Team I Genome Assembly Group

The group is conducting its discussions, planning, etc. on the Open Academic Environment. Our group is public.

Introduction

Background

Figure 1. Bacterial Genomics [1]

Bacterial genomics is the discipline concerning the genome of a bacteria and includes all hereditary information regarding that bacteria. Bacterial genomics helps study bacterial evolution as well as determine the causative agent in disease outbreaks. Bacterial genomics helps identify bacterial pathogens (and antibiotic resistance) and how these pathogens interact with their host. Deciphering bacterial genomes is in great need.

Figure 2. Klebsiella (http://healthcare.bioquell.com)

Features of Klebsiella[2,3]: a) Gram negative, non-motile, straight rods, Capsule forming; b) Singly, in pairs or short chains; c) Both respiratory and fermentative metabolism, facultative (metablolism switching based on environment); d) Oxidase negative; e) GC content: ~57%

Data

We downloaded 258 Klebsiella spp. (paired-end reads; 250 base pairs in length) from NCBI SRA database.

Objective

This study on Klebsiella spp. is motivated by finding of Colistin heteroresistance in K. pneumoniae. "Genetically identical, but phenotypically distinct, subpopulation of colistin-resistant bacteria can mediate in vivo treatment failure" --David Weiss.

Figure 3. Heteroresistant subpopulation [4]

Figure 4. Schematic representation of mechanism leading to heteroresistance [4]

Methods

Pipeline (general workflow)

References

1. Perna, Nicole T., Guy Plunkett III, Valerie Burland, Bob Mau, Jeremy D. Glasner, Debra J. Rose, George F. Mayhew et al. "Genome sequence of enterohaemorrhagic Escherichia coli O157: H7." Nature 409, no. 6819 (2001): 529.

2. Bergey, David Hendricks, Robert Stanley Breed, Everitt George Dunne Murray, and A. Parker Hitchens. Bergey's manual of determinative bacteriology. Baltimore: Williams & Wilkins, 1934.

3. Wikipedia contributors, "Klebsiella," Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/w/index.php?title=Klebsiella&oldid=821116734 (accessed February 27, 2018).

4. Jayol, Aurélie, Patrice Nordmann, Adrian Brink, and Laurent Poirel. "Heteroresistance to colistin in Klebsiella pneumoniae associated with alterations in the PhoPQ regulatory system." Antimicrobial agents and chemotherapy 59, no. 5 (2015): 2780-2784.