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

Performance of molecular tests for diagnosis of bloodstream infections in the clinical setting: a systematic literature review and meta-analysis

BACKGROUND

Rapid identification of bloodstream pathogens and associated antimicrobial resistance (AMR) profiles by molecular tests from positive blood cultures (PBCs) have the potential to improve patient management and clinical outcomes.

OBJECTIVES

A systematic review and meta-analysis were conducted to evaluate diagnostic test accuracy (DTA) of molecular tests from PBCs for detecting pathogens and AMR in the clinical setting.

METHODS

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DATA SOURCES

Medline, Embase, Cochrane, conference proceedings, and study bibliographies were searched.

STUDY ELIGIBILITY CRITERIA

Studies evaluating DTA of commercially available molecular tests vs. traditional phenotypic identification and susceptibility testing methods in patients with PBCs were eligible.

PARTICIPANTS

Patients with PBCs.

TESTS

Commercially available molecular tests.

REFERENCE STANDARD

Traditional phenotypic identification and susceptibility testing methods (standard of care, SOC).

ASSESSMENT OF RISK OF BIAS

Study quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2.

METHODS OF DATA SYNTHESIS

Summary DTA outcomes were estimated using bivariate random-effects models for gram-negative bacteria (GNB), gram-positive bacteria (GPB), yeast, GNB-AMR, GPB-AMR, and specific targets when reported by ≥ 2 studies (PROSPERO CRD42023488057).

RESULTS

Seventy-four studies including 24 590 samples were analysed, most of which had a low risk of bias. When compared with SOC, molecular tests showed 92-99% sensitivity, 99-100% specificity, 99-100% positive predictive value, and 97-100% negative predictive value for identifying total GNB (43 studies), GPB (38 studies), yeast (24 studies), GNB-AMR (35 studies), and GPB-AMR (39 studies). For individual pathogen targets, 93-100% sensitivity, 98-100% specificity, 86-100% positive predictive value, and 99-100% negative predictive value were estimated. Five of seven AMR genes had 91-99% sensitivity and 99-100% specificity. Sensitivity was lower for IMP (four studies; 62%; 95% CI, 34-83%) and VIM (four studies; 70%; 95% CI, 38-90%) carbapenemases, where genes were not detected or were not harboured in Pseudomonas aeruginosa (i.e. low prevalence). Performance of molecular tests in detecting AMR was generally comparable when grouped by geographical region (Europe, North America, and East Asia).

DISCUSSION

High DTA support the use of molecular tests in identifying a broad panel of pathogens and detecting AMR in GNB and GPB.

Guardians of resistance and virulence: detection of mec, femA, Van, pvl, hlg and spa genes in methicillin and vancomycin-resistant Staphylococcus aureus from clinical and food samples in Southwestern Nigeria

BACKGROUND

Staphylococcus aureus strains are highly virulent and associated with an eclectic range of severe nosocomial and community-acquired infections.

OBJECTIVES

This study assessed methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA/VRSA) from clinical and ready-to-eat (RTE) food sources, screened for antibiotic resistance; and molecular determinants of antibiotic and virulence genes.

METHODS

Altogether, 465 clinical and RTE food samples were analyzed via conventional microbiological techniques and S. aureus identification was confirmed by nuc gene detection. Phenotypic screening for methicillin and vancomycin-resistance was by agar-screen cum micro-broth dilution respectively, while antibiotic susceptibility testing was done by the disc-diffusion technique. VanA/vanB/VanC1, femA, mecA/mecC; pvl/hlg and spa gene detection was via Polymerase chain reaction.

RESULTS

Phenotypically, 211 Staphylococcal isolates were recovered, 138 (65.4%) of them carrying the nuc gene - all 138 (100.0%) were VRSA, while 59/138 (42.8%) were MRSA phenotypically. Overall, 114/138 (82.6%), 7/138 (5.1%), and 6/138 (4.3%) of isolates had the femA, mecA, and mecC genes, while van genes were detected in only 3 (2.2%) isolates, with virulence determinants pvl, hlg, and spa gene carriage in 8 (5.8%), 10 (7.2%), and 77 (55.8%) isolates respectively. In all, 11.6% carried resistance-associated genes, 55.8% carried virulence genes, and co-detection of resistance and virulence genes was observed in 12.3%. Overall, 96/138 (69.6%) were multidrug-resistant (MDR), while one strain was extremely drug-resistant (XDR). MAR Indices ≥ 0.2 was observed in 83.3% of isolates.

CONCLUSION

This study highlights virulence levels of MRSA and VRSA circulating strains in Osogbo, contributing to their sustained surveillance, and improving available data for successive epidemiology investigations. This study also reports the occurrence of the mecC gene in S. aureus isolates from RTE foods and human samples in Southwestern Nigeria.

Identification of sepsis-causing bacteria from whole blood without culture using primers with no cross-reactivity to human DNA

Sepsis is a major health concern globally, and identification of the causative organism usually takes several days. Furthermore, molecular amplification using whole blood from patients with sepsis remains challenging because of primer cross-reactivity with human DNA, which can delay appropriate clinical intervention. To address these concerns, we designed primers that could reduce cross-reactivity. By evaluating these primers against human DNA, we confirmed that the cross-reactivity observed with conventional primers was notably absent. In silico PCR further demonstrated the specificity and efficiency of the designed primers across 23 bacterial species that are often associated with sepsis. When tested using blood samples from sepsis patients, the designed primers showed moderate sensitivity and high specificity. Surprisingly, our method identified bacteria even in samples that were detected at other sites but tested negative using conventional blood culture methods. Although we identified some challenges, such as contamination with Acetobacter aceti due to the saponin pretreatment of samples, the developed method demonstrates remarkable potential for rapid identification of the causative organisms of sepsis and provides a new avenue for diagnosis in clinical practice.

Characterization of initial CLABSI culture results to support antimicrobial de-escalation in pediatric GI inpatients

OBJECTIVES

Central Line-associated Bloodstream Infections (CLABSIs) pose a serious mortality and morbidity risk. An institutional protocol was developed for the evaluation and empirical antibiotic treatment of possible CLABSIs. The potential impact of de-escalating antimicrobial therapy based on initial Gram stain and molecular identification was assessed.

METHODS

All positive blood cultures from patients admitted to the gastroenterology service at a large pediatric medical center were collected from 1/1/14 to 12/31/20. Cultures that were negative, repeated, or causative organisms that were unable to be identified with susceptibility data were excluded. Timepoints and organism(s) from each culture were recorded. Polymicrobial cultures were classified as containing only gram-positive organisms (polymicrobial GP), only gram-negative organisms (polymicrobial GN), or mixed spectrum.

