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

Cholera in Azov area

The purpose of research is analysis of clinical course and treatment results of patients with cholera in the Azov area. Materials and methods. During the period from 29.05.2011 to 19.08.2011 33 cases of cholera (32 adults and 1 child) and 25 vibrio carriers (22 adults and 3 children), which were caused by toxigenic strains of Vibrio cholera El Tor serogroup O1 Ogawa. Results. Likely factors of disease transmission in Mariupol are sea and river water, and the fish that were caught in the waters of the city. Typical and watery diarrhoea, vomiting, abdominal pain and lack of normal body temperature, dehydration syndrome, characterized clinical cholera for adults in most cases. The mean duration of diarrhoea was 6,6 days. At 46.9% observed atypical symptoms in 10 (31,3%) – abdominal pain (1 patient cramping in 7 cases, localized in the epigastria region, at 2-over stomach). In 5 patients (15,6%) had an increase in body temperature to 37,2–37,7 degrees Celsius. In 15 (46,9%) patients had severe nausea accompanied by vomiting. Easy for cholera was observed in 1 (3.1%), moderate – in 14 (43,8%), heavy – in 17 (53,1%) patients. Dehydration I level is set at 4 (12,5%), II – from 6 (18,7%), III – in 18 (56,3%), IV – 4 (12,5%) patients. Cholera outbreak was characterized by a predominance of severe disease and severe dehydration (III and IV), which was observed in 68.8% of patients. The decisive factor in the treatment of cholera patients was initiated in a timely manner rehydration therapy, in particular the introduction of the solution «Trisol». Against the background of rehydration therapy hyperkalaemia was observed in 9,4% of cases, vascular rehydration at 9,4%, the cell rehydration in 3,1% of patients. Fatal accidents cholera outbreaks have not been observed. Conclusion. Clinical diagnosis of cholera and the provision of medical care in the prehospital phase were poor, indicating the need for systematic conducting training seminars among experts of ambulance, as well as doctors of primary medical network. Cholera hospitals (or base hospitals) must be equipped with a mobile diagnostics (ultrasound, X-rays) and modern laboratory equipment. The required list of drug supply cholera hospitals should be expanded in view of possible complications and comorbidities

Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy

© 2017Antibiotic therapy can lead to the disruption of gut microbiota community with possible negative outcomes for human health. One of the diseases for which the treatment scheme commonly included antibiotic intake is Helicobacter pylori infection. The changes in taxonomic and functional composition of microbiota in patients can be assessed using “shotgun” metagenomic sequencing. Ten stool samples were collected from 4 patients with Helicobacter pylori infection before and directly after the H. pylori eradication course. Additionally, for two of the subjects, the samples were collected 1 month after the end of the treatment. The samples were subject to “shotgun” (whole-genome) metagenomic sequencing using Illumina HiSeq platform. The reads are deposited in the ENA (project ID: PRJEB18265)

Search for Specific Biomarkers of IFNβ Bioactivity in Patients with Multiple Sclerosis

Myxovirus A (MxA), a protein encoded by the MX1 gene with antiviral activity, has proven to be a sensitive measure of IFNβ bioactivity in multiple sclerosis (MS). However, the use of MxA as a biomarker of IFNβ bioactivity has been criticized for the lack of evidence of its role on disease pathogenesis and the clinical response to IFNβ. Here, we aimed to identify specific biomarkers of IFNβ bioactivity in order to compare their gene expression induction by type I IFNs with the MxA, and to investigate their potential role in MS pathogenesis. Gene expression microarrays were performed in PBMC from MS patients who developed neutralizing antibodies (NAB) to IFNβ at 12 and/or 24 months of treatment and patients who remained NAB negative. Nine genes followed patterns in gene expression over time similar to the MX1, which was considered the gold standard gene, and were selected for further experiments: IFI6, IFI27, IFI44L, IFIT1, HERC5, LY6E, RSAD2, SIGLEC1, and USP18. In vitro experiments in PBMC from healthy controls revealed specific induction of selected biomarkers by IFNβ but not IFNγ, and several markers, in particular USP18 and HERC5, were shown to be significantly induced at lower IFNβ concentrations and more selective than the MX1 as biomarkers of IFNβ bioactivity. In addition, USP18 expression was deficient in MS patients compared with healthy controls (p = 0.0004). We propose specific biomarkers that may be considered in addition to the MxA to evaluate IFNβ bioactivity, and to further explore their implication in MS pathogenesis

