Organisms causing secondary pneumonias in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test

Dhesi, Zaneeta; Enne, Virve I.; Brealey, David; Livermore, David M.; High, Juliet; Russell, Charlotte; Colles, Antony; Kandil, Hala; Mack, Damien; Page, Valérie; Parker, Robert; Roulston, Kerry; Singh, Suveer; Wey, Emmanuel; Swart, Ann Marie; Stirling, Susan; Barber, Julie; O’Grady, Justin; Gant, Vanya

doi:10.1101/2020.06.22.20131573

Cited by 29 publications

(34 citation statements)

References 13 publications

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“…9 This is reflected in a recent report from five UK intensive care units showing a predominance of Enterobacterales species, Staphylococcus aureus and Pseudomonal species typical of hospital-or ventilator-associated pneumonia occurring at a median of 14 days following admission. 25 We also observed that about one in ten in critical care were prescribed systemic antifungal agents and in half of these therapy was microbiology-directed. Antifungals were prescribed in combination with broad spectrum antibiotics and later in the critical care unit admission suggesting suspected nosocomial infection.…”

Section: Discussionmentioning

confidence: 94%

Survey of antibiotic and antifungal prescribing in patients with suspected and confirmed COVID-19 in Scottish hospitals

Seaton

Gibbons

Cooper

et al. 2020

Journal of Infection

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Background: Concern regarding bacterial co-infection complicating SARS-CoV-2 has created a challenge for antimicrobial stewardship. Following introduction of national antibiotic recommendations for suspected bacterial respiratory tract infection complicating COVID-19, a point prevalence survey of prescribing was conducted across acute hospitals in Scotland. Methods: Patients in designated COVID-19 units were included and demographic, clinical and antimicrobial data were collected from 15 hospitals on a single day between 20th and 30th April 2020. Comparisons were made between SARS-CoV-2 positive and negative patients and patients on non-critical care and critical care units. Factors associated with antibiotic prescribing in SARS-CoV-2 positive patients were examined using Univariable and multivariable regression analyses. Findings: There were 820 patients were included, 64.8% were SARS-CoV-2 positive and 14.9% were managed in critical care, and 22.1% of SARS-CoV-2 infections were considered probable or definite nosocomial infections. On the survey day, antibiotic prevalence was 45.0% and 73.9% were prescribed for suspected respiratory tract infection. Amoxicillin, doxycycline and co-amoxiclav accounted for over half of all antibiotics in non-critical care wards and meropenem, piperacillin-tazobactam and co-amoxiclav accounted for approximately half prescribed in critical care. Of all SARS-CoV-2 patients, 38.3% were prescribed antibiotics. In a multivariable logistic regression analysis, COPD/chronic lung disease and CRP ≥ 100 mg/l were associated with higher odds and probable or confirmed nosocomial COVID-19, diabetes and management on an elderly care ward had lower odds of an antibiotic prescription. Systemic antifungals were prescribed in 9.8% of critical care patients and commenced a median of 18 days after critical care admission. Interpretation: A relatively low prevalence of antibiotic prescribing in SARS-CoV-2 hospitalised patients and low proportion of broad spectrum antibiotics in non-critical care settings was observed potentially reflecting national antimicrobial stewardship initiatives. Broad spectrum antibiotic and antifungal prescribing in critical care units was observed indicating the importance of infection prevention and control and stewardship initiatives in this setting.

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Section: Discussionmentioning

confidence: 94%

Survey of antibiotic and antifungal prescribing in patients with suspected and confirmed COVID-19 in Scottish hospitals

Seaton

Gibbons

Cooper

et al. 2020

Journal of Infection

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“…The 2019/20 influenza season in the UK ended in late March [38]. Other UK cohorts recruited during the spring wave of COVID-19 (March - May 2020) similarly reported very little or no viral co-infection [25, 36].…”

Section: Discussionmentioning

confidence: 99%

Co-infection in critically ill patients with COVID-19: An observational cohort study from England

