Analysis of Ultra Low Genome Conservation in Clostridium difficile

Joy Scaria,Lalit Ponnala,Yung-Fu Chang,Weiwei Yan,Tavan Janvilisri,Lukas A Mueller,Malcolm James Horsburgh

doi:10.1371/journal.pone.0015147

Joy Scaria, Lalit Ponnala + Show 5 more

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https://doi.org/10.1371/journal.pone.0015147

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Abstract

Microarray-based comparative genome hybridisations (CGH) and genome sequencing of Clostridium difficile isolates have shown that the genomes of this species are highly variable. To further characterize their genome variation, we employed integration of data from CGH, genome sequencing and putative cellular pathways. Transcontinental strain comparison using CGH data confirmed the emergence of a human-specific hypervirulent cluster. However, there was no correlation between total toxin production and hypervirulent phenotype, indicating the possibility of involvement of additional factors towards hypervirulence. Calculation of C. difficile core and pan genome size using CGH and sequence data estimated that the core genome is composed of 947 to 1,033 genes and a pan genome comprised of 9,640 genes. The reconstruction, annotation and analysis of cellular pathways revealed highly conserved pathways despite large genome variation. However, few pathways such as tetrahydrofolate biosynthesis were found to be variable and could be contributing to adaptation towards virulence such as antibiotic resistance.

Highlights

Clostridium difficile is a gram-positive spore-forming anaerobic bacterium with a wide host range [1]
In its simplest form C. difficile-associated disease (CDAD) can lead to mild diarrhea, but in the extremes it results in serious sequelae, toxic megacolon, intestinal perforation, peritonitis or death [2]
Several CDAD outbreaks in the past decade in Europe and North America have been attributed to the emergence of hypervirulent C. difficile strains belonging to PCR ribotype 027/pulse-field type NAP1 (027/NAP1) which produce elevated levels of toxins A and B, the primary virulence factors of this bacterium [4,5,6,7,8,9]

Summary

Introduction

Clostridium difficile is a gram-positive spore-forming anaerobic bacterium with a wide host range [1]. A microarray-based comparative genome hybridization (CGH) of this strain against 8 other C. difficile strains showed that the up to 61% of the total coding sequences (CDS) were absent from at least one strain tested [10]. In our recent CGH analysis of a similar number of strains showed that the core genome of this species could be as low as 16% [12].

Results

Conclusion