Source: UNIVERSITY OF FLORIDA submitted to
UNDERSTANDING ANTIBIOTIC RESISTANCE OCCURENCE AND DEVELOMENT OF MITIGATION STRATEGIES IN CATTLE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1005132
Grant No.
2015-68003-22971
Project No.
FLAW-2014-05287
Proposal No.
2014-05287
Multistate No.
(N/A)
Program Code
A4171
Project Start Date
Feb 15, 2015
Project End Date
Feb 14, 2020
Grant Year
2015
Project Director
Jeong, K.
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
AG-ANIMAL SCIENCES
Non Technical Summary
The effectiveness of antibiotics has been challenged by the occurrence of dangerous infections that antibiotics can no longer treat, as pathogens are developing resistance to the drugs. Despite its negative and growing impact on not only public health, but also animal health, there are few effective strategies for reducing the prevalence of antimicrobial resistant microorganisms (ARMs) in farm animals. There is thus a compelling need to develop mitigation strategies for ARMs in food animals. Development of rational mitigation strategies requires a comprehensive understanding of when, where, and how resistance was acquired, and how resistance genes and ARMs move among animals. However, little data is available on factors contributing to the acquisition of ARMs in agricultural systems. On the basis of our findings, our central hypothesis is that current management practices for grass-fed cattle create conditions conducive to the acquisition and development of antibiotic resistance in the gastrointestinal tract. Therefore, understanding of AR occurrence from earlier in the food animal production cycle is essential to develop mitigation strategies. This integrated research and extension project focuses on identifying associated risk factors and origin for the presence of such resistance in farm animals to develop methods for reducing ARMs in farm animals. Conventional and new extension approaches will be used to better educate stakeholders and the public to reduce ARMs in cattle, enhancing the sustainability of US agriculture and global food safety and security.
Animal Health Component
10%
Research Effort Categories
Basic
40%
Applied
30%
Developmental
30%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
7124099110070%
7233310104030%
Knowledge Area
712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins; 723 - Hazards to Human Health and Safety;

Subject Of Investigation
4099 - Microorganisms, general/other; 3310 - Beef cattle, live animal;

Field Of Science
1040 - Molecular biology; 1100 - Bacteriology;
Goals / Objectives
Our long-term goal is to develop solutions for mitigating antibiotic resistance (AR) in farm animals. Much of the research to date on selection/acquisition of antimicrobial resistance in food animal production has focused on feedlots. In our preliminary studies, we have found high levels of ARMs in cow/calf operations here in Florida, suggesting that the pathways involved in acquisition of ARMs are more complex - and begin earlier in the production cycle - than had been anticipated. On the basis of our findings, our central hypothesis is that current management practices for grass-fed cattle create conditions conducive to the acquisition and development of antibiotic resistance in the gastrointestinal tract. Development of rational mitigation strategies requires a comprehensive understanding of when, where, and how resistance was acquired, and how resistance genes and ARMs move among animals. However, little data is available on factors contributing to the acquisition of ARMs in agricultural systems. Therefore, understanding of AR occurrence from earlier in the food animal production cycle is essential to develop mitigation strategies. This integrated research and extension project focusing on identifying associated risk factors and origin for the presence of such resistance in farm animals to develop methods for reducing ARMs in farm animals. Conventional and new extension approaches will be used to better educate stakeholders and the public to reduce ARMs in cattle, enhancing the sustainability of US agriculture and global food safety and security.The specific objectives of the proposal are as follows:Aim #1: Understand AR occurrence in cow/calf operations to identify risk factors raising AR in cattle that will explain how ARMs are developed and prevalent in earlier stage of production. This will be applied in the development of a farm management model to mitigate ARMs. Obj.1A: Evaluate prevalence of antibiotic resistant microorganisms in cow/calf operations. Obj. 1B: Identify associated risk factors for the presence of such resistance, including antibiotic use, environmental factors, soil, water, feeds, and animal management practices.Aim #2: Identify mechanisms of antimicrobial resistance, especially Extended-Spectrum β-Lactamases (ESBLs), to understand how and where antibiotic resistance acquired in cattle that can be applied in the development of a cattle management model to mitigate ARMs. Obj. 2A: Speciate ESBL producing microorganisms in cattle. Obj. 2B: Identify resistance genes and understand mechanisms of acquisition of ESBLs in cattle.Aim #3: Determine the points where ARMs are introduced into cattle identify critical control points that will provide the basis for development of intervention strategies for antimicrobial resistance and use this information to develop a dynamic ARM transmission model. Obj. 3A: Trace animals from birth to slaughter to understand ARM occurrence, prevalence, and transmission in cow/calf operations. Obj. 3B: Identify animal factors that affect the prevalence of ARMs in cattle, including genetic and physiological factors. Obj. 3C: Develop a mathematical model that will predict ARM occurrence in cattleAim #4: Develop and deliver a comprehensive extension/education program on best farm and cattle management practices to mitigate AR on farms. Obj. 4A: Develop best AR mitigation strategies on the basis of outcomes of this proposed research that can be applied in cow/calf operations. Obj. 4B: Transfer mitigation strategies to food animal producers and scientists by publications, training, and education through scientific journals, personal contact, and web-based resources including eXtension system. Obj. 4C: Involve undergraduate, graduate, and pre-veterinary students in best cattle management practices and research activities to reduce ARMs to stimulate interest towards graduate school and food animal oriented careers.
Project Methods
Aim #1: This aim is an integrated project combining research and extension components. The goal of the research component in Aim #1 is to understand AR occurrence in cow/calf operations in Florida to identify risk factors raising AR in cattle that will explain how ARMs are developed and prevalent in earlier stage of production and will be applied in development of farm management model to mitigate ARMs.Obj.1A: Evaluate prevalence of antibiotic resistant microorganisms in cow/calf operationsTo confirm our findings that ESBL-producing microorganisms are ubiquitous in the cattle consuming forage-based diets, we will expand our studies through investigation of farms in north Florida. The north Florida region will be used because small and medium-sized farms, which feed grass to cattle, can be easily identified for sampling compared to other regions. In addition, we found this region has different soil composition and vulnerability to ground water pollution, suggesting this region may give us unique insights to predict risk factors that raise the prevalence and transmission of ESBL-producing microorganisms1A.1. Sampling strategy in cattle operation Cattle operations in north Florida will be recruited for this project.1A. 2. Prevalence of ARMs in cow/calf operations and collection of isolates To measure ESBL prevalence in small/medium size farms in grass-fed cattle, we will analyze samples obtaining from RAJ, soil, water, and feeds.1A. 3. Statistical analyses For the prevalence analysis, we will model the probability of a positive swab sample as a function of county, farm size category, and cow/calf status using a generalized linear mixed model with a logit link, as follows:logit(pijk )=α+βLargeij + ηCowijk +ui, where i indexes county, j indexes farm, and k indicates swab, Largeij indicates whether farm ij is a large farm or not, Cowijk indicates whether swab ijk is from a cow or a calf, and ui is a random effect indicating correlation of prevalences within a county. For the risk factor analysis, we will incorporate covariates into the above model and test two-sided statistical significance at the α = 0.05 level.1A. 4. Metagenomic analysisTo understand if animal microflora affects on the prevalence of ARMs in cattle, we will conduct culture independent metagenomic analysis. We will select about 100 cattle (50 cows and 50 calves) and RAJ swab samples will be used for this analysis.1A. 4. 1. DNA sample extraction and sequencing.Fecal samples (0.1g) will be used to extract DNA sample, and 16S rRNA amplicons will be sequenced using a Illumina MiSeq instruments and reagents (47).1A. 4. 2. Sequencing data analysis and Identification of BacteriaThe sequencing processing will filter out short sequences <200bp, quality score <Q25, sequences with ambiguous base calls, and sequences with homopolymer >6bp.1A. 4. 3. Statistical Analyses for metagenomic analyses Rarefaction curves and bacterial diversity (Chao1 and Shannon) will be evaluated using the R software (http://www.r-project.org). Hierarchical clustering of microbial species will be generated by a heat map with Euclidean distance using the R. The dissimilarity of bacterial communities between samples will be analyzed by principal coordinate analysis (PCoA) of weighted UniFrac distances (http://bmf.colorado.edu/unifrac). Mean values will be plotted in the relative abundance of bacteria and data will be compared with Student's t-test using the GraphPad Prism InStat 3.1. P values ≤0.05 will be considered as statistically significant.Obj. 1B: Identify associated risk factors for the presence of such resistance, including antibiotic use, environmental factors, soil, water, feeds, and animal management practices We will accomplish the goal of objective 1B by collecting farm-specific data to assess possible risk factors for ARM carriage. We will prepare questionnaires to ask farmers and farm employees to identify high risk factors, such as antibiotic use for the therapeutic or subtherapeutic purposes, types of antibiotics if used, age of animals, types of feed, questions related to animal husbandry, source of drinking water for animals, animal migration among farms etc. (during the 1st farm visit for sampling).Aim #2: The goal of this aim is to identify mechanisms of antimicrobial resistance, especially Extended-Spectrum β-Lactamases (ESBLs), to understand how and where ESBLs are acquired in cattle. This information will be applied in the development of a cattle management model to mitigate ARMs.Obj. 2A: Speciate ESBL producing microorganisms in cattle 2A. 1. Phenotypic screening & speciationThe goal of this objective is to speciate ESBL producing microorganisms in cattle. We want a collection that includes both clinically important isolates and species that may serve as donors for resistance genes.2A. 2. Identification of resistance genes by amplifying known ESBL genes Isolates will be screened for specific ESBL-producing genes using a multiplex PCR as previously described. In brief, this method uses 9 different primer sets (blaTEM, blaSHV, blaCTX-M, blaCMY, blaOXA-1, blaOXA-2, blaACC-like, blaVEB, and blaDHA).Obj. 2B: Identify resistance genes and understand mechanisms of acquisition of ESBLs in cattle. The goal of objective 2B is to identify specific antimicrobial resistance genes and mechanisms of gene transfer among strains. All cefotaxime-resistant isolates selected from MacConkey plates (from cattle, soil, and water), as described above, will be screened.2B. 1. Functional metagenomics to identify unknown cefotaxime resistance genes Identification of resistance genes will be conducted using functional metagenomic selections, which are suited to characterize resistance because they identify any gene sufficient to confer resistance to bacteria.2A. 2. Whole genome sequencing for strain relatedness/genetic epidemiology To examine strain relatedness and to shed light on the possible transmission route of the isolated strains, we will conduct whole-genome sequencing of cefotaxime resistant strains. Next-generation sequencing will be conducted using Illumina Miseq sequcer using 250 bp paired end reads.Aim #3: The goal of this aim is to determine the points where ARMs are introduced into cattle to identify critical control points that will provide the basis for the development of intervention strategies for antimicrobial resistance. In addition, a dynamic ARM transmission model will be developed using outcomes of this proposed researchObj. 3A: Trace animals from birth to slaughter to understand ARM occurrence, prevalence, and transmission in cow/calf operations Obj. 3B: Identify animal factors that affect the prevalence of ARMs in cattle, including genetic and physiological factors. In this research we will study the animal from birth to slaughter to find potential ARM introduction points. This will help to identify critical control points that will provide the basis for development of intervention strategies for antimicrobial resistance. In addition, we will evaluate the GI tract microflora change using metagenomic analysis as animals grow to identify if microflora affect of the prevalence of ARMs in cattle.Aim #4: The goal of this aim is to develop and deliver a comprehensive extension/education program on best farm and cattle management practices to mitigate AR on farms.Obj. 4A: Develop best AR mitigation strategies based on the outcomes of the proposed research.Obj. 4B: Transfer of mitigation strategies to food animal producers and scientists

