Salmonellosis in the COVID-19 Pandemic Era

Relevance. In 2020, there was a unique situation caused by the COVID-19 pandemic and the anti-epidemic measures introduced in this regard. To date, the question of how these methods affect the spread of other infectious diseases, including salmonellosis, has not been studied. Target. To assess the impact of anti-epidemic measures during the COVID-19 pandemic on the epidemic process of salmonella infection in St. Petersburg. Materials and methods. Reporting form No. 2 of Rospotrebnadzor «Information on infectious and parasitic diseases» for 2018–2020 and data from the State report «On the state of sanitary and epidemiological well-being of the population in St. Petersburg in 2019», «On the state of sanitary and epidemiological well-being of the population in St. Petersburg in 2020». Data processing was carried out using Microsoft Excel (Microsoft®, USA), Statistica for Windows (StatSoft®, USA) with the determination of the level of significance (p), the calculation of confidence intervals (95% CI) was carried out in the EpiTools application. Results. The incidence of salmonellosis in 2020 was significantly lower than in the previous 2 years 28.86 (95% CI 27.45–30.34) per 100 ths population, and in 2019 and 2018 – 49.8 (95% CI 47.9–51.7) and 39.21 (95% CI 37.6– 40.9) per 100 ths of the population respectively. When analyzing the incidence of salmonellosis in 1995 to 2020, it was revealed that in 2020 the incidence rate was the lowest over the past 25 years and below the multi-year average (37 per 100 ths population) in St. Petersburg by 22%. A decrease in the incidence of salmonellosis was observed in 2020 and in the Russian Federation as a whole compared to 2019, the indicator increased 1.6 times and amounted to 14.71 per 100 ths rubles. population (multi-year average – 29.1). In 2020, there was a change in the intra-annual incidence of salmonellosis. While the peak incidence of salmonellosis persisted in the autumn period (September–October), in 2020 there was no characteristic rise in the spring period, as was observed in 2018 and 2019, which may be due to the spring lockdown (p = 0.03). The decrease in the incidence of salmonellosis was due to a significant decrease in the incidence among adults, while this was not observed in other age groups. In 2018–2020, diseases in the population were caused by 61 serotypes of Salmonella: in 2018 – 33, in 2019 – 32, and in 2020 – 39 serotypes. During the pandemic, the decrease in the incidence of salmonellosis was due to the decrease in the incidence caused by S. Enteritis, which in 2020 amounted to 19.91 (95% CI 18.73-21.14) per 100 thousand population, while in 2019 – 39, 01 (95% CI 37.4–40.7) and in 2018 – 31.24 (95% CI 29.8–32.8) per 100 ths population. At the same time, the decrease in the incidence rate was a decrease in the incidence rate among adults, while in other age groups no changes in the incidence rate were observed. The incidence due to other salmonella serotypes did not change. There were no significant differences in the incidence of salmonellosis by sex and age. Conclusion. The measures introduced during the pandemic in 2020 led to a decrease in the incidence of salmonellosis in St. Petersburg by reducing the incidence of salmonellosis caused by S. Enteritidis among adults. © Lubimova AV, et al.

Clinical and Epidemiological Characteristics of COVID-19 in Persons Living with HIV Complicated by Tuberculosis

Relevance. At present, three infections – HIV infection, tuberculosis, and COVID-19-are spreading simultaneously in the world. Of great practical importance is the assessment of clinical and epidemiological features of COVID-19 in HIV-infected patients with tuberculosis, COVID-19. Aim. To study the risk of COVID-19 disease and identify clinical and epidemiological features in and population of patients with HIV infection complicated by tuberculosis in comparison with patients with HIV infection and the population without these diseases. Materials and methods. Since 13.03.2020 by 31.12.2021 in the Kemerovo Region-Kuzbass, a continuous prospective analytical epidemiological study of the case-control type was performed. Of those with COVID-19, two observation groups were formed: group I (HIV +), group II (HIV/TB) and comparison group III (persons without either HIV or tuberculosis). All patients underwent: determination of SARS-CoV-2 RNA, standard examination methods in accordance with the temporary methodological recommendations «Prevention, diagnosis and treatment of a new coronavirus infection (COVID-19)», relevant at the time of treatment. Results. The incidence of COVID-19 among patients with HIV infection complicated by tuberculosis exceeded the incidence of COVID-19 among HIV-infected by 14%. There were no gender differences between patients I (HIV +) and II (HIV/TB) groups. In the comparison group, the incidence of COVID-19 was 1.26 times higher in women compared to men. COVID-19 disease in patients with co-infection (HIV/TB) was predominantly mild. Viral pneumonia developed 1.86 times less often, oxygenotherapy was required only in 18.75% of cases, which is 2.5 times lower than in group I (HIV +) and 2.47 times less than in the comparison group (III). In labeled pairs, clinical symptoms of COVID-19 in all groups occurred with the same frequency. Metabolic disorders were evident in all groups. Co-infected patients (HIV/TB) had higher levels of D-dimer, ESR, total bilirubin. Conclusion. Active tuberculosis in HIV-infected people is a factor that increases the risk of COVID-19 disease without affecting the severity of the infectious process. © 2023, Numikom. All rights reserved.

