Verigene® gram-positive blood culture nucleic acid test

Diagnostic Stewardship in Clinical Microbiology: An Indispensable Component of Patient Care

Emerging infectious diseases and increasing resistance to available antimicrobials are mapping the evolution of clinical microbiology and escalating the nature of undertakings required. Rapid diagnosis has become the need of the hour, which can affect diagnostic algorithms and therapeutic decisions simultaneously. Subsequently, the concept of 'diagnostic stewardship' was introduced into clinical practice for coherent implementation of available diagnostic modalities to ensure that these new rapid diagnostic technologies are conserved, rather than consumed as part of health care resources, with a view to improve the patient care and reduce Turnaround Time (TAT) and treatment expense. The present study highlights the requisite of diagnostic stewardship and outlines the infectious disease diagnostic modalities that can assist in its successful implementation. Diagnostic stewardship promotes precise, timely diagnostics, from the initial specimen collection and identification to reporting with appropriate TAT, so as to enable timely management of the patient. The main aim of diagnostic stewardship is to optimize the right choice of diagnostic test for the right patient to attain clinically significant reports with the least possible TAT for timely management and the least expected adverse effects for the patient, community, and the healthcare system. This underlines the requisite of a multifaceted approach to make technological advancements effective and successful for implementation as a part of diagnostic stewardship for the best patient care.

Nanomaterial-based methods for sepsis management

Sepsis is a serious disease caused by an impaired host immune response to infection, resulting in organ dysfunction, tissue damage and is responsible for high in-hospital mortality (approximately 20%). Recently, WHO documented sepsis as a global health priority. Nevertheless, there is still no effective and specific therapy for clinically detecting sepsis. Nanomaterial-based approaches have appeared as promising tools for identifying bacterial infections. In this review, recent biosensors are introduced and summarized as nanomaterial-based platforms for sepsis management and severe complications. Biosensors can be used as tools for the diagnosis and treatment of sepsis and as nanocarriers for drug delivery. In general, diagnostic methods for sepsis-associated bacteria, biosensors developed for this purpose are presented in detail, and their strengths and weaknesses are discussed. In other words, readers of this article will gain a comprehensive understanding of biosensors and their applications in sepsis management.

Nanomedicine: New Frontiers in Fighting Microbial Infections

Microbes have dominated life on Earth for the past two billion years, despite facing a variety of obstacles. In the 20th century, antibiotics and immunizations brought about these changes. Since then, microorganisms have acquired resistance, and various infectious diseases have been able to avoid being treated with traditionally developed vaccines. Antibiotic resistance and pathogenicity have surpassed antibiotic discovery in terms of importance over the course of the past few decades. These shifts have resulted in tremendous economic and health repercussions across the board for all socioeconomic levels; thus, we require ground-breaking innovations to effectively manage microbial infections and to provide long-term solutions. The pharmaceutical and biotechnology sectors have been radically altered as a result of nanomedicine, and this trend is now spreading to the antibacterial research community. Here, we examine the role that nanomedicine plays in the prevention of microbial infections, including topics such as diagnosis, antimicrobial therapy, pharmaceutical administration, and immunizations, as well as the opportunities and challenges that lie ahead.

REASSURED Multiplex Diagnostics: A Critical Review and Forecast

The diagnosis of infectious diseases is ineffective when the diagnostic test does not meet one or more of the necessary standards of affordability, accessibility, and accuracy. The World Health Organization further clarifies these standards with a set of criteria that has the acronym ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable to end-users). The advancement of the digital age has led to a revision of the ASSURED criteria to REASSURED: Real-time connectivity, Ease of specimen collection, Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free or simple, and Deliverable to end-users. Many diagnostic tests have been developed that aim to satisfy the REASSURED criteria; however, most of them only detect a single target. With the progression of syndromic infections, coinfections and the current antimicrobial resistance challenges, the need for multiplexed diagnostics is now more important than ever. This review summarizes current diagnostic technologies for multiplexed detection and forecasts which methods have promise for detecting multiple targets and meeting all REASSURED criteria.

