TY - JOUR

T1 - The changing spectrum of microbial aetiology of respiratory tract infections in hospitalized patients before and during the COVID-19 pandemic

AU - Serigstad, Sondre

AU - Markussen, Dagfinn L.

AU - Ritz, Christian

AU - Ebbesen, Marit H.

AU - Knoop, Siri T.

AU - Kommedal, Øyvind

AU - Heggelund, Lars

AU - Ulvestad, Elling

AU - Bjørneklett, Rune O.

AU - Grewal, Harleen M.S.

AU - Clark, Tristan W.

AU - Faurholt-Jepsen, Daniel

AU - Ravn, Pernille

AU - van Werkhoven, Cornelis H.

AU - the CAPNOR study group

N1 - Funding Information: We gratefully acknowledge the CAPNOR study group, the study nurses, the staff at the Emergency Care Clinic, and staff at the Department of Microbiology. Last, we thank all the enrolled patients. CAPNOR study group: Rune O. Bjørneklett (Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway), Tristan W. Clark (School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK), Marit H. Ebbesen (Department of Microbiology, Haukeland University Hospital, Bergen, Norway), Daniel Faurholt-Jepsen (Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway; Department of Infectious Diseases, Rigshospitalet, Denmark), Harleen M. S. Grewal (Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway), Lars Heggelund (Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway; Department of Internal Medicine, Vestre Viken Hospital Trust, Drammen, Norway), Siri T. Knoop (Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway), Øyvind Kommedal (Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway), Dagfinn L. Markussen (Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway), Pernille Ravn (Department of Internal Medicine, Section for Infectious Diseases, Herlev and Gentofte Hospital, Hellerup, Denmark), Christian Ritz (Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway; National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark), Sondre Serigstad (Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway), Elling Ulvestad (Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, University of Bergen, Bergen, Norway; Department of Microbiology, Haukeland University Hospital, Bergen, Norway), Cornelis H. van Werkhoven (Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands). Funding Information: Open access funding provided by University of Bergen. This work was supported financially by the Research Council of Norway (NORCAP; 288718), the Trond Mohn Foundation (COVID-19 CAPNOR; TMS2020TMT07 and RESPNOR; BFS2019TMT06), the University of Bergen and Haukeland University Hospital. The funders had no role in designing the study and no role in collection, analysis and interpretation of data, nor in writing the manuscript.

PY - 2022

Y1 - 2022

N2 - Background: The COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP). Methods: This study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann–Whitney’s U test was used to analyse continuous variables. Fisher’s exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values. Results: Admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort. Conclusion: During the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2.

AB - Background: The COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP). Methods: This study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann–Whitney’s U test was used to analyse continuous variables. Fisher’s exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values. Results: Admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort. Conclusion: During the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2.

KW - Community acquired pneumonia

KW - COVID-19

KW - Epidemiology

KW - FilmArray pneumonia panel

KW - Molecular testing

KW - Respiratory tract infections

KW - SARS-CoV-2

U2 - 10.1186/s12879-022-07732-5

DO - 10.1186/s12879-022-07732-5

M3 - Journal article

C2 - 36180842

AN - SCOPUS:85139411221

VL - 22

JO - B M C Infectious Diseases

JF - B M C Infectious Diseases

SN - 1471-2334

IS - 1

M1 - 763

ER -