Nasopharyngeal Smears Research Articles

Forensic assessment of maternal deaths from the COVID-19 during the 2021 pandemic

BACKGROUND: According to the literature, the mortality rate from SARS-CoV-2 infection among pregnant women is up to 25%. The high-risk group for the development of severe forms of COVID-19 includes pregnant women with extragenital pathology. Obstetric tactics are determined by the severity of the condition of the mother and fetus, as well as the duration of pregnancy. The decision on early delivery is made as a result of an interdisciplinary medical consultation. Delivery in the midst of the disease is associated with an increase in maternal mortality. According to the literature, including our own research, it has been established that the basis for favorable perinatal outcomes in patients with severe and moderate forms of COVID-19 is: an adequate assessment of the condition of the pregnant woman and fetus (especially at the outpatient stage, where the pregnant woman goes first), early hospitalization, early initiation of intensive care and timely delivery before the onset of irreversible organ changes in pregnant women. AIM: The aim of this study was to analyze the tactics of pregnancy management, delivery and perinatal outcomes, assessing the quality of medical care at the outpatient and hospital stages provided to pregnant women who died in a specialized obstetric hospital from the extremely severe new coronavirus infection COVID-19 (based on the data of commission forensic examinations). MATERIALS AND METHODS: This retrospective study of pregnancy outcomes was performed in 11 patients who died from complications of extremely severe COVID-19 in a regional specialized obstetric hospital in Russia based on the data of commission forensic examinations performed in the Bureau of Forensic Medical Examination (Saint Petersburg, Russia) in 2021, at gestation periods of 28–34 weeks (n = 7) and 37–39 weeks (n = 4) in the context of assessing the quality of medical care in the field of obstetrics and gynecology. We confirmed the diagnosis of the new coronavirus infection COVID-19 in 10 (90.9%) patients by SARS-CoV-2 RNA identification using polymerase chain reaction in a nasopharyngeal smear on an average of 4.9 ± 3.6 days from the onset of the disease. In one patient, the clinical diagnosis was confirmed postmortem by the detection of SARS-Cov-2 RNA during autopsy (in the trachea, lungs, and spleen). All patients in the hospital underwent a comprehensive anamnestic, clinical and laboratory examination in the amount regulated by the administrative regulations of the Ministry of Health of the Russian Federation that were relevant at the time of providing medical care. Nine (81.8%) patients sought medical help from a local therapist on 3.1 ± 1.6 days from the onset of the disease and received outpatient treatment for 3.4 ± 1.8 days, two patients not seeing a doctor and receiving outpatient care. The average time before admission to the specialized obstetric hospital was 6.0 ± 2.2 days from the onset of the disease. RESULTS: During the forensic assessment of the medical records of deceased patients, significant defects in the quality of medical care were identified in the framework of this study at the stages of information collection, diagnosis, treatment, and succession. An indirect causal relationship was established between the most significant defects in the quality of medical care and adverse pregnancy outcomes, since the cause of death or critical conditions were individually determined severe complications, rather than defects in medical care, which, nevertheless, does not exclude their significance in the totality of causes of severe maternal outcomes. CONCLUSIONS: The data obtained indicate the need for earlier delivery in pregnant women with the new coronavirus infection COVID-19 before the appearance of irreversible changes in patients with progressive respiratory failure, multiple organ failure syndrome, systemic inflammatory response syndrome, and cytokine storm.

The Performance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Virus Using the Colorimetric Reverse-Transcription Loop Mediated Isothermal Amplification (RT-LAMP) Method in Saliva Specimens of Suspected COVID-19 Patients.

Corona Virus Disease-19 (COVID-19) is a disease caused by Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2). The most reliable and widely accepted method for diagnosing this infection, despite facing various challenges, is the Reverse Transcription Polymerase Chain Reaction (RT-PCR) method, which utilizes nasopharyngeal swab sample. Reverse-transcription loop mediated isothermal amplification (RT-LAMP) is a simpler nucleic acid amplification method compared to the RT-PCR method. This method has several advantages, including: of amplification at constant temperature, faster results, and potentially greater examination capacity. This study aimed to compare the validity of the RT-LAMP method using saliva specimens with that of the RT-PCR method using nasopharyngeal smears. This was an analytical observational study with a cross-sectional design. The participants were inpatients in the COVID-19 special isolation building of Hasan Sadikin General Hospital, Indonesia with a probable (clinical symptoms of covid, but not confirm NAAT examination) or confirmed diagnosis of COVID-19 from September 2021 to February 2022. The inclusion criteria are COVID-19 patients with symptoms, adult subjects, and composite mentions. Patients who were unable to secrete saliva were also excluded. In total, 118 specimens were collected. The validity test results of the saliva specimens using the RT-LAMP method showed sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), of 65.5%, 100%, 100%, and 75%, respectively. The results increased in subjects treated between 3 and 7 days after symptom onset ie 73.2%, 100%, 100%, and 82.3%, respectively. The very strong specificity accompanied by good sensitivity and NPV in the group of subjects treated 3-7 days after the onset of symptoms indicates that the RT-LAMP method using saliva specimens can be an efficient and reliable alternative tool in detecting the SARS-CoV-2 virus.

