Progress 10/01/14 to 09/30/17
Outputs
Target Audience:Public health Diagnosticians Epidemiologists Changes/Problems:Analysis of metabolomics and proteomics data What opportunities for training and professional development has the project provided?MPH Capstone project Undergraduate student training in laboratory methods. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Publish manuscript. Present in conference.
Impacts
What was accomplished under these goals?
Poster and oral presentation for the capstone project of an MPH student. Abstract submitted for INFECTIOUS DISEASE DIAGNOSTICS FOR THE 21ST CENTURY symposium held on July 8-10, 2019 in Fort Collins, CO
Publications
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2019
Citation:
INFECTIOUS DISEASE DIAGNOSTICS FOR THE 21ST CENTURY, Fort Collins, CO from July 8-10, 2019
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Metabolomics and Proteomics scientists Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?CVMBS Research day poster presentation by Sean Montgomery (MS student of MIP department) 01.30.2016 How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Scientific publication in a peer review journal.
Impacts
What was accomplished under these goals?
Integron size groups that were found in dairy cattle were 1000, 1000+1200 and 1800 bp; in swine were 1000, 1000+1200; in poultry were 1000 and in humans were 1000, 1200, 1000+1200, 1000+1200+1600, and 1800. 48% of bovine samples, 83% of swine, 11.5% of poultry and 32% of human samples carried at least one integron group, 100% of them resistant to at least one antibiotic. The majority represented 1000 bp in humans and poultry, 1000+1200 in dairy cattle and swine. The most common AMR pattern among all resistant samples (23/126%=18.25%) was ampicillin, amoxicillin-clavulanate, streptomycin, sulfisoxazole, tetracyclines, chloramphenicol and florfenicol (coded as AMCAMS10SSSTECFFC). Hence, these samples are chosen for performing 'omic' profiling. All of those samples carried 1000 and 1200 bp integrons, 5 from human, 8 from bovine and 10 from swine. The samples that did not show resistance to any antibiotics did not carry any integrons, indicating that integron testing is highly specific in detecting AMR. However, there were 35% of the dairy samples not carrying integrons but showed resistance to at least one antibiotic, 83% of swine, 35% of poultry samples and 50% of human samples not carrying any integron showed resistance to at least one antibiotic. Thereby, integron testing provides high confidence in the positive result (high predictive value positive) in detecting AMR. The proteomic analysis results from 9 isolates (3 human, 3 bovine, 3 porcine) grown in ACSSuT-treated broth and no-drug broth (groups coded as FD and ND, respectively), produced 1631 confidently identified proteins (confident identification signifies a presence in at least two out of three replicates and a spectral count of 2). A total of 822 proteins significantly varied in abundance between the 2 groups, with 366 proteins significantly upregulated in the presence of the ACSSuT drug panel (Figure 2), and 456 proteins significantly upregulated in the absence of the ACSSuT drug treatment. Results of ACSSuT-exposed upregulated protein samples were organized according to cellular pathways via the Kyoto Encyclopedia of Genes and Genomes. The metabolic pathways, ribosomal pathways and biosynthesis of secondary metabolites were the top 3 cellular pathways identified to upregulate proteins with the ACSSuT drug stress.
Publications
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Scientists, graduate and undergraduate students in Veterinary Medicine and Biomedical Sciences Changes/Problems:Specific integron size was selected depicting a particular pattern of AMR to begin answering the question on what metabolites and proteins are expressed in samples carrying those patterns. An experimental approach was undertaken where 9 samples were grown with and without antibiotics to be able to identify the markers among 3 host species. The proteomic method is very expensive and hence the availablebudget was utilizedto answer an important scientific question to begin with. What opportunities for training and professional development has the project provided?The project has involved 2 undergraduate students and 1 graduate student from MIP department. It was a very good opportunity for them to learn the omics techniques in terms of sample prep and submission. How have the results been disseminated to communities of interest?Proteomic part of the project was presented on a poster for the CVMBS research day 2016. What do you plan to do during the next reporting period to accomplish the goals?Metabolomics results are yet to be received from the PMF laboratory. Once those results are received, all the data will be compiled to model statistically the associations between the metabolite and protein profiles and the antimicrobial resistance in the Salmonella isolates carrying1000+1200 bp integrons.
