Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care

Abstract

Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis. Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs. Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge’s Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records. Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation. Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.

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

“…The selection of organisms targeted on the card was crucial, and informed by our previous experience where omission of key organisms of concern significantly limited the impact of a similar card. 17 Given the case mix of our unit, with a high proportion of immunosuppressed patients, we opted to include a number of low pathogenicity organisms, such a coagulase-negative staphylococci, enterococci and Candida albicans on the card. The detection of these organisms can be challenging to interpret, and indeed given the knowledge that many critically ill patients may be immunoparietic even if not classically immunosuppressed 6 their significance remains uncertain.…”

“…Organism coverage for the TAC was selected from the known microbial flora encountered in the ICU, supplemented by the literature concerning causative organisms reported in severe pneumonia 1,2,6, 10 17,18 The species covered by the card are shown in figure 1. The card also included primers to target the endogenous control RNase P and the internal control MS2.…”

“…Organism selection was informed by review the literature concerning organisms found in severe pneumonia 1,2,6,13,18,19 . Details of organism selection and the card layout are shown in supplemental section (Supplemental Figure S1).…”

“…16 However, previous experience had demonstrated that multiplex PCR with restricted coverage of common respiratory pathogens had a limited impact on clinical decision making. 17 In this study we set out to evaluate the clinical utility of a customised TAC based syndromic diagnostic for severe pneumonia.…”

“…Although TACs have shown promising performance relative to conventional microbiology, 17 our previous experience demonstrated that a TAC with restricted coverage of common respiratory pathogens had a limited impact on clinical decision making in critically ill patients. 18 We therefore set out to develop and implement a multi-pathogen array that would have broad applicability for severe pneumonia.…”