Progress 02/15/15 to 02/14/20

Outputs
Target Audience:The target audience of the 5th year efforts of this grant was mainly food animal producers. County agents (Agriculture agents), meat processing industry workers, and beef animal producers were educated on antibiotic use and antibiotic resistance in beef cattle. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The teaching component of the project has completed all its planned activities This last year we trained the second cohort of students in their Antimicrobial Resistance and Food Safety Internship. The first four weeks of the internship took place at the North Florida Research and Education Center at UF in Marianna, Florida and were post-harvest centered. The post-harvest section included observing hygienic slaughter, assisting graduate students with carcass microbial swabbing, meat quality assessment in commercial facilities and the University Meat Laboratory, and receiving HACCP, GMP, and SSOP training for meat processing. The second half of the internship was conducted in the Department of Animal Sciences. This cohort of students, in collaboration with faculty members from the UF's Department of Animal Sciences, co-authored an EDIS (peer-reviewed extension publication) titled- Antibiotic Use and Resistance for Beef Cattle Producers. The teaching team developed a short satisfaction survey that students completed at the end of their internship. The majority of respondents reported high levels of satisfaction with different aspects of teaching and communication during their internship. Lower levels of satisfaction were reported for aspects associated with housing and compensation. Unfortunately, the teaching team missed the opportunity to include some evaluation questions in the survey focused on capturing changes in knowledge, attitudes, skills, and aspirations of the participants. Nevertheless, the experience seems to have been valuablefor the students. How have the results been disseminated to communities of interest?The extension component has made significant effort to conducth the planned activities. This is evident in the variety of extension-related materials and presentations that theteam developed and delivered over the last year. The team developed an innovative and comprehensive curriculum for professional development of extension faculty that can be used across extension to train faculty on strategies to maximize AR mitigation. Additional elements (e.g., instruction plans, learning objectives, assessments, etc.) have been developed and disseminated. The offered five field days total. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The research component (the main one in the project) has successfully completed all of the planned activities associated with Aims 1, 2. and 3. We have generated a total of 27 research articles on AMR occurrence, trnasmission, and AMR mitigation in beef cattle.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Peixin Fan, Beilei Bian, Lin Teng, Corwin D Nelson, J Driver, Mauricio A Elzo, Kwangcheol C Jeong. Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation. 2020. ISME J.14:302-317.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Lin Teng, Shinyoung Lee, Amber Ginn, Sarah M Markland, Raies A Mir, Nicolas DiLorenzo, Christina Boucher, Mattia Prosperi, Judith Johnson, J Glenn Morris, Kwangcheol C Jeong. Genomic comparison reveals natural occurrence of clinically relevant multidrug-resistant extended-spectrum-?-lactamase-producing Escherichia coli strains. 2019. Appl. Environ. Microbiol. DOI: 10.1128/AEM.03030-18.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Zhengxin Ma, Shinyoung Lee, K Casey Jeong. Mitigating antibiotic resistance at the livestock-environment interface: a review. 2019. 29:1683-1692.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Peixin Fan, Corwin Nelson, Joseph Driver, Mauricio A Elzo. and K.C. Jeong. Animal breed composition is associated with the hindgut microbiota structure and ?-lactam resistance in the multibreed Angus-Brahman herd. 2019. Frontiers in Microbiol. doi.org/10.3389/fmicb.2019.01846
  • Type: Books Status: Published Year Published: 2020 Citation: Education Curriculum for Antimicrobial Resistance Mitigation
  • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Lin Teng, Shinyoung Lee, Dongjin Park, Kwangcheol C. Jeong. Genetic and Functional Analyses of Virulence Potential of an Escherichia coli O157:H7 Strain Isolated from Super-Shedder Cattle. 2020. Frontiers in Cellular and Infection Microbiol. Accepted
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Shinyoung Lee, Lin Teng, Nicolas DiLorenzo, Thomas A Weppelmann, Kwangcheol Casey Jeong. Prevalence and Molecular Characteristics of Extended-Spectrum and AmpC ?-Lactamase Producing Escherichia coli in Grazing Beef Cattle. 2020. Frontiers in Microbiology. doi.org/10.3389/fmicb.2019.03076
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Shinyoung Lee, Raies A Mir, Si Hong Park, Donghyuk Kim, Hae-Yeong Kim, Raoul K Boughton, J Glenn Morris Jr, Kwangcheol C Jeong. 2020. Prevalence of extended-spectrum ?-lactamases in the local farm environment and livestock: challenges to mitigate antimicrobial resistance. Critical Reviews in Microbiology. 46:1-14.


Progress 02/15/18 to 02/14/19

Outputs
Target Audience: The target audience of the 4th year efforts of this grant was not only scientific community who focuses on research to reduce the prevalence of antimicrobia resistant microorganisms in food animals but also food animal producers. Gradute and postdoctorate were trained too. County agents (Agriculture agents) and meat processing industry wokers were also trained. We have also extended our dissemination efforts to public. Changes/Problems: We would like to extend this project to 2/14/2020. We are so grateful for the work that we have conducted with this grant. Since this NIFA grant has been initiated, we have performed proposed work efficiently and achieved the desired outcomes in the research, education, and extension components. However, mainly due to unexpected damages on our research and extension resources caused by natural disasters such as hurricanes, Irma (2017) and Michael (2018), this project has been significantly delayed, especially for Extension components. Hurricanes affected the sample collections from the environments and animals for Aim #3B and delayed the on-site extension activities. We have also encountered some technical challenges to collect and process data for Aim 2B. Due to these difficulties, this project has been delayed, and Co-PDs decided to request this no cost extension. For the research component, sample and data collections for research aims and objectives are almost done, except for some objectives mentioned above and an integrated objective (Obj. 3C and Obj. 4A). The extension component has made significant progress, but this component is running a little bit behind schedule due to its reliance on the outcomes of research components and damages on our key extension sites (North Florida Research and Education Center and FAMU) that have delayed our activities significantly. An external project evaluator and advisory committee members of this project have recommended asking for the NCE and the PD/Co-PDs strongly concurred with this recommendation. In addition, as the PD of this grant, I would like to acquire an approval to include new Co- PDs to complete delayed Aims and Objectives. Dr. Boucher(replacing Dr. Judith Johnson's role due to her retirement) would provide bioinformatics tools and analysis for Aim #2B (functional metagenomics to identify unknown cefotaxime genes). Dr. Corwin Nelson(replacing Dr. Mauricio Elzo's role due to his retirement) would be involved in Aim 3B (identify animal factors that affect the prevalence of ARMs in cattle). Dr. Younggu Her (replacing a post doctorate who originally intended to develop mathematical model but left for his career) would develop a mathematical model to predict ARM occurrence for Aim 3C. These three Co-PDs have already involved in this grant as collaborators or consultants to replace personnel who retired or left this project team. The remaining funds will be used to complete the proposed work, not for new aims or projects, for extension and research components. The funds will be used for supporting personnel, materials, tuition for graduate students, extension activities, data processing/dissemination, and publication to complete and acquire desired goals. What opportunities for training and professional development has the project provided? During the reporting period, training was offered for extension agents to provide update on antimicrobial resistance in food animals. Another in-service training was offered under the title of "Meat and Poultry Safety Update: Current Issues and Mitigation Strategies" on Feb 7-8 in Gainesville, FL. We had a total of 15 participants in the training. How have the results been disseminated to communities of interest? During the reporting period, training was offered for extension agents to provide update on antimicrobial resistance in food animals. Another in-service training was offered under the title of "Meat and Poultry Safety Update: Current Issues and Mitigation Strategies" on Feb 7-8 in Gainesville, FL. We had a total of 15 participants in the training. We educated public by participating 2018 Family Day at the Dairy Farm. This annual event is an Open House for the general public to come visit a working dairy farm. We presented a variety of educational information about antimicrobial resistance to prevent spread by personal hygiene to ~1500 visitors. FAMU conducted various extension activities to disseminate research outcomes that include farm fest field day multimedia presentation, creation of video, TV interview, social media posts and sharing. FAMU also developed video contents on antibiotic use. What do you plan to do during the next reporting period to accomplish the goals?As recommended by evaluator of this project, the team members would like to obtain a one-year no cost extension to complete the missing research element and allow the extension team to translate the findings from this research to develop and deliver the non-formal educational programs and products that are missing - this extension component is critical if the project intends to make a significant contribution to its long-term impact.