Clinical and Financial Impact of Rapid Antimicrobial Susceptibility Testing in Blood Cultures

The rapid identification of pathogens that cause bloodstream infections plays a vital role in the modern clinical microbiology laboratory. Despite demonstrating a significant reduction in turnaround time and a significant effect on clinical decisions, most methods do not provide complete antimicrobial susceptibility testing (AST) information. We employed rapid identification (ID) and AST using the Accelerate PhenoTest on positive blood cultures containing Gram-negative bacilli. The length of stay (LOS) significantly decreased from an average of 12.1 days prior to implementation to 6.6 days post-implementation (p = 0.02), representing potential total savings of USD 666,208.00. All-cause mortality did not differ significantly, 27 (19%) versus 18 (12%), p = 0.11. We also observed an associated decrease in the use of broad-spectrum antimicrobials, including meropenem and quinolones. The implementation of a rapid ID and AST method, along with a well-established antimicrobial stewardship program, has the potential to decrease LOS, broad-spectrum antibiotic use, and costs to the healthcare system, with no observable impact on mortality.

Nanotools for Sepsis Diagnosis and Treatment

Sepsis is one of the leading causes of death worldwide with high mortality rates and a pathological complexity hindering early and accurate diagnosis. Today, laboratory culture tests are the epitome of pathogen recognition in sepsis. However, their consistency remains an issue of controversy with false negative results often observed. Clinically used blood markers, C reactive protein (CRP) and procalcitonin (PCT) are indicators of an acute-phase response and thus lack specificity, offering limited diagnostic efficacy. In addition to poor diagnosis, inefficient drug delivery and the increasing prevalence of antibiotic-resistant microorganisms constitute significant barriers in antibiotic stewardship and impede effective therapy. These challenges have prompted the exploration for alternative strategies that pursue accurate diagnosis and effective treatment. Nanomaterials are examined for both diagnostic and therapeutic purposes in sepsis. The nanoparticle (NP)-enabled capture of sepsis causative agents and/or sepsis biomarkers in biofluids can revolutionize sepsis diagnosis. From the therapeutic point of view, currently existing nanoscale drug delivery systems have proven to be excellent allies in targeted therapy, while many other nanotherapeutic applications are envisioned. Herein, the most relevant applications of nanomedicine for the diagnosis, prognosis, and treatment of sepsis is reviewed, providing a critical assessment of their potentiality for clinical translation.

Establishment and application of a novel fluorescence-based analytical method for the rapid detection of viable bacteria in different samples

A rapid method for readily detecting the total numbers of viable bacterial cells in numerous samples (including surface water, solid inoculants, and soil samples) is reported using a newly developed hand-held fluorometer and a fluorescent dye Calcein UltraGreen™ AM. Compared to the traditional plate counting method that requires 48 hours of cultivation, the newly established method does not require any incubation time, making the detection method faster and more convenient. The portable rapid detection fluorometer has a wide dynamic range of relative fluorescence intensity from 45 to 30 133. It can detect bacterial concentration ranging from 10⁵ to 10¹⁰ cells per mL. This newly established method has good applicability for accurately and quickly detecting the cell number of viable bacteria in various samples. The results of the fluorescence-based method were compared with those of the traditional plate counting method, and it was found that the relative standard deviation was less than 6%. This new rapid measurement system provides a robust method for the rapid on-site detection of viable bacteria.

A Guide to Bacterial Culture Identification And Results Interpretation

PURPOSE

To provide a guide to interpreting bacterial culture results.

METHODS

Studies were identified via a PubMed literature search (from 1966 to January 2018). Search terms included microbial sensitivity tests, microbial drug resistance, and anti-infective agents/pharmacology. Articles were included if they were published in English. References within identified articles were also reviewed.

RESULTS

This paper reviewed core concepts of interpreting bacterial culture results, including timing of cultures, common culture sites, potential for contamination, interpreting the Gram stain, role of rapid diagnostic tests, conventional antibiotic susceptibility testing, and automated testing.

CONCLUSION

This guide can assist pharmacists in their role as integral members of the antimicrobial stewardship team in an effort to improve patient care.

