Comparative genomics for identification of clone-specific sequence blocks in Streptococcus pneumoniae

Oggioni, Marco R.

doi:10.1016/s0378-1097(01)00209-9

Cited by 11 publications

(18 citation statements)

References 21 publications

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“…Pneumococcal genome sequences (Hoskins et al ., 2001; Dopazo et al ., 2001; Tettelin et al ., 2001) were downloaded and analysed on an in‐house database using BioEdit (http://www.mbio.ncsu.edu/BioEdit/bioedit.html) (.Oggioni and Pozzi, 2001). Whole genome blast s were performed on a LINUX platform (. Oggioni and Pozzi, 2001) using the freely available blast software from the NCBI FTP site (http://www.ncbi.nlm.nih.gov/Ftp/index.html).…”

Section: Methodsmentioning

confidence: 99%

Pneumococcal zinc metalloproteinase ZmpC cleaves human matrix metalloproteinase 9 and is a virulence factor in experimental pneumonia

Oggioni¹,

Memmi

Maggi

et al. 2003

Molecular Microbiology

101

114

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SummaryThe ZmpC zinc metalloproteinase of Streptococcus pneumoniae , annotated in the type 4 genome as SP0071, was found to cleave human matrix metalloproteinase 9 (MMP-9). The previously described IgA protease activity was confirmed to be specifically linked to the IgA1-protease/SP1154 zinc metalloproteinase. MMP-9 is a protease cleaving extracellular matrix gelatin and collagen and is activated by proteolytic cleavage like most proteases. MMP-9 is a human protease and is involved in a variety of physiological and pathological matrix degrading processes, including tissue invasion of metastases and opening of the blood-brain barrier. While TIGR4 (serotype 4) and G54 (serotype 19) pneumococcal genome strains have a highly conserved copy of zmp C, the genome of R6 (a derivative of serotype 2 D39 strain) lacks zmp C. Both the analysis for zmp C presence and MMP-9 cleavage activity in various pneumococcal strains showed correlation of ZmpC with MMP-9 cleavage activity. When assaying clinical isolates of S. pneumoniae , the zmpC gene was not found in any of the nasal and conjunctival swab isolates, but it was present in 1 out of 13 meningitis isolates and in 6 out of 11 pneumonia isolates. In a murine pneumonia model, infection with a zmpC -mutant reduced mortality at 3-4 days post-infection by 75%, when compared with infection with wild-type strains. These data indicate that the ZmpC pneumococcal protease may play a role in pneumococcal virulence and pathogenicity in the lung.

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Section: Methodsmentioning

confidence: 99%

Pneumococcal zinc metalloproteinase ZmpC cleaves human matrix metalloproteinase 9 and is a virulence factor in experimental pneumonia

Oggioni¹,

Memmi

Maggi

et al. 2003

Molecular Microbiology

101

114

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“…The great majority of pneumococcal genes share from 97 to 99 % nucleotide identity among isolates (Oggioni & Pozzi, 2001;Tettelin & Hollingshead, 2004). However, the pneumococcal zinc metalloproteinases fall within a restricted group of hypervariable surface proteins that includes other important antigens, such as PspA and PspC.…”

Section: Introductionmentioning

confidence: 99%

Zinc metalloproteinase genes in clinical isolates of Streptococcus pneumoniae: association of the full array with a clonal cluster comprising serotypes 8 and 11A