RESULTS

During the 6-year period, 361 positive blood cultures were included in the study. Single isolates were identified in 79.5% (287/361) of cultures. Polymicrobial cultures from confirmed central line source accounted for 15.0% (54/361), with 6.4% (23/361) Polymicrobial GP, 4.4% (16/361) Polymicrobial GN, and 4.2% (15/361) being mixed-spectrum cultures. Both organism types were detected on initial gram-stain in 40% (6/15) of the mixed-spectrum cultures, another 26.7% (4/15) had the opposite-spectrum organism identified within an average of <3 h and the remaining 33.3% (5/15) had the opposite-spectrum organism identified by culture growth.

CONCLUSIONS

Polymicrobial mixed-spectrum cultures accounted for <5% of positive blood cultures and most isolates were identified within 3 h of first positivity. This may allow for further investigation of early de-escalation of therapy for this population and limit antimicrobial exposure.

Clinical evaluation of polymerase chain reaction coupled with quantum dot fluorescence analysis in the identification of bacteria and yeasts in patients with suspected bloodstream infections

Bloodstream infections are serious and complex infectious diseases that often require a rapid diagnosis. Polymerase chain reaction coupled with quantum dot fluorescence analysis (PCR-QDFA) is a novel diagnostic technique. This study aimed to evaluate the diagnostic performance of PCR-QDFA for pathogen detection in patients with suspected bloodstream infections (BSIs). It evaluates 29 kinds of common pathogens (24 bacteria and 5 yeasts) from blood culture bottles. The results of PCR-QDFA identification and traditional microbial laboratory identification were compared, and the latter was used as the 'gold standard' to analyse the diagnostic performance of the PCR-QDFA. In total, 517 blood culture bottles were included in this study. The PCR-QDFA identified microorganisms in 368/422 (87.2%) samples with monomicrobial growth. For the pathogens on the PCR-QDFA list, the assay showed a higher sensitivity of 97.4% (368/378). When polymicrobial growth was analysed, the PCR-QDFA successfully detected 19/25 (76%) microorganisms on the PCR-QDFA list. In addition, 82/82 negative blood culture bottles also showed no pathogens by PCR-QDFA with a specificity of 100%. In conclusion, the PCR-QDFA assay could identify a majority of the common pathogens encountered in clinical practice, showing excellent diagnostic performance for pathogen detection in patients with suspected BSIs.

Quick detection of causative bacteria in cases of acute cholangitis and cholecystitis using a multichannel gene autoanalyzer

PURPOSES

Acute cholangitis and cholecystitis can become severe conditions as a result of inappropriate therapeutic administration and thereafter become increasingly resistant to antimicrobial treatment. The simultaneous detection of the bacterial nucleic acid and antimicrobial resistance gene is covered by the national health insurance program in Japan for sepsis. In this study, we evaluate the use of a multichannel gene autoanalyzer (Verigene system) for the quick detection of causative bacteria in cases of acute cholangitis and cholecystitis.

METHODS

This study included 108 patients diagnosed with acute cholangitis or cholecystitis between June 2015 and November 2018. A bacterial culture test and Verigene assay were used to evaluate the bile samples.

RESULTS

The most commonly isolated bacteria were Escherichia coli, which includes six extended-spectrum beta-lactamase (ESBL)-producing E. coli. Among the patients with positive bile cultures, bacteria were detected in 35.7% of cases via the Verigene system. The detection rates of the Verigene system significantly increased when the number of bacterial colonies was ≥ 10⁶ colony-forming unit (CFU)/mL (58.1%). Cases with a maximum colony quantity of ≥ 10⁶ CFU/mL exhibited higher inflammation, suggesting the presence of a bacterial infection.

CONCLUSIONS

The Verigene system might be a new method for the quick detection of causative bacteria in patients with infectious acute cholangitis and cholecystitis.

Recent advances in rapid antimicrobial susceptibility testing systems

INTRODUCTION

Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged.

AREAS COVERED

Advances in rapid phenotypic and molecular-based AST systems.

EXPERT OPINION

AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.

Rapid isolation of rare targets from large fluid volumes

Rapidly isolating rare targets from larger, clinically relevant fluid volumes remains an unresolved problem in biomedicine and diagnosis. Here, we describe how 3D particle sorting can enrich targets at ultralow concentrations over 100-fold within minutes not possible with conventional approaches. Current clinical devices based on biochemical extraction and microfluidic solutions typically require high concentrations and/or can only process sub-milliliter volumes in time. In a proof-of-concept application, we isolated bacteria from whole blood as demanded for rapid sepsis diagnosis where minimal numbers of bacteria need to be found in a 1–10 mL blood sample. After sample encapsulation in droplets and target enrichment with the 3D particle sorter within a few minutes, downstream analyses were able to identify bacteria and test for antibiotic susceptibility, information which is critical for successful treatment of bloodstream infections.

Updates on Rapid Diagnostic Tests in Infectious Diseases

In the last two decades there have been dramatic advances in development of rapid diagnostic tests. Turnaround time of the assays have significantly been shortened which led to reductions in time to appropriate antimicrobial therapy and improvement of patient clinical outcomes. Molecular-based assays generally have better sensitivity than conventional methods, but the cost is higher. The results need to be interpreted cautiously as detection of colonized organisms, pathogen detection in asymptomatic patients, and false negative/positive can occur. Indications and cost-effectiveness need to be considered for appropriate utilization of rapid diagnostic tests.

Therapeutic Nanoparticles and Their Targeted Delivery Applications

Nanotechnology offers many advantages in various fields of science. In this regard, nanoparticles are the essential building blocks of nanotechnology. Recent advances in nanotechnology have proven that nanoparticles acquire a great potential in medical applications. Formation of stable interactions with ligands, variability in size and shape, high carrier capacity, and convenience of binding of both hydrophilic and hydrophobic substances make nanoparticles favorable platforms for the target-specific and controlled delivery of micro- and macromolecules in disease therapy. Nanoparticles combined with the therapeutic agents overcome problems associated with conventional therapy; however, some issues like side effects and toxicity are still debated and should be well concerned before their utilization in biological systems. It is therefore important to understand the specific properties of therapeutic nanoparticles and their delivery strategies. Here, we provide an overview on the unique features of nanoparticles in the biological systems. We emphasize on the type of clinically used nanoparticles and their specificity for therapeutic applications, as well as on their current delivery strategies for specific diseases such as cancer, infectious, autoimmune, cardiovascular, neurodegenerative, ocular, and pulmonary diseases. Understanding of the characteristics of nanoparticles and their interactions with the biological environment will enable us to establish novel strategies for the treatment, prevention, and diagnosis in many diseases, particularly untreatable ones.

