A New Type of Chronic Wound Infection after Wisdom Tooth Extraction: A Diagnostic Approach with 16S-rRNA Gene Analysis, Next-Generation Sequencing, and Bioinformatics

Böttger, Sebastian; Zechel-Gran, Silke; Streckbein, Philipp; Knitschke, Michael; Hain, Torsten; Weigel, Markus; Wilbrand, Jan-Falco; Domann, Eugen; Howaldt, Hans‐Peter; Attia, Sameh

doi:10.3390/pathogens9100798

Cited by 9 publications

(7 citation statements)

References 39 publications

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“…In this case, taking a swab can help distinguish classic mono-infections, which are often caused by easily culturable bacteria, from the typical anaerobic pathogen spectrum of odontogenic infections. In particular, infections with pyogenic Streptococci (e.g., peritonsillar abscess), abscesses caused by Staphylococci (especially S. aureus ), and infections with nonfermenting Gram-negative bacilli (NFGNB) [ 20 ] should be mentioned here, in which a possible adjuvant antibiotic therapy may need to be designed differently for the typical odontogenic abscess.…”

Section: Discussionmentioning

confidence: 99%

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Clinical Relevance of the Microbiome in Odontogenic Abscesses

Böttger

Zechel-Gran

Schmermund

et al. 2021

Biology

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Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.

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Section: Discussionmentioning

confidence: 99%

“…Irrespective of the clinical therapy and culture results thereby obtained, the microbiome of the pus was determined from the frozen samples about three months later using 16S rRNA gene analysis [ 18 , 19 , 20 ]. 16S rRNA amplicon sequencing works like a bacterial fingerprint if the base sequence can be matched with a ribosomal database.…”

Section: Methodsmentioning

confidence: 99%

Clinical Relevance of the Microbiome in Odontogenic Abscesses

Böttger

Zechel-Gran

Schmermund

et al. 2021

Biology

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“…It is not always possible to sufficiently identify the causative pathogens by culture-based methods alone [ 10 ]—some authors even speak of culture-negative odontogenic abscesses if it is not possible to cultivate any pathogens at all [ 11 ]. Recent detection methods, not based on culturing, and particularly 16S rRNA gene analysis with subsequent gene sequencing, have shown that many bacteria of the oral cavity can only be determined with difficulty or even not at all by culture-based methods [ 3 , 12 , 13 ]. It has also not yet been possible to determine which bacteria of the oral and pharyngeal microbiome are exactly responsible for the acute inflammatory process and if the oral microbiome in these patients is composed differently compared to healthy people.…”

Section: Introductionmentioning

confidence: 99%

Microbiome of Odontogenic Abscesses

et al. 2021

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Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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“…Since the introduction of the revolutionary method of bacterial characterization by Pace et al 26 , 16S rRNA-based characterization of bacterial species has been universally accepted as an accurate method for bacterial identi cation 27 . 16S rRNA metagenomic analysis has provided an objective tool to explore bacterial diversity and composition under a wide variety of clinical scenarios, in which 16S rRNA amplicon with SMS analysis was widely adopted for economic affordability and rapid microbial detection strategy 28 .To date, the use of 16S ribosomal RNA (rRNA) metagenomic analysis to study GM changes in the clinical setting have demonstrated the capability to analyze associations between GM changes and colorectal diseases 28 , COVID-19 infections 29 , prosthetic joint infections 30 , chronic wound infections after wisdom tooth extraction 31 , detection of postoperative infection sources 32 , and the potential to in uence SSI outcomes in colorectal surgery 14 . In this study, the 16S rRNA amplicon with SMS analysis was utilized to verify gut GM changes in mice.…”

Section: Discussionmentioning

confidence: 99%

Antibiotic cocktail followed by Clostridium butyricum (CBM588) supplementation improves colonic anastomotic healing in mice

Chen

Lai

et al. 2023

Preprint

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Background Microbiota manipulation through preoperative probiotic administration with Clostridium butyricum (CBM588) has shown promising results in reducing surgical site infections, but the resulting changes in gut microbiota are unclear. This study, using 16S ribosomal RNA metagenomic analysis, aimed to observe microbiome changes after CBM588 administration before murine colonic anastomosis. Materials and methods Eighteen C57BL/6 mice were divided into three groups. All mice, including group A as the control group, received oral neomycin and metronidazole before surgery. Group B received six consecutive days of CBM588 before surgery. Group C received kanamycin, gentamycin, colistin, metronidazole, and vancomycin, followed by six consecutive days of CBM588 before surgery. Results Compared with groups A and B, group C had significantly lower adhesion scores (p < 0.001), better postoperative performance (p < 0.05) and anastomotic healing scores (p < 0.001), and lower anastomotic necrosis areas (p < 0.05). Metagenomic analysis revealed that group C was enriched with the order Clostridiales, family Clostridiaceae, and genus Clostridium, with low bacterial diversity and composition. Conclusions Using a murine colonic anastomosis model, a preoperative antibiotic cocktail followed by CBM588 supplementation effectively decreased bacterial diversity and increased the percentage of Clostridiaceae. Associated outcomes included lower intra-abdominal adhesion scores, better postoperative performance and anastomotic healing scores, and lower anastomotic necrosis areas.

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A New Type of Chronic Wound Infection after Wisdom Tooth Extraction: A Diagnostic Approach with 16S-rRNA Gene Analysis, Next-Generation Sequencing, and Bioinformatics

Cited by 9 publications

References 39 publications

Clinical Relevance of the Microbiome in Odontogenic Abscesses

Clinical Relevance of the Microbiome in Odontogenic Abscesses

Microbiome of Odontogenic Abscesses

Antibiotic cocktail followed by Clostridium butyricum (CBM588) supplementation improves colonic anastomotic healing in mice

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