Engineered Nanoparticles for Effective Redox Signaling During Angiogenic and Antiangiogenic Therapy

SIGNIFICANCE

Redox signaling plays a vital role in regulating various cellular signaling pathways and disease biology. Recently, nanomedicine (application of nanotechnology in biology and medicine) has been demonstrated to regulate angiogenesis through redox signaling. A complete understanding of redox signaling pathways influenced angiogenesis/antiangiogenesis triggered by therapeutic nanoparticles is extensively reviewed in this article. Recent Advances: In recent times, nanomedicines are regarded as the Trojan horses that could be employed for successful drug delivery, gene delivery, peptide delivery, disease diagnosis, and others, conquering barriers associated with conventional theranostic approaches.

CRITICAL ISSUES

Physiological angiogenesis is a tightly regulated process maintaining a balance between proangiogenic and antiangiogenic factors. The redox signaling is one of the main factors that contribute to this physiological balance. An aberrant redox signaling cascade can be caused by several exogenous and endogenous factors and leads to reduced or augmented angiogenesis that ultimately results in several disease conditions.

FUTURE DIRECTIONS

Redox signaling-based nanomedicine approach has emerged as a new platform for angiogenesis-related disease therapy, where nanoparticles promote angiogenesis via controlled reactive oxygen species (ROS) production and antiangiogenesis by triggering excessive ROS formation. Recently, investigators have identified different efficient nano-candidates, which modulate angiogenesis by controlling intracellular redox molecules. Considering the importance of angiogenesis in health care a thorough understanding of nanomedicine-regulated redox signaling would inspire researchers to design and develop more novel nanomaterials that could be used as an alternative strategy for the treatment of various diseases, where angiogenesis plays a vital role.

Pathogen enrichment from human whole blood for the diagnosis of bloodstream infection: Prospects and limitations

Blood culture represents the current reference method for the detection of bacteria or fungi in the circulation. To accelerate pathogen identification, molecular diagnostic methods, mainly based on polymerase chain reaction (PCR), have been introduced to ensure early and targeted antibiotic treatment of patients suffering from bloodstream infection. Still, these approaches suffer from a lack of sensitivity and from inhibition of PCR in a number of clinical samples, leading to false negative results. To overcome these limitations, various approaches aiming at the enrichment of pathogens from larger blood volumes prior to the extraction of pathogen DNA, thereby also depleting factors interfering with PCR, have been developed. Here, we provide an overview of current systems for diagnosing bloodstream infection, with a focus on approaches for pre-analytical pathogen enrichment, and highlight emerging applications of pathogen depletion for therapeutic purposes as a potential adjunctive treatment of sepsis patients.

Quantamatrix Multiplexed Assay Platform system for direct detection of bacteria and antibiotic resistance determinants in positive blood culture bottles

OBJECTIVES

Rapid and accurate identification of the causative pathogens of bloodstream infections (BSIs) is crucial for initiating appropriate antimicrobial therapy, which decreases the related morbidity and mortality rates. The aim of this study was to evaluate the usefulness of a newly developed multiplexed, bead-based bioassay system, the Quantamatrix Multiplexed Assay Platform (QMAP) system, obtained directly from blood culture bottles, to simultaneously detect the presence of bacteria and identify the genes for antibiotic resistance.

METHODS

The QMAP system was used to evaluate 619 blood culture bottles from patients with BSIs and to compare the results of conventional culture methods.

RESULTS

Using conventional bacterial cultures as the reference standard, the sensitivity, specificity, positive predictive value, and negative predictive value of the QMAP system for detection of bacterial pathogens in positive blood culture (PBC) samples were 99.8% (n=592, 95% CI 0.9852-1.000, p <0.001), 100% (95% CI 0.983-1.000, p <0.001), 100% (95% CI 0.9922-1.000, p <0.001), and 99.5% (95% CI 0.9695-1.000, p <0.001), respectively. In addition, sensitivity and specificity of the QMAP system for identification of the genes for antibiotic resistance were 99.4% (n=158, 95% CI 0.9617-0.9999, p <0.009) and 99.6% (95% CI 0.9763-0.9999, p <0.0001), respectively.

CONCLUSIONS

Obtaining results using the QMAP system takes about 3 hr, while culture methods can take 48-72 hr. Therefore, analysis using the QMAP system is rapid and reliable for characterizing causative pathogens in BSIs.