Impacts
What was accomplished under these goals?
Total number of Salmonella enterica ser Typhimurium cultures retrieved from culture banks of various laboratories were 183 representing dairy cows, swine, poultry and humans. Among the 183 samples tested against 16 antimicrobial drugs for resistance, 69% of were resistant to at least one antibiotic. The number of samples resistant to at least 5 antibiotics were 42%, mostly representing humans followed by bovine and then swine; birds showed the least number of AMRs. Integron size groups that were found in dairy cattle were 1000, 1000+1200 and 1800 bp; in swine were 1000, 1000+1200; in poultry were 1000 and in humans were 1000, 1200, 1000+1200, 1000+1200+1600, and 1800. Forty eight percent of bovine samples, 83% of swine, 11.5% of poultry and 32% of human samples carried at least one integron group, 100% of them resistant to at least one antibiotic. The majority represented 1000 bp in humans and poultry, 1000+1200 in dairy cattle and swine. The most common AMR pattern among all resistant samples (23/126%=18.25%) was ampicillin, amoxicillin-clavulanate, streptomycin, sulfisoxazole, tetracyclines, chloramphenicol and florfenicol (coded as AMCAMS10SSSTECFFC). Hence, these samples are chosen for performing 'omic' profiling. All of those samples carried 1000 and 1200 bp integrons, 5 from human, 8 from bovine and 10 from swine (Table 4). The samples that did not show resistance to any antibiotics did not carry any integrons, indicating that integron testing is highly specific in detecting AMR. However, there were 35% of the dairy samples not carrying integrons but showed resistance to at least one antibiotic, 83% of swine, 35% of poultry samples and 50% of human samples not carrying any integron showed resistance to at least one antibiotic. Thereby, integron testing provides high confidence in the positive result (high predictive value positive) in detecting AMR. Proteomic analysis: The proteomic analysis results from 9 isolates (3 human, 3 bovine, 3 porcine) grown in ACSSuT-treated broth and no-drug broth (groups coded as FD and ND, respectively), produced 1631 confidently identified proteins (confident identification signifies a presence in at least two out of three replicates and a spectral count of 2). A total of 822 proteins significantly varied in abundance between the 2 groups, with 366 proteins significantly upregulated in the presence of the ACSSuT drug panel (Figure 2), and 456 proteins significantly upregulated in the absence of the ACSSuT drug treatment. Results of ACSSuT-exposed upregulated protein samples were organized according to cellular pathways via the Kyoto Encyclopedia of Genes and Genomes (Table 5). The metabolic pathways, ribosomal pathways and biosynthesis of secondary metabolites were the top 3 cellular pathways identified to upregulate proteins with the ACSSuT drug stress. Table 5. KEGG Pathway Enrichment Analysis for upregulated proteins under ACSSuT drug stress Cellular Pathways/Processes Protein Count1 p-value2 Metabolic pathways 93 1.01E-04 Ribosome 49 3.73E-45 Biosynthesis of secondary metabolites 38 4.21E-01 Purine metabolism 19 1.17E-03 Aminoacyl-tRNA biosynthesis 17 1.03E-10 Pyrimidine metabolism 15 2.39E-03 Protein export 11 2.03E-06 Bacterial secretion system 11 8.53E-02 Fatty acid biosynthesis 10 7.71E-08 Fatty acid metabolism 10 1.18E-04 RNA degradation 8 8.13E-04 Biotin metabolism 6 5.55E-02 RNA polymerase 4 4.99E-03 1The number of enriched proteins upregulated during exposure to the ACSSuT drug panel, organized by their cellular pathway/process in the cell. 2Bonferroni corrected. Host Specific Differences: The total number of proteins upregulated within the drug group (FD) were 142 in humans, 80 in bovine and 32 in porcine samples. When the 3 host species were compared, there were 91 unique proteins in humans, 39 in bovine and 33 in porcine in the drug group.
Publications
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