Impacts
What was accomplished under these goals? Obj. 1A: We found that ESBL-producing bacteria is probably originated from the environment, rather than occurring on farms in cow/calf operations. These findings propose new insights into development of mitigation strategies for AMR (Mir et. al. Frontiers in Microbiology, published). Obj. 1B: We found soil is major AMR reservoir. Soil microbiota from farms with high prevalence of CRB in beef cattle clustered closer. (Markland et. al. Frontiers in Microbiology, accepted). Farm management affects on the prevalence of AMR. Large farming operations were associated with higher likelihood of CRB detection. Regular cleaning of drinking troughs and the addition of ionophores to feed were associated with CRB reduction in fecal samples (Markland et. al. Frontiers in Microbiology, accepted). Taken together, the widespread of CRB into both cattle seldom treated with cephalosporin antibiotics and the surrounding environment suggests the environment is a natural source of antimicrobial resistance in beef cattle. Obj. 2A Using whole genome sequencing and comparative genomics of 30 extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, isolated from beef cattle with no previous exposure to antibiotics, we provide evidence for acquisition of the ESBL isolates from environment, rather than raised on farms by antibiotic use (Teng et. al. Applied and Environmental Microbiology, Under review). Phylogenic relatedness with reference ESBLs from various geographic locations and hosts, such as animals, the environment, and humans suggests that transmission of ESBLs occurs intercontinentally without host preference (Teng et. al. Applied and Environmental Microbiology, Under review). Dairy cows with metritis infected with ESBL-producing Escherichia coli were failed to be treated with antibiotics, indicating antibiotic treatment failure in dairy cattle is probably associated with AMR (Ma et. al. Frontiers in Microbiology, published) Dairy cows with mastitis were infected with various AMR and microbiome of mastitic cows carried more antibiotic producers, suggesting antibiotic treatment failure in mastitic cows is probably associated with AMR (Ma et. al. Applied and Environmental Microbiology, submitted) Obj. 2B Multi-drug resistant ESBL-producing bacteria are pandemic in animals raised without antibiotics. MDR ESBL-producing bacteria encoded various virulence genes, providing insight into not only the evolution of bacterial pathogenesis, but a potential threat for public health. Obj. 3A We found beef cattle are infected with MDR ESBL-producing bacteria in the uterus (manuscript in preparation) ESBL-producing E. coli was detected in the range of 50-10.5% (34/322) of fecal samples. Whole Genome Sequencing (WGS) of ~400 ESBL strains were conducted. Following WGS, phylogenetic analysis revealed that these strains clustered into 8 groups that coincided with their STs. All the isolates carried a variety of virulence genes and were resistant to multiple antibiotics, suggesting that these strains may threaten public health if they contaminate food products. Obj. 3B We found that animal genetics affects on the prevalence of specific microbiota We found that AMR colonization in the GI tract is dynamic process, affected by animal age and maturation of microbiota. These data suggest that we may reduce AMR by modulation of the gut microbiota in the GI tract. Taken together, our results provide insights into how to develop mitigation strategies to reduce ESBLs in cattle.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mir RA, Weppelmann TA, Teng L, Kirpich A, Elzo MA, Driver JD, Jeong KC. Colonization Dynamics of Cefotaxime Resistant Bacteria in Beef Cattle Raised Without Cephalosporin Antibiotics. Frontiers in microbiology, 2018; 9:500.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: 1. Ma ZX, Ginn A, Kang M, Galvao K, Jeong KC. Genomic and virulence characterization of intrauterine pathogenic Escherichia coli with multi-drug resistance isolated from cow uteri with metritis. Frontiers in microbiology, 2018; 9, p.3137.
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Markland, S., Thomas A. Weppelmann, Zhengxin Ma, Shinyoung Lee, Raies A. Mir, Lin Teng, Amber Ginn, Choonghee Lee, Maria Ukhanova, Sebastian Galindo, Chad Carr, Nicolas DiLorenzo, SooHyoun Ahn, Jae Hyung Mah, Volkar Mai, Mobley Ray, J Glenn Morris, and K.C. Jeong. 2019. High Prevalence of Cefotaxime Resistant Bacteria in grazing Beef Cattle: A Cross Sectional Study. Accepted. Frontiers in Microbiology.
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Teng L, Lee S, Ginn A, Markland S, Mir R, DiLorenzo N, Boucher C, Prosperi M, Johnson J, Morris G, Jeong KC. Genomic comparison reveals natural occurrence of clinically relevant multi-drug resistant extended-spectrum ?-lactamase producing Escherichia coli. Under review.
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Zhengxin Ma, Shinyoung Lee, Peixin Fan, Jaehyun Lim,b, Klibs N. Galvao, Corwin Nelson, and K. Casey Jeonga. Diversity of ?-lactam antibiotic resistant bacteria in mastitic cows and its potential association with antibiotic treatment failure. Under Review
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Lee S, Teng L, Jeong KC. Prevalence and molecular characteristics of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in commercial cattle farms. EPI Research Day, Gainesville, FL, Feb. 15, 2018
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Lee S, Teng L, Kim H, Jeong KC. Prevalence and molecular characteristics of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in commercial cattle farms. American Society for Microbiology annual meeting, Atlanta, GA, June 07-11, 2018.
  • Type: Book Chapters Status: Published Year Published: 2018 Citation: Si Hong Park, Mushin Aydin, Peixin Fang, Shinyoung Lee, Lin Teng, Sun Ae Kim, Soohyoun Ahn, Steven C Ricke, Zhaohao Shi, and K. C. Jeong. 2018. Detection strategies for foodboren Salmonella and prospects for utilization of whole genome sequencing. Food and Feed Safety Systems and Analysis. Safety Systems and Analysis. Steven Ricke [et al.]. Academic Press. 289-308.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Lee S, Boughton RK, Jeong KC. Occurrence and genomic characteristics of cefotaxime resistant bacteria in wildlife. Animal Sciences Symposium, St. Augustine, FL, Nov. 1-2, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Teng L, Lee S, Fan P, Mir RA, Jeong KC. Cycling of antimicrobial resistance from farms to hospitals. One Health Symposium, Gainesville, FL, Jan. 16, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Teng L, Fan P, Boucher C, Nelson CD, and Jeong KC. Prevalence and Characterization of Extended-spectrum ?-lactamase-producing Escherichia coli Isolated from Meconium of Newborn Calves, Emerging Pathogens Institute Research Day, Gainesville, FL, Feb. 15, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Teng L, Fan P, Boucher C, Noyes NR, Park S, Nelson CD, Ginn A, Driver JD, Morris JG, Jeong KC. Extended-spectrum ?-lactamase-producing Escherichia coli from meconium of newborn calves. Animal Sciences Seminar, Gainesville, FL, Mar. 15, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Teng L, Fan P, Ginn A, Noyes NR, Park S, Nelson CD, Driver JD, Boucher C, Ricke S, Jeong KC. Extended-spectrum ?-lactamase-producing Escherichia coli from meconium of Newborn Calves. American Society for Microbiology Annual Meeting, Atlanta, GA, Jun. 7-11, 2018
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Teng L, Fan P, Boucher C, Nelson CD, and Jeong KC. Extended-spectrum ?-lactamase-producing Escherichia coli from meconium of newborn calves. Animal Sciences Symposium, St. Augustine, FL, Nov. 1-2, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Fan P, Teng L, Nelson CD, Driver DJ, Elzo MA, Jeong KC. Animal breed composition shapes gut microbiota, and its effects on the host metabolic and immunological status. EPI Research Day, Gainesville, FL, Feb. 15, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Fan P, Nelson C, Driver J, Elzo M, Jeong KC. Bovine meconium microbiota varies with birthweight and influences the gut microbiota establishment during early stage of life. AMCB Symposium, Crystal River, FL, Apr.6-7, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Fan P, Teng L, Nelson CD, Driver DJ, Elzo MA, Jeong KC. Animal breed composition shapes gut microbiota, and its effects on the host metabolic and immunological status. Animal Science Seminar, Gainesville, FL, Apr. 10, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Fan P, Teng L, Nelson CD, Driver DJ, Elzo MA, Jeong KC. Animal breed composition shapes gut microbiota, and its effects on the host metabolic and immunological status. American Society for Microbiology annual meeting, Atlanta, GA, June 07-11, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: 1. Fan P, Poindexter M, Nelson CD, Driver DJ, Elzo MA, Jeong KC. Development of gut microbiota through life in an Angus-Brahman multibreed herd. Animal Sciences Symposium, St. Augustine, FL, Nov. 1-2, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jeong, K.C. Understanding cross-talk between gut microbiota and host that modulates immune response and physiological performance. International Association for Food Protection. Salt-Lake City, UT, USA. Jul. 18-21, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jeong, K.C. Impact of the use of polymyxin antimicrobials on the emergence of antimicrobial resistance and safety of foods of animal origin. Korean Society of Food Science and Technology. Korea. Jun. 27-29, 2018.


