|Year : 2017 | Volume
| Issue : 2 | Page : 274-276
Genome sequence of an invasive strain of Streptococcus gordonii
Thangam Menon, V Naveen Kumar
Department of Microbiology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
|Date of Web Publication||5-Jul-2017|
Department of Microbiology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu
Source of Support: None, Conflict of Interest: None
We report the genome sequence of IE35, a strain of Streptococcus gordonii isolated from the blood of a patient with prosthetic valve endocarditis. Whole-genome sequencing of S. gordonii IE35 strain by the combination of Illumina HiSeq2000 paired-end, Ion Torrent single-end sequencing and gap closing by Illumina NextSeq yielded a single, circular chromosome of 2,190,105 bp. It had 2106 predicted coding sequences, of which 2014 genes encoded proteins involved in various cellular processes and 66 genes coded for RNA. The predicted RNA genes were annotated up to pathway level and genes responsible for various metabolic processes and virulence were identified.
Keywords: Endocarditis, Genome sequence, Streptococcus gordonii
|How to cite this article:|
Menon T, Kumar V N. Genome sequence of an invasive strain of Streptococcus gordonii. Indian J Med Microbiol 2017;35:274-6
|How to cite this URL:|
Menon T, Kumar V N. Genome sequence of an invasive strain of Streptococcus gordonii. Indian J Med Microbiol [serial online] 2017 [cited 2017 Sep 26];35:274-6. Available from: http://www.ijmm.org/text.asp?2017/35/2/274/209597
| ~ Introduction|| |
Streptococcus gordonii is a member of the Streptococcus mitis group and a part of the oral microbiota. It forms dental plaque by creating biofilms on tooth surfaces eventually leading to periodontal disease and dental cavities. S. gordonii is well known for its ability to colonise damaged heart valves and is an important etiological agent of bacterial endocarditis. It enters the blood stream usually after oral trauma and is known to possess genes contributing to adhesion, fibrinogen binding and platelet binding, which are important for the pathogenesis of infective endocarditis.
The complete genome sequence of two isolates of S. gordonii reported so far, S. gordonii Challis substr. CH1 (NC_009785) and S. gordonii KCOM 1506 (NZ_CPO12648) are both from dental samples. The complete genome sequence of an isolate from invasive infections such as infective endocarditis has not been reported till date.
We report the whole-genome sequence of a strain of S. gordonii IE 35, which was isolated from a case of infective endocarditis.
| ~ Materials and Methods|| |
The S. gordonii strain IE35 had been isolated from a 25-year-old patient with prosthetic valve endocarditis. Fresh subcultures were made on 5% sheep blood agar and colonies were inoculated into 45 mL of brain–heart infusion broth, incubated for 24 h, centrifuged at 5000 rpm for 15 min at 4°C and pellet was used for DNA extraction using Qiagen DNeasy kit (QIAGEN, Germany). Concentration and purity of extracted DNA were assessed by NanoDrop1000 UV spectrophotometer (Thermo Scientific, USA) at 260 and 280 Š and by agarose gel electrophoresis.
Whole-genome sequencing of S. gordonii strain IE35 was carried out in Illumina and Ion Torrent platforms (Genotypic Technology Pvt Ltd., Bengaluru, India).
Illumina paired-end sequences data along with Ion Torrent single-end sequences data were used for the contig merging and scaffolds were generated from contigs using the software SSPACE-2.0. The smaller scaffolds (500 bp) were filtered out from the draft assembly by using MUMmer v3.23 software.
The gap sequences in the genome were sequenced by preparing libraries using Illumina TruSeq kit, sequencing was performed on Illumina NextSeq and gap closing was carried out using GapCloser v1.12 software.
The gene prediction and pathway annotation was carried out using RAST web server at http://rast.nmpdr.org/. Whole-genome sequence of S. gordonii strain IE35 was submitted to GenBank and accession number was obtained (NZ_CP017295).
| ~ Results|| |
Whole-genome sequencing of S. gordonii IE35 strain by the combination of Illumina HiSeq2000 paired-end, Ion Torrent single-end sequencing and gap closing by Illumina NextSeq yielded a single, circular chromosome of 2,190,105 bp with 3000-fold genome coverage with a G + C content of 40.48%.