et al. 2006

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Zinc metalloproteinase genes in clinical isolates of Streptococcus pneumoniae: association of the full array with a clonal cluster comprising serotypes 8 and 11A Pneumococci display large zinc metalloproteinases on the surface, including the IgA protease, which cleaves human IgA1 in the hinge region, the ZmpC proteinase, which cleaves human matrix metalloproteinase 9 (MMP-9), and two other proteinases, ZmpB and ZmpD, whose substrates have not yet been identified. Surface metalloproteinases are antigenic and have been linked to virulence. The genes encoding these proteinases reside in three distinct loci: two loci specific for zmpB and zmpC, and a third, the iga locus, containing iga and zmpD. Data obtained by this and other groups have shown that pneumococcal metalloproteinase genes are transcribed and yield mature and enzymatically active proteins. Since the presence of the four proteinase genes is variable in the pneumococcal strains whose genomes have been sequenced, the presence of these genes in a collection of 218 pneumococcal isolates, mostly from invasive disease, was investigated. The data showed that zmpB and iga were present in all the isolates examined, while zmpC and zmpD were present in a variable proportion of the isolates (in 18 and 49 %, respectively). Interestingly, isolates carrying both zmpC and zmpD were found to belong mainly to two serotypes (sts), 8 and 11A. By molecular typing, st 8 and st 11A isolates appeared to belong to the same clonal cluster. The presence of these two additional metalloproteinases could contribute to the fitness of particular pneumococcal clones. INTRODUCTIONStreptococcus pneumoniae (pneumococcus) is a common and important human pathogen. Pneumococci are the chief cause of community-acquired pneumonia and bacterial meningitis, the second-most-prevalent cause of sepsis, and one of the main causes of otitis media (Gillespie, 1989). The main virulence factors of S. pneumoniae are the capsule, the pneumolysin that is a cholesterol-dependent cytolysin, and some pneumococcal surface proteins and enzymes, including PspA, PspC, neuraminidase and hyaluronidase (Paton et al., 1993;Mitchell, 2000;Chapuy-Regaud et al., 2003;Iannelli et al., 2004). A characteristic feature of S. pneumoniae is the presence of large zinc metalloproteinases on the cell surface. These enzymes have a common structure (Pfam Accession no. PF02395) and are present not only in S. pneumoniae but also in related oral streptococci, such as Streptococcus sanguis, Streptococcus gordonii, Streptococcus mitis and Streptococcus oralis .From the published genome sequences, it can be inferred that S. pneumoniae possesses two (strain R6, rough derivative of serotype 2; Hoskins et al., 2001), three (strain TIGR4, serotype 4; Tettelin et al., 2001) or even four (strain G54, serotype 19F;Dopazo et al., 2001) zinc metalloproteinase genes, depending on the strain. All the above-mentioned strains possess iga and zmpB, encoding the IgA protease and ZmpB, respectively. In addition, strains TIGR4 and G54 possess the metal...

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“…Computational genomics has led the way to efficient and customized mining of genomics for species‐specific nucleotide sequences. The BLAST program, a frequently used tool for nucleotide sequence comparisons, has been applied to identify specific targets for the detection and identification of bacterial pathogens (Oggioni and Pozzi ; Kim et al . , ).…”

Section: Resultsmentioning

confidence: 99%

“…Computational genomics has been applied to identify specific targets for the detection and identification of bacterial pathogens (Oggioni and Pozzi ; Kim et al . , ).…”

Section: Introductionmentioning

confidence: 99%

Development of a PCR Assay for Rapid Detection of Cronobacter sakazakii from Powdered Infant Formula Using a Target Sequence Identified by Comparative Genomic Analysis

Chen

Ren

et al. 2015

Journal of Food Safety

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The occurrence of outbreaks of Cronobacter sakazakii causing necrotizing meningitis in China highlights the need for strain characterization of this pathogenic species. In this study, SMM system was utilized to mine for new molecular markers of C. sakazakii. One C. sakazakii‐specific CDS (>ref|NC_009778.1|:c1077329‐1076055) with a length of 1,275 bp was used to design a primer set. A PCR assay was developed and optimized to detect C. sakazakii. The PCR assay amplified a 498 bp DNA product from all 43 C. sakazakii strains tested but not from 30 other bacteria strains. The detection limit was 7.11 pg/PCR (equivalent 1,422 genomic copies) when the genomic DNA of C. sakazakii ATCC 29544 was 10‐fold diluted. Three powdered infant formulas from different commercial brands were inoculated with the strain ATCC 29544 at the level of 56 cells contamination, and the target fragments (498 bp) were produced after samples were enriched for 6 h at 37C.Thirty food samples were detected simultaneously by this PCR assay and the conventional method, and a coincident detecting result was found between the PCR assay and the conventional method. This method provides a useful tool for rapid identification of C. sakazakii in food and environmental matrices. Practical Applications The gold standard based on the FDA‐recommended methods for isolation and identification of Cronobacter sakazakii from powdered infant formula is time consuming and labor intensive. A PCR assay has been established to detect C. sakazakii. This method provides a useful tool for rapid and accurate identification of C. sakazakii in food when a large number of food samples need to be rapidly isolated and identified.

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Comparative genomics for identification of clone-specific sequence blocks in Streptococcus pneumoniae

Cited by 11 publications

References 21 publications

Pneumococcal zinc metalloproteinase ZmpC cleaves human matrix metalloproteinase 9 and is a virulence factor in experimental pneumonia

Pneumococcal zinc metalloproteinase ZmpC cleaves human matrix metalloproteinase 9 and is a virulence factor in experimental pneumonia

Zinc metalloproteinase genes in clinical isolates of Streptococcus pneumoniae: association of the full array with a clonal cluster comprising serotypes 8 and 11A

Development of a PCR Assay for Rapid Detection of Cronobacter sakazakii from Powdered Infant Formula Using a Target Sequence Identified by Comparative Genomic Analysis

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