Infectious Morbidity in Closed Long-Term Care Facilities in the «Pre-COVID Stage»

Relevance. Elderly people have become the fastest growing segment of the global population over the past few decades. The number of people over the working age in Russia, and with them citizens living in closed long-term care facilities (CLTFS), is growing. Residents of these organizations belong to the risk group, and CLTFS have a number of characteristics that turn these institutions into a unique environment for the spread of infectious diseases. Aims. To analyze the CLTFS residents infectious morbidity in the "pre-covid stage" (according to literature sources). A scientific review of research in Russian and English using information portals and platforms has been carried out eLIBRARY.ru, Web of Science, PubMed, Google Academy and Scopus for the period 1981-2022. The search was carried out by keywords. Information about the most frequent infectious diseases affecting residents of closed long-term care institutions was the criterion for inclusion in the sample of publications. Out of 16171 initially identified articles, 61 publications were selected after initial analysis. Conclusions. According to various estimates, the leading infectious diseases in CLTFS were: acute respiratory infections, pneumonia, urinary tract infections, skin and mucous infections, acute intestinal infections. The article describes pathogens and their prevalence in CLTFS including pathogens with multiple drug resistance (MDR), describes the resistance of bacteria to antimicrobial drugs formation problem in these organizations, as well as development of certain diseases risk factors. Studies conducted in various CLTFS in Europe, Russia, the USA, and Asia indicate a high prevalence of infectious diseases among their residents, high colonization of residents with antimicrobial-resistant pathogens, as well as the infection transmission probability from the CLTFS and its spread to other long-term care institutions and medical and preventive organizations. © 2023, Numikom. All rights reserved.

Characteristic of Viral and Bacterial Contaminationin Objects of the Infection Hospital Environment of the Hospital for the Treatment of Patients with COVID-19 During the Pandemic Period

Relevance. Due to the COVID-19 pandemic a infectious diseases hospitals nationwide network has been deployed to treat patients infected with SARS-CoV-2. The principles of their formation with a strict division into «infectious» and «clean» zones, despite the epidemiological justification, lead to the formation of a dynamic artificially created closed ecosystem. In such an ecosystem, on the one hand, patients who undergo a wide range of invasive and aggressive therapeutic and diagnostic manipulations, and medical personnel stay for a long time, on the other hand, pathogens of a viral and bacterial nature that can adapt to hospital conditions and form resistant strains circulate. As a result, high risks of contamination of environmental objects of hospitals and patients themselves are created, which can lead to the development of exogenous nosocomial infection. Aims. To study the features of viral and bacterial contamination of objects in the hospital environment of the infectious diseases hospital for the treatment of patients infected with SARS-CoV-2 during the COVID-19 pandemic. Materials and methods. A study was conducted on 343 samples from the external environment of the infectious diseases hospital for COVID-19 patients' treatment during its planned work. Sample collection was performed during three days (Tuesday, Thursday, Sunday) at 20 unified sampling points: in the area where patients general hospital area as well as from the outer surface of personal protective equipment for medical personnel (overalls, gloves). The study used epidemiological (descriptive-evaluative and analytical), molecular genetic (SARS-CoV-2 PCR-RT, sequencing), bacteriological (isolation, cultivation and MALDI-TOF identification of bacterial cultures) methods. Statistical significance of differences was assessed by Fisher's point test (φ). Differences were considered significant at p≤0.05. Statistical data processing was carried out using the Microsoft Office 2010 application package, the online resource https://medstatistic. ru/, ST Statistica 10. Results. The study demonstrated a high level of viral and bacterial contamination of environmental objects in the intensive care unit of the infectious diseases hospital for COVID-19 patients treatment – 11.1%, incl. objects of the general hospital environment – 9.3% (doctor's workplace – 16.7%);patient location area – 13.9% (electric pump – 27.8%, mechanical ventilation, manipulation table – 16.7% each);the outer surface of personnel gloves – 21.1–38.9%;the outer surface of protective overalls for personnel – 44.4–50.0%. SARS-CoV-2 isolated from the objects of the external environment of the hospital belonged to the genetic variant B.1.617.1 DELTA, which corresponded to the epidemiological situation at sampling collection period. The opportunistic microflora structure was dominated by Enterococcus faecalis (38.1%), Klebsiella pneumoniaе (21.4%) and Escherichia coli (16.7%), which demonstrated a high level of resistance (to 3 or more groups of antibiotics). Conclusion. Initially, the main sources of the infectious diseases hospital environmental objects contamination with SARS-CoV-2 are most likely patients. Further contamination of the infectious diseases hospital environmental objects with viruses and opportunistic microflora occurs with the medical personnel direct participation. The current situation requires a review of approaches to the rules for disinfection, the PPE use and employees hands antiseptic treatment in infectious diseases hospital during the COVID-19 pandemic, as well as the length of staff work period length. © 2022, Numikom. All rights reserved.

