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Tuesday, July 28 • 11:30 - 11:35
iJump: a fast tool for tracking bacterial mobile elements rearrangements in course of adaptive laboratory evolution

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Mobile elements rearrangements in bacteria may lead to gene inactivation or deregulation providing an important contribution to adaptation. While the challenge of mapping these rearrangements was addressed for individual genomes, no efficient tools are available for tracking their dynamics in evolving populations, such as in adaptive laboratory evolution (ALE).
We are using ALE in a custom-engineered continuous culture device (morbidostat) to study dynamics and mechanisms of antibiotic resistance in major gram-negative bacterial pathogens. Acquisition of mutations in evolving populations is monitored by deep sequencing of samples in time-series.
To observe evolutionary paths driven by “jumping” of IS elements we have developed the iJump software, which is using soft-clipped reads from the SAM/BAM alignment extracted from the boundaries of known mobile elements to find new junctions and estimate their frequencies. The performance of iJump was first tested on a simulated data set where it showed 1-4% error in frequency estimation. Application of the iJump tool to our ALE studies with Escherichia coli, Acinetobacter baumannii and Pseudiomonas aeruginosa confirmed its practical utility and revealed IS-driven bacterial adaptations to known antibiotics and novel drug candidates. The results were verified by Nanopore-based sequencing and MIC determination of selected individual clones. Software available at https://github.com/sleyn/ijump

Posters
avatar for Semen Leyn

Semen Leyn

Postdoctoral Associate, Sanford Burnham Prebys Medical Discovery Institute
Doing bioinformatics on several bacterial genomics projects including study of antibiotics resistance development for novel drug candidates and metabolic reconstruction in human gut microbiome.



Tuesday July 28, 2020 11:30 - 11:35 MSK
Zoom Conference https://zoom.us/j/94321101353?pwd=QlJBb09uM0NVVnVyK0FkbTJ3Nkcrdz09