Dynamic surveillance of fatal pneumonia pathogens during the COVID-19 pandemic and postpandemic period
Authors:   Khabarovsk Research Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Khabarovsk, Russian Federation, Bondarenko A.P. , Trotsenko O.E. ,   Khabarovsk Research Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Khabarovsk, Russian Federation, Ogienko O.N. ,   Khabarovsk Research Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Khabarovsk, Russian Federation, Golubeva A.O. ,   Khabarovsk Research Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Khabarovsk, Russian Federation, Pshenichcnaya N.Yu. ,   Central Research Institute of Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russian Federation, Zapregalova L.A. ,   A.M.Voyno-Yasenetsky City Clinical Hospital, Khabarovsk, Russian Federation, Bobrovnikova M.Yu. ,   A.M.Voyno-Yasenetsky City Clinical Hospital, Khabarovsk, Russian Federation, Bazykina E.A. ,   Khabarovsk Research Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Khabarovsk, Russian Federation, Yarovenko V.V. ,   Khabarovsk anti-plague station of Rospotrebnadzor, Khabarovsk, Russian Federation, Bakhmetyeva S.V. ,   Khabarovsk anti-plague station of Rospotrebnadzor, Khabarovsk, Russian Federation, Dobrova S.A. ,   Khabarovsk anti-plague station of Rospotrebnadzor, Khabarovsk, Russian Federation, Kovalsky A.G. ,   Khabarovsk anti-plague station of Rospotrebnadzor, Khabarovsk, Russian Federation, Kurganova O.P. ,   Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Department for the Amur Region, Blagoveshchensk, Russian Federation, Natykan Yu.A. ,   Khabarovsk Research Institute of Epidemiology and Microbiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Khabarovsk, Russian Federation,   Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing Department for the Amur Region, Blagoveshchensk, Russian Federation,   Center of Hygiene and Epidemiology in the Amur Region, Blagoveshchensk, Russian Federation
Published: September 2024

Objective. To determine the trend of circulating pneumonia pathogens and their levels of antimicrobial resistance (AMR) during the pandemic of new coronavirus infection (NCI) and in the early postpandemic period with terminal episodes. Materials and Methods. The peculiarity of this study is the study material – autopsy specimens (lung tissue) obtained from fatal pneumonia cases. Surveillance was conducted from April 2021 to June 2022 in different phases of the epidemic process of the pandemic with the inclusion of periods of decline and wave rises in incidence (I, II, III periods, a total of 435 samples were studied). Postpandemic IV period was considered from August 2022 to July 2023 – 111 samples were examined. A total of 608 bacterial isolates were isolated during postmortem examination of samples from 546 pneumonia patients. Bacteriological examination was performed by the classical method, identification of pathogens and determination of their sensitivity to germicide was performed using a Vitek 2 Compact 30 bacterial analyzer. Results. During four periods of observation there was a change in the rank position of the leading and other pathogens of pneumonia by the frequency of detection from patients: Klebsiella pneumoniae (42.7; 61.1; 62.9; 40.5%), Acinetobacter baumannii (34.0; 20.4; 12.9; 18.9%), Staphylococcus aureus (9.7; 4.3; 12.9; 20.7%), Escherichia coli (14.6; 1.8; 7.6; 11.7%), Proteus mirabilis (2.9; 0.62; 3.5; 8.1%), Pseudomonas aeruginosa (6.8; 11.1; 6.5; 7.2%), and Stenotrophomonas maltophilia (0.8; 0.6; 1.6; 2.7%). The group Enterobacter aerogenes, Serratia marcescens was isolated in 3.9; 1.9; 4.1; 3.6% of cases. Achromobacter xylosoxidans was detected in periods 2 and 4 (1.2; 0.9%). The proportion of carbapenem-resistant strains (carbR) decreased in the postpandemic period for K. pneumoniae (70.5; 81.8; 76.6; 51.1%) and remained high in all periods of observation for A. baumannii (100; 97.0; 100; 95.2%) and P. aeruginosa (57.1;77.8;72.7;100%). S. aureus was represented mainly by germicide-sensitive variants during all periods of observation. Circulation of E. coli in the postpandemic period was due to BLRS producers (63.8% of cases). All 100% of P. mirabilis strains were resistant to cefepime (IV generation cephalosporin). Thus, during the first year of follow-up in the postpandemic period, there was a decrease in the share of K. pneumoniae in the etiology of fatal pneumonias with simultaneous decrease in the level of carb R-variants against the background of decreased pressure of intensive germicide use. The frequency of isolation of fungi of the genus Candida from autopsy specimens was 8.2%. The species structure was represented by 6 species of fungi: C. albicans – 33.3%, C. glabrata – 28.6%, C. krusei – 14.3%, C. tropicalis – 14.3%, C. lusitaniae – 4.8%, C. kefyr – 4.8%. Antimycotic-resistant strains were detected among the fungi C. glabrata and C. krusei, which is probably the reason for the increased proportion of these species in autopsy specimens. Conclusion. Bacteriological study of autopsy material in fatal pneumonias is a significant direction of microbiological monitoring, which allows obtaining important information about the bacterial flora that accompanies the patient's death, about the change of priority pathogens, the extent of their resistance, and the duration of circulation of resistant forms. Key words: pneumonia, fatal outcome, COVID-19 pandemic, postpandemic period, autopsy specimens, bacterial pathogens, circulation trends