Progress 02/15/17 to 02/14/18

Outputs
Target Audience:The target audience of the 3rd year effort of this grant was not only scientific community who focuses on research to reduce the prevalence of antimicrobia resistant microorganisms in food animals but also food animal producers. Gradute and undergradute students were trained too. County agents (Agriculture agents) and meat processing industry wokers were also trained. We have also extended our dissemination efforts to public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Objective 4C: Involve undergraduate, graduate, and pre-veterinary students in best cattle management practices and research activities to reduce AMR to stimulate interest towards graduate school and food animal oriented careers. We had 8 interns participating the University of Florida Preharvest and Post-harvest Food Safety Internships during the reporting period. The intent of this training program introduced undergraduates to research methods and to the variety of career options available in the fields of food safety and antimicrobial resistance. Training modules emphasized practices related to the risk of antimicrobial resistance in food animals and meat processing. The internship was divided into two phases, and each lasted for 4 weeks. The phase 1 took place at the University of Florida, North Florida Research and Education Center in Marianna, FL. The interns were introduced to research facilities and field equipment (cattle scale, cattle handling facilities, vehicles), common animal husbandry practices in beef cattle production (feeding, bedding, mineral supplementation), sample collections (blood, ruminal fluid), cattle weighing and processing, measurement of greenhouse gas emissions and laboratory techniques (determination of blood urea nitrogen concentration, volatile fatty acids in ruminal fluid). The phase 2 was held at the University of Florida, Department of Animal Sciences in Gainesville, FL. The interns leaned Standard operating procedures (SOPs) and Good Manufacturing Practices (GMPs) associated with beef slaughter and fabrication, received Hazzard Analysis Critical Control Point System (HACCP) training, and learned about primary antimicrobial interventions used in beef processing, their efficiency and application, microbiology analysis methods to evaluate antimicrobial resistant microorganism as well as sanitary dressing procedure. Five of the students were enrolled in the animal sciences program at the University of Florida, and one was enrolled at Florida A&M University. Many of the students enrolled in this internship program are now seeking graduate school opportunities because of their exposure to research and animal production. 10 graduate students were supported by this grant during the reporting period. Their dissertation projects are directly related to AMR. We are expecting 4 PhD degrees in the area of AMR will be granted by supporting this grant. A group of 20 high-school students from the Farm Bureau leadership group visited the University of Florida-NFREC station on December 13, 2017. The students belonging to STEM disciplines discussed with University of Florida researchers, the latest projects conducted at the University's research station and discussed current issues in animal agriculture and career opportunities in animal sciences and agronomy. We provided In-service training. During the reporting period, training was offered for extension agents to provide food safety update on antimicrobial resistance in food animals and food risks associated with backyard chicken and other live poultry. A 2-day in-service training was offered under the title of "Meat and Poultry Safety Update: Current Issues and Mitigation Strategies" on Feb 7-8 in Gainesville, FL. We had a total of 15 participants in the training. Based on the feedback from last year, we have adjusted the difficulty level of presentations to beginning to intermediate so the information would be easy and clear to understand for our target clients and county agents. This training covered the topics under the developed educational curriculum, including meat and poultry safety and best handling practice, antimicrobial resistance in food animals and its mitigation strategies, food safety issues associated with backyard poultry raising, shell egg safety and regulations, animal food safety, and USDA-regulated food products' labeling. According to the exit survey, 100% of participants self-assessed that their knowledge on the topics improved on the topics (67% reported significant improvement and 23% moderate improvement). This self-assessment was supported by pre- and post-test results, which showed the knowledge gain from 72% (pre-test) to 86% (post-test). Additionally, 83% of participants said they would use the information they obtained from training in their own programs including seminars, and training workshops. As all training participants are the extension agents who directly work with our target clients (cattle and poultry farm owners and employee, meat and poultry industry), we believe this "train-the-trainers" approach will effectively transfer knowledge to target stakeholders. Programs or events where agents said they would use the information include field days (average attendance of 120), Florida Cattlewomen's booth at the state fair (average attendance of 400,000), and Beef Quality Assurance program for small growers (average attendance of 200), which will further increase the impact of the training. How have the results been disseminated to communities of interest?Objective 4B: Transfer mitigation strategies to food animal producers and scientists by publications, training and education through scientific journals, personal contact, and web-based resources including eXtension system. We disseminated outcomes through various methods that include research article publications, presentations, We trained extension agents, farmers and students. We developed educational curriculum. During the reporting period, educational curriculum developed in year 2 was modified to include shell eggs safety and animal feed safety based on the feedback from county extension agents who are directly working with stakeholders or run active animal/meat/poultry programs. Additionally, educational materials have updated to include new findings in the research and updated information. The educational curriculum included the following topics: Update on food safety issues with meat and poultry products Safety risks associated with backyard chickens and best practices in raising them Antibiotic resistance in food animals: current issues in public health and agriculture Mitigation strategies to minimize antimicrobial resistance in food animals Review of USDA-regulated food labeling Animal feed safety (based on FSMA Preventive Controls for Animal Food Rule) Safe handling of shell eggs and regulatory requirements Common food safety mistakes in meat and poultry handling We developed Educational packet. During the reporting period, the extension efforts focused on creating an educational packet that can be used by both extension agents and stakeholders in farming and processing industry. Based on the developed curriculum, a 288-page reference and practice guide for extension agents in livestock, agriculture and food safety, and stakeholders which is titled "Meat and Poultry Safety Update". This guide includes recommendations for backyard poultry raising, up-to-date statistics on meat and poultry-associated foodborne illnesses, and government publications on current risks linked to antibiotic use in agriculture and strategies to reduce antimicrobial resistance. So far, 35 copies have been distributed to extension agents, who will use the packet to train stakeholders. Instructional multimedia presentations. For the extension efforts, we have created a total of 9 instructional multimedia presentations. These presentations are used in trainings, workshops, and classes offered under this project, and they are also shared with extension agents so they can use them in their own classes or trainings. Presentation at the Annual Convention of the Florida Cattlemen Association. June 17, 2017, Orlando, FL. The presentation was entitled: "Developing a Research Program to Serve the Florida Beef Industry and the World" and was an invited talk by Dr. Nicolas DiLorenzo as recipient of the 2017 Researcher of the Year Award. The audience was comprised of 600 Florida cattle producers, approximately 45 researchers and extension faculty, and University of Florida administrators (Deans of Research and Extension). The presentation highlighted the integrated project: "Understanding antibiotic resistance occurrence and development of mitigation technologies in cattle", funded by the USDA-NIFA as one of the key projects of relevance to the Florida cattle industry. NFREC Beef/Forage Day. Extension event held at the University of Florida, North Florida Research and Education Center (NFREC) in Marianna, FL. A total of 120 beef and forage producers from northern Florida and southern Alabama and Georgia attended this event. Dr. DiLorenzo gave a field talk about the various research programs conducted at NFREC, including the antimicrobial resistance project. 2018 Family Day at the Dairy Farm. We participated the 5th Family Day at the University of Florida's Dairy Unit. This annual event is an Open House for the general public to come visit a working dairy farm. We presented a variety of educational information to ~1500 visitors and introduce the works for improving Florida's dairy production, animal welfare and environmental sustainability. We introduced AMR that cause infectious disease to visitors and trained to reduce AMR at home. Sub-award institute (FAMU) conducted various extension activities to disseminate research outcomes that include farm fest field day multimedia presentation, creation of video, TV interview, social media posts and sharing. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period (NCE), we will focus on publication of research findings and dissemination of outcomes. Training and professional development, dissemination of outcomes to communities will be a top priority.

