Molecular diagnosis of bloodstream infections: planning to (physically) reach the bedside

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

INTRODUCTION

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

METHODS AND ANALYSIS

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

ETHICS AND DISSEMINATION

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

TRIAL REGISTRATION NUMBER

NCT06069206.

Concentration-polarization electroosmosis for particle fractionation

Concentration-polarization electroosmosis (CPEO) refers to steady-state electroosmotic flows around charged dielectric micro-particles induced by low-frequency AC electric fields. Recently, these flows were shown to cause repulsion of colloidal particles from the wall of a microfluidic channel when an electric field is applied along the length of the channel. In this work, we exploit this mechanism to demonstrate fractionation of micron-sized polystyrene particles and bacteria in a flow-focusing device. The results are in agreement with predictions of the CPEO theory. The ease of implementation of CPEO-based fractionation in microfluidics makes it an ideal candidate for combining with current techniques commonly used to generate particle lift, such as inertial or viscoelastic focusing, requiring no extra fabrication steps other than inserting two electrodes.

Antibiotic Stewardship in Surgical Departments

Antimicrobial resistance (AMR) has emerged as one of the leading public health threats of the 21st century. New evidence underscores its significance in patients' morbidity and mortality, length of stay, as well as healthcare costs. Globally, the factors that contribute to antimicrobial resistance include social and economic determinants, healthcare governance, and environmental interactions with impact on humans, plants, and animals. Antimicrobial stewardship (AS) programs have historically overlooked surgical teams as they considered them more difficult to engage. This review aims to summarize the evolution and significance of AS in surgical wards, including the surgical intensive care unit (SICU) and the role of diagnostic stewardship (DS). The contribution of AS team members is presented. The new diagnostic modalities and the new technologies including artificial intelligence (AI) are also reviewed.

High resolution and rapid separation of bacteria from blood using elasto-inertial microfluidics

Improved sample preparation has the potential to address unmet needs for fast turnaround sepsis tests. In this work, we report elasto-inertial based rapid bacteria separation from diluted blood at high separation efficiency. In viscoelastic flows, we demonstrate novel findings where blood cells prepositioned at the outer wall entering a spiral device remain fully focused throughout the channel length while smaller bacteria migrate to the opposite wall. Initially, using microparticles, we show that particles above a certain size cut-off remain fully focused at the outer wall while smaller particles differentially migrate toward the inner wall. We demonstrate particle separation at 1 μm resolution at a total throughput of 1 mL/min. For blood-based experiments, a minimum of 1:2 dilution was necessary to fully focus blood cells at the outer wall. Finally, Escherichia coli spiked in diluted blood were continuously separated at a total flow rate of 1 mL/min, with efficiencies between 82 and 90% depending on the blood dilution. Using a single spiral, it takes 40 min to process 1 mL of blood at a separation efficiency of 82%. The label-free, passive, and rapid bacteria isolation method has a great potential for speeding up downstream phenotypic and genotypic analysis.

Validation of an Isothermal Amplification Platform for Microbial Identification and Antimicrobial Resistance Detection in Blood: A Prospective Study

Background: Recent advances in nucleic acid amplification technique (NAAT)-based identification of pathogens in blood stream infections (BSI) have revolutionized molecular diagnostics in comparison to traditional clinical microbiology practice of blood culture. Rapid pathogen detection with point-of-care diagnostic-applicable platform is prerequisite for efficient patient management. The aim of the study is to evaluate an in-house developed, lyophilized OmiX-AMP pathogen test for the detection of top six BSI-causing bacteria along with two major antimicrobial resistance (AMR) markers of carbapenem and compare it to the traditional blood culture-based detection.

Materials and methods: One hundred forty-three patients admitted to the Medical Intensive Care Unit, Narayana Hrudayalaya, Bangalore, with either suspected or proven sepsis, of either gender, of age ≥18 years were enrolled for the study. Pathogen DNA extracted from blood culture sample using OmiX pReP method was amplified at isothermal conditions and analyzed in real time using OmiX Analysis software.

