Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra

AbstractAccurate species-level identification of alpha-hemolytic (viridans) streptococci (VGS) is very important for understanding their pathogenicity and virulence. However, an extremely high level of similarity between VGS within the mitis group (S. pneumoniae, S. mitis, S. oralis and S. pseudopneumoniae) often results in misidentification of these organisms. Earlier, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been suggested as a tool for the rapid identification of S. pneumoniae. However, by using Biotyper 3.0 (Bruker) or Vitek MS (bioMérieux) databases, Streptococcus mitis/oralis species can be erroneously identified as S. pneumoniae. ClinProTools 2.1 software was used for the discrimination of MALDI-TOF mass spectra of 25 S. pneumoniae isolates, 34 S. mitis and three S. oralis. Phenotypical tests and multilocus gene typing schemes for the S. pneumoniae (http://spneumoniae.mlst.net/) and viridans streptococci (http://viridans.emlsa.net/) were used for the identification of isolates included in the study. The classifying model was generated based on different algorithms (Genetic Algorithm, Supervised Neural Network and QuickClassifier). In all cases, values of sensitivity and specificity were found to be equal or close to 100%, allowing discrimination of mass spectra of different species. Three peaks (6949, 9876 and 9975 m/z) were determined conferring the maximal statistical weight onto each model built. We find this approach to be promising for viridans streptococci discrimination

Сравнительный анализ орофарингеальной микробиоты у больных хронической обструктивной болезнью легких и бронхиальной астмой различной степени тяжести

Backgraund: The result of comparative study of oropharyngeal microbiota taxonomic composition in patients with different severity level of bronchial asthma (BA) and chronic obstructive pulmonary disease (COPD) is presented in this paper. Aims: To compare oropharyngeal microbiota composition in case of bronchial asthma and chronic obstructive pulmonary disease in different severity levels. Metods: 138 patients, 50 with BA and 88 with COPD were studied. For each patient was collected anamnesis vitae, swab from the back of the throat and performed physical examination. High-throughput 16S ribosomal RNA gene sequencing and bioinformatic analysis was employed to characterize the microbial communities. Results: As a result of the study was found a number of differences on various taxonomic levels in microbiota’s composition within group of patients with different severity level of BA and group of patients with different severity level of COPD and between those groups. COPD patients with GOLD 1–2 in comparison with GOLD 3–4 patiens are marked by prevalence of species Brevibacterium aureum, genus Scardovia, Coprococcus, Haemophilus, Moryella, Dialister, Paludibacter and decrease of Prevotella melaninogenica species. BA patients with severe uncontrolled asthma in comparison with patients which have mild persistent asthma are marked by decrease of Prevotella and increase of species Bifidobacterium longum, Prevotella nanceiensis, Neisseria cinerea, Aggregatibacter segnis and genus Odoribacter, Alloiococcus, Lactobacillus, Megasphaera, Parvimonas, Sneathia. Patient’s microbiota in BA group in comparison with COPD group is characterized by the prevalence of Prevotella melaninogenica and genus Selenomonas, Granulicatella и Gemella, and decrease of Prevotella nigrescens, Haemophilus influenza and genus Aggregatibacter, Alloiococcus, Catonella, Mycoplasma, Peptoniphilus и Sediminibacterium. There are no differences between microbiota composition in case of severe uncontrolled BA and very severe COPD. Conclusion: Lack of differences in oropharyngeal microbiota taxonomic composition between patients with severe uncontrolled BA and very severe COPD allow us to suggest a similarity of bronchopulmonary system condition in case of diseases' severe stages.Обоснование. Характеристика орофарингеальной микробиоты при хронической обструктивной болезни легких (ХОБЛ) и бронхиальной астме (БА) в зависимости от тяжести течения заболеваний является актуальной задачей, решение которой позволит уточнить роль микробиоты в их патогенезе. Цель исследования: сравнительный анализ состава орофарингеальной микробиоты при ХОБЛ и БА разной степени выраженности симптомов. Методы. В исследование включены 138 больных, из них 88 с ХОБЛ, 50 — с БА. Для каждого пациента был собран анамнез жизни, проведено физикальное исследование и получен мазок из орофарингеальной области. Определение таксономического состава проводилось секвенированием генов бактериальной 16S рРНК с последующим биоинформатическим и статистическим анализом. Результаты. При сравнительном анализе были найдены различия в представленности микроорганизмов. Для микробиоты больных ХОБЛ 1–2-й степени тяжести в сравнении с образцами ХОБЛ 3–4-й степени на фоне снижения представленностиPrevotella melaninogenica характерно более высокое содержание Brevibacterium aureum и представителей рода Scardovia, Coprococcus, Haemophilus, Moryella, Dialister и Paludibacter. Микробиота пациентов с тяжелой БА в сравнении с таковой при легкой персистирующей форме на фоне более низкого содержания бактерий рода Prevotella характеризуется более выраженным присутствием Bifidobacterium longum, Prevotella nanceiensis, Neisseria cinerea, Aggregatibacter segnis, а также представителей рода Odoribacter, Alloiococcus, Lactobacillus, Megasphaera, Parvimonas и Sneathia. При сравнении микробиоты больных БА и ХОБЛ для пациентов с БА отмечалась более высокая представленность P. melaninogenica и микроорганизмов рода Selenomonas, Granulicatella, Gemella, а также снижение Prevotella nigrescens, Haemophilus influenzae и Aggregatibacter, Alloiococcus, Catonella, Mycoplasma, Peptoniphilus, Sediminibacterium. При этом различия в составе орофарингеальной микробиоты у больных тяжелой неконтролируемой БА и ХОБЛ очень тяжелого течения не выявлены.Заключение. Отсутствие различий в бактериальной композиции орофарингеальной микробиоты у больных с тяжелыми формами ХОБЛ и БА позволяет высказать предположение о сходстве состояния бронхолегочной системы при тяжелых стадиях развития данных заболеваний

