Rapid detection of health-care-associated bloodstream infection in critical care using multipathogen real-time polymerase chain reaction technology: a diagnostic accuracy study and systematic review

Abstract

BackgroundThere is growing interest in the potential utility of real-time polymerase chain reaction (PCR) in diagnosing bloodstream infection by detecting pathogen deoxyribonucleic acid (DNA) in blood samples within a few hours. SeptiFast (Roche Diagnostics GmBH, Mannheim, Germany) is a multipathogen probe-based system targeting ribosomal DNA sequences of bacteria and fungi. It detects and identifies the commonest pathogens causing bloodstream infection. As background to this study, we report a systematic review of Phase III diagnostic accuracy studies of SeptiFast, which reveals uncertainty about its likely clinical utility based on widespread evidence of deficiencies in study design and reporting with a high risk of bias.ObjectiveDetermine the accuracy of SeptiFast real-time PCR for the detection of health-care-associated bloodstream infection, against standard microbiological culture.DesignProspective multicentre Phase III clinical diagnostic accuracy study using the standards for the reporting of diagnostic accuracy studies criteria.SettingCritical care departments within NHS hospitals in the north-west of England.ParticipantsAdult patients requiring blood culture (BC) when developing new signs of systemic inflammation.Main outcome measuresSeptiFast real-time PCR results at species/genus level compared with microbiological culture in association with independent adjudication of infection. Metrics of diagnostic accuracy were derived including sensitivity, specificity, likelihood ratios and predictive values, with their 95% confidence intervals (CIs). Latent class analysis was used to explore the diagnostic performance of culture as a reference standard.ResultsOf 1006 new patient episodes of systemic inflammation in 853 patients, 922 (92%) met the inclusion criteria and provided sufficient information for analysis. Index test assay failure occurred on 69 (7%) occasions. Adult patients had been exposed to a median of 8 days (interquartile range 4–16 days) of hospital care, had high levels of organ support activities and recent antibiotic exposure. SeptiFast real-time PCR, when compared with culture-proven bloodstream infection at species/genus level, had better specificity (85.8%, 95% CI 83.3% to 88.1%) than sensitivity (50%, 95% CI 39.1% to 60.8%). When compared with pooled diagnostic metrics derived from our systematic review, our clinical study revealed lower test accuracy of SeptiFast real-time PCR, mainly as a result of low diagnostic sensitivity. There was a low prevalence of BC-proven pathogens in these patients (9.2%, 95% CI 7.4% to 11.2%) such that the post-test probabilities of both a positive (26.3%, 95% CI 19.8% to 33.7%) and a negative SeptiFast test (5.6%, 95% CI 4.1% to 7.4%) indicate the potential limitations of this technology in the diagnosis of bloodstream infection. However, latent class analysis indicates that BC has a low sensitivity, questioning its relevance as a reference test in this setting. Using this analysis approach, the sensitivity of the SeptiFast test was low but also appeared significantly better than BC. Blood samples identified as positive by either culture or SeptiFast real-time PCR were associated with a high probability (> 95%) of infection, indicating higher diagnostic rule-in utility than was apparent using conventional analyses of diagnostic accuracy.ConclusionSeptiFast real-time PCR on blood samples may have rapid rule-in utility for the diagnosis of health-care-associated bloodstream infection but the lack of sensitivity is a significant limiting factor. Innovations aimed at improved diagnostic sensitivity of real-time PCR in this setting are urgently required. Future work recommendations include technology developments to improve the efficiency of pathogen DNA extraction and the capacity to detect a much broader range of pathogens and drug resistance genes and the application of new statistical approaches able to more reliably assess test performance in situation where the reference standard (e.g. blood culture in the setting of high antimicrobial use) is prone to error.Study registrationThe systematic review is registered as PROSPERO CRD42011001289.FundingThe National Institute for Health Research Health Technology Assessment programme. Professor Daniel McAuley and Professor Gavin D Perkins contributed to the systematic review through their funded roles as codirectors of the Intensive Care Foundation (UK).

Early Diagnosis of Sepsis: Is an Integrated Omics Approach the Way Forward?

“…Infections can also be identified by PCR analysis of bacterial 16S ribosomal RNA (rRNA) that has been developed for species/genus level identification of bacterial infections. While the time-to-results are considerably faster than blood cultures, the results are only moderately better and are best used as a rule-in diagnostic [63, 64]. A rule-out test that relies on the host response takes into account that the host immune response can effectively control minor infections, while also differentiating between systemic inflammatory responses caused by infectious versus non-infectious etiologies.…”

Clinical Significance of Molecular Diagnostic Tools for Bacterial Bloodstream Infections: A Systematic Review

“…Some reviewed publications reported on BC as a good technique in diagnosis of bBSI but also presented its various disadvantages such as long turnaround time, easy contamination, and false negative and positive results [8, 13, 15–17, 19]. A total of 12 out of 18 reviewed papers explored the BC's performance and recommended different and improved molecular techniques to detect BSIs with a particular emphasis on bacteria.…”

“…Warhurst et al, 2015, reported that SeptiFast real-time PCR is more rapid in the detection of BSIs though it has some limitations that must be handled over time [19]; this was emphasized by Wang et al, 2014, who mentioned that sepsis is one of the main causes of mortality due to therapy delay [22]. To overcome this challenge, molecular technique has to be used for rapid screening of bacteria.…”

New Molecular Diagnostic Approaches to Bacterial Infections and Antibacterial Resistance

“…A large clinical trial involving more than 1,000 patients suspected of having bloodstream infection was recently conducted in England. 48 SeptiFast had better specificity (86%) than sensitivity (50%). This platform demonstrates a “rapid rule-in utility” for the diagnosis of bloodstream infection but low sensitivity is a significantly limiting factor.…”

“…47 Furthermore, we are now witnessing the introduction of culture independent testing directly on biological samples and next-generation sequencing (NGS), permitting the analysis of complex, polymicrobial specimens in ways never imagined two decades ago. 48 …”