Ventilator-Associated Pneumonia in Critically Ill Patients With COVID-19

Mailis Maes; Ellen Higginson; Joana Pereira-Dias; Martin D. Curran; Surendra Parmar; Fahad Khokhar; Delphine Cuchet-Lourenco; Janine Lux; Sapna Sharma-Hajela; Benjamin Ravenhill; Islam Hamed; Laura Heales; Razeen Mahroof; Amelia Solderholm; Sally Forrest; Sushmita Sridhar; Nicholas M. Brown; Stephen Baker; Vilas Navapurkar; Gordon Dougan; Josfin Bartholdson Scott; Andrew Conway Morris

Disclosures

Crit Care. 2021;25(25) 

In This Article

Materials and Methods

Setting and Study Design

This study was performed in the liver/general adult ICU in Addenbrooke's Hospital, Cambridge, UK, and also included COVID-19 patients managed in the neurotrauma and dedicated COVID-19 ICUs of the hospital. Patients were reviewed at least twice daily by consultant intensive care physicians with investigation for VAP ordered by this clinician, and discussed at a daily microbiology-intensive care multi-disciplinary team/antimicrobial stewardship meeting. We had a regularly audited ventilator bundle in place, which consisted of sub-glottic suction endotracheal tubes, mandated twice daily oral hygiene with fluoride toothpaste, daily sedation holds and head of bed elevation. One to one nursing to patient ratios were maintained throughout the first wave of COVID-19, although at times this included nurses with limited critical care training as normal ICU capacity was exceded. Sessional use of personal protective equipment (full-length fluid impermeable gowns, FFP3 mask, gloves and hat) with apron and second glove change between patients was maintained from March 15th to July 31st. Patients ventilated for at least 48 h, from March 15th (date of our first COVID-19 admission) to August 30th were retrospectively reviewed for presence of VAP. VAP was defined using a modification of the European Centre for Disease Control definitions[17] for quantitative BAL culture (termed PN1) or quantitative endotracheal aspirate (ETA) or sputum culture (termed PN2) definitions of pneumonia (see Figure 1). The modifications were to use polymerase chain reaction (PCR) positivity by TAC for BAL fluid (details below) and to use a threshold of ≥ 105 Colony Forming Units (CFU)/ml for endotracheal aspirate in keeping with UK standards.[18] Low lung pathogenicity organisms (Enterococcus spp., Candida albicans, non-pneumococcal Streptococci and coagulase negative Staphylococci) were reported but not considered a component of VAP.[19]Herpesviridae (Herpes simplex, cytomegalovirus and Epstein-Barr virus) were reported but were considered to be reactivations and not considered a component of VAP.[20]

Figure 1.

Criteria used for the diagnosis of VAP.

We also looked for evidence of invasive pulmonary aspergillosis (IPA), as there are now several case reports of this developing in patients with COVID-19[11] and recent reports of its frequency in non-COVID VAP.[21] IPA was defined using the criteria set out in the report describing influenza associated pulmonary aspergillosis[22] modified to include diagnosis by PCR. The criteria were clinical evidence of pulmonary infection, radiological evidence of pulmonary infection and detection of aspergillus by BAL galactomannan, PCR positivity or culture positivity.

Diagnostics

Samples for routine microbiology were processed according to the UK Standards for Microbiology Investigations.[18] Any significant growth with a CFU of ≥ 104/mL (on BAL) or ≥ 105/mL ETA was identified by MALDI-ToF mass spectrometry. Our lab also routinely runs a multipathogen TaqMan array on bronchoalveolar lavage samples,[16] the details of this are noted below.

TaqMan Multi-pathogen Array

Custom designed TaqMan Array Cards (TAC; Thermo Fisher Scientific) targeting 52 different common respiratory pathogens, were used to test for secondary infections as previously described.[16] Detection of a clear exponential amplification curve with a Cycles to Threshold (CT) value ≤ 32 for any single gene target was reported as a positive result for the relevant pathogen. We have previously demonstrated that CT value of ≤ 32 corresponded to growth ≥ 104/CFU/ml, hence the use of this threshold to define VAP.[16] Details of the procedures for extraction of nucleic acids for TAC, SARS-CoV-2 qPCR and 16S DNA nanopore sequencing are contained in the supplemental methods.

Statistical Analysis

The primary analysis was time to development of first VAP, censored for extubation or death, with comparison by univariable Cox proportional hazards model. Secondary analysis of VAP as an incidence density (cases per 1000 ventilator days) compared with Mid-P exact test.

Risk factors for VAP were compared using a Cox proportional hazards model, with variables rejected if their p value was > 0.05 on univariable analysis, statistically significant variables entered the final model. Analyses were conducted using SPSS (v25 IBM, Armonk, NY).

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