Analytical characterization of IgG–cTpp and IgG–Mn-cTpp conjugates

Herein, the conjugation of carboxylated tetraphenylporphyrin or its derivative containing manganese cation and model protein — immunoglobulin G is presented. The obtained IgG–cTpp and IgG–Mn-cTpp conjugates were subsequently used for model immunoassays construction. The IgG–cTpp formation was confirmed using size-exclusion chromatography. Thanks to the unique properties of applied labels the assay analysis was carried out with both spectrophotometric and spectrofluorimetric detection. The assays were performed creating semi-quantitative detection system using 96-well plates. The incubation time, ensuring full saturation of the surface with secondary antibodies was also optimized. Moreover, in the case of IgG–Mn-cTpp conjugates we present the possibility of both direct and indirect determination of the label, the latter based on the catalytic activity of Mn-cTpp, which allows for amplification of the measured signal. We proved that both cTpp and Mn-cTpp may be successfully used for protein labeling and serve as universal tracers for various formats of affinity assays and sensors.

Contemporary genomic approaches in the diagnosis and typing of Staphylococcus aureus

Staphylococcus aureus is a major human pathogen, causing disease in both community and healthcare settings. Over the past two decades, the epidemiology of S. aureus disease has changed dramatically, with the emergence and spread of community-associated methicillin-resistant S. aureus clones. This epidemiological shift, coupled with the association between delayed antimicrobial therapy and increased mortality in S. aureus bacteraemia, has greatly facilitated advances in the rapid molecular diagnosis of S. aureus. Rapid molecular testing for S. aureus can greatly reduce laboratory turnaround time, and in some circumstances, may lead to improved clinical outcomes. In addition, advances in DNA sequencing technology and bioinformatic analysis have shed new lights on the molecular epidemiology and transmission dynamics of S. aureus. In this context, we provide an overview of the key advances in the molecular diagnosis and typing of S. aureus, with a particular focus on the clinical impact and utility of genomic technologies.

A rapidly fatal sepsis caused by listeria monocytogenes type-4b in a patient with chronic renal failure

INTRODUCTION

Listeria monocytogenes is a significant zoonosis causing invasive infections in the susceptible persons. The current paper presented a patient who died due to a rapidly-progressing multiple organ failure (MOF) as a result of severe sepsis caused by L. monocytogenes.

CASE PRESENTATION

A 70-years-old patient with chronic renal failure was admitted to the infectious diseases clinic due to diarrhea for one day. He was hospitalized and the body fluid samples were collected for laboratory analyses. Within few hours, his vital findings worsened, and he developed respiratory arrest. Ceftriaxone and gentamycin were administrated. However, he died due to disseminated intravascular coagulation, septic shock and meningoencephalitis at the 22nd hour of admission. Causative agent was identified as L. monocytogenes serotype-4b in post-mortem period.

DISCUSSION

L. monocytogenes can cause progressive and rapidly fatal infections in the vulnerable persons, with multisystem involvement. Since this bacterium is not susceptible to cephalosporines, it will be better to consider effective antimicrobials in the treatment of the possible cases.

The SUCCESS model for laboratory performance and execution of rapid molecular diagnostics in patients with sepsis

Successful performance and execution of rapid diagnostics in a clinical laboratory hinges heavily on careful validation, accurate and timely communication of results, and real-time quality monitoring. Laboratories must develop strategies to integrate diagnostics with stewardship and evidence-based clinical practice guidelines. We present a collaborative SUCCESS model for execution and monitoring of rapid sepsis diagnostics to facilitate timely treatment. Six months after execution of the Verigene Gram-Positive Blood Culture (BC-GP) and the AdvanDx PNA-FISH assays, data were collected on 579 and 28 episodes of bacteremia and fungemia, respectively. Clinical testing was executed using a SUCCESS model comprising the following components: stewardship, utilization of resources, core strategies, concierge services, education, support, and surveillance. Stewardship needs were identified by evaluating the specialty services benefiting from new testing. Utilization of resources was optimized by reviewing current treatment strategies and antibiogram and formulary options. Core strategies consisted of input from infectious disease leadership, pharmacy, and laboratory staff. Concierge services included automated Micro-eUpdate and physician-friendly actionable reports. Education modules were user-specific, and support was provided through a dedicated 24/7 microbiology hotline. Surveillance was performed by daily audit by the director. Using the SUCCESS model, the turnaround time for the detailed report with actionable guidelines to the physician was ∼3 hours from the time of culture positivity. The overall correlation between rapid methods and culture was 94% (546/579). Discrepant results were predominantly contaminants such as a coagulase-negative staphylococci or viridans streptococci in mixed cultures. SUCCESS is a cost-effective and easily adaptable model for clinical laboratories with limited stewardship resources.

