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Colombo NH, Kreling PF, Ribas LFF, Pereira JA, Kressirer CA, Klein MI, Tanner ACR, Duque C. Quantitative assessment of salivary oral bacteria according to the severity of dental caries in childhood. Arch Oral Biol 2017; 83:282-288. [PMID: 28858630 DOI: 10.1016/j.archoralbio.2017.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 07/24/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022]
Abstract
This study aimed to assess differences in selected oral bacteria in children according to the severity of dental caries. One hundred and thirty-six children, 36-60 months old were divided into three groups according to caries status: caries-free (CF) (n=47), early childhood caries (ECC) (n=40) and severe-early childhood caries (S-ECC) (n=49). Saliva was collected for detection and quantification of selected oral streptococci, Actinomyces naeslundii, Lactobacillus spp., Bifidobacterium spp., and Scardovia wiggsiae by quantitative-polymerase chain reaction. The results showed that the detection and quantitative levels of S. mutans, S. sobrinus, Bifidobacterium spp. and S. wiggsiae were significantly higher in S-ECC children compared to CF and ECC children, while for S. salivarius were significantly higher in CF compared to ECC and S-ECC children. There was no statistical difference among the clinical groups for S. mitis, S. oralis, A. naeslundii and Lactobacillus spp. levels and detection. S-ECC children had a lower monthly family income, started tooth brushing later and were breastfeed for a longer duration compared to CF children. S. mutans levels were positively correlated with S. wiggsiae and Bifidobacterium spp. levels, lower mother's education and child bottle-feeding before sleeping and negatively correlated with S. salivarius. It was concluded that in addition to S. mutans, other bacterial species, including bifidobacteria, Scardovia wiggsiae and S. sobrinus, are associated with severity of early childhood caries, although their role in the progress of dental caries remains unclear.
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Affiliation(s)
- Natália H Colombo
- São Paulo State University (UNESP), School of Dentistry, Araçatuba, Department of Pediatric Dentistry and Public Health, Araçatuba, SP, Brazil
| | - Paula F Kreling
- São Paulo State University (UNESP), School of Dentistry, Araçatuba, Department of Pediatric Dentistry and Public Health, Araçatuba, SP, Brazil
| | - Laís F F Ribas
- São Paulo State University (UNESP), School of Dentistry, Araçatuba, Department of Pediatric Dentistry and Public Health, Araçatuba, SP, Brazil
| | - Jesse A Pereira
- São Paulo State University (UNESP), School of Dentistry, Araçatuba, Department of Pediatric Dentistry and Public Health, Araçatuba, SP, Brazil
| | | | - Marlise I Klein
- São Paulo State University (UNESP), School of Dentistry, Araraquara, Department of Dental Materials and Prosthodontics, Araraquara, SP, Brazil
| | - Anne C R Tanner
- The Forsyth Institute, Department of Microbiology, Cambridge, MA, USA; Harvard School of Dental Medicine, Harvard University, Boston, MA, USA
| | - Cristiane Duque
- São Paulo State University (UNESP), School of Dentistry, Araçatuba, Department of Pediatric Dentistry and Public Health, Araçatuba, SP, Brazil.
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Kim W, Park HK, Hwang WJ, Shin HS. Simultaneous detection of Streptococcus pneumoniae, S. mitis, and S. oralis by a novel multiplex PCR assay targeting the gyrB gene. J Clin Microbiol 2013; 51:835-40. [PMID: 23269740 PMCID: PMC3592088 DOI: 10.1128/jcm.02920-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 12/17/2012] [Indexed: 01/05/2023] Open
Abstract
A multiplex PCR (mPCR) protocol was developed for simultaneous detection of the gyrB gene in Streptococcus pneumoniae, Streptococcus mitis, and Streptococcus oralis, and the specificity was evaluated using 141 coccus strains. Genomic DNAs purified from S. pneumoniae, S. mitis, and S. oralis strains were efficiently detected with size differences, whereas no PCR products were amplified from any of the reference strains tested. A pilot study of 47 human oral swab specimens was conducted in parallel, and the mPCR assay identified S. pneumoniae in 1 sample, S. mitis in 8 samples, and S. oralis in 2 samples, providing a powerful means for characterization at the level of species compared with traditional culture analysis. Our results suggest that the mPCR protocol presented here is a sensitive and promising tool for the rapid detection and discrimination of S. pneumoniae, S. mitis, and S. oralis from clinical specimens.
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hee Kuk Park
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Woo-Jin Hwang
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
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Park HK, Myung SC, Kim W. Comparative transcriptomic analysis of streptococcus pseudopneumoniae with viridans group streptococci. BMC Microbiol 2012; 12:77. [PMID: 22607240 PMCID: PMC3391171 DOI: 10.1186/1471-2180-12-77] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 05/18/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Streptococcus pseudopneumoniae, is a novel member of the genus Streptococcus, falling close to related members like S. pneumoniae, S. mitis, and S. oralis. Its recent appearance has shed light on streptococcal infections, which has been unclear till recently. In this study, the transcriptome of S. pseudopneumoniae CCUG 49455T was analyzed using the S. pneumoniae R6 microarray platform and compared with those of S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, and S. oralis KCTC 13048T strains. RESULTS Comparative transcriptome analysis revealed the extent of genetic relatedness among the species, and implies that S. pseudopneumoniae is the most closely related to S. pneumoniae. A total of 489, 444 and 470 genes were upregulated while 347, 484 and 443 were downregulated relative to S. pneumoniae in S. pseudopneumoniae, S. oralis and S. mitis respectively. Important findings were the up-regulation of TCS (two component systems) and transposase which were found to be specific to S. pseudopneumoniae. CONCLUSIONS This study provides insight to the current understanding of the genomic content of S. pseudopneumoniae. The comparative transcriptome analysis showed hierarchical clustering of expression data of S. pseudopneumoniae with S. pneumoniae and S. mitis with S. oralis. This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains.
