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You are an bioinformaticians working with a local hospital to investigate a possible outbreak of the Gram negative bacteria Klebsiella pneumoniae. K. pneumoniae can be extremely difficult to treat due to acquired antibiotic resistance, and it can cause a number of different invasive infections, especially among immunocompromised patients. Over the course of 6 months, hospital infection control staff have identified 18 patients who appear to have acquired carbapenem-resistant K. pneumoniae during their stay in the intensive care unit, 11 of which died. The infection control team would like you to assist in determining whether these cases are epidemiologically linked. They have isolates from each of the patients who were identified with K. pneumoniae as well as some isolates that were collected from the environment (patient rooms, sinks, high touch objects). They are interested in using whole-genome sequencing since they heard this could help them determine if the cases are related. They ask you to submit a proposal for how you would use WGS data to resolve the possible outbreak. In the proposal, they would like you to address:
1) What sequencing technology they should use. Compare and contrast the different options and then explain your decision on which platform is most appropriate for this application.
2) Describe the bioinformatics methods you will use for your analysis. Include details on each step in the analysis. What will be your end product of the analysis?
3) What other information would you need to compliment the WGS data? How would you use those data and how would it help you investigate the outbreak?
4) How will you make your final determination about the relatedness of the strains? Detail the information you will use and who they can be interpreted together. What would be your conclusion if the environmentally collected strains were closely related to the clinical isolates?