Direct identification of Gram-positive bacteria and resistance determinants from blood cultures using a microarray-based nucleic acid assay: in-depth analysis of microarray data for undetermined results

BACKGROUND

The Verigene Gram-Positive Blood Culture (BC-GP) nucleic acid assay (Nanosphere, Inc., Northbrook, IL, USA) is a newly developed microarray-based test with which 12 Gram-positive bacterial genes and three resistance determinants can be detected using blood culture broths. We evaluated the performance of this assay and investigated the signal characteristics of the microarray images.

METHODS

At the evaluation stage, we tested 80 blood cultures that were positive for various bacteria (68 bacteria covered and 12 not covered by the BC-GP panel) collected from the blood of 36 patients and 44 spiked samples. In instances where the automated system failed and errors were called, we manually inspected microarray images, measured the signal intensities of target spots, and reclassified the results.

RESULTS

With the manual analysis of the microarray images of 14 samples for which error calls were reported, we could obtain correct identification results for 12 samples without the need for retesting, because strong signals in the target spots were clearly discriminable from background noise. With our interpretation strategy, we could obtain 97.1% sensitivity and 100% specificity for bacterial identification by using the BC-GP assay. The two unidentified bacteria were viridans group streptococci, which produced weaker target signals. During the application stage, among 25 consecutive samples positive for Gram-positive bacteria, we identified two specimens with error calls as Streptococcus spp. by using manual analysis.

CONCLUSIONS

With help of the manual review of the microarray images, the BC-GP assay could successfully identify species and resistance markers for many clinically important Gram-positive bacteria.

Technology in MicroRNA Profiling: Circulating MicroRNAs as Noninvasive Cancer Biomarkers in Breast Cancer

This report describes technologies to identify and quantify microRNAs (miRNAs) as potential cancer biomarkers, using breast cancer as an example. Most breast cancer patients are not diagnosed until the disease has advanced to later stages, which decreases overall survival rates. Specific miRNAs are up- or downregulated in breast cancer patients at various stages, can be detected in plasma and serum, and have shown promising preliminary clinical sensitivity and specificity for early cancer diagnosis or staging. Nucleic acid testing methods to determine relative concentrations of selected miRNAs include reverse transcription, followed by quantitative PCR (RT-qPCR), microarrays, and next-generation sequencing (NGS). Of these methods, NGS is the most powerful approach for miRNA biomarker discovery, whereas RT-qPCR shows the most promise for eventual clinical diagnostic applications.

Performance evaluation of the Verigene® (Nanosphere) and FilmArray® (BioFire®) molecular assays for identification of causative organisms in bacterial bloodstream infections

Molecular assays designed to provide bacterial identification and detection of resistance genes directly from positive blood cultures can significantly reduce the time to definitive results. This has the potential to improve patient management and antimicrobial stewardship. However, the extent of such an impact is yet to be fully assessed. We tested two such assays, the Verigene® System Bloodstream Infection Tests (Nanosphere, Inc., Northbrook, IL, USA) (both Gram-positive and Gram-negative cartridges) and the FilmArray® Blood Culture Identification Panel (BioFire® Diagnostics, Inc., Salt Lake City, UT, USA). We compared their accuracy and speed of organism and resistance gene identification to conventional culture-based methods for 173 positive blood cultures. We also retrospectively determined, for organisms deemed not to be contaminants, the potential impact on antimicrobial prescribing. Both the Verigene® and FilmArray® assays accurately identified organisms, on average, 27.95 and 29.17 h earlier than conventional methods, respectively. There were a significant number of false-positives for Pseudomonas aeruginosa with the FilmArray® assay, which may have been related to contamination of the bioMérieux BacT standard anaerobic blood culture bottles, which the manufacturer has acknowledged. Both panels provided results significantly faster than conventional methods. In our setting, the extent of the potential positive impact on antimicrobial prescribing was modest (9 out of 173 samples). However, this may be an underestimation, since probable contaminants were not included in this analysis. In conclusion, both panels gave accurate results with significantly improved turnaround times.