Isolation of a rare pathogen <i>Chryseobacterium indologenes</i> in patients with pneumonia

Introduction. Chryseobacterium indologenes bacteria are rarely detected, poorly studied opportunistic bacteria of the nonfermenting gram-negative bacilli group that are characterized by high intrinsic and acquired multidrug resistance and involvement in healthcare associated infections.Aim. To analyze detection rate of C. indologenes strains from various biomaterials obtained from patients with pneumonia, as well as levels of pathogen drug resistance to antimicrobial drugs.Materials and methods. The research included 1740 clinical samples obtained from patients with pneumonia hospitalized in in-patient facilities of the Khabarovsk city during the COVID-19 pandemic. Clinical samples included 1305 respiratory samples (744 sputum samples and 561 nasopharyngeal swabs), 435 samples of autopsy material (lung tissue) obtained from patients with a fatal outcome of the disease. The study was performed via classical bacteriological method. Pathogens were identified with Vitek 2 bacteriological analyzer and Vitek MS mass spectrometer. Sensitivity to antimicrobial drugs was determined by disk-diffusion method and in a bacteriological analyzer.Results. A comparative analysis of detection of the entire nonfermenting gram-negative bacteria (NFGNB) group and C. indologenes from various clinical samples was carried out. Detection rate of NFGNB equaled 17.3%. NFGNB were isolated from autopsy material most often ‒ in 31.7% of cases, less often ‒ from sputum and nasopharyngeal smears (13.8% and 10.7%, respectively). C. indologenes was detected in 0.5% of the cases (8 isolates out of 1740 samples). Isolation of this pathogen was most frequent in nasopharyngeal smears – in 1.1% (6 cases out of 561 samples), least frequent ‒ from sputum, which totaled 0.3% (2 isolates from 744 samples). The detection rate of the pathogen in respiratory samples equaled 0.6% (8 isolates out of 1305 samples). This pathogen was not found in the autopsy material. Carbapenem-resistant variants of C. indologenes were isolated in 75% (6 cases out of 8) of the cases.Conclusion. Further intensifying of diagnostic methods will result in more frequent detection of these unusual pathogens, clinical significance of which needs more justification.

The impact of COVID-19 pandemic on surveillance of influenza and influenza-like viruses: a single center experience

Aims: Influenza and the agents responsible for influenza-like illness (ILI) are a significant cause of upper and lower respiratory tract infections, with a notable pattern of seasonal incidence. The surveillance of influenza and agents causing ILI is important for the developmentof a prophylaxis approach and infection control. In the present study, we utilize the Reverse transcription-polymerase chain reaction (RT-PCR) method to identify the presence of influenza virus and other agents associated with ILI in nasopharyngeal smears obtained from patients exhibiting symptoms of influenza and ILI. The study sample included patients who were admitted to multiple clinics and intensive care units (ICU) of the Health Sciences University Ankara Training and Research Hospital in the period preceding, and in the initial months and first year following the coronavirus disease 2019 (COVID-19) outbreak. Throughthe comparisons made in the study, the intention is to gain a better understanding of the influence of the COVID-19 pandemic on other viral infectious agents transmitted via the respiratory tract.
 Methods: Included in the study were 257 admitted to different wards and ICUs of our hospital due to symptoms of upper or lower respiratory tract infection and ILI between 2015 and 2021 (excluding data from 2017–2018). The study was conducted prospectively within the scope of the Global Influenza Hospital Surveillance Network project. Using sterile swabs, nasopharyngeal swab samples were collected from inpatients who provided informed consent for their participation in the study, and the samples were placed in a viral transport medium. The presence of influenza viruses (Influenza A, subtypes of Influenza A and Influenza B) and agents causing ILI (i.e. respiratory syncytial virus, coronavirus) was investigated with an RT-PCR approach.
 Results: The most common symptoms among the 257 patients included in the study with pre-diagnoses of influenza and ILI were cough (82.2%), fever (67.7%), shortness of breath (66.1%) and myalgia (40%). The RT-PCR detected a viral agent in 60 (23.3%) of the 257 patients, whereas no agent could be detected in 197 (76.6%) patients. Furthermore, 51 (18.5%) tested positive for influenza virus, five (1.9%) for respiratory syncytial virus (RSV), and four (1.5%) for SARS-CoV-2. An analysis of the results within two distinct time frames, namely prior to the COVID-19 pandemic (2016–2017, 2019–prior to December 10, 2020) and during the COVID-19 pandemic (between December 11, 2020 and 2021), influenza viruses (influenza A H1N1 and influenza A H3N2), RSV and influenza type B were identified as the dominant viruses before the COVID-19 pandemic, while the predominant viruses were a single influenza strain and four SARS-CoV-2 variants during the COVID-19 pandemic.A significant difference was noted in the distribution of viruses between the two time frames – prior to the pandemic and during the pandemic. Of the patients, 199 (77.4%) were discharged with full recovery while 58 patients died (22.6%). Of the 58 patients that died, 25 were female (25/131 females) and 33 were male (33/126 males), 11 had tested positive for influenza virus andone for RSV, while no infectious agent could be identified in 46 patients. 
 Conclusion: The implementation of molecular testing methods for the identification of viral infectious agents among inpatients during influenza and ILI outbreaks, administering antiviral and prophylactic treatments targeting influenza, RSV and SARS-CoV-2 infections, and adopting infection control measures, could significantly decrease mortality and morbidity rates while mitigating the complications associated with these infectious agents.