Холера в Приазовье

The purpose of research is analysis of clinical course and treatment results of patients with cholera in the Azov area. Materials and methods. During the period from 29.05.2011 to 19.08.2011 33 cases of cholera (32 adults and 1 child) and 25 vibrio carriers (22 adults and 3 children), which were caused by toxigenic strains of Vibrio cholera El Tor serogroup O1 Ogawa. Results. Likely factors of disease transmission in Mariupol are sea and river water, and the fish that were caught in the waters of the city. Typical and watery diarrhoea, vomiting, abdominal pain and lack of normal body temperature, dehydration syndrome, characterized clinical cholera for adults in most cases. The mean duration of diarrhoea was 6,6 days. At 46.9% observed atypical symptoms in 10 (31,3%) – abdominal pain (1 patient cramping in 7 cases, localized in the epigastria region, at 2-over stomach). In 5 patients (15,6%) had an increase in body temperature to 37,2–37,7 degrees Celsius. In 15 (46,9%) patients had severe nausea accompanied by vomiting. Easy for cholera was observed in 1 (3.1%), moderate – in 14 (43,8%), heavy – in 17 (53,1%) patients. Dehydration I level is set at 4 (12,5%), II – from 6 (18,7%), III – in 18 (56,3%), IV – 4 (12,5%) patients. Cholera outbreak was characterized by a predominance of severe disease and severe dehydration (III and IV), which was observed in 68.8% of patients. The decisive factor in the treatment of cholera patients was initiated in a timely manner rehydration therapy, in particular the introduction of the solution «Trisol». Against the background of rehydration therapy hyperkalaemia was observed in 9,4% of cases, vascular rehydration at 9,4%, the cell rehydration in 3,1% of patients. Fatal accidents cholera outbreaks have not been observed. Conclusion. Clinical diagnosis of cholera and the provision of medical care in the prehospital phase were poor, indicating the need for systematic conducting training seminars among experts of ambulance, as well as doctors of primary medical network. Cholera hospitals (or base hospitals) must be equipped with a mobile diagnostics (ultrasound, X-rays) and modern laboratory equipment. The required list of drug supply cholera hospitals should be expanded in view of possible complications and comorbidities.Цель исследования – анализ клинического течения и результатов лечения больных холерой в Приазовье. Материалы и методы. За период с 29.05.2011 г. по 19.08.2011 г. зарегистрировано 33 случая заболевания холерой (32 взрослых и 1 ребенок) и 25 вибрионосителей (22 взрослых и 3 детей), которые были вызваны токсигенными штаммами холерного вибриона Эль-Тор серогруппы O1 Огава. Результаты. Вероятными факторами передачи заболевания в г. Мариуполе являлись морская и речная вода, а также рыба, которая была выловлена в акватории города. Клиническое течение холеры у взрослых в большинстве случаев было типичным и характеризовалось водянистой диареей, рвотой, отсутствием болей в животе, нормальной температурой тела, синдромом обезвоживания. Средняя продолжительность диареи составила 6,6 суток. У 46,9% наблюдались нетипичные симптомы: у 10 (31,3%) – боль в животе (у 1 больного схваткообразная, в 7 случаях локализовалась в эпигастральной области, у 2 – по всему животу). У 5 пациентов (15,6%) отмечено повышение температуры тела до 37,2–37,7 °С. У 15 (46,9%) пациентов рвота сопровождалась выраженной тошнотой. Легкое течение холеры отмечено у 1 (3,1%), средней тяжести – у 14 (43,8%), тяжелое – у 17 (53,1%) больных. Дегидратация I степени установлена у 4 (12,5%), II – у 6 (18,7%), III – у 18 (56,3%), IV – у 4 (12,5%) пациентов. Вспышка холеры характеризовалась преобладанием тяжелых форм болезни и выраженной дегидратацией (III и IV степени), которая отмечена у 68,8% больных. Решающим фактором в терапии больных холерой была своевременно начатая регидратационная терапия, в частности, введение раствора «Трисоль». На фоне регидратационной терапии наблюдали гиперкалиемию в 9,4% случаев, сосудистую гипергидратацию у 9,4%, клеточную гипергидратацию у 3,1% больных. Летальные случаи на вспышке холеры не наблюдались. Заключение. Клиническая диагностика холеры и оказание лечебной помощи на догоспитальном этапе были неудовлетворительными, что свидетельствует о необходимости систематического проведения учебно-зачетных семинаров среди специалистов СМП, а также врачей первичной врачебной сети. Холерные госпитали (или базовые лечебные учреждения) должны быть оснащены передвижной диагностической (УЗИ, рентген) и современной лабораторной аппаратурой. Необходимый перечень лекарственного обеспечения холерных госпиталей следует расширить с учетом возможных осложнений и сопутствующих заболеваний. 