Evaluation of Verigene Gram-Positive Blood Culture Assay performance for bacteremic patients

The Verigene Gram-Positive Blood Culture (BC-GP) Assay (Nanosphere Inc., Northbrook, IL) is a microarray-based test designed to rapidly identify directly from positive blood cultures multiple bacterial species and their antimicrobial resistance markers. Nonduplicate blood cultures from 118 patients admitted to Erasme Hospital were prospectively enrolled. All but six organisms were members of the panel (95.6 %). For the identification of pathogens and detection of the mecA gene, the agreement with routine methods was 87.6 % and 97.7 %, respectively. The performance of the BC-GP assay was lower with polymicrobial than with monomicrobial blood cultures. Another concern of the BC-GP assay was the misidentification of Streptococcus mitis as S. pneumoniae (3/8). The BC-GP assay is a rapid and accurate tool for the simultaneous detection of multiple sepsis-causing bacteria and resistant genes from blood cultures, which could have an impact on patient management and healthcare cost.

Nanomedicine in the Management of Microbial Infection - Overview and Perspectives

For more than 2 billion years, microbes have reigned on our planet, evolving or outlasting many obstacles they have encountered. In the 20th century, this trend took a dramatic turn with the introduction of antibiotics and vaccines. Nevertheless, since then, microbes have progressively eroded the effectiveness of previously successful antibiotics by developing resistance, and many infections have eluded conventional vaccine design approaches. Moreover, the emergence of resistant and more virulent strains of bacteria has outpaced the development of new antibiotics over the last few decades. These trends have had major economic and health impacts at all levels of the socioeconomic spectrum - we need breakthrough innovations that could effectively manage microbial infections and deliver solutions that stand the test of time. The application of nanotechnologies to medicine, or nanomedicine, which has already demonstrated its tremendous impact on the pharmaceutical and biotechnology industries, is rapidly becoming a major driving force behind ongoing changes in the antimicrobial field. Here we provide an overview on the current progress of nanomedicine in the management of microbial infection, including diagnosis, antimicrobial therapy, drug delivery, medical devices, and vaccines, as well as perspectives on the opportunities and challenges in antimicrobial nanomedicine.

Performance of the Verigene Gram-negative blood culture assay for rapid detection of bacteria and resistance determinants

Nonduplicate blood cultures that were positive for Gram-negative bacilli (n = 125) were tested by the Verigene Gram-negative blood culture (BC-GN) assay; 117 (90.7%) isolates were members of the panel. For identification and resistance markers, the agreements with routine methods were 97.4% (114/117) and 92.3% (12/13). The BC-GN assay is a rapid and accurate tool for the detection of pathogens from blood cultures and could be integrated alongside conventional systems to enable faster patient management, but the clinical benefits should be further evaluated.

Evaluation of three rapid diagnostic methods for direct identification of microorganisms in positive blood cultures

The identification of organisms from positive blood cultures generally takes several days. However, recently developed rapid diagnostic methods offer the potential for organism identification within only a few hours of blood culture positivity. In this study, we evaluated the performance of three commercial methods to rapidly identify organisms directly from positive blood cultures: QuickFISH (AdvanDx, Wolburn, MA), Verigene Gram-Positive Blood Culture (BC-GP; Nanosphere, Northbrook, IL), and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) with Sepsityper processing (Bruker Daltonics, Billerica, MA). A total of 159 blood cultures (VersaTREK Trek Diagnostic Systems, Cleveland, OH) positive for Gram-positive and Gram-negative bacteria as well as yeast were analyzed with QuickFISH and MALDI-TOF MS. In all, 102 blood cultures were analyzed using the BC-GP assay. For monomicrobial cultures, we observed 98.0% concordance with routine methods for both QuickFISH (143/146) and the BC-GP assay (93/95). MALDI-TOF MS demonstrated 80.1% (117/146) and 87.7% (128/146) concordance with routine methods to the genus and species levels, respectively. None of the methods tested were capable of consistently identifying polymicrobial cultures in their entirety or reliably differentiating Streptococcus pneumoniae from viridans streptococci. Nevertheless, the methods evaluated in this study are convenient and accurate for the most commonly encountered pathogens and have the potential to dramatically reduce turnaround time for the provision of results to the treating physician.