Regional Features of the Serotype Composition of Streptococcus pneumoniae isolated from Bacterial Carriers of Preschool Age in the Republic of Tatarstan

Relevance. Vaccination of the child population against pneumococcal infection (PI) has been carried out in the Republic of Tatarstan according to the national calendar of preventive vaccinations since 2014. The vaccination scheme includes vaccination with PCV-13 conjugated pneumococcal vaccine.Aim. Study of the the frequency of bacterial transmission and the serotype landscape of S. pneumoniae isolated from healthy children- bacterial carriers of preschool age in the Republic of Tatarstan (RT).Materials and methods. During the period from 2016 to 2022, 1,426 children from Kazan and the districts of the Republic of Tatarstan were examined. Examination of nasopharyngeal smears was carried out by the classical bacteriological method. Serotyping was performed using molecular genetic methods (PCR).Results. The detection rate of S. pneumoniae among healthy preschool children varied in different years from 29.5 to 63%, averaging 38.5%. In urban children, the incidence of pneumococcal transmission was significantly higher than in rural children (p<0.01). Also, when analyzing the serotype landscape, mixed colonization by several serotypes was observed. As of January 1, 2021, the immune layer to the pathogen PI among preschool children was 81.7%. Monitoring of the serotype landscape of S.pneumoniae strains circulating in the RT showed the dominance of vaccine serotypes (67.2%), of which 44.4% are PCV13 serotypes. The proportion of non–vaccinated serotypes is 26%, untyped - 6.8%. Unvaccinated serotypes 35B (21.3%) and 23A (13.6%) dominated in vaccinated children, as well as serotypes not included in the PKV-13 vaccine cocktail, but included in the PPSV-23 polysaccharide vaccine not used for vaccination of children, namely 11AD (15.3%) 9LN (9.6%). In unvaccinated children, on the contrary, vaccine serotypes included in PCV-13 prevailed: 6ABCD (17.3%), 19F (20.9%), and unvaccinated serotypes 11AD, 9LN, 35B, 23A were detected with lower frequency 11,8%, 10,0%, 4,2%, 7,3% accordingly.Conclusion. Data on the regional features of the pneumococcal serotype landscape can be the basis for expanding the vaccine cocktail due to the dominant serotypes: 9LN,11 AD, 35B, 23A.

COVID-19 a Possible Cause of Myocarditis and Pericarditis: About A Case

Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is an unparalleled challenge for the healthcare community across the globe. Angiotensin-2 converting enzyme receptors play a central role in the pathogenesis of the virus. Disruption of this receptor results in cardiomyopathy, cardiac dysfunction, and heart failure. Pericarditis is described as another cause of morbidity in patients with COVID-19. The exact mechanisms of how SARS-CoV-2 can cause myocardial damage are not clearly understood. We report the case of a 72-year-old man presenting for 17 days with retrosternal chest pain suggestive of pericarditis associated with a dry cough and a decline in general condition. He has had exertional asthma and active smoking as a history. He is taken care of in the emergency room. His clinical examination found a patient hemodynamically and respiratory stable, afebrile with a normal somatic examination apart from crackling rales. The biological assessment shows an inflammatory syndrome with slightly increased troponins HS. The scan performed in the emergency room notes typical pulmonary involvement moderate to COVID-19 and low-abundance pericardial effusion confirmed by echocardiography. The COVID-19 nasopharyngeal smear was positive. We conclude in an acute peri-myocarditis with COVID-19. The clinical and biological outcome is rapidly favorable with colchicine.

МУЛЬТИМОДАЛЬНАЯ ДИАГНОСТИКА У ПАЦИЕНТОВ С КОМПОНЕНТАМИ МЕТАБОЛИЧЕСКОГО СИНДРОМА, ПЕРЕНЕСШИХ ИНТЕРСТИЦИАЛЬНУЮ ПНЕВМОНИЮ, АССОЦИИРОВАННУЮ С COVID-19

Introduction. Coronavirus infectious disease caused by SARS-CoV-2 characterized by vast clinical variability. Extrapulmonary complications associated with endothelial damage, thrombosis and impaired regulation of immune responses provide unfavorable impact on the outcome of the disease and rehabilitation opportunities. Also, infection inflict damage to the gastrointestinal tract, hepatobiliary system. A key - roles to avoid aforementioned conditions are proper diagnosis and treatment plan, which should be make as soon as possible among the patients with elements of metabolic syndrome. The aim of the study - analyze the possibilities of multimodal diagnostics in patients with elements of the metabolic syndrome who get infected by SARS-CoV-2. Material and methods. In 41 patients with positive SARS-CoV-2, according to a nasopharyngeal smear study, the elements of the metabolic syndrome such as an increase in body mass index, serum triglycerides, and blood pressure were determined. Dynamic ultrasound of the abdominal cavity organs, CT scan of the chest in the near and distant periods were performed. Results and discussion. In the period 2020 - 2021. in patients with elements of the metabolic syndrome who have suffered of interstitial pneumonia caused by COVID-19, the predominant patterns was diffuse mosaic changes in lung tissue lesions with the spread of changes in lung parenchyma to more than one segment were identified. In a comparative aspect, dynamic multimodal diagnostics of abdominal organs was performed, confirming extrapulmonary complications from the liver: hepatosplenomegaly (p ≤ 0.01), changes of hemodynamics in hepatic vessels in patients with MS (p ≤ 0.05), increased stiffness and formation of liver parenchyma fibrosis in almost 15% (F2- F3). Conclusion. Study confirm the need for careful and long-term monitoring of patients, who are a in group of risk to develop metabolic syndrome with multimodal noninvasive ultrasound control of the condition of target organs.