Data on translatome analysis of Mycoplasma gallisepticum

Mycoplasma gallisepticum is a bacterium of class Mollicutes which encompasses wall-less bacteria with significantly reduced genomes. Due to their overall reduction and simplicity mycoplasmas serve as a model of minimal cell and are used for systems biology studies. Here we present raw data on translatome (ribosome-bound mRNA) analysis of Mycoplasma gallisepticum under logarithm growth and heat stress. The data supports the publication of “Ribosomal profiling of Mycoplasma gallisepticum” (G. Y. Fisunov, D. V Evsyutina, A. A. Arzamasov, I. O. Butenko, V. M. Govorun, 2015) [1]

Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants

Background: In recent years, the damage caused by bacterial pathogens to major crops has been increasing worldwide. Pseudomonas syringae is a widespread bacterial species that infects almost all major crops. Different P. syringae strains use a wide range of biochemical mechanisms, including phytotoxins and effectors of the type III and type IV secretion systems, which determine the specific nature of the pathogen virulence. Results: Strains 1845 (isolated from dicots) and 2507 (isolated from monocots) were selected for sequencing because they specialize on different groups of plants. We compared virulence factors in these and other available genomes of phylogroup 2 to find genes responsible for the specialization of bacteria. We showed that strain 1845 belongs to the clonal group that has been infecting monocots in Russia and USA for a long time (at least 50 years). Strain 1845 has relatively recently changed its host plant to dicots. Conclusions: The results obtained by comparing the strain 1845 genome with the genomes of bacteria infecting monocots can help to identify the genes that define specific nature of the virulence of P. syringae strains. © 2016 The Author(s)

Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants

Background: In recent years, the damage caused by bacterial pathogens to major crops has been increasing worldwide. Pseudomonas syringae is a widespread bacterial species that infects almost all major crops. Different P. syringae strains use a wide range of biochemical mechanisms, including phytotoxins and effectors of the type III and type IV secretion systems, which determine the specific nature of the pathogen virulence. Results: Strains 1845 (isolated from dicots) and 2507 (isolated from monocots) were selected for sequencing because they specialize on different groups of plants. We compared virulence factors in these and other available genomes of phylogroup 2 to find genes responsible for the specialization of bacteria. We showed that strain 1845 belongs to the clonal group that has been infecting monocots in Russia and USA for a long time (at least 50 years). Strain 1845 has relatively recently changed its host plant to dicots. Conclusions: The results obtained by comparing the strain 1845 genome with the genomes of bacteria infecting monocots can help to identify the genes that define specific nature of the virulence of P. syringae strains. © 2016 The Author(s)

