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Metaproteome analysis of endodontic infections in association with different clinical conditions.

ABSTRACT: Analysis of the metaproteome of microbial communities is important to provide an insight of community physiology and pathogenicity. This study evaluated the metaproteome of endodontic infections associated with acute apical abscesses and asymptomatic apical periodontitis lesions. Proteins persisting or expressed after root canal treatment were also evaluated. Finally, human proteins associated with these infections were identified. Samples were taken from root canals of teeth with asymptomatic apical periodontitis before and after chemomechanical treatment using either NaOCl or chlorhexidine as the irrigant. Samples from abscesses were taken by aspiration of the purulent exudate. Clinical samples were processed for analysis of the exoproteome by using two complementary mass spectrometry platforms: nanoflow liquid chromatography coupled with linear ion trap quadrupole Velos Orbitrap and liquid chromatography-quadrupole time-of-flight. A total of 308 proteins of microbial origin were identified. The number of proteins in abscesses was higher than in asymptomatic cases. In canals irrigated with chlorhexidine, the number of identified proteins decreased substantially, while in the NaOCl group the number of proteins increased. The large majority of microbial proteins found in endodontic samples were related to metabolic and housekeeping processes, including protein synthesis, energy metabolism and DNA processes. Moreover, several other proteins related to pathogenicity and resistance/survival were found, including proteins involved with adhesion, biofilm formation and antibiotic resistance, stress proteins, exotoxins, invasins, proteases and endopeptidases (mostly in abscesses), and an archaeal protein linked to methane production. The majority of human proteins detected were related to cellular processes and metabolism, as well as immune defense. Interrogation of the metaproteome of endodontic microbial communities provides information on the physiology and pathogenicity of the community at the time of sampling. There is a growing need for expanded and more curated protein databases that permit more accurate identifications of proteins in metaproteomic studies.

SUBMITTER: Provenzano JC

PROVIDER: S-EPMC3797121 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Metaproteome analysis of endodontic infections in association with different clinical conditions.

Provenzano José Claudio JC Siqueira José F JF Rôças Isabela N IN Domingues Romênia R RR Paes Leme Adriana F AF Silva Márcia R S MR

PloS one 20131015 10

Analysis of the metaproteome of microbial communities is important to provide an insight of community physiology and pathogenicity. This study evaluated the metaproteome of endodontic infections associated with acute apical abscesses and asymptomatic apical periodontitis lesions. Proteins persisting or expressed after root canal treatment were also evaluated. Finally, human proteins associated with these infections were identified. Samples were taken from root canals of teeth with asymptomatic a ...[more]

PMID: 24143178

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Project description:Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and reliability of metaproteomic results. Specifically, the use of iterative searches and of suitable filters for taxonomic assignments is proposed with the aim of increasing coverage and trustworthiness of metaproteomic data.

Project description:BackgroundTo assess the financial impact of incorporating a new (reciprocal) technology into endodontic treatments in the public health system (SUS).MethodsThis was a economic evaluation study (comparing the 3 different endodontic instrumentation techniques-manual, rotary and reciprocating), allocative efficiency analysis to optimize existing resources in the SUS, and financial contribution impact analysis of incorporation of a new technology. Thirty-one (31) 12 years-old volunteers were evaluated.ResultsThe incremental cost-effectiveness ratio (ICER) was calculated at R$1.34/min, - R$0.60/min and BRL 0.10/min for the single-rooted, bi-rooted and tri-rooted teeth, respectively, when the rotary technique was compared with the manual type. In turn, the ICER was R$ 21.04/min, - R$ 0.73/min and - R$ 2.81/min for the 3 types of teeth, respectively, when the reciprocating technique was compared with the manual type. The incremental financial impact of replacing manual endodontic with rotary endodontic treatments would be - R$ 2060963.66 in the case of single-rooted teeth, but the number of treatments would also be reduced (- 19,379). In the case of two-rooted teeth, the incremental financial impact would be BRL 34921540.62 with the possibility of performing an additional 204,110 treatments. In turn, BRL 11523561.50 represented the incremental financial impact for teeth with 3 or more roots and with an increase of 72,545 procedures. When we analyzed the incremental financial impact of replacing manual endodontic with reciprocating endodontic treatments, it would be - R$ 730227.80 in the case of single-rooted teeth, allowing for an additional 2538 treatments. In turn, R$ 21674853.00 represented the incremental financial impact for bi-radicular teeth, with an increase of 121,700 procedures. In the case of two-rooted teeth, the incremental financial impact would be BRL 13591742.90 with the possibility of performing an additional 40,670 treatments.ConclusionsThe reciprocating technique could improve access to endodontic treatment in the SUS as it allowed a simultaneous reduction in clinical time and associated costs. However, the higher number of endodontic treatments performed would have a financial impact.

Dataset Information

Metaproteome analysis of endodontic infections in association with different clinical conditions.

Publications

Metaproteome analysis of endodontic infections in association with different clinical conditions.

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