COVID-19 pandemic: epidemiological features in the Jalal-Abad region of the Kyrgyz Republic

The coronavirus pandemic has caused massive economic, social and moral damage to humanity. Repeated waves of morbidity three years after the start of the COVID-19 pandemic require a comprehensive analysis of the epidemic situation and the problems of organizing and conducting preventive and anti-epidemic measures. A retrospective analysis of the incidence of COVID-19 and community-acquired pneumonia in the Jalal-Abad region of the Kyrgyz Republic in 2020 and 2021 was carried out. The frequency of detection of virus genetic material in nasopharyngeal smears was studied. An assessment of the coverage of vaccinations against COVID-19 and the proportion of people who sought medical care in day hospitals was carried out. It was found that several factors contributed to the decrease in the incidence of COVID-19 at once — the variability of pathogens, an increase in the proportion of the population ith specific protection, and the implementation of demarcation measures. A distinctive feature of the Jalal-Abad region was the deployment of day hospitals operating on the principle of the «red zone». This made it possible to increase the coverage of the population with medical care and prevent the further spread of the pathogen. The ongoing pandemic requires additional research and adjustment of countermeasures when new factors and circumstances are identified.

One of the possibilities of optimizing the therapy of a new coronavirus infection in children with the inclusion of an extract from marshmallow root, chamomile flowers, horsetail grass, walnut leaves, yarrow grass, oak bark and dandelion grass: prospective open comparative cohort study

Background. The issue of acute respiratory infections in children remains one of the most urgent. Therefore, in the pandemic due to the new coronavirus SARS-CoV-2, the search for effective treatment regimens for this disease is necessary.
 Aim. To compare the change of clinical symptoms, terms of virus elimination and disease-related economic cost as well as utilization of outpatient healthcare services in children with new coronavirus infection using the herbal medicine Tonsilgon N, oral solution, added to standard therapy.
 Materials and methods. A prospective open comparative cohort study of the effectiveness of coronavirus infection treatment in children using the standard of care alone and the standard of care with Tonsilgon N was conducted. Group 1 children (n=720) received the standard therapy for COVID-19 and Tonsilgon N oral solution for 10 days, and group 2 patients (n=670) only received the standard therapy for COVID-19. Treatment efficacy was evaluated according to the change of clinical symptoms in the observed patients, the results of SARS-CoV-2 coronavirus RNA detection in nasopharyngeal smears by polymerase chain reaction, the utilization of healthcare services, temporary disability of parents, the economic cost of the disease.
 Results. Studied patients of both groups had a typical clinical presentation of mild to moderate severity new coronavirus infection. Fatigue (96.599.7%) and sore throat (93.893.9%) were the most frequent symptoms. Posterior pharynx hyperemia was noted slightly less frequently. Low-grade fever was noted in 85.786.6% of the patients, equally often in patients of both groups. The significant therapeutic effect of the herbal medicine containing extract of marshmallow root, chamomile flowers, horsetail herb, walnut leaf, yarrow herb, oak bark, and dandelion herb includes reducing the time of sore throat relief in 93.2% of main group patients. After 10 days of treatment, sore throat persisted only in 6.8% of group 1 and 68.1% of group 2 patients (p=0.0001). These results indicate that Tonsilgon combined with standard of care is a promising way to improve the quality of life of children with the new coronavirus infection. The addition of Tonsilgon in therapy for new coronavirus infection in children shortens the time of acute inflammation resolution and reduces the duration of inflammatory intoxication. The therapy of new coronavirus infection under the provisional guidelines leads to a reduction in the time for clinical recovery and virus elimination in children and adolescents (p=0.0001) and a decrease in the utilization of outpatient healthcare services are observed: 3/4 of Group 1 patients and 1/2 of Group 2 patients (p=0.0001) applied for medical help twice during the observation period, 14.6% of Group 1 patients and 29.1% of Group 2 parents applied for medical help more than 3 times (p=0.0001). Thus, the direct and indirect economic costs of the disease decreased. The lower economic cost for parents of children in Group 1 was due to less need for medication and a lower reduction in family income due to temporary disability compared to those for parents in Group 2 (p=0.0001). No treatment-related adverse events was reported.
 Conclusion. The above data indicate that Tonsilgon therapy is an affordable way to optimize the treatment of new coronavirus infection in children.

Current <i>Streptococcus Pneumoniae</i> Serotypes in Sverdlovsk Region in 2020–2021

Relevance. Studying the spread of individual S. pneumoniae serotypes is of special epidemiologic and clinical importance. Sverdlovsk Region with the 20% proportion of community­-acquired pneumonia and its proportion among the causes of mortality of up to 70% is of special concern.Aims. Studying the features of the S. pneumoniae serotype landscape in individual socially significant population groups in Sverdlovsk Region in 2020 and 2021.Materials and methods. The work presents the results of testing nasopharyngeal smears collected in two observation groups, namely, that of 159 unvaccinated children aged 0 to 5 with acute respiratory infections (ARI), and that of 392 apparently healthy adults aged 19 to 27. We performed molecular genetic typing for identification of 20 leading S. рneumoniae serotypes/serogroups (1, 2, 3, 4, 5, 14, 16F, 19A, 19F, 23A, 23F, 6ABCD, 7AF, 9AV, 9LN, 11AD, 15AF, 18ABCF, 22AF, 12FAB/44/46, 33AF/37) using multiplex polymerase chain reaction (PCR).Results and discussion. In the individuals of the studied groups of observation, in 27.0% and 28.1% of the cases the study detected the S. pneumoniae in the biological material with circulation of 12 «vaccine» (19F – 2,6%, 6ABCD – 2,6%, 4 – 2,0%, 23F – 2,0%, 9AV – 1,3%, 9LN – 0,6%, 11AD – 1,3%, 18ABCF – 2,0%) and «nonvaccine» (15AF – 0.7%, 16F – 0.6%) serotypes. Nontypable strains with the highest proportion (77.3%) among the immunized adult population were predominant in the structure; in the unvaccinated children, this rate was 53.5%. Among the typable strains in children, 70.0% belonged to the vaccine ones, and most frequently the study identified 19F and 23F serotypes, while serotypes 3 and 12F/A/B/44/46 dominated among the adults.Conclusion. The study of unimmunized pediatric and immunized adult populations of Sverdlovsk Region confirmed a trend toward an increase in the circulation of nontypable S. pneumoniae strains in the Russian Federation, which sets the agenda to improve the monitoring system and optimize molecular genetic techniques for identification of the pathogens and upgrade the present specific and nonspecific preventive remedies, including the current antimicrobial ones and locally­-produced vaccine.

