Next-generation sequencing of a multi-drug resistance plasmid captured from stream sediment

Author

Kevin G. Libuit, James Madison UniversityFollow

Preferred Name

Kevin G. Libuit

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Date of Graduation

Spring 2016

Document Type

Thesis

Degree Name

Master of Science (MS)

Department

Department of Biology

Advisor(s)

James B. Herrick

Steven G. Cresawn

Kyle Seifert

Abstract

Plasmids in agriculturally-impacted bodies of water may play a significant role in the dissemination of antibiotic resistance. Previously, Erika Gehr, as part of her M.S. thesis work in our laboratory, captured environmental plasmids without cultivation of host bacteria from stream sediment into Escherichia coli. Individual plasmids were capable of conferring resistance to a surprising array of antibiotics including aminoglycosides and extended-spectrum β-lactams. In this study, we developed a method to sequence multi-drug resistance plasmids using both Oxford Nanopore MinION and Ion Torrent Personal Genome Machine sequencers. Plasmid pEG1-1 was sequenced on both platforms and a hybrid assembly utilizing data from both sequencing platforms generated a single 73,320 bp contig that was annotated using automated and manual techniques. Analysis of the genome revealed pEG1-1 to be an IncP-1β plasmid with two mobile genetic elements – a a tn21-related transposon and an in104 complex integron – both of which carry multiple antibiotic resistance genes. These findings suggest that plasmids in stream sediment are prone to the incorporation of mobile genetic elements that introduce a broad range of antibiotic resistance genes into their genome. This could cause serious risk to human health since IncP-1β plasmids are capable of transferring into nearly all Gram-negative bacteria, including fecal pathogens that get introduced to stream sediment.

Recommended Citation

Libuit, Kevin G., "Next-generation sequencing of a multi-drug resistance plasmid captured from stream sediment" (2016). Masters Theses, 2010-2019. 114.
https://commons.lib.jmu.edu/master201019/114