title: Experimental single-strain mobilomics reveals events that shape pathogen emergence.
abstract: Virulence genes on mobile DNAs such as genomic islands (GIs) and plasmids promote bacterial pathogen emergence. Excision is an early step in GI mobilization, producing a circular GI and a deletion site in the chromosome; circular forms are also known for some bacterial insertion sequences (ISs). The recombinant sequence at the junctions of such circles and deletions can be detected sensitively in high-throughput sequencing data, using new computational methods that enable empirical discovery of mobile DNAs. For the rich mobilome of a hospital Klebsiella pneumoniae strain, circularization junctions (CJs) were detected for six GIs and seven IS types. Our methods revealed differential biology of multiple mobile DNAs, imprecision of integrases and transposases, and differential activity among identical IS copies for IS26, ISKpn18 and ISKpn21 Using the resistance of circular dsDNA molecules to exonuclease, internally calibrated with the native plasmids, showed that not all molecules bearing GI CJs were circular. Transpositions were also detected, revealing replicon preference (ISKpn18 prefers a conjugative IncA/C2 plasmid), local action (IS26), regional preferences, selection (against capsule synthesis) and IS polarity inversion. Efficient discovery and global characterization of numerous mobile elements per experiment improves accounting for the new gene combinations that arise in emerging pathogens.
authors.affiliation: Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA.
authors.forename: Joseph S
authors.initials: JS
authors.lastname: Schoeniger
authors.affiliation: Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA.
authors.forename: Corey M
authors.initials: CM
authors.lastname: Hudson
authors.affiliation: Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA.
authors.forename: Zachary W
authors.initials: ZW
authors.lastname: Bent
authors.affiliation: Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA.
authors.forename: Anupama
authors.initials: A
authors.lastname: Sinha
authors.affiliation: Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA kpwilli@sandia.gov.
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Williams
mesh_terms: D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004270:DNA, Circular / Q000235:genetics; D044404:Genomic Islands / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D007711:Klebsiella pneumoniae / Q000235:genetics* / Q000472:pathogenicity*; D008826:Microbial Sensitivity Tests; D016254:Mutagenesis, Insertional / Q000235:genetics; D010957:Plasmids / Q000235:genetics*; D012093:Replicon / Q000235:genetics; D017384:Sequence Deletion; D013997:Time Factors
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D004270:DNA, Circular