The role of the microbiology laboratory in antimicrobial stewardship programs

One of the impediments to the success of antimicrobial stewardship is the lack of availability of rapid and sensitive laboratory tests. The last decade has seen an explosion in new technologies that permit, in less than 4 hours, the identification of organisms and their resistance markers. In addition, the use of biomarkers has been explored in algorithms to distinguish infections that require antimicrobial agents. Clinical microbiology laboratories also contribute to the success of stewardship programs through compilation of aggregate antimicrobial susceptibility data. This article reviews rapid diagnostics, the use of biomarkers, and antibiogram development to antimicrobial stewardship activities and the subsequent impact on patient outcomes.

Nonculture techniques for the detection of bacteremia and fungemia

ABSTRACT: 

Bacteremia and fungemia account for a substantial proportion of all cases of severe sepsis. Antibiotic resistance is a contributing factor in many hospital-acquired infection deaths. Traditional phenotypic methods for the identification of bacteria and yeasts from positive blood cultures and determining antimicrobial susceptibility require 48–72 h, delaying optimal therapy and negatively impacting patient outcomes. Molecular methods, including nonamplified DNA probe panels and peptide nucleic acid probes, and nucleic acid amplification methods such as PCR, proteomic methods (matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry) and direct biochemical tests provide more rapid identification of bacteria and fungi, and in some cases antimicrobial resistance markers, from positive blood cultures, as well as directly from whole blood. These methods vary in the breadth of organisms that they detect, and equally important, their ease of use. This article examines the principles, performance and practicality of the various rapid, nonculture techniques for the detection of bacteremia and fungemia.

Direct identification of bacteria in positive blood cultures: comparison of two rapid methods, FilmArray and mass spectrometry

We evaluated the accuracy and performance of the FilmArray Direct from Positive Blood Culture system (BCID) (BioFire Diagnostics, Salt Lake City, UT, USA) and the VITEK Mass Spectrometry System (Vitek MS; bioMerieux, Durham, NC, USA) to identify bacterial isolates from 161 positive blood culture bottles. The BCID uses multiplex PCR to identify 90-95% of common isolates to the genus or species/complex level as well as mecA, Van A/B, and bla(KPC) genes in approximately 1 hour. Of 151 monomicrobic isolates, the FilmArray correctly identified 48/49 (98%) to the genus and 84/84 (100%) to the species/complex level, while 18/151 (12%) gave no identification, as expected from the database. Mass spectrometry correctly identified 142/151 (94%) monomicrobic cultures to the genus level, 137/151 (91%) to the species level, with only 8/151(5%) giving no identification. Although mass spectrometry has a much larger database, the filtration system was cumbersome in contrast to the 3-5 minutes hands-on-time for the BCID.

Molecular diagnosis of sepsis: New aspects and recent developments

By shortening the time to pathogen identification and allowing for detection of organisms missed by blood culture, new molecular methods may provide clinical benefits for the management of patients with sepsis. While a number of reviews on the diagnosis of sepsis have recently been published we here present up-to-date new developments including multiplex PCR, mass spectrometry and array techniques. We focus on those techniques that are commercially available and for which clinical studies have been performed and published.