Impacts
What was accomplished under these goals? Aim #1: Objective 1A: Evaluate prevalence of antibiotic resistant microorganisms in cow/calf operations. We found that the widespread distribution of cefotaxime resistant bacteria into cattle and the environment in the absence of antibiotic usage, suggesting a natural source of antimicrobial resistance. Objective 1B: Identify associated risk factors for the presence of AMR organisms. Results indicated that animal age and parity are critical factor influencing the prevalence of STEC. In a cross-sectional study, the prevalence and concentration of CRB in beef cattle on grazing farms were investigated. Fecal samples from the recto-anal junction of cattle (n = 840) and environmental samples (n = 258) were collected from 17 farms in North and Central Florida in the US, and a survey of farm characteristics, animal husbandry practices and antibiotic usage was administered. CRB were detected in fecal samples from 47.4% of all cattle, with the prevalence ranging from 21.1% to 87.5% on farms that was significantly higher (P < 0.001) in calves compared to adult cows (54.1 vs 41.8%). Environmental samples had a higher prevalence than fecal samples (P < 0.001), with CRB detected in 88.6% of water, 98.7% of soil, and 95.7% of forage samples. Compared to the concentration (log CFU) of CRB in fecal samples (2.95, 95% CI: 2.89, 3.02), the concentration of CRB was higher (P < 0.001) in soil and forage samples (5.37, 95% CI: 5.16, 5.57) and lower (P < 0.001) in water samples (1.08, 95% CI: 0.82, 1.36). Aim #2: Objective 2A: Speciate ESBL-producing organisms in cattle. Using whole genome sequencing and comparative genomics of 30 extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBLs), isolated from beef cattle with no previous exposure to antibiotics, we provide evidence for acquisition of the ESBL isolates from environment, rather than raised on farms by antibiotic use. Phylogenic relatedness with reference ESBLs from various geographic locations and hosts, such as animals, the environment, and humans suggests that transmission of ESBLs occurs intercontinentally without host preference. Objective 2B: Identify virulence and resistance genes and understand mechanisms of acquisition of ESBLs in cattle. We described multidrug resistance of the ESBL isolates against 12 different antibiotics and comprehensive antibiotic resistance profiles. We found the ESBL isolates encoded various virulence genes, providing insight into not only the evolution of bacterial pathogenesis, but a potential threat for public health. We identified the ESBL genes are carried on chromosomal DNA and plasmids. The ESBL genes are transmitted by horizontal gene transfer by conjugation and plasmid transformation. Aim #3: Objective 3A: Trace animals from birth to slaughter to understand AMR occurrence, prevalence and transmission in cow/calf operations To identify the earliest time when animals are exposed to ESBL-producing E. coli. We conducted a cohort study using 322 calves. We collected meconium samples from the rectal anal junction of 322 newborn calves within 12 hours after their births. Fecal samples were collected from the recto anal junction of cattle at the age of ~0, 3, 6, 9, 12, 15, and 18 months and tested for cefotaxime resistant bacteria (CRB) and the presence of extended spectrum β-lactamases (ESBLs). ESBL-producing E. coli was detected in the range of 50-10.5% (34/322) of fecal samples Whole Genome Sequencing (WGS) of ~400 ESBL strains were conducted. Following WGS, phylogenetic analysis revealed that these strains clustered into 8 groups that coincided with their STs. All the isolates carried a variety of virulence genes and were resistant to multiple antibiotics, suggesting that these strains may threaten public health if they contaminate food products. In particular, we identified hyper-virulent strains of ST117 that harbored Shiga toxin-encoding genes (stxAB), which may cause severe human diseases. This was the first study that accessed the prevalence and characterization of ESBL-producing E. coli in meconium of newborn calves, indicating animals are even start to be exposed to AMR bacteria in the uterus. Furthermore, we isolated ESBLs from the cow uterus with mastitis. The pathogenicity of these ESBL isolates were confirmed by invasion assay, minimal inhibitory concentration test and antimicrobial susceptibility test. In addition, these ESBL producing IUPEC had high virulence and multidrug resistance, which were similar to the reference human clinical E. coli isolates. Objective 3B: Identify animal factors that affect the prevalence of ARMs in cattle. To identify animal factors that affect on the prevalence of ESBLs in the gastrointestinal tract, we conducted 16S rRNA metagenomics analysis. Fecal samples were collected from the recto anal junction of cattle at the age of ~0, 3, 6, 9, 12, 15, and 18 months. We analyzed ~2,000 fecal samples to understand microbe-host and microbe-microbe interactions. Metagenomic analysis revealed significant differences in microflora of the calves with and without ESBL colonization at different ages. We found that the mature microbiota reduces colonization of ESBLs in the gastrointestinal tract. We found specific genera that showed negative correlation with ESBLs. Taken together, our results provide insights into how to develop mitigation strategies to reduce ESBLs in cattle. Objective 3C: Develop a mathematical model that will predict ARM occurrence in cattle In a cohort study, a herd of beef calves with no previous exposure to antibiotics was followed during the first year of life in order to investigate the rate of colonization by bacteria resistant to the third-generation cephalosporin cefotaxime. Fecal samples were collected from the recto anal junction of cattle at the age of ~3, 6, 9, and 12 months and tested for cefotaxime resistant bacteria (CRB) and the presence of extended spectrum β-lactamases (ESBLs). The colonization dynamics of CRB in calves (n= 188) was evaluated with samples collected from four periods using longitudinal statistical analyses. Colonization by CRB was a dynamic process with over 92% of the calves testing positive for CRB at least once during the first year of life. Cattle were assumed to be born without CRB colonization and classified at each sampling into one of four groups: calves not previously colonized that remain uncolonized (−/−), calves not previously colonized that became colonized (−/+), calves previously colonized that remain colonized (+/+), and calves previously colonized that became uncolonized (+/−). Using Markov chain assumptions, the probability of colonization between sampling periods was assumed to only be dependent on the previous state of colonization and calculated directly Objective 4A: Develop best AR mitigation strategies on the basis of outcomes of this proposed research that can be applied in cow/calf operations. We found that farm management practices can be used to reduce AMR in animals that include frequent cleaning of water troughs, decomposing dead animals, feeding ionophores, quarantine new animal into herds, and keeping farming size small/medium. We have developed alternative antimicrobial agents to feed cattle to reduce AMR.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mir RA, Weppelmann TA, Teng L, Kirpich A, Elzo MA, Driver JD, Jeong KC. Colonization Dynamics of Cefotaxime Resistant Bacteria in Beef Cattle Raised Without Cephalosporin Antibiotics. Frontiers in microbiology, 2018; 9:500.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Ma ZX, Garrido-Maestu A, Jeong KC. Application, mode of action, and in vivo activity of chitosan and its micro-and nanoparticles as antimicrobial agents: A review. Carbohydrate polymers, 2017; 176, 257-265.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Ma, Z.X., A. Garrido-Maestu, C. Lee, J. Chon, D. Jeong, Y. Yue, K. Sung, Y. Park, and K.C. Jeong. 2018. Comprehensive in vitro and in vivo evaluation of chitosan microparticles for risk assessments using epithelial cells and Caenorhabditis elegans. Hazardous Materials. J. Hazardous Materials. 341:248-256.
  • Type: Journal Articles Status: Under Review Year Published: 2018 Citation: Alejandro Garrido-Maestu, Zhengxin Ma, Sae-Yeol-Rim Paik, Nusheng Chen, Sanghoon Ko, Zhaohui Tong, K.C. Jeong. Engineering of Chitosan-derived nanoparticles to enhance antimicrobial activity against foodborne pathogen Escherichia coli O157:H7. Under review.
  • Type: Journal Articles Status: Under Review Year Published: 2018 Citation: Markland, S., Thomas A. Weppelmann, Zhengxin Ma, Shinyoung Lee, Raies A. Mir, Lin Teng, Amber Ginn, Choonghee Lee, Maria Ukhanova, Sebastian Galindo, Chad Carr, Nicolas DiLorenzo, SooHyoun Ahn, Jae Hyung Mah, Volkar Mai, Mobley Ray, J Glenn Morris, and K.C. Jeong. High Prevalence of Cefotaxime Resistant Bacteria in grazing Beef Cattle: A Cross Sectional Study. Under review.
  • Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Fan P, Teng L, Nelson CD, Driver DJ, Elzo MA, Jeong KC. Animal breed composition shapes the gut microbiota, and its effects on the host metabolic and immunological status.
  • Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Fan P, Nelson CD, Driver DJ, Elzo MA, Jeong KC. Meconium microbiota varies with birthweight and influences the gut microbiota establishment during early stage of life.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Teng L, Lee S, Fan P, Mir RA, Jeong KC. Cycling of antimicrobial resistance from farms to hospitals. One Health Symposium, Gainesville, FL, Jan. 16, 2018.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Ma ZX, Kang MY, Meng S, Tong Z, Jeong KC. Development of antibody-conjugated chitosan microparticles selectively targeting Shiga toxin producing Escherichia coli. Animal Sciences Symposium of University of Florida, St. Augustine, FL, Oct. 13-14, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Fan P, Nelson CD, Driver JD, Elzo MA, Jeong KC. Understanding cross-talk between gut microflora and host that modulate growth performance and immune responses. Animal Sciences Symposium of University of Florida. St. Augustine, FL. Oct. 13-14.2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Lee S, Teng L, Jeong KC. Isolation and Characterization of Extended-spectrum ?-lactamase (ESBL)-producing E. coli from cow-calf operations in Florida. Animal Sciences Symposium of University of Florida, St. Augustine, FL. Oct. 13-14.2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Teng L, Fan P, Boucher C, Nelson CD, Jeong KC. Extended-spectrum ?-lactamase-producing Escherichia coli from meconium of newborn calves, Animal Sciences Symposium of University of Florida, St. Augustine, FL. Oct. 13-14.2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Teng, L, P.X. Fang, C. Boucher, N.R. Noyes, S. Park, C.D. Nelson, A. Ginn, J.D. Driver, J.G. Morris, K.C. Jeong. Extended-spectrum ?-lactamase-producing Escherichia coli from meconium of newborn calves. EPI Research Day, Gainesville, FL, Feb. 23, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Lee S, Teng L, Jeong KC. Isolation and characterization of extended-spectrum beta-lactamase producing Escherichia coli from beef cattle farms. EPI Research Day, Gainesville, FL, Feb. 23, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Ma ZX, Ginn A, Mir RA, Kang MY, Galvao KN, Jeong KC. Genomic characterization of intrauterine pathogenic Escherichia coli from cows with metritis. EPI Research Day, Gainesville, FL, Feb. 23, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Teng L, Fan P, A. Ginn&, J.D. Driver&, and K.C. Jeong. Extended-spectrum beta-lactamase-producing Escherichia coli from meconium of newborn calves. International Association for Food Protection Annual Meeting, Tampa, FL, Jul. 9-12, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Lee, S, Teng L, Lim J, Park J, Jeong KC. Isolation and characterization of extended-spectrum beta-lactamase producing Escherichia coli from beef cattle farms. International Association for Food Protection Annual Meeting, Tampa, FL, Jul. 9-12, 2017.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Ma ZX, Ginn A, Mir RA, Kang MY, Galvao KN, Jeong KC. Genomic characterization of intrauterine pathogenic Escherichia coli from cows with metritis. American Association of Animal Science Annual Meeting, Baltimore, MD, Jul. 8-12, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jeong, K.C. Understanding cross-talk between host and gut microflora to enhance health and growth performance. ISNFF. Gunsan, Korea. Oct. 22-25, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jeong, K.C. Development of antibody-conjugated chitosan microparticles selectively targeting Shiga toxin producing Escherichia coli. KyungHee University. Suwon, Korea. Oct. 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: K.C. Jeong. Enhancing animal health through multiple modes of action. American Dairy Science Association, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: K.C. Jeong. Antibiotic Resistance and Food Safety in the Genomic Era: Occurrence, Transmission, and Source Tracking. KosFost. Jeju, Korea. June 21-23, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jeong, K.C. Understanding antibiotic resistance occurrence and development of mitigation strategies in cattle. USDA AFRI Antimicrobial Resistance program grantees annual meeting. Tampa. FL. July 2017.
  • Type: Book Chapters Status: Published Year Published: 2018 Citation: Si Hong Park, Mushin Aydin, Peixin Fang, Shinyoung Leeg, Lin Teng, Sun Ae Kim, Soohyoun Ahn, Steven C Ricke, Zhaohao Shi, and K. C. Jeong. 2018. Detection Strategies for Foodborne Salmonella and Prospects for Utilization of Whole Genome Sequencing Approaches. Pages:289-308. Food and Feed Safety Systems and Analysis. Steven Ricke [et al.]. Academic Press.


Progress 02/15/16 to 02/14/17

Outputs
Target Audience:The target audience of the second year effort of this grant was not only scientific community who focuses on research to reduce the prevalence of antimicrobia resistant microorganisms in food animals but also food animal producers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Activities and outcomes: Professional Development Workshops Metagenomics and Whole Genome Sequencing Workshop at Emerging Pathogens Institute at the University of Florida. Provided support to invite a scientist to come to EPI to provide training to lab members for metagenomics and whole genome sequencing preparation in regards to this project. Workshop held December 2016, at the Emerging Pathogens Institute at the University of Florida in Gainesville, FL. This program trained total of 8 scientists. Undergraduate internship training Two-month internship for undergraduate students for antimicrobial resistance at pre- and post-harvest level. Provided training for animal management to reduce AMR on beef cattle farms. Provided training to reduce AMR prevalence during meat processing. Provided training to experimental techniques to isolate and identify AMR in animals. 6 students from University of Florida and FAMU were trained in the summer of 2016. How have the results been disseminated to communities of interest?Research findings have been disseminated to scientific groups and animal producers through publications, conference posters, and invited talks. What do you plan to do during the next reporting period to accomplish the goals?We have successfully accomplished the second year's goals and will continue to accomplish 3rd year's goals proposed in the grant proposal. We will continue to disseminate our accomplishments from research findings to scientific groups and animal producers through publications, conference posters, and invited talks.

