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ARTICLE

Bringing Culture-Independent Diagnostic Tests for Bloodstream Infections Into Rational Patient Management

JUN 06, 2019 | CORNELIUS J. CLANCY, MD, AND M. HONG NGUYEN, MD
Blood cultures remain the gold standard for diagnosing bacterial and Candida bloodstream infections (BSIs), but they are limited by slow turnaround and suboptimal sensitivity.1,2 Data from some but not all retrospective studies suggest that rapid initiation of active antimicrobial therapy correlates with reduced mortality among patients with bacterial or Candida BSIs.3-8 Although such findings have not been validated in prospective studies,5 the limitations of blood cultures and quality standards for sepsis and septic shock provide a rationale for aggressive empiric broad-spectrum antimicrobial therapy.5,9 These practices may promote unnecessary antimicrobial usage, drug toxicity, and emergence of resistance.5,10,11
 
Culture-independent diagnostic tests (CIDTs) that detect pathogens and antimicrobial resistance genes within clinical samples are transforming clinical practice.2,12 Syndromic CIDT panels for respiratory specimens, stool, and cerebrospinal fluid facilitate rapid identification or exclusion of infections due to particular organisms and antimicrobial initiation or de-escalation strategies.12 Likewise, commercial molecular tests of positive blood cultures for pathogen or resistance determinant identification are valuable patient care and stewardship tools.12-14 CIDTs of whole blood samples from patients with suspected BSIs have not gained widespread acceptance, in part because costs are high and clinicians are unsure how to incorporate testing into rational management paradigms.12,15 This paper reviews the performance of blood cultures and direct-from-whole-blood CIDTs for bacterial and Candida BSIs and provides a conceptual framework for using CIDTs in the clinic. 

PERFORMANCE OF BLOOD CULTURES AND CIDTS 

Blood culture sensitivity for detecting bacteremia is ~73%, 90%, and 98% if 1, 2 and 3 sets of aerobic and anaerobic bottles, respectively, are collected in the absence of antimicrobial treatment.16 Such performance is contingent upon collecting ≥20 mL of blood in each culture set. Smaller volumes, as often collected in hospitalized patients, increase false negativity.2 Blood cultures may require several days for bacteria to achieve detectable concentrations and additional time for species identification and resistance testing.2 Blood cultures are ~50% sensitive for diagnosing invasive candidiasis.1 Moreover, blood cultures become positive late in the course of invasive candidiasis, and incubation times prior to positivity are typically longer than those for detecting bacteria.1 Antimicrobial treatment reduces sensitivity for bacteria and Candida by ~50%,17-20 which is notable because 28% to 63% of blood cultures are collected from patients who are receiving antimicrobial agents.2
 
Several direct-from-whole-blood CIDTs couple nucleic acid amplification with novel technologies for target detection, including Iridica, SeptiFast, SepsiTest, Magicplex, and T2Direct (T2Bacteria, T2Candida) assays.2 T2Direct is the only FDA-cleared system.17,21,22 Assay characteristics and performance are summarized in the Table2,17,21,26,36,37. Interpretation of performance is complicated by study heterogeneity and limitations of blood cultures as gold standard. CIDTs require ≤5 mL of blood and provide results within 4 to 10 hours. In general, DNA amplification-based technologies are more sensitive than blood cultures in patients receiving antimicrobials.17,23-25 

We will focus on SeptiFast and T2Direct as examples of broad- and narrow-spectrum platforms, respectively.17,21,22,26 Concepts presented here can be applied to other tests. 

CIDTS AS BAYESIAN DIAGNOSTICS 

CIDTs assign a probability of BSI due to a given pathogen.27-29 Positive and negative predictive values (PPVs, NPVs) are determined by sensitivity and specificity of the test and the patient’s likelihood of BSI. Anticipated PPVs and NPVs in different types of patients can be calculated for pathogens targeted by SeptiFast (sensitivity/ specificity: 75%/90%), T2Bacteria (85%/95%), and T2Candida (90%/98%; Table 2). Tests are unlikely to be useful if performed every time a blood culture is collected,30 because false positivity exceeds true positivity, and excellent NPVs provide only marginal value over already low pretest likelihoods. 

