Experimental single-strain mobilomics reveals events that shape pathogen emergence

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Virulence genes on mobile DNA elements like genomic islands (GIs) and plasmids drive bacterial pathogen emergence.
• Excision of GIs and some insertion sequences (ISs) can lead to circular forms, a crucial step in their mobilization.

Purpose of the Study:

• To develop and apply novel computational methods for the sensitive detection and characterization of mobile DNA elements.
• To investigate the mobilome of a hospital-associated Klebsiella pneumoniae strain, focusing on circularization junctions (CJs).

Main Methods:

• Utilized high-throughput sequencing data to detect recombinant sequences at CJ sites.
• Employed computational approaches for empirical discovery of mobile DNAs.
• Used exonuclease resistance assays, calibrated with native plasmids, to confirm circular dsDNA molecules.

Main Results:

• Detected CJs for six GIs and seven IS types in Klebsiella pneumoniae.
• Revealed differential biology, imprecision of mobilization enzymes (integrases, transposases), and varied activity of identical IS copies (IS26, ISKpn18, ISKpn21).
• Identified transpositions, replicon preference (ISKpn18), local action (IS26), regional preferences, selection pressures (e.g., against capsule synthesis), and IS polarity inversion.

Conclusions:

• The developed methods enable efficient discovery and global characterization of numerous mobile elements.
• This approach improves the understanding of novel gene combinations contributing to the emergence of bacterial pathogens.
• Findings highlight the dynamic nature and complex biology of mobile DNA in Klebsiella pneumoniae.