Results: Among the processed 143 samples, 54 were true negative, 83 were true positive, 3 were false negative, and 2 were false positive as analyzed by OmiX READ software. Gram-negative bacteria (91.3%) and gram-positive bacteria (75%) were detected with 100% specificity and 95.6% sensitivity along with the AMR marker pattern with a turnaround time of 4 hours from sample collection to results.

Conclusion: OmiX-AMP pathogen test detected pathogens with 96.5% concordance in comparison to traditional blood culture. Henceforth, OmiX-AMP pathogen test could be used as a readily deployable diagnostic kit even in low-resource settings.

How to cite this article: Maheshwarappa HM, Guru P, Mundre RS, Lawrence N, Majumder S, Sigamani A, et al. Validation of an Isothermal Amplification Platform for Microbial Identification and Antimicrobial Resistance Detection in Blood: A Prospective Study. Indian J Crit Care Med 2021;25(3):299–304.

Utilization of Red Nonionogenic Tenside Labeling, Isoelectric Focusing, and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry in the Identification of Uropathogens in the Presence of a High Level of Albumin

Cellulose-based preparative isoelectric focusing was used for preseparation and concentration of uropathogens Staphylococcus aureus, Escherichia coli, Enterococcus faecalis, Staphylococcus epidermidis, Candida albicans, and Candida parapsilosis in a urine sample containing a high concentration of human serum albumin. For the visibility of the colorless microbial zones in the separation medium, the microbial cells were labeled with red nonionogenic tenside (1-[[4-(phenylazo)phenyl]azo]-2-hydroxy-3-naphthoic acid polyethylene glycol ester, PAPAN). A very short incubation time, about 2 min, was sufficient for the adsorption of 0.001% (w/v) PAPAN onto the cell surface at the optimized conditions. As low as 10³ cells of E. coli (pI 4.6) resuspended in 100 μL of urine sample and spiked with 0.1 mg mL^-1 of human serum albumin (pI 4.8) were successfully preseparated and concentrated using this method. Because the pI values of the labeled microorganisms remained unchanged, the focused red zones of microbial cells were collected from the separation media and further analyzed by either capillary isoelectric focusing or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The viability of the cells extracted from the collected zones was also confirmed. The proposed method provides reliable, relatively fast, and cost-effective identification of uropathogens in urine specimens with a high level of albumin.

Molecular Pathology Techniques: Advances in 2018

Molecular pathology techniques continue to evolve. Although polymerase chain reaction (PCR) remains the cornerstone methodology for nucleic acid amplification, improvements in nucleic acid detection methodologies (i.e. PCR) have increased the detection sensitivity by using fluorescent and bead based array technologies. Single base pair lesions can be detected via sequencing and related techniques to discern point mutations in disease pathogenesis. Novel technologies, such as high- resolution melting analysis, provide fast high throughput post PCR analysis of genetic mutations or variance in nucleic acid sequences. These and other technologies such as hybrid capture, fluorohore and chemiluminescence detections assays allow for rapid diagnosis and prognosis for expeditious and personalized patient management.

Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends

Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.

Rapid separation of very low concentrations of bacteria from blood

A rapid and accurate diagnosis of the species and antibiotic resistance of bacteria in septic blood is vital to increase survival rates of patients with bloodstream infections, particularly those with carbapenem-resistant enterobacteriaceae (CRE) infections. The extremely low levels in blood (1 to 100CFU/ml) make rapid diagnosis difficult. In this study, very low concentrations of bacteria (6 to 200CFU/ml) were separated from 7ml of whole blood using rapid sedimentation in a spinning hollow disk that separated plasma from red and white cells, leaving most of the bacteria suspended in the plasma. Following less than a minute of spinning, the disk was slowed, the plasma was recovered, and the bacteria were isolated by vacuum filtration. The filters were grown on nutrient plates to determine the number of bacteria recovered from the blood. Experiments were done without red blood cell (RBC) lysis and with RBC lysis in the recovered plasma. While there was scatter in the data from blood with low bacterial concentrations, the mean average recovery was 69%. The gender of the blood donor made no statistical difference in bacterial recovery. These results show that this rapid technique recovers a significant amount of bacteria from blood containing clinically relevant low levels of bacteria, producing the bacteria in minutes. These bacteria could subsequently be identified by molecular techniques to quickly identify the infectious organism and its resistance profile, thus greatly reducing the time needed to correctly diagnose and treat a blood infection.

