Team I Comparative Genomics Group

Introduction and Objectives

Comparative genomics is a field in biomedical research in which the genomic features of different organisms are compared. In short, it involves the comparison of one genome to another. This type of comparative analysis can be utilized to discover what lies hidden within the sequences of genomes by comparing sequencing information. Comparative genomics has utilities in gene prediction, regulatory element prediction, phylogenomics, pharmacogenomics, and more. For the purposes of our analysis, we will employ comparative genomics tools to compare bacterial genomes generated from next-generation sequence data generate knowledge that will help us identify and characterize a bacterial outbreak strain of Escherichia coli (E. coli) and propose treatment and outbreak identification and containment to public health professional.

Our Data:

• 50 isolates of Escherichia coli from an outbreak of foodborne illnesses. The genomes have been assembled and fully annotated.
• Epidemiological data consisting of: times, locations (states), and ingested foods of each case.

Stages of analysis and interpretation of data

1. genome assembly
2. gene prediction
3. functional annotation
4. comparative genomics
5. production of a predictive webserver

Team Objectives

• Compare and contrast functional & structural features of isolates.
  • Antibiotic Resistance profile
  • Virulence profile
• Differentiate outbreak vs. sporadic strains.
• Characterize the virulence and antibiotic resistance functional features of outbreak isolates.
• Identify the source and spread of the outbreak.
• Recommend outbreak response and treatment.

In-Class Presentations

• Comparative Genomics Background and Strategy:

• Comparative Genomics Final Results:

References

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3. Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, et al. (2018) MUMmer4: A fast and versatile genome alignment system. PLOS Computational Biology 14(1): e1005944. https://doi.org/10.1371/journal.pcbi.1005944
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6. Sultan, I., Rahman, S., Jan, A. T., Siddiqui, M. T., Mondal, A. H., & Haq, Q. M. R. (2018). Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective. Frontiers in Microbiology, 9(2066). doi:10.3389/fmicb.2018.02066
7. Trees E, Rota P, Maccannell D, Gerner-smidt P.. Molecular Epidemiology, p 131-159. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. 2015. doi: 10.1128/9781555817381.ch10