T2Bacteria magnetic resonance assay for the rapid detection of ESKAPEc pathogens directly in whole blood

Multidrug-resistant Gram-negative bacterial infections

Multidrug-resistant Gram-negative bacterial infections cause significant morbidity and mortality globally. These pathogens easily acquire antimicrobial resistance (AMR), further highlighting their clinical significance. Third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales (eg, Escherichia coli and Klebsiella spp), multidrug-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii are the most problematic and have been identified as priority pathogens. In response, several new diagnostic technologies aimed at rapidly detecting AMR have been developed, including biochemical, molecular, genomic, and proteomic techniques. The last decade has also seen the licensing of multiple antibiotics that have changed the treatment landscape for these challenging infections.

Examining the effect of direct-from-blood bacterial testing on antibiotic administration and clinical outcomes: a protocol and statistical analysis plan for a pragmatic randomised trial

INTRODUCTION

Patients with suspected bacterial infection frequently receive empiric, broad-spectrum antibiotics prior to pathogen identification due to the time required for bacteria to grow in culture. Direct-from-blood diagnostics identifying the presence or absence of bacteria and/or resistance genes from whole blood samples within hours of collection could enable earlier antibiotic optimisation for patients suspected to have bacterial infections. However, few randomised trials have evaluated the effect of using direct-from-blood bacterial testing on antibiotic administration and clinical outcomes. This manuscript describes the protocol and statistical analysis plan for a randomised trial designed to evaluate the effect of blood cultures plus direct-from-blood bacterial testing results compared with blood culture results alone on antibiotic administration and clinical outcomes.

METHODS AND ANALYSIS

We are conducting a prospective, single-centre, parallel-group, non-blinded, pragmatic, randomised trial. The trial will enrol 500 adult patients presenting to the emergency department at Vanderbilt University Medical Center with suspected bacterial infection who have been initiated on empiric intravenous vancomycin. Eligible patients are randomised 1:1 to receive Food and Drug Administration-approved direct-from-blood bacterial testing in addition to blood cultures or blood cultures alone. The primary outcome is the time to the last dose of intravenous vancomycin within 14 days of randomisation. The secondary outcome is the time to the last dose of systemic antipseudomonal beta-lactam antibiotics within 14 days of randomisation. Additional outcomes include highest stage of acute kidney injury, lowest platelet count and receipt of kidney replacement therapy within 14 days of randomisation, as well as hospital-free days, intensive care unit-free-days and all-cause, in-hospital mortality within 28 days of randomisation. Enrolment began on 13 December 2023.

ETHICS AND DISSEMINATION

The trial involves human participants and was approved by the Vanderbilt University Medical Center institutional review board with a waiver of informed consent (IRB#231229). Results will be submitted in a peer-reviewed journal and presented at scientific conferences.

TRIAL REGISTRATION NUMBER

NCT06069206.

Performance of T2Bacteria in relationship to blood cultures - a retrospective comparative study

PURPOSE

Blood culture (BC) is the gold standard for diagnosing blood stream infections (BSI) but is limited by long turnaround times (TAT) and low detection rate. The T2 Magnetic Resonance method (T2MR) offers a rapid, culture-independent alternative. The objective of this study was to compare the performance of the T2Bacteria assay to BCs in a real-world setting.

METHODS

Retrospective comparative study consisting of T2Bacteria samples and BCs sampled within 72 h from the T2Bacteria sample. The primary outcome was detections by BC and T2Bacteria, respectively. The secondary outcome was difference in TAT.

RESULTS

In total, 640 episodes were included, consisting of 640 T2Bacteria samples and 2,117 BCs. A median of three BCs was collected for each T2Bacteria sample. Overall positivity was 101 (15.8%) by either method. In 29 (28.7%) episodes, both T2Bacteria and BC were concordantly positive. In discordant episodes, 46/101 (45.5%) episodes were T2Bacteria positive/BC negative and 26/101 (25.7%) were T2Bacteria negative/BC positive (McNemar χ2, p < 0,05). In T2Bacteria positive/BC negative episodes, eight had growth of the same microorganism in a non-BC culture. Median (IQR) TAT for BC was 35 h and 30 min (25 h 50 min - 45 h 24 min), compared to 21 h and 3 min (17 h 6 min - 27 h 30 m) for T2Bacteria (p < 0.001), with longer delays for samplings occurring outside work hours.

CONCLUSIONS

The study highlights a high discordance between T2Bacteria and BC and suggests complementary roles of the methods in BSI diagnostics. Furthermore, it is crucial to improve TAT by reducing preanalytical delays.

Evaluation of T2 Magnetic Resonance (T2MR®) Technology for the Early Detection of ESKAPEc Pathogens in Septic Patients

Bloodstream infections (BSIs) and sepsis are a major cause of morbidity and mortality. Appropriate early antibiotic therapy is crucial for improving the survival of patients with sepsis and septic shock. T2 magnetic resonance (T2MR®) technology may enable fast and sensitive detection of ESKAPEc pathogens directly from whole-blood samples. We aimed to evaluate concordance between the T2Bacteria® Panel and standard blood culture and its impact on antibiotic therapy decisions. We conducted a single-centre retrospective study on patients with sepsis-induced hypotension or septic shock admitted to general, post-operative/neurosurgical, and cardiothoracic Intensive Care Units who were tested with the T2Bacteria® Panel from January 2021 to December 2022. Eighty-five consecutively admitted patients were included, for a total of 85 paired tests. A total of 48 ESKAPEc pathogens were identified by the T2Bacteria® Panel. The concordance rate between the T2Bacteria® Panel and blood cultures was 81% (69/85), with 20 concordant-positive and 49 concordant-negative cases. For the 25 microorganisms grown from accompanying blood cultures, blood pathogen coverage by the T2Bacteria® Panel was 88%. In this cohort of severely ill septic patients, the T2Bacteria® Panel was highly concordant and was able to detect more ESKAPEc pathogens, with a significantly shorter turn-around time compared to conventional blood cultures. The T2Bacteria® Panel also significantly impacted decisions on antibiotic therapy.

Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Time to receive effective therapy is a primary determinant of mortality in patients with sepsis. Blood culture is the reference standard for the microbiological diagnosis of bloodstream infections, despite its low sensitivity and prolonged time to receive a pathogen detection. In recent years, rapid tests for pathogen identification, antimicrobial susceptibility, and sepsis identification have emerged, both culture-based and culture-independent methods. This rapid narrative review presents currently commercially available approved diagnostic molecular technologies in bloodstream infections, including their clinical performance and impact on patient outcome, when available. Peer-reviewed publications relevant to the topic were searched through PubMed, and manufacturer websites of commercially available assays identified were also consulted as further sources of information. We have reviewed data about the following technologies for pathogen identification: fluorescence in situ hybridization with peptide nucleic acid probes (Accelerate PhenoTM), microarray-based assay (Verigene®), multiplex polymerase chain reaction (cobas® eplex, BioFire® FilmArray®, Molecular Mouse, Unyvero BCU SystemTM), matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (Rapid MBT Sepsityper®), T2 magnetic resonance (T2Bacteria Panel), and metagenomics-based assays (Karius©, DISQVER®, Day Zero Diagnostics). Technologies for antimicrobial susceptibility testing included the following: Alfed 60 ASTTM, VITEK® REVEALTM, dRASTTM, ASTar®, Fastinov®, QuickMIC®, ResistellTM, and LifeScale. Characteristics, microbiological performance, and issues of each method are described, as well as their clinical performance, when available.

