Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

Abstract

Background The diagnosis of infectious diseases has been hampered by reliance on microbial culture. Cultures take several days to return a result and organisms frequently fail to grow. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and mitigates against stewardship. Methods Single ICU observational cohort study with contemporaneous comparator group. We developed and implemented a TaqMan array card (TAC) covering 52 respiratory pathogens in ventilated patients undergoing bronchoscopic investigation for suspected pneumonia. The time to result was compared against conventional culture, and sensitivity compared to conventional microbiology and metagenomic sequencing. We observed the clinician decisions in response to array results, comparing antibiotic free days (AFD) between the study cohort and comparator group. Findings 95 patients were enrolled with 71 forming the comparator group. TAC returned results 61 hours (IQR 42-90) faster than culture. The test had an overall sensitivity of 93% (95% CI 88-97%) compared to a combined standard of conventional culture and metagenomic sequencing, with 100% sensitivity for most individual organisms. In 54% of cases the TAC results altered clinical management, with 62% of changes leading to de-escalation, 30% to an increase in spectrum, and investigations for alternative diagnoses in 9%. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). Interpretation Implementation of a customised syndromic diagnostic for pneumonia led to faster results, with high sensitivity and measurable impact on clinical decision making. Funding Addenbrookes Charitable Trust, Wellcome Trust and Cambridge NIHR BRC

Ventilator-associated pneumonia in critically ill patients with COVID-19

“…Any significant growth with a CFU of ≥ 10 4 /mL (on BAL) or ≥ 10 5 /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.…”

“…We performed conventional microbiological culture on all lower respiratory tract samples. Bronchoalveolar lavage (BAL) was also analysed using a multi-pathogen TaqMan array card (TAC) we have developed and reported previously [16]. In a sub-set of BALs we assessed the composition of the bacterial lung microbiome in bronchoalveolar lavage (BAL) by 16S sequencing.…”

Secondary pneumonia in critically ill ventilated patients with COVID-19

“…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 [13]. Fifty microlitres of extracted nucleic acid was used in a 200 μl final reaction volume with TaqMan™ Fast Virus 1-step Master Mix (Thermo Fisher Scientific), and cards were run on the QuantStudio 7 Flex platform (Thermo Fisher Scientific) as per the manufacturer's instructions.…”

“…Finally, we wish to acknowledge our funders the NIHR BRC. In addition we would like to acknowledge the grant awarded by Addenbrooke's Charitable Trust for the initial study of the clinical utility of the TaqMan microarray [13]. .…”

“…In this study, we aimed to identify and compare the distribution of secondary infections and VAP in critically ill ventilated COVID-19 patients against ventilated non-SARS-CoV-2 infected patients. We performed conventional microbiology, multi-pathogen molecular testing using a TaqMan array card developed and validated previously [13], and assessed the composition of the bacterial lung microbiome in bronchoalveolar lavage (BAL) samples of COVID-19 positive and COVID-19 negative patients in the same hospital over a certain time period.…”