Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence

I-Hsuan Lin,Tze-Tze Liu,Keh-Ming Wu,Chuan-Hsiung Chang,Yu-Ting Teng,Hui-Lun Wu,Yen-Ming Liu,Ming-Ta Hsu,Niyaz Ahmed

doi:10.1371/journal.pone.0020519

Abstract

Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

Highlights

Streptococcus bovis, a member of Lancefield group D streptococci, comprises a group of Gram–positive bacteria which are normal inhabitants of the gastrointestinal tract of human and animals, such as cattle, sheep, pigs, horses and dogs
The S. gallolyticus is a known human pathogen which has been shown to be associated with serious illnesses such as infective endocarditis (IE) and colorectal cancer, whereas S. pasteurianus causes neonatal sepsis and meningitis in infants and adults
Through analyzing the regions of genomic plasticity (RGPs), we provided evidence of an association between genome plasticity and genome adaptive evolution

Summary

Introduction

Streptococcus bovis, a member of Lancefield group D streptococci, comprises a group of Gram–positive bacteria which are normal inhabitants of the gastrointestinal tract of human and animals, such as cattle, sheep, pigs, horses and dogs. In human, it is the causative agent of bacteremia [1,2,3], neonatal sepsis [4], neonatal meningitis [5], adult meningitis [6] and has a well-known association with infective endocarditis (IE) [3,7,8,9], colorectal carcinoma [10,11,12,13,14] and liver diseases [15,16,17]. Because of the clear association between S. bovis and several human diseases, it is vital to accurately distinguish these organisms and identify the differences between them in a genomic scale

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Results

Conclusion