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.
2. Methods
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.
3. Results
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.
4. Discussion
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.
5. Abstract
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.
6. References
a. Include a list of references for your individual research for this report. Format it using the APA.
https://owl.purdue.edu/owl/research_and_citation/apa6_style/apa_formatting_and_style_guide/apa_ powerpoint_slide_presentation.html
Appendix: Research Links
• Google Scholar
• PubMed Database
• CARD Database
1. Presentation Pioneers inside human services associations have customarily seen their job as a value-based action (Vanvactor, 2012). The meaning of medicinal services the board will in general be various leveled and regularly grounded in encouraging administration directly. To encourage change, medicinal services associations are starting to assess characterized the board jobs outside of conventional parameters. The way to fruitful change, as indicated by Cohn (2009), lies in every individual accepting a proactive job toward improving group execution, perceiving that each individual from a group has a position of authority in the human services condition. As indicated by Hurley (2011) viable initiative in the present monetary and social atmosphere requires an alternate type of pioneers who as opposed to driving through sheer power, mystique and authoritative opinion, are centered around accomplishing change and advancement by working at a similar level with their subordinates. This sort of authority is called synergistic administration. In spite of the fact that there are a few meanings of the term, there is an agreement among social researchers that community oriented authority is an open procedure which includes collective critical thinking and basic leadership (Hurley 2011; De Meyer, 2011). Instead of driving the gathering, a community oriented pioneer is centered around the way toward bringing change. Coordinated effort has become a fundamental element for authoritative achievement. As an ever increasing number of associations push toward a community oriented culture including the NHS, another administration model is rising – one that replaces direction and control with trust and consideration (Stadtler, 2009; Vanvactor, 2012). The pioneer’s new job is to urge colleagues to consider themselves to be esteemed donors, to assist them with building their insight base and grow their own systems, and to spur them to offer their thoughts and points of view in administration of a shared objective. Cooperative pioneers see how to make a situation in which individuals decide to take an interest and contribute. Moving, intelligent and empowering (Hofstetter, 2006). The method of reasoning for this exploration is to see how current pioneers are driving change inside the association and which authority qualities are predominant among them. 1.1 Research points There are two unequivocal points of the exploration which are; to comprehend and investigate community authority attributes among pioneers in a NHS Trust and to investigate whether and if so how shared initiative qualities are common during an adjustment in Trust esteems. 1.2 Background data The Trust that is being inquired about has as of late changed their dreams and qualities proclamation. Vision and qualities are a center piece of a Trust’s character and how change happens is generally adjusted to these qualities. Because of a grieved notoriety, the Trust executed the new qualities to now concentrate on working in coordinated effort and improving nature of care. The qualities were executed in March 2018 and this examination started in July 2018. 2. Writing Review 2.1 Introduction Authority of human services experts is important to encourage the mix and nature of care, particularly when there is an association change of both the vision and qualities (Orchard and Rhykoff, 2015). A suitable group authority expands partner commitment and prosperity to encourage persistent improvement, change the executives, advancement and an emphasis on quality (Yang and Mossholder, 2010). There is a need to encourage the way toward making and continuing societies of receptiveness and straightforwardness. The change endeavors made in a NHS trust are not coordinated with ideas of economy basic leadership, corporate practice and the strategy making power. Working in cooperation can, consequently, improve group execution and increment interest in both arranging and basic leadership (Powell, 2016). The writing survey applied a checking philosophy (Cacchione, 2016) to blend too examine a general class of research material. In this manner, there are expanded conceivable outcomes of getting calculated lucidity on community and fair administration in the medicinal services condition. 