Impacts
What was accomplished under these goals? Objective 1A: Evaluate prevalence of antibiotic resistant micoorganisms in cow/calf operations. RESEARCH ARTICLE - Published Mir RA, Weppelmann TA, Johnson J, Archer D, Morris JG, Jeong KC. Identification and characterization of cefotaxime resistant bacteria in beef cattle. PLoS One 2016; 11(9). Abstract The prevalence of cefotaxime-resistant bacteria was examined by a combination of culture based and molecular typing methods in beef cattle (n = 1341) from 8 herds located in North Central Florida. The overall prevalence of cefotaxime-resistant bacteria was 15.8% (95% CI: 13.9, 17.8), varied between farms, and ranged from 5.2% to 100%. A subset of isolates (n = 23) was further characterized for the cefotaxime minimum inhibitory concentration (MIC) and antibiotic susceptibility against 10 different antibiotics, sequencing of nine β- lactamase genes, and species identification by 16S rRNA sequencing. Most of the bacterial isolates were resistant to cefotaxime (concentrations, > 64 μg/mL) and showed high levels of multi-drug resistance. Full length 16S rRNA sequences (~1300 bp) revealed that most of the isolates were not primary human or animal pathogens; rather were more typical of commensal, soil, or other environmental origin. Six extended spectrum β-lactamase (ESBL) genes identical to those in clinical human isolates were identified. Our study highlights the potential for carriage of cefotaxime resistance (including "human" ESBL genes) by the bacterial flora of food animals with no history of cefotaxime antibiotic exposure. A better understanding of the origin and transmission of resistance genes in these pre-harvest settings will be critical to development of strategies to prevent the spread of antimicrobial resistant microorganisms to hospitals and communities. Objective 1B: Identify associated risk factors for the presence of AMR organisms. RESEARCH ARTICLE - Manuscript in Preparation Weppelmann TA, Markland S, Ma ZX, Lee S, Mir RA, Teng L, Ginn A, Lee C, Cangiano LR, Galindo S, Carr C, DiLorenzo N, Ukhanova M, Mai K, Jeong KC. High prevalence of cefotaxime resistant bacteria in grazing beef cattle: a cross sectional study. In preparation Objective 2A: Speciate ESBL-producing organisms in cattle. RESEARCH ARTICLE - Published Teng L, Ginn A, Jeon SJ, Jeong KC. Complete genome and plasmid sequence of an E. coli O157:H7 strain isolated from a supper-shedder steer. Genome Announc. 2016; 4(2) e00228-16. Abstract We report here the complete genome sequence ofEscherichia coliO157:H7 strain JEONG-1266 isolated from a super- shedder steer in northwest Florida. Cattle are considered a primary reservoir ofE.coliO157:H7, and those cattle that excrete this pathogen in their feces at levels ≥10(4)CFU/g are known as super-shedders. Ginn A, Ma ZX, Galvao KN, Jeong KC. Draft genome sequence of an Escherichia coli O8:H19 ST708 Strain isolated from a Holstein dairy cow with metritis. Genome Announc. 2016; 4(2) e00261-16. Abstract We present here the genome sequence ofEscherichia coliO8:H19 strain KCJ852, belonging to multilocus sequence type (MLST) 708, isolated from the uterus of a cow with a bovine postpartum uterine infection known as metritis. Genomic investigation of KCJ852 will help us understand its virulence potential. RESEARCH ARTICLE - Manuscript in Preparation Amber Ginn, Lin Teng, Sarah M. Markland, Raies Mir, J. Glenn Morris, Jr., and Kwangcheol C. Jeong. Genomic Comparison Reveals Natural Dissemination of Extended Spectrum β-lactamase producing Escherichia coli in the environment. Objective 2B: Identify virulence and resistance genes and understand mechanisms of acquisition of ESBLs in cattle. RESEARCH ARTICLE - Manuscript Prepared for Submission Lin Teng1, 2, Peixin Fan1, 2, Amber Ginn1, 2, Noelle R Noyes4, Sihong Park5, Corwin D. Nelson2, J. Danny Driver2, Christina Boucher3, Steven Ricke5, J. Glenn Morris, Jr., and Kwangcheol Casey Jeong. Unexpected isolation of Extended-spectrum β-lactamase-producing Escherichia coli from Meconium of Newborn Calves. RESEARCH ARTICLE - Manuscript In preparation Zhengxin Ma1, 2, Amber Ginn1, 2, Minyoung Kang1,2, Klibs N. Galvao, and K.C. Jeong1,2 . Genomic evolution of Extended Spectrum β-lactamase-producing intrauterine pathogenic Escherichia coli from dairy cattle with metritis Objective 3A: Trace animals from birth to slaughter to understand AMR occurrence, prevalence and transmission in cow/calf operations RESEARCH ARTICLE - data collection on going Teng Lin1,2, S. Lee1,2, Z. Ma1,2, Peixin Fan1,2, C.Lora1,2, C. Nelson2, M. Elzo2, J.D. Driver2, and K.C. Jeong1,2 Tracking prevalence of antibiotic resistant organisms in beef calves from birth to slaughter and transmission from cows to calves Results: We have collected fecal samples from the RAJ of 324 new borne claves every three months for 15 months. We also collected meconium samples from their respective calves within 24 h of birth. We determined that approximately 10-20% of calves were positive for ESBLs during sampling season. Objective 3B: Identify animal factors that affect the prevalence of ARMs in cattle. Outcomes: RESEARCH ARTICLE - Published Mir RA, Weppelmann TA, Elzo M, Ahn S, Driver JD, Jeong KC. Colonization of beef cattle by Shiga toxin-producing Escherichia coli during the first year of life: a cohort study. PLoS One 2016; 11(2):e0148518. Abstract This study evaluated if animal physiological factors such as age, breed, sex, and weight gain influenced the shedding of STEC in beef cattle. A cohort of beef calves (n = 260) from a multi-breed beef calf population was sampled every three months after birth to measure prevalence and concentration of STEC during the first year of life. Metagenomic analysis was also used to understand the association between the STEC colonization and the composition of gut microflora. This study identified that beef calves were more likely to shed STEC during the first 6 months and that STEC shedding decreased as the animal matured. Animal breed group, sex of the calf, and average weight gain were not significantly associated with STEC colonization. The metagenomic analysis revealed for the first time that STEC colonization was correlated with a lower diversity of gut microflora, which increases as the cattle matured. Given these findings, intervention strategies that segregate younger animals, more likely to be colonized by STEC from older animals that are ready to be harvested, could be investigated as a method to reduce zoonotic transmission of STEC from cattle to humans. Objective 4A: Develop best AR mitigation strategies on the basis of outcomes of this proposed research that can be applied in cow/calf operations. RESEARCH ARTICLE - Under review Mir RA, Weppelmann TA, Teng L, Kirpich A, Elzo MA, Driver JD, Jeong KC. Colonization dynamics of cefotaxime resistant bacteria in beef cattle raised without cephalosporin antibiotics. 2017. Under review.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Teng L, A. Ginn, S.J. Jeon, and K.C. Jeong. 2016. Complete genome and plasmid sequence of an E. coli O157:H7 strain isolated from a supper-shedder steer. genomeA. 4(2) e00228-16.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ginn A., Z.X. Ma, K.N. Galvao, and K.C. Jeong. 2016. Draft genome sequence of an Escherichia coli O8:H19 ST708 strain isolated from a Holstein dairy cow with metritis. genomeA. 4(2) e00261-16.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ma Z.X., D. Kim, A.T. Adesogan, S. Ko, K.N. Galvao, and K.C. Jeong. 2016. Chitosan microparticles exert broad spectrum antimicrobial activity against antibiotic resistant microorganisms without increasing resistance. ACS Appl. Mater. Interfaces. 8:10700-9
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Jeon, S.J., Z.X. Ma, M.Y. Kang, K. Galv�o, and K.C. Jeong. 2016. Application of chitosan microparticles for treatment of metritis and in vivo evaluation of broad spectrum antimicrobial activity in cow uteri. Biomaterials. 110:71-80.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mir R.A., T.A. Weppelmann, J. Johnson, D. Archer, J.G. Morris, and K.C. Jeong. 2016. Identification and characterization of cefotaxime resistant bacteria in beef cattle. PLoS One. doi: 10.1371/journal.pone.0163279
  • Type: Journal Articles Status: Under Review Year Published: 2017 Citation: Ma Z.X., A. Garrido-Maestu, and K.C. Jeong. 2017. Engineering, applications, and mode of action of chitosan and its derivatives as antimicrobial agents.
  • Type: Journal Articles Status: Under Review Year Published: 2017 Citation: Ma, Z.X., A. Garrido-Maestu, C. Lee, J. Chon, D. Jeong, Y. Yue, K. Sung, Y. Park, and K.C. Jeong. 2017. Comprehensive in vitro and in vivo evaluation of chitosan microparticles for risk assessments using epithelial cells and Caenorhabditis elegans.
  • Type: Journal Articles Status: Under Review Year Published: 2017 Citation: Mir RA, Weppelmann TA, Teng L, Kirpich A, Elzo MA, Driver JD, Jeong KC. Colonization dynamics of cefotaxime resistant bacteria in beef cattle raised without cephalosporin antibiotics. 2017. Under review.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Teng L, Ginn A, DiLorenzo N, Ahn S, Jeong KC. Comparative genomics of Escherichia coli O157:H7 from super-shedder and low shedder cattle. Animal Sciences Symposium, St. Augustine, FL, Oct. 21-22, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Lee S, Teng L, Ginn A, Jeong KC. Isolation and characterization of ESBL-producing E. coli isolated on commercial farms. Animal Sciences Symposium, St. Augustine, FL, Oct. 21-22, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Ma ZX, Lee C, Chon J, Jeong D, Sung K, Park Y, Jeong KC. Comprehensive in vitro and in vivo evaluation of chitosan nanoparticles for risk assessments with intestinal epithelial cells and Caenorhabditis elegans. Animal Sciences Symposium, St. Augustine, FL, Oct. 21-22, 2016
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Teng L, Kang M, Markland S, Lee C, Mir RA, Ma ZX, Park D, Jeong KC. Comparative genome analysis reveals a hyper-virulent Escherichia coli O157:H7 strain isolated from a super-shedder. International Association for Food Protection Annual Meeting, St. Louis, MO, Jul 31-Aug 3, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Markland S, Mir RA, Ginn A, Jeong KC. Genomic comparison of extended-spectrum beta-lactamase-producing bacteria isolated from beef cattle grazing on pasture. International Association for Food Protection Annual Meeting, St. Louis, MO, Jul 31-Aug 3, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Markland S, Ginn A, Mir RA, Ma ZX, Teng L, Lee C, Henry D, Garcia M, Rostoll L, DiLorenzo N, Carr C, Jeong KC. Prevalence of extended-spectrum beta-lactamase-producing bacteria and Escherichia coli O157:H7 on commercial beef cattle farms in north Florida. International Association for Food Protection Annual Meeting, St. Louis, MO, Jul 31-Aug 3, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Ma ZX, Lee C, Chon J, Jeong D, Sung K, Park Y, Jeong KC. Evaluation of toxicity of chitosan nanoparticles with intestinal epithelial cells and Caenorhabditis elegans. International Association for Food Protection Annual Meeting, St. Louis, MO, Jul 31-Aug 3, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Teng L, Fan P, Boucher C, Noyes NR, Park S, Nelson CD, Ginn A, Driver JD, Morris JG Jr, Jeong KC. Extended-spectrum ?-lactamase-producing Escherichia coli from meconium of newborn calves. EPI Research Day, Gainesville, FL, Feb. 23, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Lee S, Teng L, Jeong KC. Isolation and characterization of extended-spectrum beta-lactamase producing Escherichia coli from beef cattle farms. EPI Research Day, Gainesville, FL, Feb. 23, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Ma ZX, Ginn A, Mir R, Kang M, Galvao KN, Jeong KC. Genomic characterization of intrauterine pathogenic Escherichia coli from cows with metritis. EPI Research Day, Gainesville, FL, Feb. 23, 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Teng L, Fan P, Ginn A, Driver J, Jeong KC. Extended-spectrum beta-lactamase-producing Escherichia coli from meconium of newborn calves. International Association for Food Protection Annual Meeting, Tampa, FL, Jul. 9-12, 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Lee S, Teng L, Lim J, Park J, Jeong KC. Isolationand characterization of extended-spectrum beta-lactamase producing Escherichia coli from beef cattle farms. International Association for Food Protection Annual Meeting, Tampa, FL, Jul. 9-12, 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Ma ZX, Ginn A, Mir R, Kang M, Galvao KN, Jeong KC. Genomic characterization of intrauterine pathogenic Escherichia coli from cows with metritis. American Association of Animal Science Annual Meeting, Baltimore, MD, July. 8-12, 2017.


