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J Bacteriol. 2019 Sep 9. pii: JB.00365-19. doi: 10.1128/JB.00365-19. [Epub ahead of print]

Chromosomal recombination targets in Chlamydia interspecies lateral gene transfer.

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University of Washington, Division of Allergy and Infectious Diseases, Department of Medicine, Seattle, Washington, USA.
Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA.
Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA.
Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA


Lateral gene transfer (LGT) among C. trachomatis strains is common, both in isolates generated in the laboratory and those examined directly from patients. In contrast, there are very few examples of recent acquisition of DNA by any Chlamydia spp. from any other species. Interspecies LGT in this system was analyzed using crosses of tetracycline (Tc)-resistant Chlamydia trachomatis L2/434 and chloramphenicol (Cam)-resistant C. muridarum VR-123. Parental C. muridarum strains were created using a plasmid-based Himar transposition system, which led to integration of the CamR marker randomly across the chromosome. Fragments encompassing 79% of the C. muridarum chromosome were introduced into a C. trachomatis background, with the total coverage contained on 142 independent recombinant clones. Genome sequence analysis of progeny strains identified candidate recombination hotspots, a property not consistent with in vitro C. trachomatis × C. trachomatis (intraspecies) crosses. In both interspecies and intraspecies crosses there were examples of duplications, mosaic recombination endpoints, and recombined sequences that were not linked to the selection marker. Quantitative analysis of the distribution and constituency of inserted sequences indicated that there are different constraints on interspecies LGT as compared to intraspecies crosses. These constraints may help explain why there is so little evidence of interspecies genetic exchange in this system, which is in contrast to very widespread intraspecies exchange in C. trachomatis IMPORTANCE Genome sequence analysis has demonstrated that there is widespread lateral gene transfer among strains within the species C. trachomatis, and with other closely related Chlamydia species in laboratory experiments. This is in contrast to the complete absence of foreign DNA in the genomes of sequenced clinical C. trachomatis strains. There is no understanding of any mechanisms of genetic transfer in this important group of pathogens. In this report, we demonstrate that interspecies genetic exchange can occur, but that the nature of the fragments exchanged is different than those observed in intraspecies crosses. We also generate a large hybrid strain library that can be exploited to examine important aspects of chlamydial disease.


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