Значимость вирусной нагрузки при оценке клинического и эпидемиологического статуса пациентов с COVID-19

Objective. To assess the clinical and epidemiological significance of the viral load over time in patients with varying degrees of severity of COVID-19. Patients and methods. The observation group is represented by 586 patients hospitalized at the Infectious Diseases Hospital No 1 of the Moscow Department of Health with a initially verified diagnosis of COVID-19 during the period 2020–2021. The article presents data on the assessment of the viral load level in patients with COVID-19. A representative sample of inpatients hospitalized during the first waves of the pandemic in 2020–2021 was analyzed. The dynamics of the infectious process was studied basing on the following indicators: detection of SARS-CoV-2 virus RNA by days of illness, determination of the threshold number of cycles in the PCR test (Ct), determination of SARS-CoV-2 viral load in genomic equivalents per 1 ml of sample (GE/ml). Results. Viral load in nasopharyngeal smears in the groups of observation was characterized by variability of values and high level of this indicator in patients with severe course of the disease: median Ctmax was 27.99 (2.83 × 105 GE/ml) exceeding similar indicators 1.97 times in patients with moderately severe course of the disease. Maintenance of stable viral load indicators in the course of the disease in the group of severely-ill patients by the end of the second week may indicate re-infection in the hospital. Conclusion. The results of the study can be used to substantiate the epidemiologic danger of a sick person in the course of the disease as a possible source of infection. Further studies are needed to assess the detection of SARS-CoV-2 virus viability in patients in the course of the disease as an indicator of infectious activity of the virus. Key words: SARS-CoV-2, clinical and epidemiologic markers, viral load, COVID-19

The antimicrobial activity of <i>Thymus marshallianus</i> extract against clinical cultures <i>S. aureus</i> and <i>C. albicans</i>

Aim to study the antimicrobial activity of the Thymus marshallianus extract against clinical cultures of microorganisms isolated from patients' material.
 Material and methods. The extract from the herb Th. marshallianus was obtained according to the method previously described and used, since the extraction obtained by this method presented the antimicrobial activity against standard cultures of microorganisms. The antimicrobial activity of extracts was studied in accordance with the Guidelines 4.2.1890-04 for 6 clinical isolates of Staphylococcus aureus and 5 clinical isolates of Candida albicans taken from patients' material (nasopharyngeal smear, blood, wound fluid) in the laboratory of the S. R. Mirovtsev of the Saratov State Medical University. The sectoral seeding was performed on dense nutrient media from test tubes with the colonies count, compared with the control seeding.
 Results. The antimicrobial activity of Th. marshallianus extract, obtained by the patented method, against clinical cultures of microorganisms was studied for the first time. A pronounced anti-staphylococcal effect of Th. marshallianus extract was established against clinical culture of S. aureus (the minimum inhibitory concentration ranged from 0.78 mg/ml to 0.39 mg/ml). The antimycotic activity was detected only for one culture of C. albicans (minimum inhibitory concentration 25.0 mg/ml).

A clinical case of the new coronavirus infection with cardiac involvement in a child

The ongoing pandemic of the new coronavirus infection allows us to discover new information concerning the clinical course of the disease. Despite the rarer registration and mild course of COVID-19 in children, we get new data on more severe manifestations in the form of damage to various organs including cardiovascular system. SARS-CoV-2 can lead to myocarditis development, arrhythmia, heart failure, etc.According to an infectious diseases hospital in Omsk, heart changes were recorded in 5.8% of hospitalized children with COVID-19. The article presents a clinical case of the new coronavirus infection in a child of 15 years old who was on treatment in the infection diseases hospital of Budgetary Healthcare Institution of Omsk Oblast City Children's Clinical Hospital №3 of Omsk. The diagnosis was confirmed by examining nasopharyngeal smears for evidence of RNA SARS-CoV-2 by PCR. The course of infection in this patient is characterized by myocarditis development following medium severity disease without comorbid pathology.

Nachbefragung zur Qualitätssicherung der ELISA-Kohortenstudie zur COVID-19-Prävalenz: Die Sicht von Studienteilnehmerinnen und Studienteilnehmern – Was kommt gut an?