The genome sequence of S. gordonii IE35 was compared with the closest reference genome S. gordonii str. Challis substr. CH1 strain. The genome sequences length of S. gordonii IE35 strain was approximately 6.5 Kb shorter than the reference genome (S. gordonii str. Challis substr. CH1 strain) which was 2,196,662 bp. Comparative analysis of the sequence of S. gordonii IE35 with the genome sequence of the reference genome of S. gordonii str. Challis and S. gordonii KCOM 1506 are shown in [Table 1].
|Table 1: Comparison between Streptococcus gordonii IE35 and the previously published Streptococcus gordonii str. Challis and Streptococcus gordonii KCOM 1506|
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The genome of S. gordonii IE35 contained genes encoding 2106 predicted coding sequences. About 96% (2014) of these genes encodes proteins involved in various cellular processes and 3% (66) of genes encodes for RNA (tRNA and rRNA). Of the 2014 predicted proteins, about 17.3% are conserved hypothetical proteins (present in multiple species but having unknown functions). The 66 genes coding for RNA include four 5S rRNAs, two 16S rRNA, two 23S rRNA and 58 tRNAs. The genes which code for 82.7% of proteins include genes involved in general metabolic process, virulence factors, surface proteins, resistance and competency mechanism.
We identified 246 genes necessary for the carbohydrate metabolism which includes genes encoding for enzymes involved in various metabolic pathways and carbohydrate transporters. One hundred and ninety-six genes were identified to be involved in protein metabolism which includes genes coding for various proteases, peptidase and ABC transporters. The genome encodes 58 tRNAs corresponding to all essential amino acids. Genes encoding tRNAs for leucine, arginine, methionine, glycine, threonine, proline, asparagine, lysine, glutamic acid, valine, pseudo-tRNA, tyrosine, aspartic acid, glutamine, alanine, phenylalanine and isoleucine were in multiple copies and tRNAs for histidine, tryptophan, serine and cysteine amino acids were present in single copies. The genome encodes, 102 genes involved in DNA metabolism, 102 genes for RNA metabolism and 54 genes involved in phosphorus, iron, potassium and sulphur metabolism [Table 2]. A number of secreted virulence factors were found, which included glucosyltransferase GtfG, GftA and GftB, haemolysin III, ESAT-6-like secretory virulence factors, CylB protein, secreted antigen GbpB/SagA/PcsB, putative peptidoglycan hydrolase, accessory secretory protein Asp1- Asp5, ClpB protein, Xaa-Pro dipeptidyl-peptidase and foldase protein PrsA. There were 493 genes coding for hypothetical proteins which includes six putative cell surface proteins, 162 cytoplasmic membrane-associated proteins and 10 putative extracellular proteins. Other features found in the genome of IE35 were putative internalin, LemA protein, aggregation-promoting factor, ElaA protein, pore-forming protein EbsA, CrcB protein, septation ring formation regulator EzrA, shock proteins and phage shock protein. Genes encoding for insertion sequences, transposase and integrase were also present. There were no prophages in S. gordonii IE35.
|Table 2: Genes involved in cellular processes of Streptococcus gordonii IE35|
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Surface-associated adhesins are considered to play an important role in pathogenicity and genes coding for several of these proteins such as collagen adhesion protein (Cna), cell wall-associated protein (WapA), streptococcal surface protein A (SspA), C5a peptidase (Scp), IgA1 protease and enolase were identified in the genome [Table 3].
| ~ Discussion|| |
Sequencing of bacterial genomes improves our understanding of the biology of pathogens and provides valuable insights into the mechanism of pathogenesis of disease.
The rapid developments in technology and decreasing cost of whole-genome sequencing have allowed researchers to use this technique more frequently. The genome sequence of the infecting pathogen, particularly in specific diseases such as endocarditis, will contribute to research on the pathogenesis of the disease and improve our understanding of the epidemiology and virulence mechanisms involved in invasive disease.
Financial support and sponsorship
This study was financially supported by ICMR, New Delhi.
Conflicts of interest
There are no conflicts of interest.
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[Table 1], [Table 2], [Table 3]