Clinical evaluation of commercial nucleic acid amplification tests in patients with suspected sepsis

Abstract

Background: Sepsis is a serious medical condition requiring timely administered, appropriate antibiotic therapy. Blood culture is regarded as the gold standard for aetiological diagnosis of sepsis, but it suffers from low sensitivity and long turnaround time. Thus, nucleic acid amplification tests (NAATs) have emerged to shorten the time to identification of causative microbes. The aim of the present study was to evaluate the clinical utility in everyday practice in the emergency department of two commercial NAATs in patients suspected with sepsis.

Methods: During a six-week period, blood samples were collected consecutively from all adult patients admitted to the general emergency department for suspicion of a community-onset sepsis and treated with intravenous antibiotics. Along with conventional blood cultures, multiplex PCR (Magicplex™) was performed on whole blood specimens whereas portions from blood culture bottles were used for analysis by microarray-based assay (Prove-it™). The aetiological significance of identified organisms was determined by two infectious disease physicians based on clinical presentation and expected pathogenicity.

Results: Among 382 episodes of suspected sepsis, clinically relevant microbes were detected by blood culture in 42 episodes (11%), by multiplex PCR in 37 episodes (9.7%), and by microarray in 32 episodes (8.4%). Although moderate agreement with blood culture (kappa 0.50), the multiplex PCR added diagnostic value by timely detection of 15 clinically relevant findings in blood culture-negative specimens. Results of the microarray corresponded very well to those of blood culture (kappa 0.90), but were available just marginally prior to blood culture results.

Conclusions: The use of NAATs on whole blood specimens in adjunct to current culture-based methods provides a clinical add-on value by allowing for detection of organisms missed by blood culture. However, the aetiological significance of findings detected by NAATs should be interpreted with caution as the high analytical sensitivity may add findings that do not necessarily corroborate with the clinical diagnosis.

Figure 1

Algorithm for deciding on clinical relevance of microbial findings in blood by blood culture [25] or NAAT. Other cultures were made from clinically relevant sites before administration of intravenous antibiotics. On suspicion of pneumonia or sepsis with unknown focus, a pulmonary X-ray was performed. Ultrasound, computed tomography scan, and magnetic resonance imaging were used when deemed necessary for diagnosing the site of infection. BC blood culture; NAAT nucleic acid amplification test.

Figure 2

Workflows and turnaround times for the detection methods used in the present study.

Figure 3

Microbial concordances between blood culture and NAATs. A Number of microbes detected by blood culture and/or multiplex PCR. B Number of microbes detected by blood culture and/or microarray. BC blood culture; CRF clinically relevant finding; CNRF clinically not relevant finding; OUS finding of unknown significance.