Point-of-Care Method T2Bacteria®Panel Enables a More Sensitive and Rapid Diagnosis of Bacterial Blood Stream Infections and a Shorter Time until Targeted Therapy than Blood Culture

BACKGROUND

Rapid diagnosis and identification of pathogens are pivotal for appropriate therapy of blood stream infections. The T2Bacteria®Panel, a culture-independent assay for the detection of Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa in blood, was evaluated under real-world conditions as a point-of-care method including patients admitted to the internal medicine ward due to suspected blood stream infection.

METHODS

Patients were assigned to two groups (standard of care-SOC vs. T2). In the SOC group 2 × 2 blood culture samples were collected, in the T2 group the T2Bacteria®Panel was performed additionally for pathogen identification.

RESULTS

A total of 94 patients were included. Pathogens were detected in 19 of 50 patients (38%) in the T2 group compared to 16 of 44 patients (36.4%) in the SOC group. The median time until pathogen detection was significantly shorter in the T2 group (4.5 h vs. 60 h, p < 0.001), as well as the time until targeted therapy (antibiotic with the narrowest spectrum and maximal effectiveness) (6.4 h vs. 42.2 h, p = 0.043).

CONCLUSIONS

The implementation of the T2Bacteria®Panel for patients with sepsis leads to an earlier targeted antimicrobial therapy resulting in earlier sufficient treatment and decreased excessive usage of broad-spectrum antimicrobials.

Bacterial Infections in Intensive Care Units: Epidemiological and Microbiological Aspects

Intensive care units constitute a critical setting for the management of infections. The patients' fragilities and spread of multidrug-resistant microorganisms lead to relevant difficulties in the patients' care. Recent epidemiological surveys documented the Gram-negative bacteria supremacy among intensive care unit (ICU) infection aetiologies, accounting for numerous multidrug-resistant isolates. Regarding this specific setting, clinical microbiology support holds a crucial role in the definition of diagnostic algorithms. Eventually, the complete patient evaluation requires integrating local epidemiological knowledge into the best practice and the standardization of antimicrobial stewardship programs. Clinical laboratories usually receive respiratory tract and blood samples from ICU patients, which express a significant predisposition to severe infections. Therefore, conventional or rapid diagnostic workflows should be modified depending on patients' urgency and preliminary colonization data. Additionally, it is essential to complete each microbiological report with rapid phenotypic minimum inhibitory concentration (MIC) values and information about resistance markers. Microbiologists also help in the eventual integration of ultimate genome analysis techniques into complicated diagnostic workflows. Herein, we want to emphasize the role of the microbiologist in the decisional process of critical patient management.

From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification

One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences. Diagnostic sensitivity to the single molecular level is critical, particularly when identifying bloodstream infections. In cases of clinically manifest sepsis, the concentration of bacteria in the blood may reach as low as one bacterial cell/CFU per mL of blood. Therefore, it is crucial to achieve the highest level of sensitivity for accurate detection. In the present study, we have established a method that fills the analytical gap between low concentrations of molecular markers and the minimum requirements for molecular testing. For this purpose, a sample preparation of whole blood samples with a directly downstream pre-amplification was developed, which amplifies specific species and resistance markers in a multiplex procedure. When applying pre-amplification techniques, the sensitivity of the pathogen detection in whole blood samples was up to 100 times higher than in non-pre-amplified samples. The method was tested with blood samples that were spiked with several Gram-positive and Gram-negative bacterial pathogens. By applying this method to artificial spiked blood samples, it was possible to demonstrate a sensitivity of 1 colony-forming unit (CFU) per millilitre of blood for S. aureus and E. faecium. A detection limit of 28 and 383 CFU per ml of blood was achieved for E. coli and K. pneumoniae, respectively. If the sensitivity is also confirmed for real clinical blood samples from septic patients, the novel technique can be used for pathogen detection without cultivation, which might help to accelerate diagnostics and, thus, to decrease sepsis mortality rates.

Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology

The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.

Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis

rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the commercial DNA extraction and sequencing platform SepsiTest (ST). The goal was to analyze the clinical performance of ST with a focus on nongrowing pathogens and the impact on antibiotic therapy. A literature search used PubMed/Medline, Cochrane, Science Direct, and Google Scholar. Eligibility followed PRISMA-P criteria. Quality and risk of bias were assessed drawing on QUADAS-2 (quality assessment of diagnostic accuracy studies, revised) criteria. Meta-analyses were performed regarding accuracy metrics compared to standard references and the added value of ST in terms of extra found pathogens. We identified 25 studies on sepsis, infectious endocarditis, bacterial meningitis, joint infections, pyomyositis, and various diseases from routine diagnosis. Patients with suspected infections of purportedly sterile body sites originated from various hospital wards. The overall sensitivity (79%; 95% confidence interval [CI], 73 to 84%) and specificity (83%; 95% CI, 72 to 90%) were accompanied by large effect sizes. ST-related positivity was 32% (95% CI, 30 to 34%), which was significantly higher than the culture positivity (20%; 95% CI, 18 to 22%). The overall added value of ST was 14% (95% CI, 10 to 20%) for all samples. With 130 relevant taxa, ST uncovered high microbial richness. Four studies demonstrated changes of antibiotic treatment at 12% (95% CI, 9 to 15%) of all patients upon availability of ST results. ST appears to be an approach for the diagnosis of nongrowing pathogens. The potential clinical role of this agnostic molecular diagnostic tool is discussed regarding changes of antibiotic treatment in cases where culture stays negative.

Accuracy of T2 magnetic resonance assays as point-of-care methods in the intensive care unit

BACKGROUND

Novel molecular diagnostic methods are being evaluated in order to expedite pathogen identification in patients with bacteraemia.

AIMS

To evaluate the feasibility and diagnostic accuracy of the T2 magnetic resonance (T2MR) assays - T2 Bacteria (T2B) and T2 Resistance (T2R) - as point-of-care tests in the intensive care unit compared with blood-culture-based tests.

METHODS

Prospective cross-sectional study of consecutive patients with suspected bacteraemia. Diagnostic accuracy was evaluated using blood culture as the reference method.

FINDINGS

In total, 208 cases were included in the study. The mean time from sampling to report was lower for the T2MR assays compared with blood-culture-based methods (P<0.001). The rate of invalid reports was 6.73% for the T2B assay and 9.9% for the T2R assay. For the T2B assay, overall positive percentage agreement (PPA) was 84.6% [95% confidence interval (CI) 71.9-93.1%], negative percentage agreement (NPA) was 64.3% (95% CI 55.4-72.6%), positive predictive value (PPV) was 48.9% (95% CI 42.5-55.3%) and negative predictive value (NPV) was 91.2% (95% CI 84.4-95.2%). Cohen's kappa coefficient was 0.402. For the T2R assay, overall PPA was 80% (95% CI 51.9-95.7%), NPA was 69.2% (95% CI 54.9-81.3%), PPV was 42.9% (95% CI 31.7-54.8%) and NPV was 92.3% (95% CI 81.1-97.1%). Cohen's kappa coefficient was 0.376.

