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Gaeta C, Marruganti C, Ali IAA, Fabbro A, Pinzauti D, Santoro F, Neelakantan P, Pozzi G, Grandini S. The presence of Enterococcus faecalis in saliva as a risk factor for endodontic infection. Front Cell Infect Microbiol 2023; 13:1061645. [PMID: 37091670 PMCID: PMC10118032 DOI: 10.3389/fcimb.2023.1061645] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/02/2023] [Indexed: 04/09/2023] Open
Abstract
AimThe aim of the present study was to investigate and correlate the prevalence of Enterococcus faecalis in saliva and in root canals with different pulpal and periapical conditions.MethodologySixty-seven patients were divided into five groups based on pulpal and periapical tissue status: healthy vital teeth (HVT, n=7), healthy treated teeth without lesion (HTT, n=9), irreversible pulpitis (IP, n=13), necrosis (N, n=18), and post-treatment apical periodontitis (PTAP, n=20). Saliva, rubber dam, sterility control and pre-treatment root canal samples were collected and microbiologically processed by culture method. The phylogenetic relationship of E. faecalis isolates collected from root canals and saliva were investigated by whole genome sequencing. Fisher’s exact test was used to correlate the presence of E. faecalis in root canals or saliva with clinical and/or radiographic findings. Linear/logistic regression analyses were performed to establish the relationship between the presence of E. faecalis in root canals, saliva, and the status of periapical tissues.ResultsE. faecalis was found in 18 root canal and saliva samples. E. faecalis root canal isolates were recovered with the highest frequency from post-treatment apical periodontitis. The occurrence of E. faecalis in saliva was strongly associated with its detection in the root canals (P < 0.001). The pretreatment presence of E. faecalis in root canals was associated with significantly higher odds of having periapical lesions (OR=11.03; 95% CI, 1.27-95.70; p < 0.05). Saliva and root canal isolates from the same patient were highly correlated at the phylogenetic level (Jaccard index >0.95).ConclusionThis pilot study confirms the role of E. faecalis in developing peri-radicular lesions in secondary endodontic infections and suggests that saliva could be the main source of infection. Further studies are needed to investigate the exact origin of this bacteria and its true role in the pathogenesis of secondary/persistent endodontic infections.
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Affiliation(s)
- Carlo Gaeta
- Unit of Periodontology, Endodontic and Restorative Dentistry, Department of Medical Biotechnology, University of Siena, Siena, Italy
- *Correspondence: Carlo Gaeta,
| | - Crystal Marruganti
- Unit of Periodontology, Endodontic and Restorative Dentistry, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Islam A. A. Ali
- Department of Endodontics, Faculty of Dentistry, Mansoura University, Mansoura, Egypt
| | - Andrea Fabbro
- Unit of Periodontology, Endodontic and Restorative Dentistry, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - David Pinzauti
- Unit of Periodontology, Endodontic and Restorative Dentistry, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Francesco Santoro
- Unit of Periodontology, Endodontic and Restorative Dentistry, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Prasanna Neelakantan
- Faculty of Dentistry, The University of Hong Kong, Sai Ying Pun, Hong Kong, Hong Kong SAR, China
| | - Gianni Pozzi
- Unit of Periodontology, Endodontic and Restorative Dentistry, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Simone Grandini
- Unit of Periodontology, Endodontic and Restorative Dentistry, Department of Medical Biotechnology, University of Siena, Siena, Italy
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Szoboszlay M, Schramm L, Pinzauti D, Scerri J, Sandionigi A, Biazzo M. Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required. Microorganisms 2023; 11:microorganisms11030804. [PMID: 36985377 PMCID: PMC10059749 DOI: 10.3390/microorganisms11030804] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.
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Affiliation(s)
| | | | | | | | - Anna Sandionigi
- Department of Informatics, Systems and Communication, University of Milan Bicocca, 20126 Milan, Italy
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Abstract
Streptococcus mitis is a Gram-positive bacterium, member of the oral commensal microbiota, which can occasionally be the etiologic agent of diseases such as infective endocarditis, bacteraemia and septicaemia. The highly recombinogenic and repetitive nature of the S. mitis genome impairs the assembly of a complete genome relying only on short sequencing reads. Oxford Nanopore sequencing can overcome this limitation by generating long reads, enabling the resolution of genomic repeated regions and the assembly of a complete genome sequence. Since the output of a Nanopore sequencing run is strongly influenced by genomic DNA quality and molecular weight, the DNA isolation is the crucial step for an optimal sequencing run. In the present work, we have set up and compared three DNA isolation methods on two S. mitis strains, evaluating their capability of preserving genomic DNA integrity and purity. Sequencing of DNA isolated with a mechanical lysis-based method, despite being cheaper and quicker, did not generate ultra-long reads (maximum read length of 59516 bases) and did not allow the assembly of a circular complete genome. Two methods based on enzymatic lysis of the bacterial cell wall, followed by either (i) a modified CTAB DNA isolation procedure, or (ii) a DNA purification after osmotic lysis of the protoplasts allowed the sequencing of ultra-long reads up to 107294 and 181199 bases in length, respectively. The reconstruction of a circular complete genome was possible sequencing DNAs isolated using the enzymatic lysis-based methods.
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Affiliation(s)
- David Pinzauti
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
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