Complete the PARE-Seq short course. Review antibiotics and antimicrobial resistance (Chapter 20), bacterial gene transfer (Chapter 8) and epidemiology (Chapter 19). Write a report on your soil and water sample findings.
Analyzing the Prevalence of Antibiotic Resistance in the Environment: Sequencing & Bioinformatics of Soil & Water Samples
Overview: For your final project of the PARE-Seq short course, you will be completing a lab report on your findings from the Galaxy bioinformatics activity and your subsequent research into antibiotic resistance.
The Galaxy taxonomy pie chart and antimicrobial resistance gene (ARG) table you produced in samples. For this lab report, you are tasked with choosing EITHER (a) one species of interest (that may carry multiple resistance genes, for example), OR (b) one ARG, such as a specific type of Tet resistance.
Investigate this ARG or bacteria in greater detail using Google Scholar, NCBI PubMed research database, or the CARD database (used for antibiotic resistance gene research), and be sure to record your sources.
Learning Objectives of this Virtual Lab Course:
• Define antibiotics, antibiotic resistance, and trace the pathways of resistance genes through the environment and into our bodies
• Explain the public health implications of antibiotic resistance in the environment
• Describe the role of sequencing, specifically Nanopore, in environmental surveillance for antibiotic resistance
• Give ‘real-world’ examples of AMR work and improve self-efficacy of taking part in bioinformatics research
• Demonstrate your knowledge of antibiotics, resistance mechanisms, acquisition of resistance and bacterial mechanisms of gene transfer, bacterial diversity and public health from Chapters 8,11,19 & 20.
Outline of your Final Lab Report
1. Introduction Section
a. This section should briefly (in 2-3 paragraphs) describe the purpose of this experiment, what the Galaxy workflow is intended to accomplish, and why this investigation is significant. You should include an overview of antibiotic resistance in the environment from what you learned from the video lectures and Microbiology class and how it applies to this specific activity.
a. This section will describe the experimental techniques, including a summary of Nanopore sequencing, the data samples used in this study, the Galaxy platform, and any problems that occurred as you completed this activity. Describe the goal of the Galaxy workflow (you do not need to understand what each individual tool does). DO NOT simply rewrite the Galaxy instruction manual.
1. Here is where you will display your data outputs from Galaxy. You should include (a) the pie chart output of taxonomic data from your soil and water samples, (b) the table of ARGs and the species they came from, formatted in a spreadsheet tool such as Excel or Google Sheets and including the column headers mentioned in the instruction manual.
2. It is recommended that you divide this section either by soil vs. water sample or by taxonomy vs ARG table for clarity and label each subsection.
c. Tables and figures should be labeled “Table 1, 2, etc.” and should include a short 1-2 sentence caption describing the main significance of that graph/chart.
1. This section is your analysis of the data in the Results section. Discuss the meaning of the ARG table outcome. What ARGs were present in the soil and water samples? What is their clinical significance? How is this relevant in the context of their origin (Kenya and India, respectively)?
2. Explain why you selected your species or ARG, and its relevance in the public health context of antibiotic resistance. Where in the environment is it found most commonly, or what health impacts does it have and on what communities?
3. Research one know AMR bacterial pathogen (superbug), its ARG/mechanisms of resistance and speculate how your results relate to known AMR organisms, such as this.
4. This should be the body of your lab report, 3-5 paragraphs.
a. Write this part last but place it first in your report, after the title. You will open your report with a summary of your Galaxy activity findings. Restate the purpose of the activity, any relevant findings from our data and your research into one specific area of antibiotic resistance, and end with a sentence about relevance to known AMR bacterial pathogens. 1 paragraph.
a. Include a list of references for your individual research for this report. Format it using the APA.
Appendix: Research Links
• Google Scholar
• PubMed Database
• CARD Database
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