Evaluation of the Effectiveness of Immunization Saint-Petersburg Population against COVID-19

Relevance. Vaccination is being replaced by the primary and most effective means of protecting the world's population from a new coronavirus infection. Aim. Evaluation of the effectiveness of COVID-19 immunization in Saint-Petersburg. Materials and methods: We retrospectively studied the epidemiological data on the cumulative incidence of COVID-19 in St. Petersburg among adults vaccinated (1,558,030 people) and unvaccinated (2,863,050 people) for period from December 01, 2020 to November 30, 2021 on 12.01.2021. We analyzed the data presented in the Federal Register of Persons with COVID-19 and the Federal Register of Those Vaccinated against COVID-19. Results. The risk of COVID-19 infection among vaccinated is statistically significantly lower than among unvaccinated RR = 0.11 (95% CI 0.109–0.110;p < 0.001). Infected COVID-19 Vaccinated patients were less likely to need for emergency care/hospitalization RR = 0.30 (95% CI 0.29–0.30;p < 0.001). Also among the vaccinated mortality was lower RR = 0.35 (95% CI 0.33–0.37;p < 0.001). Conclusion: We have established reliable preventive effectiveness of the use of domestic vaccines by reducing morbidity, the frequency of development of forms of the disease requiring inpatient treatment;reducing mortality among vaccinated and, accordingly, reducing the burden on the healthcare system of St. Petersburg. © 2022, Numikom. All rights reserved.

Features of the Circulation of ARVI Pathogens During of Emergence and Widespread of SARS-CoV-2 in the 2018–2021

Relevance. The long-term leadership of ARVI pathogens determines their significance in the damage caused to both health and the economy of the country. Aim. To identify the features of the structure of ARVI during the emergence and widespread spread of SARS-CoV-2. Materials and methods. The article uses methods used in epidemiological surveillance of acute respiratory viral infections. Results and discussion. The results of the diagnostic available ARVI pathogens monitoring during epidemic seasons 2018-2021 are presented. The tendency of greater engagement of aged group 15 y.o. and older in epidemic process by morbidity and hospitalization due to SARI was shown. 49 818 nasal swabs from patients with influenza infection, 36 044 – with ARVI and 59 062 – with SARS-CoV-2 were tested. The top three in the structure of ARVI were INF, HEV-D and HRSV (in the 2018–2019 season);INF, SARS-CoV-2 and HEV-D (2019–2020);SARS-CoV-2, HEV-D and HPIV/HCoV (2020–2021). The activity of viral pathogens also differed: for HPIV, HAdV, HEV-D, HMPV, a decrease in activity was noted during the appearance of SARS-CoV-2 (2019–2020) and some of its growth in the following season;in relation to HRSV and INF-a decrease in activity during the last two seasons, and for INF – extremely low activity in the 2020-2021 season;the activity of seasonal HCoV even increased slightly. The data of genetic analyses of SARS-CoV-2 positive samples showed the heterogeneity of its population with a representative of variants (Alfa, Delta) as well as endemic for Russia and Moscow variants only. The recommended composition of influenza virus vaccines for use in the 2021–2022 northern hemisphere influenza season and in the 2022 southern hemisphere influenza season are presented due to their drift changeability. Conclusions. SARS-CoV-2 was influenced by the activity of ARVI pathogens with the almost complete displacement of influenza viruses from the circulation in the period 2020–2021. © Burtseva EI, et al.