IntroductionWith the outbreak of the Corona pandemic, the LübEcker longitudinal study on infections with SARS-CoV-2 (ELISA study) was conducted in the Lübeck area to provide information on the prevalence, unreported cases and symptoms of COVID-19. The aim of the present study is to evaluate defined structure and process indictors of the study conduct of the ELISA study by subjects. MethodsAfter defining and operationalizing participant-oriented quality indicators, 3,710 participants were surveyed online via LimeSurvey. Indicators defined were access to the study, time requirements, reporting of findings, ratings of the study apps used, communication, study center, tolerability of sample collection, and willingness to re-participate. In addition, comments on push and pull factors of study participation could be made. The evaluation was both quantitative and qualitative. Results45% of the follow-up respondents (n=1,684) answered the questions on the defined structural and process indicators. In the quantitative part of the survey, tolerability of venous blood sampling was rated as significantly better than that of nasopharyngeal smears. 91% of the follow-up respondents welcomed the offer to view their findings in the personal results portal. Overall, the indicators were mostly rated positively. According to the qualitative data, the study participants found the win-win situation of the test opportunity to contribute to research, the local relevance of the study, the small incentives, and the low-threshold nature of the study registration to be positive aspects of the study. According to the quantitative data, participants suggested improving the usability of the digital applications in terms of more user-friendly identification solutions, reminder functions, announcements of software updates and avoidance of double entries. DiscussionThe defined structure and process indicators appear to be suitable for assessing the quality of study implementation from the subjects' point of view and indicate a good quality of study implementation under pandemic conditions. The lowest participation rate (75%) was measured at the fifth test time of strongly declining COVID-19 infections during the summer holidays in Schleswig-Holstein. Obviously, the benefit and meaningfulness of further study participation as well as competing factors were weighted differently by the subjects at this point. The follow-up survey suggests a variety of options for motivating participants to maintain a high level of participation. Possible limitations are that a non-response bias cannot be excluded for the follow-up survey and that no suitable standardised questionnaire was available. ConclusionThe present study provides recommendations for the planning of future cohort studies. It makes sense to continuously evaluate the motives for participation or non-participation and to explicitly consider them in the course of the study. Therefore, the definition of general quality indicators for the practical implementation of studies seems desirable. Positive experiences of the participants in connection with study participation are important, such as good time management, short response times, technical support offers and additional services such as a study homepage with frequently asked questions (FAQs), timely individual notifications of results and transparent, generally understandable information about study results during the study. Digital solutions are well received, but can still be improved for specific studies.

ПАТОЛОГІЯ ЛЕГЕНЬ ПРИ COVID-19: БАГАТОІНСТИТУЦІЙНА КОГОРТА РОЗТИНІВ ЛЬВОВА ТА ЛЬВІВСЬКОЇ ОБЛАСТІ

Introduction. In Ukraine 2,2 million coronavirus disease-19 (COVID-19) cases are reported now with 51,8 thousand deaths. Methods. A retrospective analysis of 1036 consecutive autopsies at COVID-19 in 2020 was conducted on the basis of the Lviv Regional Office for Autopsy and Lviv Railway Clinical Hospital. The diagnosis of COVID-19 was confirmed by clinical signs of viral pneumonia, nasopharyngeal smear analysis, and radiological changes. Statistical study was performed with IBM SPSS Statistics 24.0. Results. The majority (72.4%) were elderly (after 60 y.o., fig.2) males (54.1%) and females (45.9%), with age range from 19 to 93 years (mean age 66.9 ± 0.4 years). All examined patients had pneumonia, which was detected during a clinical examination with CT diagnosis and confirmed at autopsy. Acute phase of pneumonia was diagnosed in 18.5% of cases, proliferative phase – in 18.6%, fibrotic phase – in 5.9%. And in 53.5% of cases prevailed signs of progressive fibrosis associated with exudative lesions. COVID-19 was single original cause of death in 88.7% cases. In the lungs were identified: the typical virus-induced changes in epithelial cells of the trachea, bronchi, bronchioles and alveoli (100%, n=1036); different phases of diffuse alveolar damage in majority of cases (96.5%); manifestations of innate/adaptive immunity were described; pathological changes in microvasculature (large vessel thrombi were detected in 37.9%). Conclusion. Our study results prove the importance of pathological examination of tissues during autopsies to determine the pathophysiological mechanisms and underlying causes of death of patients with COVID-19.  

Immunocytochemical Assessment of ACE2 and TMPRSS2 in Nasopharyngeal Swabs from SARS-CoV-2 Patients.

SARS-CoV-2 is a positive-sense single-stranded RNA virus. It is enveloped by four structural proteins. The entry of the virus into the host cells is mediated by spike protein binding to the angiotensin converting enzyme 2 (ACE2) and proteolytic cleavage by transmembrane protease serine 2 (TMPRSS2). In this study, we analyzed the expression of the ACE2 receptor and TMPRSS2 in cases under investigation for SARS-CoV-2 infection. The study was carried out using the viral transport medium of consecutive nasopharyngeal swabs from 300 people under examination for SARS-CoV-2 infection. All samples underwent the SARS-CoV-2 transcriptase-mediated amplification assay (Procleix® SARS-CoV-2) to detect the virus. Immunocytochemistry was used in each sample to detect the presence of the SARS-CoV-2 nucleoprotein, the ACE2 receptor, and TMPRSS2. An immunocytochemical study with monoclonal antibody against SARS-CoV-2 viral nucleoprotein showed positivity in squamous cells. ACE2 were not detected in the squamous cells obtained from the nasopharyngeal samples. SARS-CoV-2 predominantly localizes to squamous cells in cytology samples of patients with positive transcriptase-mediated amplification SARS-CoV-2 assay results. The immunocytochemical negativity for ACE2 evidenced in the present study could be related to the cellular heterogeneity present in the nasopharyngeal smear samples and could be related to variations at the genomic level. Our results suggest that SARS-CoV-2 might be present in the nasopharyngeal region because viral cell junctions are weaker. This facilitates viral concentration, infective capacity and migration to specific organs, where SARS-CoV-2 infects target cells by binding to their receptors and then entering.