2.2 Theories of Collaborative Leadership Shared initiative is a style that guides in getting proficient and viable outcomes crosswise over both the inward and outside authoritative limits (Archer and Cameron, 2012). As per Goman (2014), the subjectivities and power elements related with joint effort include large scale social, relational, auxiliary and institutional settings. Participation in the scholarly tries is a vital necessity for a feasible accomplishment among pioneers who try to manufacture better connections, share control and oversee clashes suitably (Orchard and Rhykoff, 2015). In the current associated worldwide setting, synergistic authority is fundamental in making comprehensive conditions that can empower a specific group joined by discharging innovativeness (Stadtler, 2009). The ideas that are identified with community initiative incorporate shared obligations, interdependency, organization and power (Bligh, 2017). Model of group viability, expository methodology of interdisciplinary joint effort, hierarchical human science, social trade hypothesis and interdisciplinary partnership model are the principle speculations that are utilized to clarify the idea of collective administration. Model of collaboration adequacy. Both joint effort and cooperation require a blend of various parts enveloping critical thinking, relational relations and relational abilities to guarantee that a specific gathering cooperates as the individuals center around achieving a shared objective spread out by their pioneers (Vanvactor, 2012). Pioneers working valuably with people in a gathering as a way to assemble a community group condition (Archer and Cameron, 2012; Orchard and Rhykoff, 2015). In this way, pioneers who unendingly perceive the advantages that accumulate from relational connections just as cross-utilitarian coordinated efforts to make authoritative progress practice this administration style. Logical methodology of interdisciplinary joint effort and coalition. Pioneers from various teaches inside the medicinal services division perform obligations and duties appropriately through cooperation and the systematic methodology has progressively become pervasive which is upheld by practices and approaches looking to challenge the conventional administration limits (Goman, 2014). Regardless, during the procedure of coordination and sharing of exercises, clashing qualities and convictions may prompt cooperation or posture requirements that ruin correspondence and collaboration (Curtis and O’Connell, 2011). Hierarchical humanism. The model conceptualizes community oriented authority from four distinct measurements, including conclusion, interiorisation, formalization, and administration (Vanvactor, 2012). Furthermore, as per Orchard and Rhykoff (2015), the yields of the procedures might be characterized regarding inventive arrangements in the expert practices, fulfillment and nature of care Governance principally manages neighborhood and focal authority alongside ability and network. Social trade hypothesis. Social structures inside an association can be comprehended through a top to bottom investigation of relational exchanges and collaborations (Nancarrow, Booth, Ariss, Smith, Enderby and Roots, 2013). From now on, fathom complex character qualities and practices of individuals in a particular gathering. The individual thereafter (Yang and Mossholder, 2010) will accomplish the part of trade results from the advantage that an individual brings to a group and what. In any case, pioneers can utilize the arrangement procedure to improve the advantages and decrease costs that can result from clashes and absence of fitting participation (Powell, 2016). The ideas of trade and arrangement can, subsequently, yield a situation of trust and job separation. 2.3 Collaborative Leadership Traits Collective pioneers share a wide scope of qualities that can encourage collaborations between colleagues and representatives from various departmental levels and have tolerance that aides in managing a general class of disappointments (Archer and Cameron, 2012). The principal attribute includes persistent interest for straightforwardness and receptiveness in basic leadership to encourage responsibility and obligation regarding moves made inside the association (Goman, 2014). At each progression of the choice’s ways, there ought to be an unmistakable clarification of the core values. Second, shared pioneers see assets as the instruments of activities instead of thinking about them as assets (Orchard and Rhykoff, 2015). Sharing of assets is a pivotal part can result to adaptability and nimbleness that require foundation of shared objectives over all the undertaking limits. When there is a shared opinion to convey and evaluate choices and assets, a straightforward domain will at last be made. Third, there is center around legitimate administration whereby there is the ability to ceaselessly finish the responsibilities (Yang and Mossholder, 2010). Moreover, joint effort requires huge codification of the relationship that exists among remunerations and responsibility (Nancarrow et al., 2013). In a NHS Trust, increasingly conveyed and engaged activities are fundamental to bring positive results and pioneers adapt new systems of increasing more contribution from the groups and in the end encourage their profitability (Curtis and O’Connell, 2011). Another quality is the conviction that power is the best apparatus in a specific aggregate group. Moreover, Powell (2016) contends that there is a part of receptiveness in sharing data together with information to make an air of coordinated effort and trust. In the NHS, conceptualizing is encouraged through expanded support of recommendations and thoughts from the individuals taking a shot at a venture with shared objectives and goals (Yang and Mossholder, 2010). Never