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity

© 2017, National Academy of Sciences. All rights reserved.Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus, and predicted which genera were associated with inhibitory activity

ISG15 Is Critical in the Control of Chikungunya Virus Infection Independent of UbE1L Mediated Conjugation

Chikungunya virus (CHIKV) is a re-emerging alphavirus that has caused significant disease in the Indian Ocean region since 2005. During this outbreak, in addition to fever, rash and arthritis, severe cases of CHIKV infection have been observed in infants. Challenging the notion that the innate immune response in infants is immature or defective, we demonstrate that both human infants and neonatal mice generate a robust type I interferon (IFN) response during CHIKV infection that contributes to, but is insufficient for, the complete control of infection. To characterize the mechanism by which type I IFNs control CHIKV infection, we evaluated the role of ISG15 and defined it as a central player in the host response, as neonatal mice lacking ISG15 were profoundly susceptible to CHIKV infection. Surprisingly, UbE1L−/− mice, which lack the ISG15 E1 enzyme and therefore are unable to form ISG15 conjugates, displayed no increase in lethality following CHIKV infection, thus pointing to a non-classical role for ISG15. No differences in viral loads were observed between wild-type (WT) and ISG15−/− mice, however, a dramatic increase in proinflammatory cytokines and chemokines was observed in ISG15−/− mice, suggesting that the innate immune response to CHIKV contributes to their lethality. This study provides new insight into the control of CHIKV infection, and establishes a new model for how ISG15 functions as an immunomodulatory molecule in the blunting of potentially pathologic levels of innate effector molecules during the host response to viral infection

Bordetella pertussis Infection Exacerbates Influenza Virus Infection through Pertussis Toxin-Mediated Suppression of Innate Immunity

Pertussis (whooping cough) is frequently complicated by concomitant infections with respiratory viruses. Here we report the effect of Bordetella pertussis infection on subsequent influenza virus (PR8) infection in mouse models and the role of pertussis toxin (PT) in this effect. BALB/c mice infected with a wild-type strain of B. pertussis (WT) and subsequently (up to 14 days later) infected with PR8 had significantly increased pulmonary viral titers, lung pathology and mortality compared to mice similarly infected with a PT-deficient mutant strain (ΔPT) and PR8. Substitution of WT infection by intranasal treatment with purified active PT was sufficient to replicate the exacerbating effects on PR8 infection in BALB/c and C57/BL6 mice, but the effects of PT were lost when toxin was administered 24 h after virus inoculation. PT had no effect on virus titers in primary cultures of murine tracheal epithelial cells (mTECs) in vitro, suggesting the toxin targets an early immune response to increase viral titers in the mouse model. However, type I interferon responses were not affected by PT. Whole genome microarray analysis of gene expression in lung tissue from PT-treated and control PR8-infected mice at 12 and 36 h post-virus inoculation revealed that PT treatment suppressed numerous genes associated with communication between innate and adaptive immune responses. In mice depleted of alveolar macrophages, increase of pulmonary viral titers by PT treatment was lost. PT also suppressed levels of IL-1β, IL-12, IFN-γ, IL-6, KC, MCP-1 and TNF-α in the airways after PR8 infection. Furthermore PT treatment inhibited early recruitment of neutrophils and NK cells to the airways. Together these findings demonstrate that infection with B. pertussis through PT activity predisposes the host to exacerbated influenza infection by countering protective innate immune responses that control virus titers