CONCLUSION

T2MR assays have high NPV for rapid exclusion of bacteraemia, and could potentially assist with antimicrobial stewardship when applied as point-of-care diagnostic tests in the intensive care unit.

Direct-from-Blood Detection of Pathogens: a Review of Technology and Challenges

Blood cultures have been the staple of clinical microbiology laboratories for well over half a century, but gaps remain in our ability to identify the causative agent in patients presenting with signs and symptoms of sepsis. Molecular technologies have revolutionized the clinical microbiology laboratory in many areas but have yet to present a viable alternative to blood cultures. There has been a recent surge of interest in utilizing novel approaches to address this challenge. In this minireview, I discuss whether molecular tools will finally give us the answers we need and the practical challenges of incorporating them into the diagnostic algorithm.

T2Bacteria and T2Resistance Assays in Critically Ill Patients with Sepsis or Septic Shock: A Descriptive Experience

The use of rapid molecular tests may anticipate the identification of causative agents and resistance determinants in the blood of critically ill patients with sepsis. From April to December 2021, all intensive care unit patients with sepsis or septic shock who were tested with the T2Bacteria and T2Resistance assays were included in a retrospective, single center study. The primary descriptive endpoints were results of rapid molecular tests and concomitant blood cultures. Overall, 38 combinations of T2Bacteria and T2Resistance tests were performed. One or more causative agent(s) were identified by the T2Bacteria assay in 26% of episodes (10/38), whereas negative and invalid results were obtained in 66% (25/38) and 8% (3/38) of episodes, respectively. The same pathogen detected by the T2Bacteria test grew from blood cultures in 30% of cases (3/10). One or more determinant(s) of resistance were identified by the T2Resistance assay in 11% of episodes (4/38). Changes in therapy based on T2Bacteria and/or T2Resistance results occurred in 21% of episodes (8/38). In conclusion, T2Bacteria/T2Resistance results can influence early treatment decisions in critically ill patients with sepsis or septic shock in real-life practice. Large, controlled studies remain necessary to confirm a favorable impact on patients' outcomes and antimicrobial stewardship interventions.

Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections

Staphylococcus aureus is an important causative pathogen of bloodstream infections. An amplification assay such as real-time PCR is a sensitive, specific technique to detect S. aureus. However, it needs well-trained personnel, and costs are high. A literature review focusing on rapid and simple methods for diagnosing S. aureus was performed. The following methods were included: (a) Hybrisep in situ hybridization test, (b) T2Dx system, (c) BinaxNow Staphylococcus aureus and PBP2a, (d) Gram staining, (e) PNA FISH and QuickFISH, (f) Accelerate Pheno^TM system, (g) MALDI-TOF MS, (h) BioFire FilmArray, (i) Xpert MRSA/SA. These rapid and simple methods can rapidly identify S. aureus in positive blood cultures or direct blood samples. Furthermore, BioFire FilmArray and Xpert MRSA/SA identify methicillin-resistant S. aureus (MRSA), and the Accelerate Pheno^TM system can also provide antimicrobial susceptibility testing (AST) results. The rapidity and simplicity of results generated by these methods have the potential to improve patient outcomes and aid in the prevention of the emergence and transmission of MRSA.

Combining T2Bacteria and T2Candida Panels for Diagnosing Intra-Abdominal Infections: A Prospective Multicenter Study

The T2Bacteria panel is a direct-from-blood assay that delivers rapid results, targeting E. coli, S. aureus, K. pneumoniae, A. baumanii, P. aeruginosa, and E. faecium (ESKAPE pathogens). In this study, T2Bacteria and T2Candida (targeting C. albicans/C. tropicalis, C. glabrata/C. krusei, and C. parapsilosis) were evaluated in parallel with blood cultures in 101 consecutive surgical patients with suspected intra-abdominal infection admitted to the intensive care unit or high dependency unit. Fifteen patients had bacteremia, with T2Bacteria correctly identifying all on-panel (n = 8) pathogens. T2Bacteria was positive in 19 additional patients, 11 of whom had supportive cultures from other normally sterile sites (newly inserted drains, perioperative cultures or blood cultures) within seven days. Six of these eleven patients (55%) received broad-spectrum antibiotics at the sampling time. T2Candida identified the two cases of blood-culture-positive candidemia and was positive in seven additional patients, three of whom were confirmed to have intra-abdominal candidiasis. Of four patients with concurrent T2Bacteria and T2Candida positivity, only one patient had positive blood cultures (candidemia), while three out of four patients had supporting microbiological evidence of a mixed infection. T2Bacteria and T2Candida were fast and accurate in diagnosing on-panel bloodstream infections, and T2Bacteria was able to detect culture-negative intra-abdominal infections.

Burden of bacterial bloodstream infections and recent advances for diagnosis

Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.

Metabolic preference assay for rapid diagnosis of bloodstream infections

Bloodstream infections (BSIs) cause >500,000 infections and >80,000 deaths per year in North America. The length of time between the onset of symptoms and administration of appropriate antimicrobials is directly linked to mortality rates. It currently takes 2–5 days to identify BSI pathogens and measure their susceptibility to antimicrobials – a timeline that directly contributes to preventable deaths. To address this, we demonstrate a rapid metabolic preference assay (MPA) that uses the pattern of metabolic fluxes observed in ex-vivo microbial cultures to identify common pathogens and determine their antimicrobial susceptibility profiles. In a head-to-head race with a leading platform (VITEK 2, BioMérieux) used in diagnostic laboratories, MPA decreases testing timelines from 40 hours to under 20. If put into practice, this assay could reduce septic shock mortality and reduce the use of broad spectrum antibiotics.

It is currently slow to identify bloodstream infection pathogens. Here the authors report a rapid metabolic preference assay that uses the pattern of metabolic fluxes observed in ex-vivo microbial cultures to identify common pathogens and determine their antimicrobial susceptibility profiles.

Molecular diagnosis of bacteremia in a pediatric intensive care unit: a step forward

Aim: T2Bacteria^® Panel detects six ESKAPE pathogens in around 3.5 h directly in whole blood. Our aim was to compare T2Bacteria with simultaneous blood culture in critically ill children with suspected bloodstream infection. Materials & methods: Retrospective study of critically ill children admitted to our tertiary-care center (2018-2020). Results: A total of 60 patients were recruited, including 63 episodes and 75 T2Bacteria/blood cultures were performed. Overall agreement between T2Bacteria and blood culture was 78.7% with a discordance of 21.3% (16/75 samples). Conclusion: T2Bacteria Panel may be useful in critically ill children providing an accurate and fast diagnosis of bacteremia directly from blood sample and detecting pathogens not recovered in blood cultures.