CORONAVIRUS DISEASECOVID-19: NEW POSSIBILITIES OF DIAGNOSIS

The аim of research – to determinine the diagnostic expediency of using lung condensateas a bioenvironment for the detection of SARS-CoV-2 virus in children with coronavirusdisease COVID-19.Materials and methods. The study was conducted on the basis of infectious diseasesdepartments of the Chernivtsi Children’s Regional Clinical Hospital during December2021 to January 2022. Verifi cation of coronavirus disease COVID-19 was performed bypolymerase chain reaction with reverse transcriptase (set COVID-19 Multiplex RT-PCRin real time regime from Labsystems Diagnostics Oy) with simultaneous detection of threemajor genes ORF1ab, nucleus (E) and envelope (E). The material for the study werenasopharyngeal swabs and pulmonary expiratory. Results. We examined 32 hospitalized children diagnosed with COVID-19 with a meanage of 10,43 ± 0,72 (min = 3, max = 17). The share of boys was 34,4%, girls – 64,6%(p = 0,05), which indicates the practical absence of diff erences in gender. Biomaterialcollection – nasopharyngeal swabs and pulmonary expiration were performed on 6,71± 0,58 (min = 2, max = 16) day of the disease. SARS-CoV-2 virus RNA was detected in46,8% of patients, which almost coincided with the PCR results of 40,62% (p> 0,05).Estimating viral load, the mean value of cycles for PCR of nasopharyngeal smear was30,86 ± 1,39, and for pulmonary expiration – 32,39 ± 1,26. Taking into account theaverage values, depending on the detected gene, it was found that the number of cyclesfor the smear gene E constituted 30,06 ± 1,37 (min = 19, max = 38), the N gene – 30,93 ±1,33 (min = 20, max = 38) for the ORF1ab gene 31,6 ± 1,48 (min = 20, max = 40). Thenumber of cycles for the condensate gene E is 32,6 ± 1,24 (min = 25, max = 38); geneN – 33,36 ± 1,09 (min = 28, max = 39), for ORF1ab – 34,08 ± 1,06 (min = 28, max = 39).The results of the correlation analysis of paraclinical examination of children hospitalizedfor coronavirus disease COVID-19 showed that the use of PCR smear test, comparedwith Ig M, increased the risk of infection with a chance ratio (OR) of 2,27 (95% CI1,26-4,08), relative risk (RR) 1,47 (95% CI 1,01-2,15), absolute risk (R) 0,20. Whenreceiving a positive test result, the post-test probability of a positive result increased12,8%, with a negative one – the result decreased 7,5%. Estimating viral load for geneE, OR = 2,8 (95% CI 1,58-4,98), RR = 1,66 (95% CI 1,22-2,28), R = 0,25, for genes N,ORF1ab OR = 3,2 (95% CI 1,79-5,71), RR = 1,77 (95% CI 1,29-2,44), R = 0,28.Conclusions. At comparative analysis of PCR, performed in diff erentbioenvironmentsof children, the obtainedresults are evidence of better specifi city in the detection of thepathogen when using a traditional smear of the nasopharyngeal mucosa compared withthe use of pulmonary expiratory. However, the study of exhaled condensate can be usedto reduce the isolation time of patients.

Etiology of community-acquired and hospital-acquired pneumonia associated with COVID-19

PurposeThe COVID-19 pandemic is accompanied by a high incidence of community-acquired pneumonia (CAP). Patients with a new coronavirus infection have an increased risk of developing hospital-acquired pneumonia. Aim: to study the etiological structure of CAP during the epidemic spread of COVID-19, to assess the risks of joining the pathogens of pneumonia associated with the provision of medical care.Methods & MaterialsBiological material from 1085 hospitalized patients with CAP was conducted from August 2020 - June 2021 in Rostov-on-Don (Russia). Verification of respiratory viruses including SARS-CoV-2 RNA was performed by polymerase chain reaction in nasopharyngeal smears. Bacteriological analysis of sputum was performed via classical methods, identification of isolated pathogens was carried out using time-of-flight mass spectrometry on an Autoflex (Bruker Daltonics) with BioTyper 3.0 software.ResultsCases of type 3 parainfluenza virus (7.8±0.9%), other types of coronaviruses (HKU-1, OC43, HL-63 and 229Е) (2.7±0.5%), respiratory syncytial virus (1.9±0.5%) were detected in patients with COVID-19. Fungi of the genus Candida (35.6±1.8%) and Staphylococcus aureus (9.1±1.1%) were prevailing in the microbiota structure. Should be noted that the number of Streptococcus pneumoniae cultures decreased from 5.5 % in August 2020 to 1.1 % in June 2021, possibly due to pneumococcal vaccination. Gramm-negative enterobacteria were presented predominantly by Klebsiella pneumoniae (3.5±0.7%), Escherichia coli (2.9±0.6%), and non-fermenting Gramm-negative bacteria – Pseudomonas aeruginosa (1.5±0.5%) and Acinetobacter baumannii (1.2±0.4%). In 30.6% of patients treated in the hospital there was a secondary infection probably associated with compromised immune system and the transmission of infection from the hospital environment. Secondary infection with Candida spp., non-fermenting Gramm-negative bacteria (A. baumannii, and P. aeruginosa) and K. pneumoniae, including those characterized by multiple drug-resistance, prevailed. The most frequently registered resistance to penicillins, cephalosporins of 3rd generation.ConclusionA feature of CAP in patients with laboratory-confirmed COVID-19 is a higher incidence of mixed infection of both viral and bacterial etiology. Patients with COVID-19 represent a high risk group for the development of mycotic lung lesions, possibly against the background of treatment with antibacterial drugs. There is a significant risk of the formation of nosocomial infections in patients.

