Objective: comparative study of the etiological structure of community-acquired pneumonia in SARSCoV-2 “+”and SARS-CoV-2 “-“ patients who sought help from medical organizations in the Rostov Region.Materials and methods. Biological material from 508 patients diagnosed with community-acquired pneumonia who were on outpatient treatment or in hospitals in Rostov-on-Don was studied. Verification of respiratory viruses, including SARS-CoV-2 RNA, as well as M. pneumoniae, C. pneumoniae, and L. pneumophila was performed by polymerase chain reaction in nasopharyngeal smears. Bacteriological analysis of sputum was carried out using differential diagnostic media, identification of isolated pathogens was carried out using time-of-flight mass spectrometry on Autoflex (Bruker Daltonics) with BioTyper 3.0 software.Results and discussion. During the spread of a new coronavirus infection in the Rostov Region, the main etiological agent of community-acquired pneumonia is the new SARS-CoV-2 coronavirus. Specific character of pneumonia in patients with laboratory-confirmed COVID-19 is a higher incidence of mixed infection of both viral and bacterial etiology. Against the background of detection of a new coronavirus infection in patients with pneumonia, cases of detection of other types of coronaviruses have been registered (HKU-1,OC43, HL-63 and 229Е). The most common etiological agent of bacterial pneumonia in patients was Streptococcus spp., both in patients with COVID-19-associated pneumonia and in patients who tested negative for SARS-CoV-2. Coronavirus patients represent a high risk group for the development of mycotic lung lesions.
Aim. Analysis of epidemic manifestations of natural-foci infections (NFI), clarification of spectrum of their causative agents, determination of epizootic activity of natural foci in the Crimea Federal District (KFD). Materials and methods. Epizootologic examination of 10 administrative districts of KDF was carried out. 291 pools (2705 specimens) of ixodes ticks and 283 samples of organs of small mammals were studied by PCR method for the presence of DNA/RNA of causative agents of a number of NFI. Results. Morbidity by NFI in KFD was registered by 6 nosologies: Lyme borreliosis, Marseilles fever, leptospirosis, tularemia, intestine yersiniosis and tick-borne viral encephalitis, wherein, transmissive infections made up 91.6%. Circulation of causative agents of Crimea hemorrhagic fever, Q fever, group of tick-borne spotted fever, Lyme borreliosis, human granulocytic anaplasmosis, human monocytic ehrlichiosis, hemorrhagic fever with renal syndrome, West Nile fever, tularemia and leptospirosis was established. Conclusion. Due to activity of natural foci of NFI further monitoring of epidemiologic and epizootologic manifestations of these infections in the Crimea, including using genetic methods of analysis, is necessary for ensuring sanitary-epidemiologic welfare of KFD population.
Федеральная служба по надзору в сфере защиты прав потребителей и благополучия человека, Москва, Российская федерация; 2 ФКУЗ «Ставропольский научно-исследовательский противочумный институт», Ставрополь, Российская Федерация; 3 ФБУЗ «Центр гигиены и эпидемиологии в Республике Крым и городе федерального значения Севастополе», Симферополь, Российская Федерация Территория Крымского полуострова является эндемичной по многим природно-очаговым инфекциям. В работе представлены результаты эпизоотологического обследования 8 административных районов Крымского федерального округа (КФО). Осуществлен учет численности мелких млекопитающих и иксодовых клещей, определен их видовой состав, проведен отбор проб полевого материала и лабораторные исследования на наличие возбудителей бактериальных и вирусных инфекций. Установлено, что доминирующим видом клещей в сборах весной является H. marginatum, доминирующим видом мелких млекопитающих -мышь домовая. В сборах осенью преобладают H. punctata и полевка обыкновенная. Результаты лабораторного исследования полевого материала свидетельствуют о циркуляции на территории КФО возбудителей лихорадки Ку, клещевых пятнистых лихорадок, иксодового клещевого боррелиоза, гранулацитарного анаплазмоза человека, моноцитарного эрлихиоза человека, геморрагической лихорадки с почечным синдромом и лептоспироза.
Q fever poses a problem, both in the Russian Federation and abroad. Thereat, a new base normative document, sanitary-epidemiological regulations on coxiellosis prevention, has been developed and approved in the Russian Federation. For the first time ever in the world history, a regulated surveillance of community-acquired pneumonias, which will help to improve diagnostics of this pathology, has been introduced in our country. Quality of Q fever control directly depends on the laboratory facilities, qualification of the personnel, and coordination of interagency cooperation. All these factors provide for the prompt assessment of the situation, in-time anti-epidemic measures, and forecasting of the events, which ensures the biological security of Russian Federation.
Introduction: Hospital-acquired bacterial superinfections in COVID-19 patients are one of the main reasons of a severer course of the disease, a higher risk of adverse outcomes, and, consequently, a longer hospital stay. Much attention is, therefore, paid to the study of genetic markers enabling identification of clonal relationships between different isolates of the causative agents of bacterial co-infections, which, in their turn, help distinguish between hospital- and community-acquired cases of infectious diseases. Objective: To study the genetic diversity and clonal relationships of A. baumannii and P. aeruginosa isolated from patients with a novel coronavirus disease (COVID-19) in Rostov-on-Don. Materials and methods: We tested biological specimens from 217 in- and outpatients with community-acquired pneumonia in the city of Rostov-on-Don. Whole-genome sequencing of A. baumannii and P. aeruginosa strains was performed using a MiSeq sequencer (Illumina, USA). SNP markers were selected using proprietary software written in Java and Python. Cluster analysis and dendrogram construction were performed using the author's software using the UPGMA method. The MEGA 5 software was used to build the dendrogram. Results: We established the spectrum of bacteria causing the development of secondary infection associated with COVID-19. Results of the whole-genome sequencing of 10 pneumonia pathogens isolated from patients with the novel coronavirus disease revealed clonality of individual strains. The nosocomial origin of two isolates of P. aeruginosa and two of A. baumannii was demonstrated and confirmed by the analysis of their plasmid composition. Secondary bacterial infection in COVID-19 patients may be attributed to the pathological development of the dominant microflora of the upper respiratory tract mucosa, which provides normal biocenosis in healthy people, or non-compliance with basic principles of hospital hygiene and infection control precautions. Conclusion: The research helped determine the etiological structure of pneumonia in patients with COVID-19. Whole-genome sequencing and the following bioinformatic analysis revealed the nosocomial origin of a number of strains of P. aeruginosa and A. baumanii.
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