Role of the T2Dx magnetic resonance assay in patients with suspected bloodstream infection: a single-centre real-world experience

BACKGROUND

T2Dx was approved by the US Food and Drug Administration for the rapid detection of a modified panel of ESKAPE bacterial species or Candida spp. causing bloodstream infection (BSI).

PATIENTS AND METHODS

We performed a retrospective, observational study from January 1, 2018 to December 31, 2019 of all hospitalised patients with suspected BSI who underwent assessment using T2Dx in addition to standard blood culture (BC). T2-positive patients (cases) were compared to a matched group of patients with BSI documented only by BC (1:2 ratio) to investigate the possible impact of T2Dx on the appropriateness of empirical antimicrobial therapy and 21-day mortality.

RESULTS

In total, 78 T2Dx-analysed samples (49 patients) were analysed. The T2Dx assay result was positive for18 patients and negative for 31 patients. The concordance rates of the T2Bacteria Panel and T2Candida Panel results with those of standard BC were 74.4% and 91.4%, respectively. In the matched analysis, inappropriate empiric antimicrobial therapy administration was significantly less frequent in cases than in comparators (5.5% vs. 38.8%). The 21-day mortality rate was twofold lower in cases than in comparators (22.2% vs. 44.4%), although the difference was not significant. No other analysed variables were significantly different between the two groups.

CONCLUSIONS

This study illustrated that T2Dx might be associated with an increase in the appropriateness of empiric antimicrobial therapy in patients with BSI. Further studies are needed to evaluate whether the T2Dx assay can improve patient outcomes.

New evidence for managing Gram-negative bloodstream infections

PURPOSE OF REVIEW

Gram-negative bloodstream infections (GNBSI) are common and carry considerable mortality. Treatment is complicated by increasing antimicrobial resistance, posing a challenge for timely appropriate antibiotics and limiting the choices of effective definitive therapy. The present review aims to summarize recent studies addressing the management of GNBSI.

RECENT FINDINGS

New rapid diagnostic tests (RDT) for pathogen identification and antibiotic susceptibility are associated with improved antimicrobial stewardship and reduced length of stay. No mortality benefit or patient-related outcomes are reported. Data regarding the use of new beta-lactam beta-lactamase inhibitors (BLBLIs) for treating multidrug resistance Gram-negative bacteria is supportive, though questions regarding combinations, optimal dosing, mode of administration, and resistance emergence remain to be clarified. Current data regarding cefiderocol necessitates further studies in order to support its use in GNBSI. Shortened (≤7 days) duration of therapy and early oral step down for GNBSI are supported by the literature. The role of repeated blood cultures should be further defined.

SUMMARY

RDTs should be implemented to improve antibiotic stewardship. Clinical implications on patient-related outcomes should be evaluated. New BLBLIs show promise in the treatment of GNBSI. Additional data are needed regarding the use of cefiderocol. Antibiotic therapy should be shortened and early oral step down should be considered.

Culture independent detection systems for bloodstream infection

BACKGROUND

Sepsis and bloodstream infection are associated with significant morbidity and mortality, and early effective antimicrobial therapy has been demonstrated to improve patient outcomes. Traditional culture-based methods, however, have several limitations which hamper a prompt diagnosis in bloodstream infection, including long turnaround times and limited sensitivity. In the last years, advances have been made in the development of several technologies which allow the identification of pathogens and their resistance markers directly from whole blood, possibly representing promising alternatives to conventional culture methods.

OBJECTIVES

To review the currently commercially available emerging assays for the diagnosis of bloodstream infections directly from whole blood, including their performance and the available data about their impact on patients' outcome.

SOURCES

Peer-reviewed publications relevant to the topic have been searched through PubMed; manufacturers' websites have also been consulted as a data source.

CONTENT

We have reviewed available data about the following technologies: multiplex real-time PCR working directly from whole blood (Magicplex Sepsis Real-Time test, Seegene), PCR combined with T2 Magnetic Resonance (T2Candida and T2Bacteria panel, T2Biosystem), and metagenomics-based assays (including SepsiTest, Molzym; iDTECT Dx Blood, PathoQuest; Karius NGS plasma Test, Karius). Performance characteristics, advantages and pitfalls of each method are described, and available data about their impact on patients' clinical outcomes are discussed.

IMPLICATIONS

The potential of rapid diagnostic tests applied on whole blood in improving the management of patients with bloodstream infection and sepsis is high, both in terms of reducing turnaround times and improving the sensitivity of pathogen and antimicrobial resistance detection. However, overall, there is still a scarcity of data about the real-life performance of such tests, and well-designed studies are awaited for assessing the impact of these emerging technologies on patients' outcomes.

Accuracy and Impact on Patient Management of New Tools for Diagnosis of Sepsis: Experience with the T2 Magnetic Resonance Bacteria Panel

The rapid and accurate identification of pathogens responsible for sepsis is essential for prompt and effective antimicrobial therapy. Molecular technologies have been developed to detect the most common causative agents, with high sensitivity and short time to result (TTR). T2 Bacteria Panel (T2), based on a combination of PCR and T2 magnetic resonance, can identify directly in blood samples Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecium, and Acinetobacter baumannii pathogens. This study evaluates the role of T2 in the diagnosis of sepsis and its impact on patient management, specifically in terms of TTR and the switch from empirical to directed therapy, comparing results of blood culture (BC) and T2 assay in 82 patients with sepsis. T2 significantly improved the detection of the causative agents of sepsis. For pathogens included in the panel, T2 sensitivity was 100% (95% CI 86.3–100.0), significantly higher than that of BC (54.8%, 95% CI 36.0–72.7). The TTR (median, IQR) of positive T2 (3.66 h, 3.59–4.31) was significantly shorter than that of the positive BC (37.58 h, 20.10–47.32). A significant reduction in the duration of empiric therapy and an increase in the percentage of patients with switched therapy was observed in patients with a positive T2 result. In conclusion, T2 can shorten and improve the etiological diagnosis of sepsis with a positive impact on patient management.

Direct Testing for KPC-Mediated Carbapenem Resistance from Blood Samples Using a T2 Magnetic Resonance Based Assay

Molecular-based carbapenem resistance testing in Gram-negative bacterial bloodstream infections (BSIs) is currently limited because of the reliance on positive blood culture (BC) samples. The T2Resistance™ panel may now allow the detection of carbapenemase- and other β-lactamase encoding genes directly from blood samples. We detected carbapenem resistance genes in 11 (84.6%) of 13 samples from patients with BC-documented BSIs (10 caused by KPC-producing Klebsiellapneumoniae and 1 caused by VIM/CMY-producing Citrobacter freundii). Two samples that tested negative for carbapenem resistance genes were from patients with BC-documented BSIs caused by KPC-producing K. pneumoniae who were receiving effective antibiotic therapy. In conclusion, our findings suggest that the T2Resistance™ panel can be a reliable tool for diagnosing carbapenem-resistant Gram-negative bacterial BSIs.