A nanoparticle-based method for culture-free bacterial DNA enrichment from whole blood

Point-of-care (POC) diagnostics are one of the quick and sensitive detection approaches used in current clinical applications, but always face a performance tradeoff between time-to-result and assay sensitivity. One critical setting where these limitations are evident is the detection of sepsis, where 6-10mL of whole blood may contain as little as one bacterial colony forming unit (cfu). The large sample volume, complex nature of the sample and low analyte concentration necessitates signal enhancement using culture-based or molecular amplification techniques. In the time-critical diagnosis of sepsis, waiting for up to 24h to produce sufficient DNA for analysis is not possible. As a consequence, there is a need for integrated sample preparation methods that could enable shorter detection times, whilst maintaining high analytical performance. We report the development of a culture-free bacterial enrichment method to concentrate bacteria from whole blood in less than 3h. The method relies on triple-enrichment steps to magnetically concentrate bacterial cells and their DNA with a 500-fold reduction in sample volume (from 10 to 0.02mL). Using this sample preparation method, sensitive qPCR detection of the extracted S. aureus bacterial DNA was achieved with a detection limit of 5±0.58cfu/mL within a total elapsed time of 4h; much faster than conventional culture-based approaches. The method could be fully automated for integration into clinical practice for point-of-care or molecular detection of bacterial DNA from whole blood.

Rapid separation of bacteria from blood - Chemical aspects

To rapidly diagnose infectious organisms causing blood sepsis, bacteria must be rapidly separated from blood, a very difficult process considering that concentrations of bacteria are many orders of magnitude lower than concentrations of blood cells. We have successfully separated bacteria from red and white blood cells using a sedimentation process in which the separation is driven by differences in density and size. Seven mL of whole human blood spiked with bacteria is placed in a 12-cm hollow disk and spun at 3000rpm for 1min. The red and white cells sediment more than 30-fold faster than bacteria, leaving much of the bacteria in the plasma. When the disk is slowly decelerated, the plasma flows to a collection site and the red and white cells are trapped in the disk. Analysis of the recovered plasma shows that about 36% of the bacteria is recovered in the plasma. The plasma is not perfectly clear of red blood cells, but about 94% have been removed. This paper describes the effects of various chemical aspects of this process, including the influence of anticoagulant chemistry on the separation efficiency and the use of wetting agents and platelet aggregators that may influence the bacterial recovery. In a clinical scenario, the recovered bacteria can be subsequently analyzed to determine their species and resistance to various antibiotics.

Development of a magnetic separation method to capture sepsis associated bacteria in blood

Bloodstream infections are important public health problems, associated with high mortality due to the inability to detect the pathogen quickly in the early stages of infection. Such inability has led to a growing interest in the development of a rapid, sensitive, and specific assay to detect these pathogens. In an effort to improve diagnostic efficiency, we present here a magnetic separation method for bacteria that is based on mutated lysozyme (LysE35A) to capture S. aureus from whole blood. LysE35A-coated beads were able to bind different MSSA and MRSA isolates in the blood and also other six Gram-positive and two Gram-negative species in whole blood. This system was capable to bind bacteria at low concentrations (10CFU/ml) in spiked blood. Samples captured with the mutated lysozyme showed more responsive amplification of the 16S gene than whole blood at concentrations of 10(3)-10(5)CFU. These data demonstrate detection of S. aureus directly in blood samples, without in vitro cultivation. Our results show that capture with LysE35A-coated beads can be useful to develop a point of care diagnostic system for rapid and sensitive detection of pathogens in clinical settings.