Progress 02/15/15 to 02/14/16

Outputs
Target Audience:The target audience of first year effort of this grant was not only scientific community who focuses on research to reduce the prevalence of antimicrobia resistant microorganismsin food animals but also food animal producers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Education and Professional Development Workshops Metagenomics and Whole Genome Sequencing Workshop at Emerging Pathogens Institute at the University of Florida. Provided support to invite a scientist to come to EPI to provide training to lab members for metagenomics and whole genome sequencing preparation in regards to this project. Workshop held January 19-22 at the Emerging Pathogens Institute at the University of Florida in Gainesville, FL. International Clinics on Infectious Disease Dynamics and Data (ICID3) Program. Clinic on Dynamical Approaches to Infectious Disease Data (DAIDD). Provided support for one student to participate in this workshop to learn to develop a dynamical model involving the data collected in this project. Workshop Held December 12-19, 2015 at the White Oak Conservation Center in Yulee, FL. http://www.ici3d.org/daidd/ PacBio User Group Meeting Provided support for one student to participate in this workshop to learn whole genome sequencing techniques in regards to this project. Workshop held June 16-18 at the University Of Maryland School Of Pharmacy in Baltimore, MD. http://programs.pacificbiosciences.com/l/1652/2015-03-25/31k95f How have the results been disseminated to communities of interest?Research findings have been disseminated to scientific groups and animal producers through publications, conference posters, and invited talks. What do you plan to do during the next reporting period to accomplish the goals?We have successfully accomplished the first year's goals and will continue to accomplish second year's goals proposed in the grant proposal.