Социально-экономическая эффективность проведения неонатального скрининга на спинальную мышечную атрофию в Российской Федерации

Background. Spinal muscular atrophy (SMA) is a severe rare disease that has been widely discussed in recent years. Achievements in etiopathogenetic therapy and the social significance of the disease (child population, high mortality), the cost of treatment attracted the attention of the public and the goverment, which, among other things, led to the formation of a separate area with the creation of a fund to finance the treatment of patients with orphan diseases.Aim. To conduct an analysis of the socio-economic efficiency of mass neonatal screening for SMA in the Russian Federation.Materials and methods. A survey of patients (their parents) and doctors was conducted. The current clinical guidelines and the standard of medical care for children with SMA were studied. The cost of medicines is taken from the State Register of Maximum Selling Prices. If the drug is not included in the List of Vital Essential and Necessary Drugs, cost information from the procurement data is used.Results. The socioeconomic burden of SMA on identified patients was about 3,994,289,548 rubles per year prior to screening. The very introduction of mass neonatal screening will amount to about 679,224,000 rubles in year. At the same time, a disease detected in a timely manner due to neonatal screening and timely prescribed effective treatment can lead to a reduction in the cost of specialized and palliative care by 54,073,271 rubles, direct non-medical costs by 88,137,423 rubles, and indirect costs by 154,197,900 rubles per year, which together is more than 7 % of the calculated burden of SMA.Conclusion. The introduction of mass screening will lead to the fact that the number of annually detected patients will increase from current values to the actual value of the prevalence when registering patients with milder forms of SMA. The need for drug supply with drugs and medical care in general will increase. At the same time, children diagnosed with SMA will not die in the early years of life, their survival rate, life expectancy will increase, the quality of life will improve, infant mortality will decrease, which is the main task of neonatal screening and one of the goals of the National Healthcare Project.Введение. Спинальная мышечная атрофия (СМА) – тяжелое редкое заболевание, которое в последние годы широко обсуждается. Достижения этиопатогенетической терапии и социальная значимость болезни (детская популяция, высокая смертность), стоимость лечения привлекли внимание общественности и правительства, что среди прочего привело к формированию отдельного направления с созданием фонда по финансированию лечения пациентов с орфанными болезнями.Цель исследования – провести анализ социально-экономической эффективности массового неонатального скрининга на СМА в Российской Федерации.Материалы и методы. Проведено анкетирование пациентов (их родителей) и врачей. Изучены действующие клинические рекомендации и стандарт медицинской помощи детям при СМА. Стоимость лекарственных препаратов взята из Государственного реестра предельных отпускных цен. Для препаратов, не входящих в Перечень жизненно необходимых и важнейших лекарственных препаратов, использовалась информация о стоимости из данных о закупках.Результаты. Социально-экономическое бремя СМА на выявленных пациентов составило порядка 3 994 289 548 руб. в год до введения скрининга. Затраты на внедрение массового неонатального скрининга составят около 679 224 000 руб. в год. При этом своевременное выявление болезни благодаря неонатальному скринингу и назначенное эффективное лечение позволяют снижать затраты на специализированную и паллиативную помощь на 54 073 271 руб., прямые немедицинские затраты на 88 137 423 руб., а также непрямые затраты на 154 197 900 руб. в год, что в совокупности составляет >7 % от рассчитанного бремени СМА. Выводы. Введение массового скрининга приведет к ежегодному выявлению пациентов и увеличению их числа с текущих значений до реальной величины распространенности при регистрации больных с более легкими формами СМА. Потребность в лекарственном обеспечении препаратами и медицинской помощи в целом возрастает. При этом дети со СМА не будут умирать в ранние годы жизни, их выживаемость, продолжительность жизни увеличатся, улучшится качество жизни, снизится младенческая смертность, что является основной задачей неонатального скрининга и одной из целей национального проекта «Здравоохранение»

колективна монографія

Кримінальний процесуальний кодекс 2012 року: ідеологія та практика правозастосування: колективна монографія / за заг. ред. Ю. П. Аленіна ; відпов. за вип. І. В. Гловюк. - Одеса : Видавничий дім «Гельветика», 2018. - 1148 с