Baskaran

Lawrence

Lansbury

et al. 2020

Preprint

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Objective: To describe the incidence and nature of co-infection in critically ill adults with COVID-19 infection in England. Methods: A retrospective cohort study of adults with COVID-19 admitted to seven intensive care units (ICUs) in England up to 18 May 2020, was performed. Patients with completed ICU stays were included. The proportion and type of organisms were determined at <48 and >48 hours following hospital admission, corresponding to community and hospital-acquired co-infections. Results: Of 254 patients studied (median age 59 years (IQR 49-69); 64.6% male), 139 clinically significant organisms were identified from 83(32.7%) patients. Bacterial co-infections were identified within 48 hours of admission in 14(5.5%) patients; the commonest pathogens were Staphylococcus aureus (four patients) and Streptococcus pneumoniae (two patients). The proportion of pathogens detected increased with duration of ICU stay, consisting largely of Gram-negative bacteria, particularly Klebsiella pneumoniae and Escherichia coli. The co-infection rate >48 hours after admission was 27/1000 person-days (95% CI 21.3-34.1). Patients with co-infections were more likely to die in ICU (crude OR 1.78,95% CI 1.03-3.08, p=0.04) compared to those without co-infections. Conclusion: We found limited evidence for community-acquired bacterial co-infection in hospitalised adults with COVID-19, but a high rate of Gram-negative infection acquired during ICU stay.

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“…However, approved for use with BLS and SLS, BioFire PNplus allows for easy specimen testing for CAP [6,7] and meets IDSA/ATS recommendations [13] for non-invasive diagnostic testing as a preferred method for VAP and ERS guidelines to test distal quantitative specimens [16]. Additionally, studies that used BioFire PNplus panels in COVID-19 patients demonstrated not only improved diagnosis of bacterial coinfections but enhanced options for appropriate therapy [35,44,45]. Verroken et al demonstrated that BioFire PNplus Panel speeded up therapeutic changes in 46.9% of COVID-19 patients, five patients having antibiotics stopped and one third remained antibiotic free [35].…”

Section: Number and Type Of Microorganisms Reported By Soc Notmentioning

confidence: 99%

Multinational evaluation of the BioFire® FilmArray® Pneumonia plus Panel as compared to standard of care testing

Ginocchio

Garcia-Mondragon

Mauerhofer

et al. 2021

Eur J Clin Microbiol Infect Dis

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This study compared standard of care testing (SOC) to BioFire® FilmArray® Pneumonia plus Panel (PNplus). PNplus detects 15 bacteria with semiquantitative log bin values, 7 antibiotic resistance markers, three atypical bacteria (AB), and eight viral classes directly from bronchoalveolar lavage-like specimens (BLS) and sputum-like specimens (SLS). Fifty-two laboratories from 13 European countries and Israel tested 1234 BLS and 1242 SLS with PNplus and SOC. Detection rates and number of pathogens/samples were compared for PNplus pathogens. PNplus bin values and SOC quantities were compared. Three thousand two hundred sixty-two bacteria in PNplus were detected by PNplus and/or SOC. SOC detected 57.1% compared to 95.8% for PNplus (p ≤ 0.0001). PNplus semiquantitative bin values were less than SOC, equal to SOC, or greater than SOC in 5.1%, 25.4%, and 69.6% of results, respectively. PNplus bin values were on average ≥ 1 log than SOC values (58.5% 1–2 logs; 11.0% 3–4 logs). PNplus identified 98.2% of MRSA and SOC 55.6%. SOC detected 73/103 AB (70.9%) and 134/631 viruses (21.2%). PNplus detected 93/103 AB (90.3%) and 618/631 viruses (97.9%) (p ≤ 0.0001). PNplus and SOC mean number of pathogens/samples were 1.99 and 1.44, respectively. All gram-negative resistance markers were detected. PNplus and SOC results were fully or partially concordant for 49.1% and 26.4% of specimens, respectively. PNplus was highly sensitive and detected more potential pneumonia pathogens than SOC. Semiquantification may assist in understanding pathogen significance. As PNplus generates results in approximately 1 h, PNplus has potential to direct antimicrobial therapy in near real time and improve antimicrobial stewardship and patient outcomes.

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Organisms causing secondary pneumonias in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test

Cited by 29 publications

References 13 publications

Survey of antibiotic and antifungal prescribing in patients with suspected and confirmed COVID-19 in Scottish hospitals

Survey of antibiotic and antifungal prescribing in patients with suspected and confirmed COVID-19 in Scottish hospitals

Co-infection in critically ill patients with COVID-19: An observational cohort study from England

Multinational evaluation of the BioFire® FilmArray® Pneumonia plus Panel as compared to standard of care testing

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