New Microbiological Techniques for the Diagnosis of Bacterial Infections and Sepsis in ICU Including Point of Care

Purpose of Review

The aim of this article is to review current and emerging microbiological techniques that support the rapid diagnosis of bacterial infections in critically ill patients, including their performance, strengths and pitfalls, as well as available data evaluating their clinical impact.

Recent Findings

Bacterial infections and sepsis are responsible for significant morbidity and mortality in patients admitted to the intensive care unit and their management is further complicated by the increase in the global burden of antimicrobial resistance. In this setting, new diagnostic methods able to overcome the limits of traditional microbiology in terms of turn-around time and accuracy are highly warranted. We discuss the following broad themes: optimisation of existing culture-based methodologies, rapid antigen detection, nucleic acid detection (including multiplex PCR assays and microarrays), sepsis biomarkers, novel methods of pathogen detection (e.g. T2 magnetic resonance) and susceptibility testing (e.g. morphokinetic cellular analysis) and the application of direct metagenomics on clinical samples. The assessment of the host response through new “omics” technologies might also aid in early diagnosis of infections, as well as define non-infectious inflammatory states.

Summary

Despite being a promising field, there is still scarce evidence about the real-life impact of these assays on patient management. A common finding of available studies is that the performance of rapid diagnostic strategies highly depends on whether they are integrated within active antimicrobial stewardship programs. Assessing the impact of these emerging diagnostic methods through patient-centred clinical outcomes is a complex challenge for which large and well-designed studies are awaited.

Antimicrobial and resource utilization with T2 magnetic resonance for rapid diagnosis of bloodstream infections: systematic review with meta-analysis of controlled studies

Objectives: To compare antimicrobial and resource utilization with T2 Magnetic Resonance (T2MR) versus blood culture (BC) in patients with suspected bloodstream infection.Methods: We systematically searched MEDLINE, EMBASE, and CENTRAL for randomized trials or observational controlled studies of patients with suspected bloodstream infection receiving a diagnosis with T2MR or BC. Using an inverse variance meta-analysis model, we reported mortality using the risk ratio (RR) and the remaining outcomes as the mean difference (MD).Results: Fourteen studies were included in the meta-analysis. Time to detection (MD = -81 hours; p < 0.001) and time to species identification (MD = -77 hours; p < 0.001) were faster with T2MR. Patients testing positive on T2MR received targeted antimicrobial therapy faster (-42 hours; p < 0.001) and patients testing negative on T2MR were de-escalated from empirical therapy faster (-7 hours; p = 0.02) vs. BC. Length of intensive care unit stay (MD = -5.0 days; p = 0.03) and hospital stay (MD = -4.8 days; p = 0.03) were shorter with T2MR. Mortality rates were comparable between T2MR and BC (28.9% vs. 29.9%, RR = 1.02, p = 0.86).Conclusion: Utilization of T2MR for identification of bloodstream pathogens provides faster time to detection, faster transition to targeted microbial therapy, faster de-escalation of empirical therapy, shorter ICU and hospital stay, and with comparable mortality rate versus BC.

Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis

In the microbiological diagnosis of bloodstream infections (BSI), blood culture (BC) is considered the gold standard test despite its limitations such as low sensitivity and slow turnaround time. A new FDA-cleared and CE-marked platform utilizing magnetic resonance to detect amplified DNA of the six most common and/or problematic BSI pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli; referred to as ESKAPEc) is available and may shorten the time to diagnosis and potentially improve antimicrobial utilization. Whole blood samples from hospitalized patients with clinical signs of sepsis were analyzed using the T2Bacteria Panel (T2Biosystems) and compared to simultaneously collected BC. Discrepant results were evaluated based on clinical infection criteria, combining supporting culture results and the opinion of treating physicians. A total of 55 samples from 53 patients were evaluated. The sensitivity and specificity of the T2Bacteria panel was 94% (16 out of 17 detections of T2Bacteria-targeted organisms) and 100%, respectively, with 36.4% (8 of 22) causes of BSI detected only by this method. The T2Bacteria Panel detected pathogens on average 55 hours faster than standard BC. In our study, 9 of 15 patients with positive T2Bacteria Panel results received early-targeted antibiotic therapy and/or modification of antimicrobial treatment based on T2Bacteria Panel findings. Given the high reliability, faster time to detection, and easy workflow, the technique qualifies as a point-of-care testing approach.

Evaluation of Rapid Sepsityper® protocol and specific MBT-Sepsityper module (Bruker Daltonics) for the rapid diagnosis of bacteremia and fungemia by MALDI-TOF-MS

During bloodstream infections, rapid adaptation of empirical treatment according to the microorganism identified is essential to decrease mortality. The aim of the present study was to assess the microbiological performances of a new rapid version of the Sepsityper® kit (Bruker Daltonics) allowing identification of bacteria and yeast by MALDI-TOF mass spectrometry directly from positive blood cultures in 10 min and of the specific MBT-Sepsityper module for spectra analysis, designed to increase identification performance. Identification rates were determined prospectively on 350 bacterial and 29 fungal positive blood cultures, and compared to conventional diagnostic method. Our rapid diagnosis strategy (Rapid Sepsityper® protocol: one spot with and one without formic acid extraction step) combined to MBT-Sepsityper module provided 65.4%, 78.9% and 62% reliable identification to the species level of monomicrobial positive blood cultures growing respectively Gram-positive, Gram-negative bacteria or yeast. Importantly, identification rates of Gram-positive bacteria were higher in anaerobic than in aerobic bottles (77.8% vs 22.2%; p = 0.004), if formic acid extraction step was performed (60.8% vs 39.2%; p = 1.8e⁻⁶) and if specific MBT-Sepsityper module was used (76.2% vs 61.9%, p = 0.041) while no significant differences were observed for Gram-negative bacteria. For yeasts identification, formic acid extraction step improved rapid identification rate by 37.9% while the specific MBT-Sepsityper module increased overall performances by 38%, providing up to 89.7% reliable identification if associated with the standard Sepsityper® protocol. These performances, associated with a reduce turnaround time, may help to implement a rapid identification strategy of bloodstream infections in the routine workflow of microbiology laboratories.

Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Blood for the Diagnosis of Bloodstream Infections: A Mini-Review

Staphylococcus aureus represents a major human pathogen able to cause a number of infections, especially bloodstream infections (BSI). Clinical use of methicillin has led to the emergence of methicillin-resistant S. aureus (MRSA) and MRSA-BSI have been reported to be associated with high morbidity and mortality. Clinical diagnosis of BSI is based on the results from blood culture that, although considered the gold standard method, is time-consuming. For this reason, rapid diagnostic tests to identify the presence of methicillin-susceptible S. aureus (MSSA) and MRSA isolates directly in blood cultures are being used with increasing frequency to rapidly commence targeted antimicrobial therapy, also in the light of antimicrobial stewardship efforts. Here, we review and report the most common rapid non-molecular and molecular methods currently available to detect the presence of MRSA directly from blood.