Impacts
What was accomplished under these goals? Aim #1: Understand AR occurrence in cow/calf operations to identify risk factors raising AR in cattle that will explain how ARMs are developed and prevalent in earlier stages of production. This will be applied in the development of a farm management model to mitigate ARMs. Objective 1A: Evaluate prevalence of antibiotic resistant micoorganisms in cow/calf operations. Outcomes: RESEARCH ARTICLE - Manuscript Prepared for Submission Identification and characterization of naturally occurring cefotaxime resistant microorganisms in beef cattle Raies A. Mir, Thomas A. Weppelmann, Judith A. Johnson, Douglas Archer, Glenn J. Morris, Jr., and Kwangcheol Casey Jeong* Results We report the isolation of bacteria from cattle with no previous antibiotic treatment. 1365 fecal samples were collected from cows from 11 different herds located in N. Florida. Overall prevalence of cefotaxime resistant bacteria was 15.8% Most of the bacterial isolates were resistant to therapeutic concentrations (> 64 µg/mL) of cefotaxime. Most of the isolates were of commensal, soil, or environmental origin. This is the first study to demonstrate the natural phenomena of cephalosporin resistance in food animals with no history of antibiotic treatment. Objective 1B: Identify associated risk factors for the presence of AMR organisms. Results indicated that animal age and parity are critical factor influencing the prevalence of STEC. Outcomes RESEARCH ARTICLE - In Preparation Prevalence of extended-spectrum β-lactamase producing bacteria and E. coli O157:H7 on commercial beef cattle farms in North Florida Markland, S.M.1,2, R.A. Mir1,2, Z. Ma1,2, L. Teng1,2, C. Lee1,2, D. Henry1,3, M. Garcia1,3, L. Rostoll1,3, S. Turner2, G. Hidalgo2, C. Lora2, G.C. Lamb1,3, N. DiLorenzo1,3, C. Carr1and K.C. Jeong1,2 Results: We collected fecal, soil, forage and water samples from 17 commercial cow/calf operations in 9 counties across North Florida. The prevalence of cefotaxime resistance on farms ranges from 28.9% to 92.3%. The prevalence of E. coli O157:H7 on farms ranges from 24.4% - 72.2%. Prevalence of cefotaxime resistant organisms is highest in soil samples. Prevalence of E. coli O157:H7 is highest in forage samples. Aim #2: Identify mechanisms of antimicrobial resistance, especially extended-spectrum β-lactamases (ESBLs), to understand how and where antibiotic resistance acquired in cattle can be applied in the development of cattle management model to mitigate AMR organisms. Objective 2A: Speciate ESBL-producing organisms in cattle. Outcomes: RESEARCH ARTICLE - Manuscript in Preparation Genomic comparison of extended spectrum β-lactamase- producing bacteria from beef cattle grazing on pasture Markland, S.M.1,2, R.A. Mir1,2, A. Ginn1,2and K.C. Jeong1,2 Results: We established our own NCBI BioProject # PRJNA298331. We have sequenced 30 isolates that were cefotaxime resistant based on their ability to grow on MacConkey agar supplemented with 4µg/ml of cefotaxime from 2013 and 2014. Whole genome sequencing analysis revealed that all of these isolates were E. coli. Isolates contained one of two CTX-M genes (blaCTX-M-1 and blaCTX-M-32) which clustered together according to phylogenic tree analysis. All isolates from 2014 were found to be multi-drug resistant compared to 11.8% of isolates from 2013. Virulence gene profiles were unique to isolates within each clade of the phylogenic tree. Isolates with specific adherence types (fimH) also clustered together. All isolates were found to be MDR. Objective 2B: Identify virulence and resistance genes and understand mechanisms of acquisition of ESBLs in cattle. Outcomes: RESEARCH ARTICLE - Manuscript Prepared for Submission Comparative genome analysis reveals a hyper-virulent Escherichia coli O157: H7 strain isolated from a super-shedder Teng, L.1,2, A. Ginn1,2, M. Kang1,2, S.M. Markland1,2, C. Lee1,2, D. Park3and K.C. Jeong1,2 Results: We isolated a predominant strain from cattle at the UF North Florida Research & Education Center (NFREC). We determined that this isolate possesses the stx2a and stx2c genes which encode, Shiga-toxin. This isolate is a clade 8 E. coli strain that is of lineage I/II. Adherence assay analysis revealed KCJ1266 has significantly higher affinity for attachment to Hep-2 cells compared to controls. Genome annotation of KCJ1266 was performed to determine whether there are specific genes present within this isolate to identify genetic factors associated with the super-shedding phenotype. RESEARCH ARTICLE - Manuscript Inpreparation Genomic evolution of Extended Spectrum β-lactamase-producing intrauterine pathogenic Escherichia coli from dairy cattle with metritis Ma, Z.1,2, M. Kang1,2, A. Ginn1,2, K. Galvao3,4, and K.C. Jeong1,2 Results: 23 Escherichia coli were isolated from dairy cattle suffering from metritis. 13 out of 23 isolates (56.5%) were found to contain AMR genes related to ESBLs. 3 out of 23 isolates (13%) were found to contain CTX-M genes which confer resistance to cefotaxime. 3 isolates from CTX-M positive isolates were multi-drug resistant. Aim #3: Determine the points where AMR organisms are introduced into cattle to identify critical control points that will provide the basis for development of intervention strategies for antimicrobial resistance and use this information to develop a dynamic AMR transmission model. Objective 3A: Trace animals from birth to slaughter to understand AMR occurrence, prevalence and transmission in cow/calf operations Outcomes: RESEARCH ARTICLE - Manuscript in Preparation Tracking prevalence of antibiotic resistant organisms in beef calves from birth to slaughter and transmission from cows to calves Markland, S.M.1,2, R.A. Mir, 1,2, S. Turner2, G. Hidalgo2, C.Lora2, C. Nelson2, M. Elzo2, J.D. Driver2, and K.C. Jeong1,2 Results: We collected fecal samples from the RAJ of 324 pregnant cows prior to giving birth. We also collected meconium samples from their respective calves within 24 h of birth. We determined that approximately 39.5% (128/324) of all cow fecal samples (pregnant cows) were positive for cefotaxime resistance. We determined that approximately 35.58% (95/267) of all calf meconium samples (collected within 24 h of birth) were positive for cefotaxime resistance. Objective 3B: Identify animal factors that affect the prevalence of ARMs in cattle. Outcomes: RESEARCH ARTICLE - Published in PLoS One Colonization of Beef Cattle by Shiga Toxin-producing Escherichia coli during the First year of Life: a Cohort Study Raies A. Mir1, 2, Thomas A. Weppelmann2,3, Mauricio Elzo1, Soohyoun Ahn4, Danny Driver1, and Kwangcheol Casey Jeong1,2 * Results: We evaluated a cohort of beef cattle one to eleven years of age to better understand the effect of cattle age on the prevalence of STEC in animals. We also sampled a subset of animals in both years of the project. Results indicated that age and parity are critical factor influencing the prevalence of STEC. Heifers had the lowest prevalence and cows of age two had the highest prevalence. Aim #4: Develop and deliver a comprehensive extension/education program on best farm and cattle management practices to mitigate antibiotic resistance on farms. Objective 4A: Develop best AR mitigation strategies on the basis of outcomes of this proposed research that can be applied in cow/calf operations. Outcomes: RESEARCH ARTICLE - Manuscript Submitted Chitosan microparticles exert broad spectrum antimicrobial activity against antibiotic resistant microorganisms without increasing resistance Zhengxin Ma1,2, Donghyeon Kim2, 3, Adegbola T. Adesogan2, Sanghoon Ko4, Klibs Galvao5,6, and Kwangcheol Casey Jeong1,2? Results: CN were previously identified to have broad-spectrum antimicrobial activity. We determined that CM exert broad spectrum antimicrobial activity against AMR bacteria without acquiring resistance toward CM over time. CM also did not induce cross resistance toward other antibiotics.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mir, R.A., T.A. Weppelmann, M. Elzo, S. Ahn, J. D. Driver and K.C. Jeong. 2016. Colonization of Beef Cattle by Shiga Toxin-Producing Escherichia coli during the First Year of Life: A Cohort Study. PLOS One. DOI: 10.1371/journal.pone.0148518
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: ? Mir, R.A., S.M. Markland, M. Elzo, S. Ahn, N. DiLorenzo, G. Cliff Lamb, J. Wasdin, D. Driver and K. Casey Jeong. 2015. Prevalence of Shiga-Toxin Producing Escherichia coli in Two Cohorts of Beef Cattle is Associated with Diversity of Microflora and Animal Age. 2015 Florida Beef Research Report. 75-80.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: ? Mir, R.A., S.M. Markland, T.A. Weppelmann, M. Elzo, K. Casey Jeong. 2015. Prevalence of Cefotaxime Resistant Enterobacteriaceae in Beef Cattle in Florida. 2015 Florida Beef Research Report. 81-86.
  • Type: Journal Articles Status: Submitted Year Published: 2016 Citation: Ma Z.X., A. Garrido-Maestu, and K.C. Jeong. 2016. Engineering, applications, and mode of action of chitosan and its derivatives as antimicrobial agents. Submitted.
  • Type: Journal Articles Status: Submitted Year Published: 2016 Citation: Ginn A., Z.X. Ma, K.N. Galvao, and K.C. Jeong. 2016. Draft genome sequence of an Escherichia coli O8:H19 ST708 strain isolated from a Holstein dairy cow with metritis. Submitted.
  • Type: Journal Articles Status: Submitted Year Published: 2016 Citation: Teng L, A. Ginn, S. Jeon, and K.C. Jeong. 2016. Complete genome and plasmid sequence of an E. coli O157:H7 strain isolated from a supper-shedder steer. Submitted.
  • Type: Journal Articles Status: Submitted Year Published: 2016 Citation: Ma Z.X., Donghyeon Kim, Adegbola T. Adesogan, Sanghoon Ko, Klibs Galvao, and K.C. Jeong. 2016. Chitosan microparticles exert broad spectrum antimicrobial activity against antibiotic resistant microorganisms without increasing resistance. Submitted.
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2016 Citation: Lee, C., L. Teng, D. Park and K.C. Jeong. 2016. Whole Genome Analysis of a Predominant Escherichia coli O157:H7 in Animals Reveals Unique Genetic Features That May Confer Persistency in Hosts. American Society for Microbiology Annual Meeting. ASM Microbe. Poster Presentation. June 16-20, 2016. Boston, MA.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Markland, S.M., R. Mir, A. Ginn and K.C. Jeong. 2016. Comparative genomic analysis of bacteria isolated from cattle and environmental sources on farms harboring extended-spectrum ?-lactamase genes. University of Florida Emerging Pathogens Institute Research Day. Poster Presentation. February 16, 2016. Gainesville, FL
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Markland, S.M., R. Mir, Z. Ma, L. Teng, C. Lee, S. Turner, G. Hidalgo, C. Lora, N. DiLorenzo, C. Carr and K.C. Jeong. 2016. Prevalence of antibiotic resistant bacteria and E. coli O157:H7 from animal and environmental sources in North Florida. University of Florida Emerging Pathogens Institute Research Day. Poster Presentation. February 16, 2016. Gainesville, FL.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: L. Teng, M. Kang, S. M. Markland. C. Lee, R. Mir, Z. Ma, D. Park and K.C. Jeong. 2016. Utilization of PacBio whole genome sequencing to characterize a hyper-virulent Escherichia coli O157:H7 strain isolated from super-shedding cattle. University of Florida Emerging Pathogens Institute Research Day. Poster Presentation. February 16, 2016. Gainesville, FL.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mir, R. and K.C. Jeong. 2015. University of Florida Department of Animal Science Research Symposium. Tracking cefotaxime resistance in beef cattle from birth to slaughter weight. Camp Weed & Cerveny Conference Center. Oral Presentation. Oct. 8-9, 2015. Live Oak, FL.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Teng, L., C. Lee, R. Mir, Z. Ma, D. Park and K.C. Jeong. 2015. Comparative Analysis of super-shedder strains of Escherichia coli O157:H7 reveals distinctive genome features. Camp Weed & Cerveny Conference Center. Poster Presentation. Oct. 8-9, 2015. Live Oak, FL
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mir, R.A., T. Weppelmann, M. Elzo and K.C. Jeong. 2015. Animal factors that influence the prevalence of Shiga toxin-producing Escherichia coli in beef cattle. Verotoxigeneic Escherichia coli Annual Meeting. Sept. 13-16, 2015. Poster 43. Boston, MA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mir, R.A. and K.C. Jeong. 2015. Tracking cefotaxime resistance in beef cattle from birth to slaughter weight. International Association for Food Protection Annual Meeting. July 25-28, 2015. P2-76. Portland, OR
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mir, R.A. and K.C. Jeong. 2015. Dynamics of Shiga Toxin-producing Escherichia coli (STEC) Shedding in Beef Cattle. International Association for Food Protection Annual Meeting. July 25-28, 2015. P2-228. Portland, OR.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: L. Teng, R. Mir, Z. Ma, and K.C. Jeong. 2015. Comparative genomic analysis of persistent E. coli O157:H7 strains isolated from super-shedders in subtropical and continental climates. Florida Association for Food Protection Annual Educational Conference. May. 2015. Poster Presentation. Crystal River, FL.
  • Type: Other Status: Published Year Published: 2015 Citation: Invited talk. Jeong, KC. 2015. Engineering of Chitosan-based Nanoparticles for Multidrug Resistant Microorganisms. UKC meeting. Atlanta, GA. July 29-Aug. 1.
  • Type: Other Status: Published Year Published: 2015 Citation: Invited talk, Jeong, KC. 2015. Nanotechnology to Enhance Safety and Security in Food Distribution and Preservation. KSFE meeting, Jeju Island, Korea. Nov. 11-13.
  • Type: Other Status: Published Year Published: 2015 Citation: Invited talk, Jeong, KC. 2015. Challenges and opportunities in food safety on animal farms. Konkuk Univsersity. Seoul, Korea. Nov. 19
  • Type: Other Status: Published Year Published: 2015 Citation: Invited talk, Jeong, KC. 2015. From bench to the real world: Translational research to intervene pathogens at pre-harvest, Kyunghee University. Korea. Nov. 18.
  • Type: Other Status: Published Year Published: 2015 Citation: Invited talk, Markland, S.M. UF Antibiotic Resistance Project: Antibiotic Resistance in Food Producing Animals and Plants. Florida Association for Food Production Educational Luncheon. December 9, 2015. IFAS Orange County Extension Office. Orlando, FL. Attendance: ~20 people
  • Type: Other Status: Published Year Published: 2015 Citation: Invited talk, Markland, S.M. USDA Antimicrobial Resistance Research Project. Florida Cattlemans Association Quarterly Meeting. September 29, 2015. Straughn IFAS Extension Center, University of Florida. Gainesville, FL. Attendance: ~50 people
  • Type: Websites Status: Published Year Published: 2015 Citation: UF Antimicrobial Resistance Research: http://epi.ufl.edu/amr/