Evaluation of the nanosphere verigene gram-positive blood culture assay with the VersaTREK blood culture system and assessment of possible impact on selected patients

The Verigene Gram-positive blood culture (BC-GP) assay (Nanosphere, Northbrook, IL) is a molecular method for the rapid identification of Gram-positive organisms and resistance markers directly from blood culture bottles. A total of 148 VersaTREK REDOX 1 40-ml aerobic bottles demonstrating Gram-positive bacteria were tested. Results were compared with those from conventional biochemical and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identifications. We obtained isolates of methicillin-resistant Staphylococcus aureus (MRSA) (24), methicillin-susceptible Staphylococcus aureus (MSSA) (14), methicillin-resistant Staphylococcus epidermidis (MRSE) (17), methicillin-susceptible Staphylococcus epidermidis (MSSE) (9), other coagulase-negative staphylococci (19), Streptococcus salivarius (5), Streptococcus parasanguinis (2), Streptococcus sanguinis (1), Streptococcus cristatus (1), the Streptococcus bovis group (5), Streptococcus agalactiae (9), the Streptococcus anginosus group (1), Streptococcus pneumoniae (6), vancomycin-resistant Enterococcus faecium (VRE FCM) (16), vancomycin-susceptible Enterococcus faecalis (3), Aerococcus viridans (2), Bacillus (6), Corynebacterium (8), Lactobacillus (2), Micrococcus (2), Neisseria mucosa (1), Escherichia coli (3), Candida tropicalis (1), Propionibacterium (1), and Rothia (1). Overall agreement with the culture results was 95%. A total of 137 of 138 (99%) monomicrobial cultures were concordant. We tested 9 polymicrobial samples and found 33% agreement. A chart review of 31 patients with MRSA, MSSA, or VRE demonstrated that the Nanosphere BC-GP assay might have led to more appropriate antibiotic selection for these patients an average of 42 h earlier. Additionally, contact isolation could have been initiated an average of 37 h earlier for patients with MRSA or VRE. The BC-GP assay may have a positive impact on patient care, health care costs, and antibiotic stewardship.

Commercial multiplex technologies for the microbiological diagnosis of sepsis

In patients with suspected sepsis, rapid and accurate diagnosis of the causative infectious agent is critical. Although clinicians often use empiric antimicrobial therapy until the blood cultures are available to potentially adjust treatment, this approach is often not optimum for patient care. Recently, several commercial molecular multiplex technologies have shown promise for fast and comprehensive diagnosis of microorganisms and their antimicrobial resistance signatures. While one class of multiplex technologies is directed at improving the speed and diagnostic information obtained from positive blood cultures, the other identifies the causative microorganisms directly from clinical blood samples. This review provides an overview of these molecular technologies and describes their performance capabilities compared to standard blood cultures and in some cases to each other. We discuss the current clinical impact, limitations, and likely futures advances these multiplex technologies may have in guiding the management of patients with sepsis.

Evaluation of the Verigene Gram-positive blood culture nucleic acid test for rapid detection of bacteria and resistance determinants

Rapid identification of pathogens from blood cultures can decrease lengths of stay and improve patient outcomes. We evaluated the accuracy of the Verigene Gram-positive blood culture (BC-GP) nucleic acid test for investigational use only (Nanosphere, Inc., Northbrook, IL) for the identification of Gram-positive bacteria from blood cultures. The detection of resistance genes (mecA in Staphylococcus aureus and Staphylococcus epidermidis and vanA or vanB in Enterococcus faecium and Enterococcus faecalis) by the BC-GP assay also was assessed. A total of 186 positive blood cultures (in BacT/Alert FA bottles) with Gram-positive cocci observed with Gram staining were analyzed using the BC-GP assay. The BC-GP results were compared with the identification and susceptibility profiles obtained with routine methods in the clinical laboratory. Discordant results were arbitrated with additional biochemical, cefoxitin disk, and repeat BC-GP testing. The initial BC-GP organism identification was concordant with routine method results for 94.6% of the blood cultures. Only 40% of the Streptococcus pneumoniae identifications were correct. The detection of the mecA gene for 69 blood cultures with only S. aureus or S. epidermidis was concordant with susceptibility testing results. For 3 of 6 cultures with multiple Staphylococcus spp., mecA detection was reported but was correlated with oxacillin resistance in a species other than S. aureus or S. epidermidis. The detection of vanA agreed with susceptibility testing results for 45 of 46 cultures with E. faecalis or E. faecium. Comparison of the mean times to results for each organism group showed that BC-GP results were available 31 to 42 h earlier than phenotypic identifications and 41 to 50 h earlier than susceptibility results.