Experience in the Development and Use of a New Test System for Screening and Diagnosis of Acute Respiratory Infections

Relevance. Acute respiratory infections (ARI) are a serious health problem not only because of the high frequency of their occurrence, but also because of the economic damage they cause both in the form of direct costs (the cost of diagnosis and treatment) and indirect costs (disability, reduced labor productivity, etc.). Pregnant women and children under 5 years of age are included in the group of patients with risk factors for complications of influenza and other ARI, therefore, an analysis of the etiological structure of ARI and influenza in obstetric hospitals is an urgent task. In recent years, there has been an urgent need to create a national complex diagnostic test system based on molecular genetic methods for detecting infectious agents that cause ARI. Aims. The aim of the study is to analyze the etiological structure of ARI and influenza in patients with clinical symptoms and to develop and implement a new test system for rapid screening and diagnosis of infections that cause ARI. Materials & methods. When studying the etiological structure of ARI and influenza, cultural studies of the nasal and pharyngeal mucosa were carried out, followed by identification of microorganisms using MALDI-TOF mass spectrometry and molecular genetic study (real-time PCR) using an experimental test panel containing primers that allow detecting the following viruses: influenza A, B viruses, parainfluenza viruses of the 1st, 2nd, 3rd and 4th types, coronaviruses OS43, HKU1, NL63, E229, respiratory syncytial virus, metapneumovirus, rhinovirus and adenovirus, as well as bacterial pathogens of ARI: Haemophilus influenzae, Streptococcus pneumoniae, Streptococcus pyogenes, Moraxella catarrhalis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa. The test system was developed using the following methods: real-time PCR, a combination of reverse transcription and real-time PCR (RT-PCR) and the next generation sequencing (NGS) method. Results. The etiological structure of ARI and influenza was analyzed in patients with clinical manifestations (cough, tickling/sore throat/hyperemia of the mucous membrane of the palate and the back wall of the pharynx, shortness of breath/difficulty breathing, acute runny nose/nasal congestion). The species spectrum of bacterial and viral pathogens was revealed. A new test system based on PCR, real-time RT-PCR and NGS has been created for complex diagnostics of both viral and bacterial pathogens of ARI, consisting of three separate components: the main test system «ARI», which detects the main viral and bacterial pathogens of ARI, and two additional sets of reagents: «Oseltamivir resistance» and «Oseltamivir/ Zanamivir resistance». Conclusions. The new test system can be used to detect and differentiate nucleic acids of pathogens of ARI of humans. The test system seems to us promising for further use. As a result of the analysis of the etiological structure of acute respiratory infections and influenza, attention is drawn to a significantly smaller variety of identified pathogens in 2020 and a much more pronounced dominance of rhinovirus infection compared to our previous study in 2019. © 2022, Numikom. All rights reserved.

COVID-19 Outbreak at Sports Club: Conditions of Occurrence and Causes of the Spread of Infection

