Evolution of Streptococcus pneumoniae and its close commensal relatives

Streptococcus pneumoniae is a member of the Mitis group of streptococci which, according to 16S rRNA-sequence based phylogenetic reconstruction, includes 12 species. While other species of this group are considered prototypes of commensal bacteria, S. pneumoniae is among the most frequent microbial killers worldwide. Population genetic analysis of 118 strains, supported by demonstration of a distinct cell wall carbohydrate structure and competence pheromone sequence signature, shows that S. pneumoniae is one of several hundred evolutionary lineages forming a cluster separate from Streptococcus oralis and Streptococcus infantis. The remaining lineages of this distinct cluster are commensals previously collectively referred to as Streptococcus mitis and each represent separate species by traditional taxonomic standard. Virulence genes including the operon for capsule polysaccharide synthesis and genes encoding IgA1 protease, pneumolysin, and autolysin were randomly distributed among S. mitis lineages. Estimates of the evolutionary age of the lineages, the identical location of remnants of virulence genes in the genomes of commensal strains, the pattern of genome reductions, and the proportion of unique genes and their origin support the model that the entire cluster of S. pneumoniae, S. pseudopneumoniae, and S. mitis lineages evolved from pneumococcus-like bacteria presumably pathogenic to the common immediate ancestor of hominoids. During their adaptation to a commensal life style, most of the lineages gradually lost the majority of genes determining virulence and became genetically distinct due to sexual isolation in their respective hosts.     

Genome sequence of Streptococcus mutans bacteriophage M102

Bacteriophage M102 is a lytic phage specific for serotype c strains of Streptococcus mutans, a causative agent of dental caries. In this study, the complete genome sequence of M102 was determined. The genome is 31,147 bp in size and contains 41 ORFs. Most of the ORFs encoding putative phage structural proteins show similarity to those from bacteriophages from Streptococcus thermophilus. Bioinformatic analysis indicated that the M102 genome contains an unusual lysis cassette, which encodes a holin and two lytic enzymes.     

Complete genome sequence of the African dairy isolate Streptococcus infantarius subsp. infantarius strain CJ18

Streptococcus infantarius subsp. infantarius, a member of the Streptococcus bovis/Streptococcus equinus complex, is highly prevalent in artisanal dairy fermentations in Africa. Here the complete genome sequence of the dairy-adapted S. infantarius subsp. infantarius CJ18 strain--a strain predominant in traditionally fermented camel milk (suusac) from Kenya--is presented.     

Complete Genome Sequence of Streptococcus pyogenes M1 476, Isolated from a Patient with Streptococcal Toxic Shock Syndrome

Here, we report the completely annotated genome sequence of Streptococcus pyogenes M1 476 isolated from a patient with streptococcal toxic shock syndrome (STSS) during pregnancy. The genome sequence will provide new insights into the mechanisms underlying STSS.     

Complete genome sequence of Streptococcus thermophilus strain ND03

Streptococcus thermophilus strain ND03 is a Chinese commercial dairy starter used for the manufacture of yogurt. It was isolated from naturally fermented yak milk in Qinghai, China. We present here the complete genome sequence of ND03 and compare it to three other published genomes of Streptococcus thermophilus strains.     

变形链球菌反应调控蛋白ComE结合序列的初步筛选

目的：从变形链球菌基因组中筛选反应调控蛋白ComE结合的核酸序列。方法：⑴提取变形链球菌UA159 基因组,进行超声剪切处理。以基因组片段为模板,用随机引物进行延伸,切胶纯化和PCR 扩增后获得基因组文库。⑵应用基因组 SELEX 技术,以ComE 蛋白为靶物质,与变形链球菌基因组文库共同孵育,循环筛选8轮。筛选产物TA克隆后送去测序,测序结果进行生物信息学分析。⑶将分析得到的2个序列分别克隆入pFW5-luc载体中,然后分别重组到变形链球菌UA159野生株和comE突变株的基因组中,采用RT-PCR的方法检测luc片段的表达。结果：⑴获得了变形链球菌UA159 的基因组文库,片段范围约为100～300bp。⑵随机挑取54个克隆送去测序,经生物信息学分析和RT-PCR初步验证,最终获得1个ComE 蛋白可能的结合序列。结论：采用基因组 SELEX 技术,筛选反应调控蛋白ComE可能的结合序列,并进行了初步验证,为后续进行变形链球菌反应调控蛋白ComE调控机制的研究奠定了基础。     

Characterization of a streptococcal cholesterol-dependent cytolysin with a lewis y and b specific lectin domain

The cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins that often exhibit distinct structural changes that modify their pore-forming activity. A soluble platelet aggregation factor from Streptococcus mitis (Sm-hPAF) was characterized and shown to be a functional CDC with an amino-terminal fucose-binding lectin domain. Sm-hPAF, or lectinolysin (LLY) as renamed herein, is most closely related to CDCs from Streptococcus intermedius (ILY) and Streptococcus pneumoniae (pneumolysin or PLY). The LLY gene was identified in strains of S. mitis, S. pneumoniae, and Streptococcus pseudopneumoniae. LLY induces pore-dependent changes in the light scattering properties of the platelets that mimic those induced by platelet aggregation but does not induce platelet aggregation. LLY monomers form the typical large homooligomeric membrane pore complex observed for the CDCs. The pore-forming activity of LLY on platelets is modulated by the amino-terminal lectin domain, a structure that is not present in other CDCs. Glycan microarray analysis showed the lectin domain is specific for difucosylated glycans within Lewis b (Le (b)) and Lewis y (Le (y)) antigens. The glycan-binding site is occluded in the soluble monomer of LLY but is apparently exposed after cell binding, since it significantly increases LLY pore-forming activity in a glycan-dependent manner. Hence, LLY represents a new class of CDC whose pore-forming mechanism is modulated by a glycan-binding domain.     

Complete genome sequence of Streptococcus pneumoniae strain ST556, a multidrug-resistant isolate from an otitis media patient

Streptococcus pneumoniae is a major pathogen causing bacterial infection in the middle ear of humans. We previously used S. pneumoniae strain ST556, a low-passage 19F isolate from an otitis media patient, to perform a whole-genome screen for ear infection-associated genes in a chinchilla model. This report presents the complete genome sequence of ST556. The genome sequence will provide information complementary to the experimental data from our genetic study of this strain.     

Complete genome sequence of the dairy isolate Streptococcus macedonicus ACA-DC 198

The species Streptococcus macedonicus is associated with the food environment, especially with fermented dairy products. Here we present the complete 2.1-Mb genome sequence of strain ACA-DC 198, which was isolated from naturally fermented Greek kasseri cheese.     

Complete genome sequence of the serotype k Streptococcus mutans strain LJ23

Streptococcus mutans is the major pathogen of dental caries and occasionally causes infective endocarditis. Here we report the complete genome sequence of serotype k S. mutans strain LJ23, which was recently isolated from the oral cavity of a Japanese patient.     

Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis

This work describes a whole-genome sequence of Streptococcus agalactiae strain GD201008-001, a pathogen causing meningoencephalitis in cultural tilapia in China. The genome sequence provides opportunities to understand the piscine GBS pathogenicity and its genetic basis associated with host tropism.     

Genome Sequence of the Lantibiotic Bacteriocin Producer Streptococcus salivarius Strain K12

Streptococcus salivarius is a prevalent commensal species of the oropharyngeal tract. S. salivarius strain K12 is an isolate from the saliva of a healthy child, used as an oral probiotic. Here, we report its genome sequence, i.e., the full sequence of the 190-kb megaplasmid pSsal-K12 and a high-quality draft 2.2-Gb chromosomal sequence.     

Differentiation of Streptococcus pneumoniae conjunctivitis outbreak isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Streptococcus pneumoniae (pneumococcus [Pnc]) is a causative agent of many infectious diseases, including pneumonia, septicemia, otitis media, and conjunctivitis. There have been documented conjunctivitis outbreaks in which nontypeable (NT), nonencapsulated Pnc has been identified as the etiological agent. The use of mass spectrometry to comparatively and differentially analyze protein and peptide profiles of whole-cell microorganisms remains somewhat uncharted. In this report, we discuss a comparative proteomic analysis between NT S. pneumoniae conjunctivitis outbreak strains (cPnc) and other known typeable or NT pneumococcal and streptococcal isolates (including Pnc TIGR4 and R6, Streptococcus oralis, Streptococcus mitis, Streptococcus pseudopneumoniae, and Streptococcus pyogenes) and nonstreptococcal isolates (including Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus) as controls. cPnc cells and controls were grown to mid-log phase, harvested, and subsequently treated with a 10% trifluoroacetic acid-sinapinic acid matrix mixture. Protein and peptide fragments of the whole-cell bacterial isolate-matrix combinations ranging in size from 2 to 14 kDa were evaluated by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Additionally Random Forest analytical tools and dendrogramic representations (Genesis) suggested similarities and clustered the isolates into distinct clonal groups, respectively. Also, a peak list of protein and peptide masses was obtained and compared to a known Pnc protein mass library, in which a peptide common and unique to cPnc isolates was tentatively identified. Information gained from this study will lead to the identification and validation of proteins that are commonly and exclusively expressed in cPnc strains which could potentially be used as a biomarker in the rapid diagnosis of pneumococcal conjunctivitis.     