Emerging Microbiology Diagnostics for Transplant Infections: On the Cusp of a Paradigm Shift

In light of the heightened risk for infection associated with solid organ and hematopoietic stem cell transplantation, rapid and accurate microbiology diagnostics are essential to the practice of transplant clinicians, including infectious diseases specialists. In the last decade, diagnostic microbiology has seen a shift toward culture-independent techniques including single-target and multiplexed molecular testing, mass-spectrometry, and magnetic resonance-based methods which have together greatly expanded the array of pathogens identified, increased processing speed and throughput, allowed for detection of resistance determinants, and ultimately improved the outcomes of infected transplant recipients. More recently, a newer generation of diagnostics with immense potential has emerged, including multiplexed molecular panels directly applicable to blood and blood culture specimens, next-generation metagenomics, and gas chromatography mass spectrometry. Though these methods have some recognized drawbacks, many have already demonstrated improved sensitivity and a positive impact on clinical outcomes in transplant and immunocompromised patients.

The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update

The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.

Feasibility of precise and reliable glucose quantification in human whole blood samples by 1 tesla benchtop NMR

The standard procedure for blood glucose measurements is enzymatic testing. This method is cheap, but requires small samples of open blood with direct contact to the test medium. In principle, NMR provides non-contact analysis of body fluids, but high-field spectrometers are expensive and cannot be easily utilized under clinical conditions. Low-field NMR systems with permanent magnets are becoming increasingly smaller and more affordable. The studies presented here aim at exploring the capabilities of low-field NMR for measuring glucose concentrations in whole blood. For this purpose, a modern 1 T benchtop NMR spectrometer was used. Challenges arise from broad spectral lines, the glucose peak locations close to the water signal, low SNR and the interference with signals from other blood components. Whole blood as a sample comprises even more boundary conditions: crucial for reliable results are avoiding the separation of plasma and cells by gravitation and reliable reference values. First, the accuracy of glucose levels measured by NMR was tested using aqueous glucose solutions and commercially available bovine plasma. Then, 117 blood samples from oral glucose tolerance testing were measured with minimal preparation by simple pulse-acquire NMR experiments. The analysis itself is the key to achieve high precision, so several approaches were investigated: peak integration, orthogonal projection to latent structure analysis and support vector machine regression. Correlations between results from the NMR spectra and the routine laboratory automated analyzer revealed an RMSE of 7.90 mg/dL for the best model. 91.5% of the model output lies within the limits of the German Medical Association guidelines, which require the glucose measurement to be within 11% of the reference method. It is concluded that spectral quantification of glucose in whole blood samples by high-quality NMR spectrometers operating at 1 T is feasible with sufficient accuracy.

The challenge of recognising sepsis: Future nanotechnology solutions

The urgent need to start anti-infective therapeutic interventions in suspected sepsis, and the lack of specific time-critical diagnostic information often lead to the widespread administration of broad-spectrum antimicrobial therapies, increasing the risk of unwanted patient harms and contributing to rising pathogen antimicrobial resistance. Nanotechnology, which involves engineering at the nanoscale, allows for the bespoke development of diagnostic solutions with multi-functionality and high sensitivity that has the potential to help provide time-critical information to make more accurate diagnoses and treatment decisions for sepsis. Nanotechnologies also have the potential to improve upon the current strategies used for novel biomarker discovery. Here we describe some of the current limitations to identifying sepsis and explore the potential role for nanotechnology solutions.

New and novel rapid diagnostics that are impacting infection prevention and antimicrobial stewardship

PURPOSE OF REVIEW

The current review summarizes advances in rapid diagnostic testing that impacts infection prevention and antimicrobial stewardship programs.

RECENT FINDINGS

A variety of rapid diagnostic technologies to identify organisms in cultured blood are now available. When coupled with antimicrobial stewardship (ASP), these rapid technologies can optimize antimicrobial utilization and patient outcomes. Two rapid molecular panels that detect organisms related to pneumonia are available and may impact infection prevention surveillance definitions. Three molecular tests are available for the detection of meningitis and encephalitis pathogens. Still, the clinical impact of these broad, multiplexed panels need additional clarification. For Clostridioides difficile infections, ultrasensitive toxin A/B assays may provide enhanced sensitivity and specificity compared with enzyme immunoassay and molecular testing respectively. Finally, the adoption of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI TOF MS) for rapid organism identification is growing. Recent US Food and Drug Administration-clearance of a MALDI TOF MS platform for identification of Nocardia, Mycobacteria, and molds may expedite antimicrobial decisions for infections that traditionally required days to weeks for an identification.

SUMMARY

Tests with broad diagnostic scope and swift turnaround time are rapidly entering the market. Many impact infection prevention and ASP programs. Collaboration with the microbiology laboratory is crucial to ensure that new tests successfully optimize patient care.

A case study on Staphylococcus aureus bacteraemia: available treatment options, antibiotic R&D and responsible antibiotic-use strategies

Objectives

This case study addresses: (i) antibiotic treatment options for Staphylococcus aureus bacteraemia (SAB), for both empirical and targeted therapy; (ii) the current status of and priorities for the antibiotic pipeline to ensure access of effective antibiotics for SAB; and (iii) strategies for responsible antibiotic use relevant to the clinical management of SAB.

Methods

Evidence to address the aims was extracted from the following information sources: (i) EUCAST and CLSI recommendations, summaries of product characteristics (SPCs), antibiotic treatment guidelines and the textbook Kucers’ The Use of Antibiotics; (ii) the www.clinicaltrial.gov database; and (iii) quality indicators for responsible antibiotic use.

Results

Current monotherapy treatment options for SAB include only three drug classes (β-lactams, glycopeptides and lipopeptides), of which two also cover MRSA bacteraemia (glycopeptides and lipopeptides). The analysis of the antibiotic pipeline and ongoing clinical trials revealed that several new antibiotics with S. aureus (including MRSA) coverage were developed in the past decade (2009–19). However, none belonged to a new antibiotic class or had superior effectiveness and their added clinical value for SAB remains to be proven. Responsible antibiotic use for the treatment of SAB was illustrated using 11 quality indicators.

Conclusions

Awareness of the problem of a limited antibiotic arsenal, together with incentives (e.g. push incentives), is needed to steer the R&D landscape towards the development of novel and effective antibiotics for treating SAB. In the meantime, responsible antibiotic use guided by quality indicators should preserve the effectiveness of currently available antibiotics for treating SAB.

Molecular Diagnostic Advances in Transplant Infectious Diseases

PURPOSE OF REVIEW

The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases.

RECENT FINDINGS

Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.