A new culture-based method for rapid identification of microorganisms in polymicrobial blood cultures by MALDI-TOF MS

Background

The application of matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) to microbial identification has allowed the development of rapid methods for identification of microorganisms directly in positive, blood cultures (BCs). These methods can yield accurate results for monomicrobial BCs, but often fail to identify multiple microorganisms in polymicrobial BCs. The present study was aimed at establishing a rapid and simple method for identification of bacteria and yeast in polymicrobial BCs from patients with bloodstream infection.

Results

The rapid method herein proposed is based on short-term culture in liquid media allowing selective growth of microorganisms recovered from polymicrobial BCs, followed by rapid identification by MALDI-TOF MS. To evaluate the accuracy of this method, 56 polymicrobial BCs were comparatively analyzed with the rapid and routine methods. The results showed concordant identification for both microbial species in 43/50 (86%) BCs containing two different microorganisms, and for two microbial species in six BCs containing more than two different species. Overall, 102/119 (85.7%) microorganisms were concordantly identified by the rapid and routine methods using a cut-off value of 1.700 for valid identification. The mean time to identification after BC positivity was about 4.2 h for streptococci/enterococci, 8.7 h for staphylococci, 11.1 h for Gram-negative bacteria, and 14.4 h for yeast, allowing a significant time saving compared to the routine method.

Conclusions

The proposed method allowed rapid and reliable microbial identification in polymicrobial BCs, and could provide clinicians with timely, useful information to streamline empirical antimicrobial therapy in critically ill patients.

A Healthcare Improvement Intervention Combining Nucleic Acid Microarray Testing With Direct Physician Response for Management of Staphylococcus aureus Bacteremia

Background

Nucleic acid microarray (NAM) testing for detection of Staphylococcus aureus bacteremia (SAB) and S. aureus resistance gene determinants can reduce time to targeted antibiotic administration. Evidence-based management of SAB includes bedside infectious diseases (ID) consultation. As a healthcare improvement initiative at our institution, with the goal of improving management and outcomes for subjects with SAB, we implemented NAM with a process for responding to positive NAM results by directly triggered, mandatory ID consultation.

Methods

Preintervention, SAB was identified by traditional culture and results passively directed to antibiotic stewardship program (ASP) pharmacists. Postintervention, SAB in adult inpatients was identified by Verigene Gram-Positive Blood Culture test, results paged directly to ID fellow physicians, and consultation initiated immediately. In the new process, ASP assisted with management after the initial consultation. A single-center, retrospective, pre-/postintervention analysis was performed.

Results

One hundred six preintervention and 120 postintervention subjects were assessed. Time to ID consultation after notification of a positive blood culture decreased 26.0 hours (95% confidence interval [CI], 45.1 to 7.1 hours, P < .001) postintervention compared with preintervention. Time to initiation of targeted antibiotic decreased by a mean of 21.2 hours (95% CI, 31.4 to 11.0 hours, P < .001) and time to targeted antibiotics for methicillin-sensitive S. aureus decreased by a mean of 40.7 hours (95% CI, 58.0 to 23.5 hours, P < .001). The intervention was associated with lower in-hospital (13.2% to 5.8%, P = .047) and 30-day (17.9% to 8.3%, P = .025) mortality.

Conclusions

Compared with an ASP-directed response to traditionally detected SAB, an efficient physician response to NAM was associated with improved care and outcomes for SAB.

Accelerating Initiation of Adequate Antimicrobial Therapy Using Real-Time Decision Support and Microarray Testing

Introduction:

Bloodstream infections (BSI) represent a common cause of sepsis and mortality in children. Early and adequate empirical antimicrobial therapy is a critical component of successful treatment of BSI. Rapid PCR-based diagnostic technologies, such as nucleic acid microarrays, can decrease the time needed to identify pathogens and antimicrobial resistance and have the potential to ensure patients are started on adequate antibiotics as early as possible. However, without appropriate processes to support timely and targeted interpretation of these results, these advantages may not be realized in practice.

Methods:

Our Antimicrobial Stewardship Program (ASP) implemented a quality improvement initiative using the Institute for Healthcare Improvement’s Model for Improvement to decrease the time between a nucleic acid microarray result for Gram-positive bacteremia and the time a patient was placed on adequate antimicrobial therapy. The primary effective intervention was a near real-time notification system to the managing physicians of inadequate antimicrobial therapy via a call from the ASP team.

Results:

Following the intervention, the average time to adequate antimicrobial therapy in patients with Gram-positive BSI and inadequate coverage decreased from 38 hours with the nucleic acid microarray result alone to 4.7 hours when results were combined with an ASP clinical decision support intervention, an 87% reduction.

Conclusions:

The positive effects of rapid-detection technologies to improve patient care are enhanced when combined with clinical decision support tools that can target inadequate antimicrobial treatments in near real time.

A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections

With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.

Reliability of the Verigene system for the identification for Gram-positive Bacteria and detection of antimicrobial resistance markers from children with bacteremia

BACKGROUND

Targeted antimicrobial therapy can reduce morbidity in patients with sepsis. Molecular methodologies used in the clinical laboratory can provide information about infectious agents faster than traditional culture methods. Using molecular information to make clinical decisions more quickly has been shown to improve patient outcomes, and reduce length of stay and healthcare cost in adults. Its effect on pediatric care is less well described.

METHODS

Blood cultures growing Gram-positive cocci or Gram-positive bacilli on Gram stain were evaluated by molecular and traditional methodologies. Results from the molecular platform, Luminex Verigene® Blood Culture - Gram-positive Panel (BC-GP) were compared to results from standard culture and susceptibility testing (Vitek™ MS, Vitek™, E-test®). Overall statistical agreement is evaluated.

RESULTS

1231 positive pediatric blood cultures grew single isolates detectable by the BC-GP panel. 899 were correctly identified to species, 282 to genus, 50 isolates were not detected. All organisms detected by BC-GP that grew in single isolate cultures were identified as the same organism by Vitek™ MS with the exception of 7 organisms.112 cultures were found to have polymicrobial growth of Gram-positive organisms. Excellent overall agreement was noted for antimicrobial resistance markers with only 5 samples displaying discordant results.

DISCUSSION

In general, clinicians can use the identification and antimicrobial resistance marker data gained from Luminex Verigene® BC-GP with confidence to alter empiric coverage. Rare instances of disagreement with traditional culture data led to maintaining the empiric clinical approach and did not result in patient harm.

Smartphone-based pathogen diagnosis in urinary sepsis patients

Background

There is an urgent need for rapid, sensitive, and affordable diagnostics for microbial infections at the point-of-care. Although a number of innovative systems have been reported that transform mobile phones into potential diagnostic tools, the translational challenge to clinical diagnostics remains a significant hurdle to overcome.