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Affiliation(s)
- Hee Kuk Park
- Department of Microbiology & Research Center for Medical Sciences, Chung-Ang University College of Medicine, Seoul, 156-756, Republic of Korea
| | - Soon Chul Myung
- Department of Urology, Chung-Ang University College of Medicine, Seoul, 156-756, Republic of Korea
| | - Wonyong Kim
- Department of Microbiology & Research Center for Medical Sciences, Chung-Ang University College of Medicine, Seoul, 156-756, Republic of Korea
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Identification of a pheA gene associated with Streptococcus mitis by using suppression subtractive hybridization. Appl Environ Microbiol 2012; 78:3004-9. [PMID: 22307284 DOI: 10.1128/aem.07510-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We performed suppression subtractive hybridization to identify genomic differences between Streptococcus mitis and Streptococcus pneumoniae. Based on the pheA gene, a primer set specific to S. mitis detection was found in 18 out of 103 S. mitis-specific clones. Our findings would be useful for discrimination of S. mitis from other closely related cocci in the oral environment.
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Kim MH, Cho MS, Kim BK, Choi HJ, Hahn JH, Kim C, Kang MJ, Kim SH, Park DS. Quantitative Real-Time Polymerase Chain Reaction Assay for Detection of Pectobacterium wasabiae Using YD Repeat Protein Gene-Based Primers. PLANT DISEASE 2012; 96:253-257. [PMID: 30731799 DOI: 10.1094/pdis-06-11-0511] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The aim of this study was to develop a quantitative polymerase chain reaction (qPCR) assay for specific detection of Pectobacterium wasabiae using a primer pair based on the YD repeat protein gene for amplification of a 140-bp DNA fragment from infected wasabi (Wasabia japonica), a member of the crucifer family. The soft rot caused by P. wasabiae is an emerging disease that is present in many wasabi-producing areas. However, specific and reliable methods for identifying the pathogen are not available. Therefore, a qPCR primer set for accurate diagnosis of P. wasabiae was developed from publically available genome sequences. A SYBR Green qPCR primer set was designed based on a YD repeat protein gene of P. wasabiae WPP163 because it is known that this gene is structurally diverse among species, pathovars, or subspecies. The specificity of the primer set was evaluated using genomic DNA from 5 isolates of P. wasabiae, 5 different species of Pectobacterium, and 16 other pathogenic reference bacteria. The primer set used in the PCR assay successfully amplified a 140-bp amplicon for all five P. wasabiae strains. No amplification was obtained from 29 other pathogenic bacteria. The assay was also able to detect at least two genomic DNA, or 3 CFU per reaction, when using calibrated cell suspension.
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Affiliation(s)
- Myeong Ho Kim
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Min Seok Cho
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Byoung Kyu Kim
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Hyeon Jin Choi
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Jang Ho Hahn
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - ChangKug Kim
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Man Jung Kang
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Seong Hwan Kim
- Department of Microbiology, Dankook University, 330-714 Cheonan, Republic of Korea
| | - Dong Suk Park
- National Academy of Agricultural Science, Rural Development Administration, Republic of Korea
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Kim W, Park HK, Thanh HD, Lee BY, Shin JW, Shin HS. Comparative genome analysis of Lactococcus garvieae using a suppression subtractive hybridization library: discovery of novel DNA signatures. FEMS Microbiol Lett 2011; 325:77-84. [PMID: 22092865 DOI: 10.1111/j.1574-6968.2011.02414.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/04/2011] [Accepted: 09/06/2011] [Indexed: 12/01/2022] Open
Abstract
Lactococcus garvieae, the pathogenic species in the genus Lactococcus, is recognized as an emerging pathogen in fish, animals, and humans. Despite the widespread distribution and emerging clinical significance of L. garvieae, little is known about the genomic content of this microorganism. Suppression subtractive hybridization was performed to identify the genomic differences between L. garvieae and Lactococcus lactis ssp. lactis, its closest phylogenetic neighbor, and the type species of the genus Lactococcus. Twenty-seven clones were specific to L. garvieae and were highly different from Lactococcus lactis in their nucleotide and protein sequences. Lactococcus garvieae primer sets were subsequently designed for two of these clones corresponding to a pyrH gene and a novel DNA signature for application in the specific detection of L. garvieae. The primer specificities were evaluated relative to three previously described 16S rRNA gene-targeted methods using 32 Lactococcus and closely related strains. Both newly designed primer sets were highly specific to L. garvieae and performed better than did the existing primers. Our findings may be useful for developing more stable and accurate tools for the discrimination of L. garvieae from other closely related species.
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Korea
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