In patients presenting to the hospital with fever or those with sepsis in the absence of septic shock, anticipated SeptiFast and T2Bacteria PPVs for targeted bacteria are each ~50% to 75%. SeptiFast offers an advantage of detecting ~85% to 90% of bacteria and fungi that cause BSIs, whereas T2Bacteria detects 5 bacteria that account for ~50% of BSIs.26,31-33 A potential disadvantage of broad-spectrum panels is that some targets are uncommon causes of BSI and therefore more likely to generate false-positive results. Although T2Bacteria NPVs are excellent for targeted bacteria, they are inferior to SeptiFast NPVs in excluding BSIs due to any bacteria. Candida are typically rare causes of BSI in these populations,15,27-29 and T2Candida PPVs and NPVs are unlikely to be useful in most cases. Anticipated T2Candida PPVs may approach 67%, and NPVs are 99.7% among septic patients with risk factors for candidemia in whom a causative bacterium is not identified. T2Candida detects species that account for >95% of candidemia at most centers.17,21 

The likelihood of bacterial or Candida BSI increases in septic shock, and anticipated PPVs of each test are ≥70%. However, SeptiFast and T2Bacteria NPVs are just 78% and 62%, respectively, for excluding BSIs in the setting of septic shock; T2Candida NPV remains excellent (99.5%). 

INCORPORATING CIDTS INTO CLINICAL AND STEWARDSHIP PRACTICES 

Surviving Sepsis guidelines endorse empiric broad-spectrum antibiotic therapy within 1 hour of triage for suspected sepsis and septic shock and rapid de-escalation based on susceptibility of causative organisms or if infection is excluded.9 Other experts propose more nuanced, case-by-case approaches, in which empiric antibiotics are administered immediately for suspected septic shock, but clinical observation and diagnostic testing may be undertaken prior to treatment decisions in at least some patients with suspected sepsis in the absence of shock.5,10,11 

In patients with possible sepsis in whom treatment decisions have been deferred pending workup, positive SeptiFast or T2Bacteria results may shorten the time to antibiotic treatment compared with waiting for positive blood cultures. If blood or other cultures are negative and an alternative, noninfectious diagnosis is not established, there is a good chance based on predictive values that a positive CIDT has identified a BSI that would have been missed otherwise. In such cases, continuing antibiotic treatment against the CIDT-identified pathogen is reasonable. Detection of resistance genes by SeptiFast may guide early selection of active antibiotics. T2Bacteria does not include resistance genes, but the panel is directed against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter species) that are often resistant to first-line antibiotics.22,34 In high-risk patients, such as those colonized by a resistant pathogen included in the panel, a positive T2Bacteria result may justify use of an alternative agent. 

If SeptiFast or T2Bacteria results are negative and a patient with suspected sepsis is stable, clinicians may decide to withhold antimicrobials pending blood and other culture results. This strategy is reasonable because empiric treatment has not proved superior to culture-directed treatment of BSIs or suspected sepsis, and ~50% of suspected sepsis is ultimately ascribed to noninfectious etiologies.5,10,11 If antimicrobials have been administered, combined negative CIDT and culture results may offer an argument for de-escalation. Approaches to using CIDTs similar to those described for possible sepsis also may be useful for managing febrile patients in the emergency department. 

In patients with presumed septic shock, clinicians will not wait for CIDT results before initiating broad-spectrum antibiotics (often in combination). In these patients, SeptiFast and T2Bacteria may have value if antibiotics are administered before blood cultures or whole blood samples are collected. Positive CIDT results may help in streamlining empiric antibiotic regimens. T2Candida is likely to be useful in septic shock (and perhaps in sepsis with risk factors for candidemia),35 since empiric antifungals are not recommended routinely.9 T2Candida PPVs and NPVs would justify initiating and withholding (or discontinuing) antifungal therapy, respectively. Sensitivity and specificity of SeptiFast are lower than T2Candida for Candida species,17,21,26 but the former test still may have value in patients with septic shock who are at risk of candidemia. 

CONCLUSIONS 

We propose a conceptual framework for thinking about how to incorporate CIDTs for BSIs into rational patient management and antimicrobial stewardship strategies. Similar exercises can be undertaken for other populations at risk of BSIs, such as patients with neutropenic fever or transplant recipients with sepsis. CIDT-based management paradigms will require validation in clinical trials. An important question is whether shorter turnaround times and identification of more potential pathogens and resistance determinants using direct-from-whole-blood CIDTs can lead to improved patient outcomes compared with those obtained with molecular testing of positive blood cultures. 

Clancy is chief of infectious diseases at the VA Pittsburgh Healthcare System and director of the XDR Pathogen Laboratory at the University of Pittsburgh. His research lab is funded by the Department of Veterans Affairs and National Institutes of Health. 

Nguyen is director of the Antimicrobial Stewardship and Transplant Infectious Diseases programs at the University of Pittsburgh Medical Center. Her translational and basic science research lab is funded by the National Institutes of Health and other sources. 

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