Complete Genome Sequence of Streptococcus agalactiae ZQ0910, a Pathogen Causing Meningoencephalitis in the GIFT Strain of Nile Tilapia (Oreochromis niloticus)

Streptococcus agalactiae (group B streptococcus [GBS]) is a pathogen that causes meningoencephalitis in Nile tilapia (Oreochromis niloticus). Here, we reported the complete genome sequence of S. agalactiae strain ZQ0910, which was isolated from the GIFT strain of Nile tilapia in Guangdong, China.     

Complete genome sequence of the commensal Streptococcus salivarius strain JIM8777

The commensal bacterium Streptococcus salivarius is a prevalent species of the human oropharyngeal tract with an important role in oral ecology. Here, we report the complete 2.2-Mb genome sequence and annotation of strain JIM8777, which was recently isolated from the oral cavity of a healthy, dentate infant.     

Genome sequence of the bacteriocin-producing oral probiotic Streptococcus salivarius strain M18

Streptococcus salivarius is a Gram-positive bacterial commensal and pioneer colonizer of the human oral cavity. Many strains produce ribosomally synthesized proteinaceous antibiotics (bacteriocins), and some strains have been developed for use as oral probiotics. Here, we present the draft genome sequence of the bacteriocin-producing oral probiotic S. salivarius strain M18.     

Structure of a conjugative element in Streptococcus pneumoniae.

We have cloned and mapped a 69-kilobase (kb) region of the chromosome of Streptococcus pneumoniae DP1322, which carries the conjugative omega (cat-tet) insertion from S. pneumoniae BM6001. This element proved to be 65.5 kb in size. Location of the junctions was facilitated by cloning a preferred target region from the wild-type strain Rx1 recipient genome. This target site was preferred by both the BM6001 element and the cat-erm-tet element from Streptococcus agalactiae B109. Within the BM6001 element cat and tet were separated by 30 kb, and cat was flanked by two copies of a sequence that was also present in the recipient strain Rx1 DNA. Another sequence at least 2.4 kb in size was found inside the BM6001 element and at two places in the Rx1 genome. Its role is unknown. The ends of the BM6001 element appear to be the same as those of the B109 element, both as seen after transfer to S. pneumoniae and as mapped by others in pDP5 after transposition in Streptococcus faecalis. We see no homology between the ends of the BM6001 element and find no evidence suggesting that it ever circularizes.     

Complete genome sequence of Streptococcus suis serotype 14 strain JS14

Streptococcus suis is an important zoonotic agent leading to a variety of diseases in swine and can be transmitted to human beings upon close contact. Here, we report the complete genome sequence of S. suis serotype 14 strain JS14 which was isolated from a diseased pig in Jiangsu Province, China.     

Conservation of the mosaic structure of the four internal transcribed spacers and localisation of the rrn operons on the Streptococcus pneumoniae genome

The detection of heterogeneity of the 16S-23S ribosomal intergenic transcribed spacer (ITS) region has become rather common over the past years for identification and typing purposes of bacteria. The ITS not only varies in sequence and length, but also in number of alleles per genome and in their position on the chromosome together with the ribosomal clusters. The ITS characterisation has allowed discrimination of several species within a genus and variation in ITS sequences between the multiple rrn operons present within a genome may be as high or greater than between strains of the same species or subspecies. It is important to understand the variability of ITS sequences in a given genome to gain insights into bacterial physiology and taxonomy. The present study describes the possibility to type Streptococcus pneumoniae by PCR-ribotyping of the spacer region, the determination of the molecular structure of the ITS, and the determination of the number and localisation of rrn operons in this microorganism. Our results show that the genome of S. pneumoniae contains four ribosomal operons, showing the same genomic organisation among strains, each containing a single ITS allele of 270 bp. The ITS sequence presents a mosaic organisation of blocks highly conserved intra- and inter-species within the genus Streptococcus, giving no possibility for variations to arise.     

Complete Genome Sequence of Streptococcus thermophilus Strain MN-ZLW-002

Streptococcus thermophilus MN-ZLW-002 was originally isolated from traditionally fermented Chinese dairy products. One of the strain-dependent characteristics of this bacterium is its ability to produce exopolysaccharides (EPSs). This study determined and analyzed the genome sequence of MN-ZLW-002. Its complete genome comprised 2,046 genes and 1,848,520 nucleotides with an average GC content of 39%. The EPS cluster of MN-ZLW-002 includes 25 open reading frames (ORFs), and some results indicate a horizontal gene transfer between MN-ZLW-002 and other lactic acid bacteria (LAB).