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Title: Experimental single-strain mobilomics reveals events that shape pathogen emergence

Abstract

Virulence and resistance genes carried on mobile DNAs such as genomic islands (GIs) and plasmids promote bacterial pathogen emergence. An early step in the mobilization of GIs is their excision, which produces both a circular form of the GI and a deletion site in the chromosome; circular forms have also been described for some bacterial insertion sequences (ISs). We demonstrate that the recombinant sequence produced at the junction of such circles, and their corresponding deletion sites, can be detected sensitively in high throughput sequencing data, using new computational methods that enable empirical discovery of new mobile DNAs. Applied to the rich mobilome of a single strain (Kpn2146) of the emerging multidrug-resistant pathogen Klebsiella pneumoniae, our approach detected circular junctions for six GIs and seven IS types (several of the latter not previously known to circularize). Our methods further revealed differential biology of multiple mobile DNAs, imprecision of integrases and transposases, and differential activity among identical IS copies for IS26, ISKpn18 and ISKpn21. Exonuclease was used to enrich for circular dsDNA molecules, and internal calibration with the native Kpn2146 plasmids showed that not all molecules bearing GI and IS circular junctions were circular dsDNAs. Transposition events were also detected, revealing repliconmore » preference (ISKpn18 preferring a conjugative IncA/C2 plasmid), local action (IS26), regional preferences, selection (against capsule synthesis), and left-right IS end swapping. Efficient discovery and global characterization of numerous mobile elements per experiment will allow detailed accounting of bacterial evolution, explaining the new gene combinations that arise in emerging pathogens.« less

Authors:
 [1];  [1];  [1];  [1];  [1]
  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States). Systems Biology Dept.
Publication Date:
Research Org.:
Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1263512
Report Number(s):
SAND-2016-6520J
Journal ID: ISSN 0305-1048; 644838
Grant/Contract Number:  
AC04-94AL85000
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Name: Nucleic Acids Research; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; genomic island; pathogenicity; bioinformatics; transposition; insertion sequence

Citation Formats

Schoeniger, Joseph S., Hudson, Corey M., Bent, Zachary W., Sinha, Anupama, and Williams, Kelly P. Experimental single-strain mobilomics reveals events that shape pathogen emergence. United States: N. p., 2016. Web. https://doi.org/10.1093/nar/gkw601.
Schoeniger, Joseph S., Hudson, Corey M., Bent, Zachary W., Sinha, Anupama, & Williams, Kelly P. Experimental single-strain mobilomics reveals events that shape pathogen emergence. United States. https://doi.org/10.1093/nar/gkw601
Schoeniger, Joseph S., Hudson, Corey M., Bent, Zachary W., Sinha, Anupama, and Williams, Kelly P. Mon . "Experimental single-strain mobilomics reveals events that shape pathogen emergence". United States. https://doi.org/10.1093/nar/gkw601. https://www.osti.gov/servlets/purl/1263512.
@article{osti_1263512,
title = {Experimental single-strain mobilomics reveals events that shape pathogen emergence},
author = {Schoeniger, Joseph S. and Hudson, Corey M. and Bent, Zachary W. and Sinha, Anupama and Williams, Kelly P.},
abstractNote = {Virulence and resistance genes carried on mobile DNAs such as genomic islands (GIs) and plasmids promote bacterial pathogen emergence. An early step in the mobilization of GIs is their excision, which produces both a circular form of the GI and a deletion site in the chromosome; circular forms have also been described for some bacterial insertion sequences (ISs). We demonstrate that the recombinant sequence produced at the junction of such circles, and their corresponding deletion sites, can be detected sensitively in high throughput sequencing data, using new computational methods that enable empirical discovery of new mobile DNAs. Applied to the rich mobilome of a single strain (Kpn2146) of the emerging multidrug-resistant pathogen Klebsiella pneumoniae, our approach detected circular junctions for six GIs and seven IS types (several of the latter not previously known to circularize). Our methods further revealed differential biology of multiple mobile DNAs, imprecision of integrases and transposases, and differential activity among identical IS copies for IS26, ISKpn18 and ISKpn21. Exonuclease was used to enrich for circular dsDNA molecules, and internal calibration with the native Kpn2146 plasmids showed that not all molecules bearing GI and IS circular junctions were circular dsDNAs. Transposition events were also detected, revealing replicon preference (ISKpn18 preferring a conjugative IncA/C2 plasmid), local action (IS26), regional preferences, selection (against capsule synthesis), and left-right IS end swapping. Efficient discovery and global characterization of numerous mobile elements per experiment will allow detailed accounting of bacterial evolution, explaining the new gene combinations that arise in emerging pathogens.},
doi = {10.1093/nar/gkw601},
journal = {Nucleic Acids Research},
number = ,
volume = ,
place = {United States},
year = {2016},
month = {7}
}

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