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Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms
Tatiana Murillo1, Gabriel Ramírez-Vargas1, Thomas Riedel2,3
1Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica.
Genome Biology and Evolution
|April 5, 2018
Summary
Nonhomologous recombination via lateral gene transfer (NHR-LGT) significantly drives Clostridioides difficile NAP1/ST54 strain diversification, unlike NAP1/ST01 strains where mutation is key. This highlights differing evolutionary paths for C. difficile outbreaks.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Clostridioides difficile outbreaks are caused by distinct strains, including NAP1/ST54 and NAP1/ST01.
- These strains exhibit differences in genome diversity, necessitating an understanding of their evolutionary mechanisms.
Purpose of the Study:
- To compare the roles of mutation, homologous recombination (r), and nonhomologous recombination (NHR) through lateral gene transfer (LGT) in the microdiversification of C. difficile NAP1/ST54 and NAP1/ST01 strains.
- To elucidate the distinct evolutionary trajectories of these two major C. difficile outbreak strains.
Main Methods:
- Whole genome sequencing of 32 NAP1/ST54 and 17 NAP1/ST01 C. difficile isolates.
- Analysis of single nucleotide polymorphisms (SNPs), dN/dS ratios, recombination blocks, and pangenome content.
- Quantification of gene content changes and mobile genetic elements (MGEs) associated with LGT.
Main Results:
- Comparable SNP counts and densities were observed between NAP1/ST54 and NAP1/ST01 strains.
- NAP1/ST01 strains exhibited higher dN/dS rates, while NAP1/ST54 strains showed a larger, more heterogeneous pangenome with significant gene content changes attributed to MGEs.
- NHR-LGT played a substantially greater role in NAP1/ST54 microdiversification compared to NAP1/ST01, evidenced by a 4x higher LGT/SNP rate.
Conclusions:
- Nonhomologous recombination via lateral gene transfer (NHR-LGT) is a primary driver of microdiversification in Clostridioides difficile NAP1/ST54 strains.
- Mutation appears to be a more significant factor in the evolution of NAP1/ST01 strains.
- These findings reveal divergent evolutionary strategies employed by key C. difficile outbreak strains.
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