Scope and limitations of MALDI-TOF MS blood serum peptide profiling in cancer diagnostics

Serum samples (33 healthy women, 34 ovarian cancer, 28 colorectal cancer, 34 syphilis patients and 136 patients with various benign gynecological diseases) were analyzed by MALDI-TOF MS peptide profiling and respective predictive models were generated by genetic and supervised neural network algorithms. Classification models for pathology versus healthy control showed up to 100% sensitivity and specificity for all target diseases. However, the specificity dropped to unsatisfactory 25–40% in case of target versus nontarget disease diagnostics. Expansion of the control group to an artificial “nominal control” group by adding profiles of benign gynecological diseases considerably improved specificity of the models distinguishing ovarian cancer from healthy control and benign gynecological diseases. The suggested version of MALDI-TOF MS profiling of sera could be applied to differentiate between cancers and benign neoplasms of the same localization which is a challenging task for classical methods. To increase the specificity of diagnostic methods based on peptidome analysis of blood samples, it is necessary to identify sets of concrete peptide structures which qualitatively or quantitatively differ among patients with different diseases. © 2016, Pleiades Publishing, Ltd

Scope and limitations of MALDI-TOF MS blood serum peptide profiling in cancer diagnostics

Serum samples (33 healthy women, 34 ovarian cancer, 28 colorectal cancer, 34 syphilis patients and 136 patients with various benign gynecological diseases) were analyzed by MALDI-TOF MS peptide profiling and respective predictive models were generated by genetic and supervised neural network algorithms. Classification models for pathology versus healthy control showed up to 100% sensitivity and specificity for all target diseases. However, the specificity dropped to unsatisfactory 25–40% in case of target versus nontarget disease diagnostics. Expansion of the control group to an artificial “nominal control” group by adding profiles of benign gynecological diseases considerably improved specificity of the models distinguishing ovarian cancer from healthy control and benign gynecological diseases. The suggested version of MALDI-TOF MS profiling of sera could be applied to differentiate between cancers and benign neoplasms of the same localization which is a challenging task for classical methods. To increase the specificity of diagnostic methods based on peptidome analysis of blood samples, it is necessary to identify sets of concrete peptide structures which qualitatively or quantitatively differ among patients with different diseases. © 2016, Pleiades Publishing, Ltd

Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain

© 2020, Springer Science+Business Media, LLC, part of Springer Nature. Antimicrobial peptides (AMPs) are natural antagonistic tools of many bacteria and are considered as attractive antimicrobial agents for the treatment of bacteria with multidrug resistance. Lactic acid bacteria from the gastrointestinal tract of animals and human produce various AMPs inhibiting the growth of pathogens. Here we report the isolation and identification of novel Lactobacillus fermentum strain HF-D1 from the human gut producing AMPs which prevents the growth of P. aeruginosa and S. marcescens. The active fraction of peptides was obtained from the culture liquid by precipitation at 80% saturation of ammonium sulphate. For peptides identification, the precipitate was treated with guanidine hydrochloride to desorb from proteins, separated with ultrafiltration on spin columns with 10,000 MWCO, desalted with a reversed-phase chromatography and subjected to LC–MS/MS analysis. The in silico analysis of the identified 1111 peptides by using ADAM, CAMPR3 and AMPA prediction servers led to identification of the linear peptide with highly probable antimicrobial activity and further investigation of its antibacterial activity mechanism is promising. By using the dereplication algorithm, the peptide highly similar to non-ribosomal cyclic AMPs originally isolated from Staphylococcus epidermidis has been identified. This indicates that L. fermentum HF-D1 represents a novel strain producing antimicrobial peptides targeting P. aeruginosa and S. marcescens