Methods

A smartphone-based real-time loop-mediated isothermal amplification (smaRT-LAMP) system was developed for pathogen ID in urinary sepsis patients. The free, custom-built mobile phone app allows the phone to serve as a stand-alone device for quantitative diagnostics, allowing the determination of genome copy-number of bacterial pathogens in real time.

Findings

A head-to-head comparative bacterial analysis of urine from sepsis patients revealed that the performance of smaRT-LAMP matched that of clinical diagnostics at the admitting hospital in a fraction of the time (~1 h vs. 18–28 h). Among patients with bacteremic complications of their urinary sepsis, pathogen ID from the urine matched that from the blood – potentially allowing pathogen diagnosis shortly after hospital admission. Additionally, smaRT-LAMP did not exhibit false positives in sepsis patients with clinically negative urine cultures.

Interpretation

The smaRT-LAMP system is effective against diverse Gram-negative and -positive pathogens and biological specimens, costs less than $100 US to fabricate (in addition to the smartphone), and is configurable for the simultaneous detection of multiple pathogens. SmaRT-LAMP thus offers the potential to deliver rapid diagnosis and treatment of urinary tract infections and urinary sepsis with a simple test that can be performed at low cost at the point-of-care.

Fund

National Institutes of Health, Chan-Zuckerberg Biohub, Bill and Melinda Gates Foundation.

Multicenter assessment of the rapid Unyvero Blood Culture molecular assay

Purpose

Bloodstream infections remain an important cause of morbidity and mortality. Rapid diagnosis can reduce the time from empiric antimicrobial therapy to targeted therapy and improve patient outcomes.

Methodology

The fully automated Unyvero Blood Culture (BCU) Application (Curetis GmbH) can identify a broad panel of pathogens (36 analytes covering over 50 pathogens) and 16 antibiotic resistance gene markers simultaneously in about 5 h. The assay was evaluated in three clinical laboratories in comparison to routine microbiological procedures.

Results

A total of 207 blood cultures were included in the study, and 90.5 % of the species identified by culture were covered by the Unyvero BCU panel with an overall sensitivity of 96.8 % and specificity of 99.8 %. The time to result was reduced on average by about 34 h. The assay accurately identified 95 % of the species, including 158/164 monomicrobial and 7/9 polymicrobial cultures. The Unyvero BCU Cartridge detected a large number of resistance markers including mecA (n=57), aac(6′)aph(2′′) (n=40), one vanB resistance gene, and six instances of bla_CTX-M.

Conclusion

The Unyvero BCU Application provided fast, reliable results, while significantly improving turnaround time in blood culture diagnostics.

Sustained impact of a rapid microarray-based assay with antimicrobial stewardship interventions on optimizing therapy in patients with Gram-positive bacteraemia

Objectives

To compare antibiotic optimization and outcomes of patients before implementation of the Verigene Gram-Positive Blood Culture (Verigene BC-GP) nucleic acid microarray assay to after implementation with antimicrobial stewardship (AS) interventions and after discontinuation of AS interventions.

Methods

A retrospective pre-post-post quasi-experimental study was conducted to compare the three periods. AS interventions consisted of real-time guidance to clinicians on antibiotic selection. The primary outcome was median time from Gram stain to optimal therapy. Secondary outcomes included median time to effective therapy, median duration of therapy for contaminant organisms, median length of stay after blood cultures were collected, and all-cause in-hospital mortality.

Results

Out of a total of 923 patients, 390 (125 baseline, 134 intervention, 131 post-intervention) who were not on optimal therapy at the time of Gram stain or had contaminated blood cultures were assessed. Compared with baseline, only the median time to optimal therapy for MSSA bacteraemia was reduced in both the intervention and post-intervention periods (17 versus 17 versus 50 h; P < 0.001), respectively. In an analysis adjusted for baseline differences among the groups using quantile regression models, use of the Verigene BC-GP assay in both periods significantly reduced time to optimal therapy by 14-22 h in patients who would achieve optimal therapy at ≥ 26 h without the assay. There were no differences in in-hospital mortality or hospital length of stay between study periods.

Conclusions

A real-time AS intervention implemented alongside introduction of the Verigene BC-GP assay led to improvements in antibiotic therapy for patients with bacteraemia due to Gram-positive cocci, even after the AS intervention was discontinued.

New paradigm for rapid achievement of appropriate therapy in special populations: coupling antibiotic dose optimization rapid microbiological methods

INTRODUCTION

Some special patient populations (e.g. critically ill, burns, hematological malignancy, post-major surgery, post-major trauma) have characteristics that lead to higher rates of failure and mortality associated with infection. Choice of effective antibiotics and optimized doses are challenging in these patients that are commonly infected by multidrug-resistant pathogens. Areas covered: A review of the importance of diagnosis and the place of newer microbiological methods (e.g. whole-genome sequencing) to ensure rapid transition from empiric to directed antibiotic therapy is provided. The effects of pathophysiological changes on antibiotic pharmacokinetics are also provided. Expert opinion: Product information dosing regimens do not address the pharmacokinetic alterations that can occur in special patient populations and increase the likelihood of therapeutic failure and the emergence of bacterial resistance. Altered dosing approaches, supplemented with the use of dosing software and therapeutic drug monitoring, may be needed to ensure optimal antibiotic exposure and better therapeutic outcomes in these patients with severe infection. Dose optimization needs to be coupled with advanced microbiological techniques that enable rapid microbiological identification and characterization of resistance mechanism to ensure that maximally effective directed therapy can be chosen.

A review of novel technologies and techniques associated with identification of bloodstream infection etiologies and rapid antimicrobial genotypic and quantitative phenotypic determination

INTRODUCTION

The antimicrobial aspect of management of patients with blood stream infections (BSI) and sepsis is time critical. In an era of increasing antimicrobial resistance, rapid detection and identification of bacteria with antimicrobial susceptibility is crucial to direct therapy early in the course of illness. Molecular techniques offer a potential solution to this. Areas covered: In the present review the authors have discussed a number of novel solutions utilizing a variety of molecular techniques for pathogen detection, identification and antimicrobial susceptibility. The review is not designed to be an exhaustive literature review covering all diagnostic solutions ever developed, instead the authors have focused on what they have had experience using, evaluating or currently view as new and exciting with potential to revolutionize BSI diagnosis. The authors searched PubMed (Medline) and Google Scholar with terms: BSI, Bacteraemia, Candidaemia, Diagnostics, AST, Rapid, AMR, Novel and Blood Culture. The authors attended recent clinical microbiology technology congresses. Expert commentary: There are multiple exciting novel technologies at differing stages of development with potential to revolutionize diagnosis of BSI. More work is needed as well as a standardized assessment of different platforms in order to better understand the clinical and financial impacts these will have in clinical microbiology laboratories.

