at the symposia ofthe Norht Central Avian Disease Conference annual meeting in Minneapolis, MN, March 2019. 3. Informal outreach: This work was discussed extensively with members of the MN poultry industry and allied industry. This includes primarily broiler and turkey companies in MN, and several agricultural feed additive companies. Meetings were conducted at the Mid-Central Research and Outreach Center in Willmar, MN. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has provided the opportunity to train and mentor twopostdoctoral students and two PhD students (National Needs Fellows)in bioinformatics and laboratory techniques related to Objectives 2 and 3. How have the results been disseminated to communities of interest?The PI has made a number of presentations at local high schools and community colleges in the central MN area using the goals and results of this project as an example of cutting-edge science that occurs in the heart of agriculture in the USA. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. The CRISPR/Cas tools developed will be tested against field strains in vitro to assess the efficacy of the system towards eliminating plasmids. A conugative system using IncP-type plasmid vectors will be developed as a means to naturally deliver the CRISPR/Cas system to other bacteria, and this will be tested in vitro using natural conjugation experiments. Objective 2. Longitudunal field studies will be conducted to assess ORT and E. coli ecology across farms, geographical locations, and time in the US turkey production sector. The database to harbor genomic data used to predictors of ecological pathogen shifts in response to vaccination and other mitigation strategies will continue to be developed. Objective 3. A systematic will be started to survey literature for determination of the effectiveness of prebiotic and probiotic approaches towards enhancing performance and reducing disease in poultry production. In vitro screens will be conducted to determine host adaptive properties of probiotic strains in turkeys and chickens. In vitro pathogen inhibition studies will be conducted. Objective 4. A symposium will be proposed for the Midwest Poultry Federation meeting in Minneapolis in March 2020. Similarly, a symposia will be proposed for upcoming meetings at the American Association for Avian Pathologists and IPPE.
Impacts
What was accomplished under these goals?
Objective 1. The CRISPR/Cas system targeting different plasmid types has been developed in the laboratory. These tools will be used towards in vitro testing to determine the theoretical ability of a CRISPR-Cas delivery system to target multiple plasmids circulating in poultry production systems in the US. Objective 2. Genome sequences of approximately 100 ORT and 500 avian pathogenic E. coli have been obtained and analyzed. Tools used to analyze strains included whole genome SNP-based typing, pangenome analysis, and mining of genomic data for molecular serotype, virulence genotype, plasmid content, resistance gene content, MLST type, cgMLST type, and wgMLST type. The database that will harbor these strains is in development. Poultry companies have been contacted for enrollment into studies examining on-farm ORT and E. coli ecology using clinical, commensal, and environmental isolates collected in longitudinal manner. Objective 3. In vitro avian and mammalian epithelial cell line modelshave been established in the laboratory and are currently being tested using strains of Lactobacillus, E. coli, and Salmonella. In vitro pathogen inhibition models are in development using supernaten-based and direct cell-cell inhibition models. Objective 4. Two articles were published in trade magazines for turkey producers to introduce the concepts of bacterial strain typing, and why this matters for the producer.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Jahan N and Johnson T. Comparative genome analyses of avian pathogenic Escherichia coli (APEC) from commercial turkey production in the U.S. The Poultry Science Association Annual Meeting, San Antonio, TX, July 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Correlating phenotype and genotype in turkey-derived Lactobacillus johnsonii to discover effective probiotic strains for use in commercial turkeys. The Poultry Science Association Annual Meeting, San Antonio, TX, July 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Thomas J, Weber B, Wakil A, and Johnson T. Identifying turkey-specific Lactobacillus strains that inhibit poultry pathogens, and exploring prebiotic-probiotic combinations that enhance their growth. The Poultry Science Association Annual Meeting, San Antonio, TX, July 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Johnson A, Weber B, and Johnson T. Using probiotic performance assays and comparative genome analysis of Lactobacillus johnsonii strains to discover effective probiotics for use in commercial turkeys. The Gut Health Symposium, St. Louis, MO, November 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Jahan N and Johnson T. Comparative genome analyses of avian pathogenic Escherichia coli from commercial turkey and broiler production. The Conference for Research Workers in Animal Diseases, Chicago, IL, December 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Smith E and Johnson T. Pangenome analysis of Ornithobacterium rhinotracheale clinical isolates and vaccine strains from US turkeys. The Conference for Research Workers in Animal Diseases, Chicago, IL, December 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Persistence against resistance: human vs. animal antibiotics. Invited keynote presentation at the 72nd North Dakota Poultry Industries Annual Meeting, Fargo, ND, December 2018.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2018
Citation:
Ornithobacterium rhinotracheale: what can we learn from its DNA? Invited talk at the American College of Turkey Veterinarians annual meeting, Denver, CO, July 2018.
|
|