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

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Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Organisms causing secondary pneumonias in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test
Creator	Gant, Vanya Parker, Robert Wey, Emmanuel Martin, Daniel Barber, Julie Brealey, David Colles, Antony Dhesi, Zaneeta High, Juliet Kandil, Hala Livermore, David Mack, Damien O'grady, Justin Page, Valerie Roulston, Kerry Russell, Charlotte Singh, Suveer Stirling, Susan Swart, Ann
Source	MedRxiv
abstract	ABSTRACT Introduction. Several viral respiratory infections - notably influenza - are associated with secondary bacterial infection and additional pathology. The extent to which this applies for COVID-19 is unknown. Accordingly, we aimed to define the bacteria causing secondary pneumonias in COVID-19 ICU patients using the FilmArray Pneumonia Panel, and to determine this tests potential in COVID-19 management. Methods. COVID-19 ICU patients with clinically-suspected secondary infection at 5 UK hospitals were tested with the FilmArray at point of care. We collected patient demographic data and compared FilmArray results with routine culture. Results. We report results of 110 FilmArray tests on 94 patients (16 had 2 tests): 69 patients (73%) were male, the median age was 59 yrs; 92 were ventilated. Median hospital stay before testing was 14 days (range 1-38). Fifty-nine (54%) tests were positive, with 141 bacteria detected. Most were Enterobacterales (n=55, including Klebsiella spp. [n= 35]) or Staphylococcus aureus (n=13), as is typical of hospital and ventilator pneumonia. Community pathogens, including Haemophilus influenzae (n=8) and Streptococcus pneumoniae (n=1), were rarer. FilmArray detected one additional virus (Rhinovirus/Enterovirus) and no atypical bacteria. Fewer samples (28 % vs. 54%) were positive by routine culture, and fewer species were reported per sample; Klebsiella species remained the most prevalent pathogens. Conclusion. FilmArray had a higher diagnostic yield than culture for ICU COVID-19 patients with suspected secondary pneumonias. The bacteria found mostly were Enterobacterales, S. aureus and P. aeruginosa, as in typical HAP/VAP, but with Klebsiella spp. more prominent. We found almost no viral co-infection. Turnaround from sample to results is around 1h 15 min compared with the usual 72h for culture, giving prescribers earlier data to inform antimicrobial decisions.
has issue date	2020-06-23(xsd:dateTime)
bibo:doi	10.1101/2020.06.22.20131573
has license	medrxiv
sha1sum (hex)	5bdda24bcbee5be96aa71ff382078d888504a5f9
schema:url	https://doi.org/10.1101/2020.06.22.20131573
resource representing a document's title	Organisms causing secondary pneumonias in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test
resource representing a document's body	covid:5bdda24bcbee5be96aa71ff382078d888504a5f9#body_text
is schema:about of	named entity 'Pneumonia' named entity 'COVID-19' named entity 'detected' named entity 'REDCap' named entity '16S rDNA' named entity 'SARS-CoV2' named entity 'ICU' named entity 'secondary' named entity 'secondary bacterial infection' named entity 'respiratory infections' named entity 'COVID-19' named entity 'ICUs' named entity 'COVID-19' named entity 'NIHR' named entity 'CTX-M' named entity 'COVID-19' named entity 'Klebsiella pneumoniae' named entity 'viral infections' named entity 'patient outcomes' named entity 'microbiology' named entity 'antibiotics' named entity 'COVID-19' named entity 'invasive ventilation' named entity 'COVID-19' named entity 'COVID-19' named entity 'penicillin allergy' named entity 'SARS-CoV2' named entity 'RCT' named entity 'COVID-19 pandemic' named entity 'secondary bacterial infection' named entity 'bioMérieux' named entity 'ventilator-associated pneumonia' named entity 'CC-BY-ND' named entity 'Citrobacter koseri' named entity 'ICUs' named entity 'S. pneumoniae' named entity 'anamnestic response' named entity 'ICUs' named entity 'pathogens' named entity 'Enterobacterales' named entity 'K. pneumoniae' named entity 'California' named entity 'medRxiv' named entity 'microbiology' named entity 'species group' named entity 'China' named entity 'Viral' named entity 'K. oxytoca' named entity 'peer review' named entity 'K. pneumoniae' named entity 'clinical indication' named entity 'March 2020' named entity 'mecA' named entity 'Antibiotic' named entity 'K. pneumoniae' named entity 'secondary bacterial infection' named entity 'community-acquired' named entity 'medRxiv' named entity 'COVID' named entity 'medRxiv' named entity 'CC-BY-ND' named entity 'VAP' named entity 'S. aureus' named entity 'hospital-acquired' named entity 'respiratory tract' named entity 'medRxiv' named entity 'ICU'

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