Acute pulmonary embolism in COVID-19 pandemic: prevalence and intrahospital outcome: a single center experience

Abstract Funding Acknowledgements Type of funding sources: None. Purpose We want to evaluate clinical, laboratory profiles and intra-hospital outcome in patients with acute PE treated in intensive care unit in the period of COVID-19 pandemic. Methods This is a single center, retrospective cohort study of patients with confirmed acute PE admitted in Intensive Cardiac Care Unit of a tertiary level university hospital between January and December 2020. Detailed history, risk factors, laboratory parameters and treatment strategy based on patient risk were assessed. All patients underwent 2-dimensional echocardiography, lower limb venous Doppler and CT pulmonary angiography (CTPA). sPESI score and intra-hospital outcomes were evaluated in all patients. Nasopharyngeal smear and real-time reverse transcriptase–polymerase chain reaction (RT-PCR) assay was performed in order to confirm COVID-19 infection. Results We studied 47 patients with acute PE treated in our ICU, with mean age 58.6 ± 19.4 years. Eight patients (17%) had massive PE (central thrombus) and 39 (83%) had sub massive PE (subsegmental thrombus) confirmed by CTPA. Six patients (12,7%) had history of deep vein thrombosis (DVT), 3 patients (6,3%) had history of prior PE, 4 patients (8,5%) were operated within 3 months, 7 patients (14,8%) had history of malignancy, 24 patient’s had increased body weight and obesity (51%). Twelve patients (25,5%) were tested for COVID 19 with real-time reverse transcriptase–polymerase chain reaction (RT-PCR) assay, and 3 come positive (12.5%). Eight patients were high risk with shock (17%), intermediate high risk were 29 patients (61.7%) and intermediate low risk were 10 patients (21.3%). sPESI score was >1 in all 47 patients. Abnormal RV function with PAH was found in 32 patients (68%). Five high risk, unstable patients died within 72 hours of admission, resulting in an overall ICU mortality rate of 10,6% and 62.5% mortality rate in patients with cardiogenic shock. Patients with PE and COVID-19 had significantly higher D-dimer and hs-Troponin I levels comparing to the patients with patients negative for COVID-19. Multivariate logistic regression analysis showed thrombolytic therapy OR 2.145 (95% CI: 1.105−4,512), D-Dimers >4.500 ng/ml OR 1.893 (95% CI: 0.932–3.241), high risk PE OR 3.98 (95% CI: 1.396−5.641) and acute renal failure OR 2.421 (95% CI: 1.105−4.762) as independent mortality predictors. Eight patients have been treated with fibrinolysis (t-PA), and 39 patients with Heparin therapy. 40 survived patients were discharged with NOAC treatment (95,2%). Conclusions Pulmonary embolism cardiology clinic ICU admission in the period of COVID-19 pandemic decreased, with increase of PE severity, patients risk and mortality rate. Thrombolytic therapy, D-Dimers >4.500 ng/ml, high risk PE and acute renal failure were independent mortality predictors. Thrombolysis was successful treatment for high risk patients with low bleeding risk.

Оценка роли микробиоты носоглотки в формировании хронического лимфопролиферативного синдрома ЛОР-органов у детей младшего возраста

To assess the nasopharyngeal microbiota role in the development of chronic lymphoproliferative syndrome of ENT organs in young children, 40 children aged 2–3 years were examined. Cytological and cultural bacteriological studies of nasopharyngeal smears were carried out. Serological and molecular genetic analyzes of markers of herpesvirus infections (Epstein–Barr virus (EBV), cytomegalovirus (CMV), and human herpes virus type 6 (HHV-6)) in the blood, polymerase chain reaction (PCR), and immunofluorescence reaction (RIF) were performed with generic antiherpetic sera of the same name in scrapings of the pharyngeal tonsil. In the rhinocytogram, 57,14% of children had poor gram-positive cocci, characteristic of the normal state of the mucosa. In nasopharyngeal smears, the growth of microorganisms of opportunistic and saprophytic microbiota was not detected in a diagnostically significant amount in 19,44% of children; isolated growth of normal aerobic and/or facultative anaerobic microbiota was observed with the same frequency. Opportunistic microbiota was detected in 61,11% of cases, including associations of saprophytic microbiota and opportunistic microorganisms were detected in 27,78% of children. Most often, Staphylococcus aureus 54,55% was detected in children; known respiratory pathogens were found less frequently: Streptococcus pneumoniae 31,82%, Haemophilus influenzae 13,64%, Moraxella catarrhalis 13,64%. In the majority of patients, 77,27%, one type of pathobiont was identified. 100% infection with herpesvirus infections was established, including EBV 66,67%, CMV 56,41%, HHV-6 61,54%. Mixed infections dominated 69,23%, EBV infection prevailed among mono infections. The active stage of herpesvirus infection was established in 56,41% of children, of which 77,27% were mono infections, and 22,73% were mixed infections, among which 80% were EBV + HHV-6. Most frequently, there were detected the signs of active EBV infection 46,15%, HHV-6 reactivation was detected in 20,51% of cases, active CMV persistence was much less common 7,69%. The active stage of herpesvirus infections was confirmed by the study of brush-smears of the nasopharyngeal mucosa with immunofluorescence test and PCR. In general, the traditional semi-quantitative studies of cultures of bacterial colonies from samples of the pharyngeal tonsil biotope did not reveal a unified causative agent (pathogen) of chronic lymphoproliferative syndrome of ENT organs in young children.