From Nano to Micro: using nanotechnology to combat microorganisms and their multidrug resistance

The spread of antibiotic resistance and increasing prevalence of biofilm-associated infections is driving demand for new means to treat bacterial infection. Nanotechnology provides an innovative platform for addressing this challenge, with potential to manage even infections involving multidrug-resistant (MDR) bacteria. The current review summarizes recent progress over the last 2 years in the field of antibacterial nanodrugs, and describes their unique properties, mode of action and activity against MDR bacteria and biofilms. Biocompatibility and commercialization are also discussed. As opposed to the more common division of nanoparticles (NPs) into organic- and inorganic-based materials, this review classifies NPs into two functional categories. The first includes NPs exhibiting intrinsic antibacterial properties and the second is devoted to NPs serving as a cargo for delivering antibacterial agents. Antibacterial nanomaterials used to decorate medical devices and implants are reviewed here as well.

Probing the modulated formation of gold nanoparticles-beta-lactoglobulin corona complexes and their applications

Understanding the interactions between proteins and nanoparticles (NPs) along with the underlying structural and dynamic information is of utmost importance to exploit nanotechnology for biomedical applications. Upon adsorption onto a NP surface, proteins form a well-organized layer, termed the corona, that dictates the identity of the NP-protein complex and governs its biological pathways. Given its high biological relevance, in-depth molecular investigations and applications of NPs-protein corona complexes are still scarce, especially since different proteins form unique corona patterns, making identification of the biomolecular motifs at the interface critical. In this work, we provide molecular insights and structural characterizations of the bio-nano interface of a popular food-based protein, namely bovine beta-lactoglobulin (β-LG), with gold nanoparticles (AuNPs) and report on our investigations of the formation of corona complexes by combined molecular simulations and complementary experiments. Two major binding sites in β-LG were identified as being driven by citrate-mediated electrostatic interactions, while the associated binding kinetics and conformational changes in the secondary structures were also characterized. More importantly, the superior stability of the corona led us to further explore its biomedical applications, such as in the smartphone-based point-of-care biosensing of Escherichia coli (E. coli) and in the computed tomography (CT) of the gastrointestinal (GI) tract through oral administration to probe GI tolerance and functions. Considering their biocompatibility, edible nature, and efficient excretion through defecation, AuNPs-β-LG corona complexes have shown promising perspectives for future in vitro and in vivo clinical settings.

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.

Ventilator-Associated Pneumonia: The Role of Emerging Diagnostic Technologies

Antibiotic resistance has emerged as a key determinant of outcome in patients with serious infections along with the virulence of the underlying pathogen. Within the intensive care unit (ICU) setting, ventilator-associated pneumonia (VAP) is a common nosocomial infection that is frequently caused by multidrug-resistant bacteria. Antimicrobial resistance is a growing challenge in the care of critically ill patients. Escalating rates of antibiotic resistance add substantially to the morbidity, mortality, and cost related to infection in the ICU. Both gram-positive organisms, such as methicillin-resistant Staphylococcus aureus and vancomycin-intermediate S. aureus, and gram-negative bacteria, including Pseudomonas aeruginosa, Acinetobacter species, carbapenem-resistant Enterobacteriaceae, such as the Klebsiella pneumoniae carbapenemase-producing bacteria, and extended spectrum β-lactamase organisms, have contributed to the escalating rates of resistance seen in VAP and other nosocomial infections. The rising rates of antimicrobial resistance have led to the routine empiric administration of broad-spectrum antibiotics even when bacterial infection is not documented. Moreover, there are several new broader-spectrum antibiotics that have recently become available and others scheduled for approval in the near future. The challenge to ICU clinicians is how to most effectively utilize these agents to maximize patient benefits while minimizing further emergence of resistance. Use of rapid diagnostics may hold the key for achieving this important balance. There is an urgent need for integrating the administration of new and existing antibiotics with the emerging rapid diagnostic technologies in a way that is both cost-effective and sustainable for the long run.

Advances in Rapid Identification and Susceptibility Testing of Bacteria in the Clinical Microbiology Laboratory: Implications for Patient Care and Antimicrobial Stewardship Programs

Early availability of information on bacterial pathogens and their antimicrobial susceptibility is of key importance for the management of infectious diseases patients. Currently, using traditional approaches, it usually takes at least 48 hours for identification and susceptibility testing of bacterial pathogens. Therefore, the slowness of diagnostic procedures drives prolongation of empiric, potentially inappropriate, antibacterial therapies. Over the last couple of years, the improvement of available techniques (e.g. for susceptibility testing, DNA amplification assays), and introduction of novel technologies (e.g. MALDI-TOF) has fundamentally changed approaches towards pathogen identification and characterization. Importantly, these techniques offer increased diagnostic resolution while at the same time shorten the time-to-result, and are thus of obvious importance for antimicrobial stewardship. In this review, we will discuss recent advances in medical microbiology with special emphasis on the impact of novel techniques on antimicrobial stewardship programs.

The detection of microbial DNA but not cultured bacteria is associated with increased mortality in patients with suspected sepsis-a prospective multi-centre European observational study

OBJECTIVES

Blood culture results inadequately stratify the mortality risk in critically ill patients with sepsis. We sought to establish the prognostic significance of the presence of microbial DNA in the bloodstream of patients hospitalized with suspected sepsis.

METHODS

We analysed the data collected during the Rapid Diagnosis of Infections in the Critically Ill (RADICAL) study, which compared a novel culture-independent PCR/electrospray ionization-mass spectrometry (ESI-MS) assay with standard microbiological testing. Patients were eligible for the study if they had suspected sepsis and were either hospitalized or were referred to one of nine intensive care units from six European countries. The blood specimen for PCR/ESI-MS assay was taken along with initial blood culture taken for clinical indications.

RESULTS

Of the 616 patients recruited to the RADICAL study, 439 patients had data on outcome, results of the blood culture and PCR/ESI-MS assay available for analysis. Positive blood culture and PCR/ESI-MSI result was found in 13% (56/439) and 40% (177/439) of patients, respectively. Either a positive blood culture (p 0.01) or a positive PCR/ESI-MS (p 0.005) was associated with higher SOFA scores on enrolment to the study. There was no difference in 28-day mortality observed in patients who had either positive or negative blood cultures (35% versus 32%, p 0.74). However, in patients with a positive PCR/ESI-MS assay, mortality was significantly higher in comparison to those with a negative result (42% versus 26%, p 0.001).

CONCLUSIONS

Presence of microbial DNA in patients with suspected sepsis might define a patient group at higher risk of death.