Development of a Multiplex PCR Platform for the Rapid Detection of Bacteria, Antibiotic Resistance, and Candida in Human Blood Samples

The diagnosis of bloodstream infections (BSIs) still relies on blood culture (BC), but low turnaround times may hinder the early initiation of an appropriate antimicrobial therapy, thus increasing the risk of infection-related death. We describe a direct and rapid multiplex PCR-based assay capable of detecting and identifying 16 bacterial and four Candida species, as well as three antibiotic-resistance determinants, in uncultured samples. Using whole-blood samples spiked with microorganisms at low densities, we found that the MicrobScan assay had a mean limit of detection of 15.1 ± 3.3 CFU of bacteria/Candida per ml of blood. When applied to positive BC samples, the assay allowed the sensitive and specific detection of BSI pathogens, including bla _KPC-, mecA-, or vanA/vanB-positive bacteria. We evaluated the assay using prospectively collected blood samples from patients with suspected BSI. The sensitivity and specificity were 86.4 and 97.0%, respectively, among patients with positive BCs for the microorganisms targeted by the assay or patients fulfilling the criteria for infection. The mean times to positive or negative assay results were 5.3 ± 0.2 and 5.1 ± 0.1 h, respectively. Fifteen of 20 patients with MicrobScan assay-positive/BC-negative samples were receiving antimicrobial therapy. In conclusion, the MicrobScan assay is well suited to complement current diagnostic methods for BSIs.

Direct Detection of Pathogens in Bloodstream During Sepsis: Are We There Yet?

Background

Advances in medicine have improved our understanding of sepsis, but it remains a major cause of morbidity and mortality. The detection of pathogens that cause sepsis remains a challenge for clinical microbiology laboratories.

Content

Routine blood cultures are time-consuming and are negative in a large proportion of cases, leading to excessive use of broad-spectrum antimicrobials. Molecular testing direct from patient blood without the need for incubation has the potential to fill the gaps in our diagnostic armament and complement blood cultures to provide results in a timely manner. Currently available platforms show promise but have yet to definitively address gaps in sensitivity and specificity.

Summary

Significant strides have been made in the detection of pathogens directly from blood. A number of hurdles, however, remain before this technology can be adapted for routine use.

Diagnostic Challenges and Laboratory Considerations for Pediatric Sepsis

Background

Sepsis is a leading cause of death for children in the US and worldwide. There is a lack of consensus how sepsis is clinically defined, and sepsis definitions and diagnostic guidelines for the pediatric population have remained unchanged for more than a decade now. Current pediatric definitions are largely based on adult guidelines and expert opinion rather than evidence based on outcomes in the pediatric populations. Without a clear definition of sepsis, it is challenging to evaluate the performance of new laboratory tests on the diagnosis and management of sepsis.

Content

This review provides an overview of common etiologies of sepsis in pediatric populations, challenges in defining and diagnosing pediatric sepsis, and current laboratory tests used to identify and monitor sepsis. Strengths and limitations of emerging diagnostic strategies will also be discussed.

Summary

Currently there is no single biomarker that can accurately diagnose or predict sepsis. Current biomarkers such as C-reactive protein and lactate are neither sensitive nor specific for diagnosing sepsis. New biomarkers and rapid pathogen identification assays are much needed. Procalcitonin, although having some limitations, has emerged as a biomarker with demonstrated utility in management of sepsis in adults. Parallel studies analyzing the utility of procalcitonin in pediatric populations are lagging but have shown potential to affect sepsis care in pediatric populations. Multibiomarker approaches and stepwise algorithms show promise in the management of pediatric sepsis. However, a major hurdle is the lack of validated clinical criteria for classification of pediatric sepsis, which is necessary for the development of well-designed studies that can assess the clinical impact of these emerging biomarkers.

Rapid microbiological tests for bloodstream infections due to multidrug resistant Gram-negative bacteria: therapeutic implications

BACKGROUND

Treating severe infections due to multidrug-resistant Gram-negative bacteria (MDR-GNB) is one of the most important challenges for clinicians worldwide, partly because resistance may remain unrecognized until identification of the causative agent and/or antimicrobial susceptibility testing (AST). Recently, some novel rapid test for identification and/or AST of MDR-GNB from positive blood cultures or the blood of patients with bloodstream infections (BSIs) have become available.

OBJECTIVES

The objective of this narrative review is to discuss the advantages and limitations of different rapid tests for identification and/or AST of MDR-GNB from positive blood cultures or the blood of patients with BSI, as well as the available evidence on their possible role to improve therapeutic decisions and antimicrobial stewardship.

SOURCES

Inductive PubMed search for publications relevant to the topic.

CONTENT

The present review is structured in the following way: (a) rapid tests on positive blood cultures; (b) rapid tests directly on whole blood; (c) therapeutic implications.

IMPLICATIONS

Novel molecular and phenotypic rapid tests for identification and AST show the potential for favourably influencing patients' outcomes and results of antimicrobial stewardship interventions by reducing both the time to effective treatment and the misuse of antibiotics, although the interpretation about their impact on actual therapeutic decisions and patients' outcomes is still complex. Factors such as feasibility and personnel availability, as well as the detailed knowledge of the local microbiological epidemiology, need to be considered very carefully when implementing novel rapid tests in laboratory workflows and algorithms. Providing high-level, comparable evidence on the clinical impact of rapid identification and AST is becoming of paramount importance for MDR-GNB infections, since in the near future rapid identification of specific resistance mechanisms could be crucial for guiding rapid, effective, and targeted therapy against specific resistance mechanisms.

Recovery of Gram-Negative Bacteria from Aerobic Blood Culture Bottles Containing Antibiotic Binding Resins after Exposure to β-Lactam and Fluoroquinolone Concentrations

Blood culture bottles containing antibiotic binding resins are routinely used to minimize artificial sterilization in the presence of antibiotics. However, the resin binding kinetics can differ between antibiotics and concentrations. This study assessed the impact of clinically meaningful peak, midpoint, and trough concentrations of meropenem, imipenem, cefepime, cefazolin, levofloxacin, and piperacillin-tazobactam on the recovery of Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae from resin-containing BacT/Alert FA Plus and Bactec Aerobic/F blood culture bottles. P. aeruginosa-inoculated bottles alarmed positive in 4/20 (20%), 16/20 (80%), and 20/20 (100%) of those with peak, midpoint, and trough concentrations of antipseudomonal agents, respectively (P ≤ 0.001). E. coli was recovered from 8/24 (33%), 11/24 (46%), and 14/24 (58%) of bottles with peak, midpoint, and trough concentrations, respectively (P = 0.221). K. pneumoniae was recovered from 8/16 (50%) at all concentrations of the studied antibiotics (P = 1.0). BacT/Alert and Bactec bottles inoculated with antibiotics and P. aeruginosa had similar times to detection (TTD) (P = 0.352); however, antibiotic-containing BacT/Alert bottles had a shorter TTD compared with antibiotic-containing Bactec bottles for E. coli (P = 0.026) and K. pneumoniae (P ≤ 0.001). Pathogen recovery in BacT/Alert FA Plus and Bactec Aerobic/F blood culture bottles containing antibiotic binding resins was greatly reduced in the presence of antibiotics, especially at higher concentrations. These data support the practice of drawing blood cultures immediately before an antibiotic dose to maximize the chances of pathogen recovery.