Relevance. The new coronavirus infection (COVID-19), which appeared in late 2019 in China, has spread to almost all countries of the world in just a few months. The explosive nature of its spread was accompanied by the formation of large epidemic foci in organizations of various profiles, including leisure and sports. Aims. To establish the conditions and causes of the spread of SARS-CoV-2 among the members of one of the sports clubs based on an in-depth epidemiological analysis. Materials and methods. To study the features of the spread of the SARS-CoV-2 virus in a sports organization, the following documents were used previously developed by the authors and successfully tested in practice: «Act of epidemiological investigation of group and outbreak morbidity of new coronavirus infection (COVID-19) at an enterprise/organization/institution» and «Individual card of a patient with a new coronavirus infection (COVID-19) at the enterprise / organization/institution». In the process of epidemiological investigation, in order to detect SARS-CoV-2 RNA in PCR, a laboratory examination of sports club participants (sick and contact) was conducted, followed by genome-wide sequencing of isolated SARS-CoV-2 viruses on the basis of the Laboratory of Molecular Virology of the A. A. Smorodintsev Influenza Research Institute, which performs these types of studies. Results. Within 17 days, 26 cases of COVID- 19 were registered among the sports team members and staff from the support group (coaching staff, medical staff, administrators), which was 74.3% of their actual number. The majority of patients (76.9%) had mild acute respiratory infection, two (7.7%) had no symptoms, and four (15.4%) had interstitial pneumonia. Of the clinical manifestations of the disease, the most frequent were weakness, fever, headache, muscle and joint pain, difficulty in nasal breathing and serous-mucous discharge from the nose, sore throat, cough, shortness of breath, anosmia and dyspeptic manifestations in the form of diarrhea, nausea or vomiting. The occurrence of the outbreak was the result of the introduction of infection from the opposing team at the tournament. The leading factors that contributed to the spread of COVID-19 among sports club members were the admission to games and training of athletes with acute respiratory infections, prolonged close contact between players during training and competitions, violations in the use of personal protective equipment, compliance with hygiene and hand antiseptics, disinfection measures in the premises of sports institutions and defects in the implementation of the regulations for the examination of teams for SARS-CoV-2 during tournaments. Conclusion. Based on the results of the study, data were obtained on the features of the spread of SARS-CoV-2 in sports organizations, which can be used in conducting preventive and anti-epidemic measures in sports and leisure institutions. © 2022, Numikom. All rights reserved.

Assessing of Humoral Immunity to SARS-COV-2 in Residents of Orenburg During the Epidemic Period

Relevance. The formation of humoral immunity is one of the most important manifestations of the protective mechanism against an infectious disease. The formation of antibodies with neutralizing activity is a key factor in preventing infection. Aims. Analysis of the esults of an ELISA study for the presence of IgM and IgG antibodies to the causative agent of a new coronavirus infection (COVID-19) in the population of the Central Orenburg region. Materials and methods. Immunoassay of blood serum for the presence of IgM and IgG antibodies using ELISA test by Vectro-Best (Novosibirsk, Russia). Results and discussion. The analysis revealed the presence of more than half of the cases of sero conversion among the examined individuals. The most surveyed was the group aged 21 to 65 years. The most typical humoral immune response to SARS-CoV-2 has been established, and the age-related characteristics of its formation have been determined. The dependence of the positivity coefficient on the age of the patients was revealed. Conclusions. According to the results of the study, the formed humoral (collective) immunity to the SARS-CoV-2 virus was registered in more than half of the studied sample. © Pankov AS et al.

Comparison of the First Three Waves of the COVID-19 Pandemic in Russia in 2020-21

Relevance. The ongoing COVID-19 pandemic in the world, which is characterized by a long undulating course, requires an in-depth study of the features of the epidemic process, including the influence of natural, climatic and social factors on it. Aim. Compare the intensity of three waves of the COVID-19 pandemic in Russia. To identify the features of the parameters of the COVID-19 pandemic in Russia in the age groups of the population and in the federal districts. Materials and methods. Data from the computer database of the Influenza Research Institute and the Stop-coronavirus website were used. Results. The construction of the weekly dynamics of COVID-19 made it possible to clarify the start, peak and end dates of each wave in megacities, federal districts and among the population of the Russia. Conclusion. In the dynamics of the incidence of COVID-19 in the population of the Russian Federation from March 2020 to September 2021, three waves were detected: I spring-summer wave, II autumn-winter, III spring -summer. All three waves started in megacities, first in Moscow, and spread across federal districts. The rise of morbidity in Russia as a whole began and peaked in the autumn-winter wave later than in the spring-summer waves (immediately after the megacities). The total duration of the epidemic and the period of its development in the autumn-winter wave were longer than in the spring-summer waves. Morbidity, hospitalization and mortality depended on age, and in all three waves were higher among people over 65 years of age. The intensity of COVID-19 in the first spring-summer wave was the lowest. The II autumn-winter wave was the most intense in terms of morbidity, hospitalization rate and mortality in all age groups. The III spring-summer wave in terms of morbidity and hospitalization was less intensive, than the II autumn-winter wave, but there were no significant differences between the mortality rates in the II and III wave hospitalization and fatal outcomes were revealed. © Karpova LS, et al.