Potential Impact of Rapid Blood Culture Testing for Gram-Positive Bacteremia in Japan with the Verigene Gram-Positive Blood Culture Test

Background. Early detection of Gram-positive bacteremia and timely appropriate antimicrobial therapy are required for decreasing patient mortality. The purpose of our study was to evaluate the performance of the Verigene Gram-positive blood culture assay (BC-GP) in two special healthcare settings and determine the potential impact of rapid blood culture testing for Gram-positive bacteremia within the Japanese healthcare delivery system. Furthermore, the study included simulated blood cultures, which included a library of well-characterized methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) isolates reflecting different geographical regions in Japan. Methods. A total 347 BC-GP assays were performed on clinical and simulated blood cultures. BC-GP results were compared to results obtained by reference methods for genus/species identification and detection of resistance genes using molecular and MALDI-TOF MS methodologies. Results. For identification and detection of resistance genes at two clinical sites and simulated blood cultures, overall concordance of BC-GP with reference methods was 327/347 (94%). The time for identification and antimicrobial resistance detection by BC-GP was significantly shorter compared to routine testing especially at the cardiology hospital, which does not offer clinical microbiology services on weekends and holidays. Conclusion. BC-GP generated accurate identification and detection of resistance markers compared with routine laboratory methods for Gram-positive organisms in specialized clinical settings providing more rapid results than current routine testing.

Early Identification and Treatment of Pathogens in Sepsis: Molecular Diagnostics and Antibiotic Choice

Sepsis and septic shock are serious conditions associated with high morbidity and mortality. Rapid molecular methods for detection of microorganisms and antimicrobial resistance genes from positive blood cultures or whole blood have evolved over the past 10 years. Such diagnostic methods coupled with therapeutic interventional programs are desirable to improve the overall clinical outcome and mortality. This article discusses the usefulness of current molecular test methods for the diagnosis of sepsis and their potential to enhance the success of antimicrobial stewardship programs. Clinicians and laboratories alike must appreciate key factors influencing the appropriate use and potential impact of these methods.

Multicenter Evaluation of the Portrait Staph ID/R Blood Culture Panel for Rapid Identification of Staphylococci and Detection of the mecA Gene

Bloodstream infections are a leading cause of morbidity and mortality in the United States and are associated with increased health care costs. We evaluated the Portrait Staph ID/R blood culture panel (BCP) multiplex PCR assay (Great Basin Scientific, Salt Lake City, UT) for the rapid and simultaneous identification (ID) of Staphylococcus aureus, Staphylococcus lugdunensis, and Staphylococcus species to the genus level and the detection of the mecA gene directly from a positive blood culture bottle. A total of 765 Bactec bottles demonstrating Gram-positive cocci in singles or clusters were tested during the prospective trial at 3 clinical sites. The Portrait Staph ID/R BCP results were compared with results from conventional biochemical and cefoxitin disk methods performed at an independent laboratory. Discordant ID and mecA results were resolved by rpoB gene sequencing and mecA gene sequencing, respectively. A total of 658 Staphylococcus species isolates (S. aureus, 211 isolates; S. lugdunensis, 3 isolates; and Staphylococcus spp., 444 isolates) were recovered from monomicrobial and 33 polymicrobial blood cultures. After discrepant analysis, the overall ratios of Portrait Staph ID/R BCP positive percent agreement and negative percent agreement were 99.4%/99.9% for Staphylococcus ID and 99.7%/99.2% for mecA detection.

Utilization Management in a Large Community Hospital

The utilization management of laboratory tests in a large community hospital is similar to academic and smaller community hospitals. There are numerous factors that influence laboratory utilization. Outside influences like hospitals buying physician practices, increasing numbers of hospitalists, and hospital consolidation will influence the number and complexity of the test menu that will need to be monitored for over and/or under utilization in the central laboratory and reference laboratory. CLIA’88 outlines the four test categories including point-of-care testing (waived) and provider-performed microscopy that need laboratory test utilization management. Incremental cost analysis is the most efficient method for evaluating utilization reduction cost savings. Economies of scale define reduced unit cost per test as test volume increases. Outreach programs in large community hospitals provide additional laboratory tests from non-patients in physician offices, nursing homes, and other hospitals. Disruptive innovations are changing the present paradigms in clinical diagnostics, like wearable sensors, MALDI-TOF, multiplex infectious disease panels, cell-free DNA, and others. Obsolete tests need to be universally defined and accepted by manufacturers, physicians, laboratories, and hospitals, to eliminate access to their reagents and testing platforms.

A Retrospective Study of the Impact of Rapid Diagnostic Testing on Time to Pathogen Identification and Antibiotic Use for Children with Positive Blood Cultures

Introduction

Rapid identification of bloodstream pathogens provides crucial information that can improve the choice of antimicrobial therapy for children. Previous impact studies have primarily focused on adults. Our objective was to evaluate the impact of rapid testing in a children’s hospital on time to organism identification and antibiotic use in the setting of an established antimicrobial stewardship program.

Methods

We conducted a retrospective study over three consecutive time periods (spanning January 2013–August 2015) as our hospital sequentially introduced two rapid testing methods for positive blood cultures. An antimicrobial stewardship program was active throughout the study. In the baseline period, no rapid diagnostic methods were routinely utilized. In the second period (PNAFISH), a fluorescent in situ hybridization test was implemented for gram-positive organisms and in the third a rapid multiplex PCR (rmPCR) test was employed. For children with positive blood cultures, time to organism identification use and duration of select antimicrobial therapies were compared between periods.

Results

Positive blood cultures were analyzed. Median overall time to organism identification was 23, 11, and 0 h in the baseline, PNAFISH, and rmPCR periods, respectively (p < 0.001 for both PNAFISH and rmPCR vs. baseline). For gram-negative organisms, only rmPCR performed significantly faster than baseline (p < 0.001). The duration of vancomycin use for coagulase-negative staphylococci was shorter in both the PNAFISH and rmPCR periods (mean 31 h in the baseline period, 12 and 14 h in the PNAFISH and rmPCR periods, respectively). For MSSA bacteremia, use of vancomycin was significantly decreased only in the rmPCR period (32% of patients vs. 64 and 72% in the baseline and PNAFISH periods; mean duration of 9 h vs. 30 and 26 h). There was no difference in use or duration of broad-spectrum gram-negative therapy across the three time periods.

Conclusion

Rapid diagnostic testing for children with positive blood cultures results in faster time to identification and can influence antibiotic prescribing in the setting of active antimicrobial stewardship particularly for gram-positive pathogens.

Funding

Merck.

Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology

The microbiological management of patients with suspected bacterial infection includes the identification of the pathogen and the determination of the antibiotic susceptibility. These traditional approaches, based on the pure culture of the microorganism, require at least 36-48h. A new method, Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS), has been recently developed to profile bacterial proteins from whole cell extracts and obtain a bacterial fingerprint able to discriminate microorganisms from different genera and species. By whole cell-mass spectrometry, microbial identification can be achieved within minutes from cultured isolate, rather than traditional phenotypic or genotypic characterizations. From the year 2009 an explosion of applications of this technology has been observed with promising results. Several studies have been performed and showed that MALDI-TOF represents a reliable alternative method for rapid bacteria and fungi identification in clinical setting. A future area of expansion is represented by the application of MALDI-TOF technology to the antibiotic susceptibility test. In conclusion, the revision of the literature available up to date demonstrated that MALDI-TOF MS represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates in clinical settings. By an earlier microbiological diagnosis, MALDI-TOF MS contributes to a reduced mortality and hospitalization time of the patients and consequently has a significant impact on cost savings and public health.

Rapid Detection of Bacteria from Blood with Surface-Enhanced Raman Spectroscopy

Traditional methods for identifying pathogens in bacteremic patients are slow (24-48+ h). This can lead to physicians making treatment decisions based on an incomplete diagnosis and potentially increasing the patient's mortality risk. To decrease time to diagnosis, we have developed a novel technology that can recover viable bacteria directly from whole blood and identify them in less than 7 h. Our technology combines a sample preparation process with surface-enhanced Raman spectroscopy (SERS). The sample preparation process enriches viable microorganisms from 10 mL of whole blood into a 200 μL aliquot. After a short incubation period, SERS is used to identify the microorganisms. We further demonstrated that SERS can be used as a broad detection method, as it identified a model set of 17 clinical blood culture isolates and microbial reference strains with 100% identification agreement. By applying the integrated technology of sample preparation and SERS to spiked whole blood samples, we were able to correctly identify both Staphylococcus aureus and Escherichia coli 97% of the time with 97% specificity and 88% sensitivity.

Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure

Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The "holy grail" of AST is a phenotype-based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibiotic exposure. Herein, digital PCR (dPCR) was employed to test whether measuring DNA replication of the target pathogen through digital single-molecule counting would shorten the required time of antibiotic exposure. Partitioning bacterial chromosomal DNA into many small volumes during dPCR enabled AST results after short exposure times by 1) precise quantification and 2) a measurement of how antibiotics affect the states of macromolecular assembly of bacterial chromosomes. This digital AST (dAST) determined susceptibility of clinical isolates from urinary tract infections (UTIs) after 15 min of exposure for all four antibiotic classes relevant to UTIs. This work lays the foundation to develop a rapid, point-of-care AST and strengthen global antibiotic stewardship.

Rapid Diagnosis of Infection in the Critically Ill, a Multicenter Study of Molecular Detection in Bloodstream Infections, Pneumonia, and Sterile Site Infections

Supplemental Digital Content is available in the text.

Early identification of causative microorganism(s) in patients with severe infection is crucial to optimize antimicrobial use and patient survival. However, current culture-based pathogen identification is slow and unreliable such that broad-spectrum antibiotics are often used to insure coverage of all potential organisms, carrying risks of overtreatment, toxicity, and selection of multidrug-resistant bacteria. We compared the results obtained using a novel, culture-independent polymerase chain reaction/electrospray ionization-mass spectrometry technology with those obtained by standard microbiological testing and evaluated the potential clinical implications of this technique.

Evaluation of Verigene Blood Culture Test Systems for Rapid Identification of Positive Blood Cultures

The performance of molecular tests using the Verigene Gram-Positive and Gram-Negative Blood Culture nucleic acid tests (BC-GP and BC-GN, resp.; Naosphere, Northbrook, IL, USA) was evaluated for the identification of microorganisms detected from blood cultures. Ninety-nine blood cultures containing Gram-positive bacteria and 150 containing Gram-negative bacteria were analyzed using the BC-GP and BC-GN assays, respectively. Blood cultures were performed using the Bactec blood culture system (BD Diagnostic Systems, Franklin Lakes, NJ, USA) and conventional identification and antibiotic-susceptibility tests were performed using a MicroScan system (Siemens, West Sacramento, CA, USA). When a single strain of bacteria was isolated from the blood culture, Verigene assays correctly identified 97.9% (94/96) of Gram-positive bacteria and 93.8% (137/146) of Gram-negative bacteria. Resistance genes mecA and vanA were correctly detected by the BC-GP assay, while the extended-spectrum β-lactamase CTX-M and the carbapenemase OXA resistance gene were detected from 30 cases cultures by the BC-GN assay. The BC-GP and BC-GN assays showed high agreement with conventional identification and susceptibility tests. These tests are useful for rapid identification of microorganisms and the detection of clinically important resistance genes from positive Bactec blood cultures.

Current applications of nanoparticles in infectious diseases

For decades infections have been treated easily with drugs. However, in the 21st century, they may become lethal again owing to the development of antimicrobial resistance. Pathogens can become resistant by means of different mechanisms, such as increasing the time they spend in the intracellular environment, where drugs are unable to reach therapeutic levels. Moreover, drugs are also subject to certain problems that decrease their efficacy. This requires the use of high doses, and frequent administrations must be implemented, causing adverse side effects or toxicity. The use of nanoparticle systems can help to overcome such problems and increase drug efficacy. Accordingly, there is considerable current interest in their use as antimicrobial agents against different pathogens like bacteria, virus, fungi or parasites, multidrug-resistant strains and biofilms; as targeting vectors towards specific tissues; as vaccines and as theranostic systems. This review begins with an overview of the different types and characteristics of nanoparticles used to deliver drugs to the target, followed by a review of current research and clinical trials addressing the use of nanoparticles within the field of infectious diseases.