Time to First Culture Positivity Among Critically Ill Adults With Methicillin-Resistant Staphylococcus aureus Growth in Respiratory or Blood Cultures

Background: For critically ill adults receiving empirical vancomycin, the duration of negative cultures after which vancomycin may be discontinued without risking subsequent growth of methicillin-resistant Staphylococcus aureus (MRSA) remains unknown. Objective: We hypothesized that if sputum cultures did not grow MRSA or blood cultures did not grow Gram-positive cocci on Gram stain by 48 hours, those cultures would not subsequently demonstrate MRSA. Methods: We conducted an ancillary analysis from patients enrolled in the Isotonic Solutions and Major Adverse Renal Events Trial (SMART). In this cohort of patients, we collected data on the time of either MRSA identification in culture or Gram-positive cocci identification on Gram stain and rate of vancomycin discontinuation. Results: Of the 15 802 patient admissions in the SMART study, 6553 (41.5%) received empirical intravenous vancomycin. Respiratory sputum cultures demonstrated MRSA during 178 patient admissions. Among respiratory cultures that would ultimately grow MRSA, 85% were positive within 48 hours, and 97% were positive within 72 hours. Cultures demonstrated MRSA bacteremia during 85 patient admissions. In 83 cases (97.6%) of MRSA bacteremia, Gram-positive cocci were identified within 48 hours after the culture was obtained. Conclusion and Relevance: This analysis of a large cohort of critically ill adults receiving empirical vancomycin found that Staphylococcus aureus was present in all but 15% of cases of MRSA-positive respiratory cultures after 48 hours, whereas Gram-positive cocci were identified within 48 hours during nearly all episodes of MRSA bacteremia. These findings may inform the timing of discontinuation of empirical vancomycin among critically ill adults.

Moderate positive predictive value of a multiplex real-time PCR on whole blood for pathogen detection in critically ill patients with sepsis

A novel multiplex real-time PCR for bloodstream infections (BSI-PCR) detects pathogens directly in blood. This study aimed at determining the positive predictive value (PPV) of BSI-PCR in critically ill patients with sepsis. We included consecutive patients with presumed sepsis upon admission to the intensive care unit (ICU). The multiplexed BSI-PCR included 17 individual PCRs for a broad panel of species- and genus-specific DNA targets. BSI-PCR results were compared with a reference diagnosis for which plausibility of infection and causative pathogen(s) had been prospectively assessed by trained observers, based on available clinical and microbiological evidence. PPV and false positive proportion (FPP) were calculated. Clinical plausibility of discordant positive results was adjudicated by an expert panel. Among 325 patients, infection likelihood was categorized as confirmed, uncertain, and ruled out in 210 (65%), 88 (27%), and 27 (8%) subjects, respectively. BSI-PCR identified one or more microorganisms in 169 (52%) patients, of whom 104 (61%) had at least one detection in accordance with the reference diagnosis. Discordant positive PCR results were observed in 95 patients, including 30 subjects categorized as having an "unknown" pathogen. Based on 5525 individual PCRs yielding 295 positive results, PPV was 167/295 (57%) and FPP was 128/5525 (2%). Expert adjudication of the 128 discordant PCR findings resulted in an adjusted PPV of 68% and FPP of 2%. BSI-PCR was all-negative in 156 patients, including 79 (51%) patients in whom infection was considered ruled out. BSI-PCR may complement conventional cultures and expedite the microbiological diagnosis of sepsis in ICU patients, but improvements in positive predictive value of the test are warranted before its implementation in clinical practice can be considered.

Performance of the T2Bacteria Panel for Diagnosing Bloodstream Infections: A Diagnostic Accuracy Study

BACKGROUND

Blood cultures, the gold standard for diagnosing bloodstream infections (BSIs), are insensitive and limited by prolonged time to results. The T2Bacteria Panel (T2 Biosystems) is a direct-from-blood, nonculture test that identifies the most common ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli).

OBJECTIVE

To assess performance of the T2Bacteria Panel in diagnosing suspected BSIs in adults.

DESIGN

Prospective patient enrollment (8 December 2015 through 4 August 2017).

SETTING

Eleven U.S. hospitals.

PATIENTS

1427 patients for whom blood cultures were ordered as standard of care.

INTERVENTION

Paired blood culture and T2Bacteria testing.

MEASUREMENTS

Performance of T2Bacteria compared with a single set of blood cultures in diagnosing proven, probable, and possible BSIs caused by T2Bacteria-targeted organisms.

RESULTS

Blood culture and T2Bacteria results were positive for targeted bacteria in 3% (39 of 1427) and 13% (181 of 1427) of patients, respectively. Mean times from start of blood culture incubation to positivity and species identification were 38.5 (SD, 32.8) and 71.7 (SD, 39.3) hours, respectively. Mean times to species identification with T2Bacteria were 3.61 (SD, 0.2) to 7.70 (SD, 1.38) hours, depending on the number of samples tested. Per-patient sensitivity and specificity of T2Bacteria for proven BSIs were 90% (95% CI, 76% to 96%) and 90% (CI, 88% to 91%), respectively; the negative predictive value was 99.7% (1242 of 1246). The rate of negative blood cultures with a positive T2Bacteria result was 10% (146 of 1427); 60% (88 of 146) of such results were associated with probable (n = 62) or possible (n = 26) BSIs. If probable BSIs and both probable and possible BSIs were assumed to be true positives missed by blood culture, per-patient specificity of T2Bacteria was 94% and 96%, respectively.

LIMITATION

Low prevalence of positive blood cultures, collection of a single set of culture specimens, and inability of T2Bacteria to detect nontargeted pathogens.

CONCLUSION

The T2Bacteria Panel rapidly and accurately diagnoses BSIs caused by 5 common bacteria.

PRIMARY FUNDING SOURCE

T2 Biosystems.

T2 magnetic resonance for the diagnosis of bloodstream infections: charting a path forward

We discuss four studies in this issue of the Journal of Antimicrobial Chemotherapy that describe experience with T2 magnetic resonance (T2MR) nanodiagnostics for Candida and bacterial bloodstream infections, in the context of the T2MR literature. T2Candida and T2Bacteria panels use a dedicated instrument to detect amplified DNA from microbial cells directly in whole blood. T2Candida gives positive or negative results for C. albicans/C. tropicalis, C. glabrata/C. krusei, and C. parapsilosis. T2Bacteria detects Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli. In recent trials, T2Candida sensitivity and specificity for candidaemia were ∼90% and ∼98%, respectively. Two studies from Spanish hospitals now provide the first data on T2Candida as a prognostic tool. T2Candida was superior to cultures or serum β-d-glucan in identifying patients with complicated candidaemia, and in predicting the outcomes of empirical antifungal therapy for suspected candidiasis. In a retrospective study from US community hospitals, use of T2Candida was reported to reduce times to appropriate antifungal therapy, shorten courses of empirical therapy, and save an average of US$280 in antifungal costs per patient tested. Finally, a study from a hospital in Rome provides the first clinical data for T2Bacteria: sensitivity and specificity were 89% and 98%, respectively, among patients with positive blood cultures for bacteria detected by the panel, or fulfilling criteria for infection. We conclude that T2MR diagnostics are promising both for detecting bloodstream infections due to Candida and bacteria, and for providing prognostic information. More studies that present real-world performance data are needed.