Carriage, Clinical Microbiology and Transmission of Staphylococcus aureus

Staphylococcus aureus is one of the most important bacterial pathogens in clinical practice and a major diagnostic focus for the routine microbiology laboratory. It is carried as a harmless commensal in up to two-thirds of the population at any one time predominantly not only in the anterior nares, but also in multiple other sites such as the groin, axilla, throat, perineum, vagina and rectum. It colonizes skin breach sites, such as ulcers and wounds, and causes superficial and deep skin and soft tissue infections and life-threatening deep seated infections particularly endocarditis and osteomyelitis. S. aureus is constantly evolving through mutation and uptake of mobile genetic elements that confer increasing resistance and virulence. Since the 1960s, hospitals have had to contend with emergence of methicillin-resistant S. aureus (MRSA) strains that spread better in hospitals than methicillin-susceptible S. aureus (MSSA) and are harder to treat. Since the 1980s, distinct community MRSA strains have also emerged that cause severe skin and respiratory infections. Conventional identification of MSSA and MRSA in the microbiology laboratory involves microscopy, culture and biochemical analysis that for most samples is straightforward but slow, taking at least 48 h. This delay has significant consequences for individual patient care and public health, through inadequate or excessive empiric antibiotic use, and failure to implement appropriate infection control measures for MRSA-colonized patients during those first 48 h. This unmet need has driven development of rapid molecular diagnostics that either complement or replace conventional culture techniques in the laboratory, or can be placed in the clinical environment as point-of-care (POC) devices. These new technologies provide results to clinicians anything from within an hour to 24 h, depending on sample and clinical setting, and should transform management of patients with S. aureus and other bacterial diseases; however, uptake is often slow due to the disruptive effect of new technologies, costs of transition and uncertainty of the optimal solution given successive advances. More evidence of the health economic, clinical and antimicrobial resistance benefit will help support introduction of these new technologies. Finally, preventing MRSA transmission has been a priority for healthcare organizations for many years. There have been significant recent reductions in transmission following local and national campaigns to re-enforce basic and heightened infection control interventions such as universal hand hygiene, barrier nursing, decolonization and isolation of MRSA-colonized patients detected through routine culture or screening policies. Developments in whole genome sequencing are providing greater insight into reservoirs and routes of transmission that should help better target interventions to ensure sustainable control of endemic strains and to identify and prevent emergence of new strains.

Nanomedicine concepts in the general medical curriculum: initiating a discussion

Various applications of nanoscale science to the field of medicine have resulted in the ongoing development of the subfield of nanomedicine. Within the past several years, there has been a concurrent proliferation of academic journals, textbooks, and other professional literature addressing fundamental basic science research and seminal clinical developments in nanomedicine. Additionally, there is now broad consensus among medical researchers and practitioners that along with personalized medicine and regenerative medicine, nanomedicine is likely to revolutionize our definitions of what constitutes human disease and its treatment. In light of these developments, incorporation of key nanomedicine concepts into the general medical curriculum ought to be considered. Here, I offer for consideration five key nanomedicine concepts, along with suggestions regarding the manner in which they might be incorporated effectively into the general medical curriculum. Related curricular issues and implications for medical education also are presented.

Prospective intervention study with a microarray-based, multiplexed, automated molecular diagnosis instrument (Verigene system) for the rapid diagnosis of bloodstream infections, and its impact on the clinical outcomes

The Verigene Gram-positive blood culture test (BC-GP) and the Verigene Gram-negative blood culture test (BC-GN) identify representative Gram-positive bacteria, Gram-negative bacteria and their antimicrobial resistance by detecting resistance genes within 3 h. Significant benefits are anticipated due to their rapidity and accuracy, however, their clinical utility is unproven in clinical studies. We performed a clinical trial between July 2014 and December 2014 for hospitalized bacteremia patients. During the intervention period (N = 88), Verigene BC-GP and BC-GN was used along with conventional microbiological diagnostic methods, while comparing the clinical data and outcomes with those during the control period (N = 147) (UMIN registration ID: UMIN000014399). The median duration between the initiation of blood culture incubation and the reporting time of the Verigene system results was 21.7 h (IQR 18.2-26.8) and the results were found in 88% of the cases by the next day after blood cultures were obtained without discordance. The hospital-onset infection rate was higher in the control period (24% vs. 44%, p = 0.002), however, no differences were seen in co-morbidities and severity between the control and intervention periods. During the intervention period, the time of appropriate antimicrobial agents' initiation was significantly earlier than that in the control period (p = 0.001) and most cases (90%; 79/88) were treated with antimicrobial agents with in-vitro susceptibility for causative bacteria the day after the blood culture was obtained. The costs for antimicrobial agents were lower in the intervention period (3618 yen vs. 8505 yen, p = 0.001). The 30-day mortality was lower in the intervention period (3% vs. 13%, p = 0.019).

Clinical and microbiological outcomes in patients with Streptococcus anginosus group bacteraemia identified through use of a rapid microarray assay

Limited data exist evaluating outcomes in patients with serious Streptococcus anginosus group infections, particularly bacteraemia. A retrospective, single-centre cohort study was conducted to characterize potential risk factors along with clinical and microbiological outcomes in patients with S. anginosus group bacteraemia (SAGB). Adult inpatients with SAGB identified using the Verigene Gram-positive blood culture assay between March 2013 and April 2014 were included. Patients aged ≤ 18 or >89 years, those with SAGB identified at an outside facility and those who were incarcerated were excluded. Differences between groups were explored using a Wilcoxon rank-sum test, χ2 test, Student's t-test or Fisher's exact test as appropriate and a two-tailed P value of ≤ 0.05 was considered statistically significant. The 34 patients who met the inclusion criteria were 57 ± 14 (mean ± SD) years old and had a median Charlson co-morbidity index of 4 [interquartile range (IQR) 1-6] and 10 (29%) were immunosuppressed at baseline. Almost half (47%) had received antibiotics in the previous 90 days. Twelve (35%) patients had gastrointestinal malignancies and the commonest source of bacteraemia was the gastrointestinal tract (53%). The primary species responsible for SAGB was S. anginosus (68%), and overall susceptibility to penicillin was 91%. Patients were most often treated with a β-lactam/β-lactamase inhibitor combination (36%) for a duration of 8 (IQR 4-13) days. Length of stay (LOS) and infection-related LOS were 10 (IQR 5-17) and 9 (IQR 4-12) days, respectively. Twenty [59%] patients achieved a clinical cure, while 29 (85%) achieved a microbiological cure. Four (12%) patients died and one patient was readmitted within 30  days. In the largest cohort of patients with SAGB to date, gastrointestinal malignancies may have been an important risk factor for SAGB, while rapid identification via a microarray assay likely contributed to improved disease recognition and timely pharmacological and non-pharmacological therapy.

Emerging technologies for the clinical microbiology laboratory

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.

Emerging commercial molecular tests for the diagnosis of bloodstream infection

Bloodstream infection (BSI) by microorganisms can lead to sepsis. This condition has a high mortality rate, which rises significantly with delays in initiation of appropriate antimicrobial treatment. Current culture methods for diagnosing BSI have long turnaround times and poor clinical sensitivity. While clinicians wait for culture diagnosis, patients are treated empirically, which can result in inappropriate treatment, undesirable side effects and contribute to drug resistance development. Molecular diagnostics assays that target pathogen DNA can identify pathogens and resistance markers within hours. Early diagnosis improves antibiotic stewardship and is associated with favorable clinical outcomes. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews recent commercially available molecular methods that use pathogen DNA to diagnose BSI, either by testing positive blood cultures or directly testing patient blood. We critically assess these tests and their application in clinical microbiology. A view of future directions in BSI diagnosis is also provided.