Rapid separation of bacteria from blood-review and outlook

The high morbidity and mortality rate of bloodstream infections involving antibiotic-resistant bacteria necessitate a rapid identification of the infectious organism and its resistance profile. Traditional methods based on culturing the blood typically require at least 24 h, and genetic amplification by PCR in the presence of blood components has been problematic. The rapid separation of bacteria from blood would facilitate their genetic identification by PCR or other methods so that the proper antibiotic regimen can quickly be selected for the septic patient. Microfluidic systems that separate bacteria from whole blood have been developed, but these are designed to process only microliter quantities of whole blood or only highly diluted blood. However, symptoms of clinical blood infections can be manifest with bacterial burdens perhaps as low as 10 CFU/mL, and thus milliliter quantities of blood must be processed to collect enough bacteria for reliable genetic analysis. This review considers the advantages and shortcomings of various methods to separate bacteria from blood, with emphasis on techniques that can be done in less than 10 min on milliliter-quantities of whole blood. These techniques include filtration, screening, centrifugation, sedimentation, hydrodynamic focusing, chemical capture on surfaces or beads, field-flow fractionation, and dielectrophoresis. Techniques with the most promise include screening, sedimentation, and magnetic bead capture, as they allow large quantities of blood to be processed quickly. Some microfluidic techniques can be scaled up. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:823-839, 2016.

Rapid detection of Gram-negative bacteria and their drug resistance genes from positive blood cultures using an automated microarray assay

We evaluated the performance of the Verigene Gram-negative blood culture (BC-GN) assay (CE-IVD version) for identification of Gram-negative (GN) bacteria and detection of resistance genes. A total of 163 GN organisms (72 characterized strains and 91 clinical isolates from 86 patients) were tested; among the clinical isolates, 86 (94.5%) isolates were included in the BC-GN panel. For identification, the agreement was 98.6% (146/148, 95% confidence interval [CI], 92.1-100) and 70% (7/10, 95% CI, 53.5-100) for monomicrobial and polymicrobial cultures, respectively. Of the 48 resistance genes harbored by 43 characterized strains, all were correctly detected. Of the 19 clinical isolates harboring resistance genes, 1 CTX-M-producing Escherichia coli isolated in polymicrobial culture was not detected. Overall, BC-GN assay provides acceptable accuracy for rapid identification of Gram-negative bacteria and detection of resistance genes, compared with routine laboratory methods despite that it has limitations in the number of genus/species and resistance gene included in the panel and it shows lower sensitivity in polymicrobial cultures.

Quality indicators on the use of antimicrobials in critically ill patients

Quality indicators have been applied to many areas of health care in recent years, including intensive care. However, they have not been specifically developed and validated for antimicrobial use in critically ill patients. Antimicrobials play a key role in intensive care units not only in the prognosis of each individual patient, but also in the development of resistance and changes in the flora in this setting. Evaluating the use of these agents is complex in the intensive care unit, however, because the indications vary greatly and antimicrobial treatment is often changed during admission. We designed and developed specific quality indicators regarding the use of antimicrobials in critically ill patients admitted to the intensive care unit. These indicators are proposed as a tool for application in intensive care units to detect problems in the use of antimicrobials. Future trials are needed, however, to validate these indicators in a large population over time.

Diagnostic utility of broad range bacterial 16S rRNA gene PCR with degradation of human and free bacterial DNA in bloodstream infection is more sensitive than an in-house developed PCR without degradation of human and free bacterial DNA

We compared a commercial broad range 16S rRNA gene PCR assay (SepsiTest) to an in-house developed assay (IHP). We assessed whether CD64 index, a biomarker of bacterial infection, can be used to exclude patients with a low probability of systemic bacterial infection. From January to March 2010, 23 patients with suspected sepsis were enrolled. CD64 index, procalcitonin, and C-reactive protein were measured on admission. Broad range 16S rRNA gene PCR was performed from whole blood (SepsiTest) or blood plasma (IHP) and compared to blood culture results. Blood samples spiked with Staphylococcus aureus were used to assess sensitivity of the molecular assays in vitro. CD64 index was lower in patients where possible sepsis was excluded than in patients with microbiologically confirmed sepsis (P = 0.004). SepsiTest identified more relevant pathogens than blood cultures (P = 0.008); in three patients (13%) results from blood culture and SepsiTest were congruent, whereas in four cases (17.4%) relevant pathogens were detected by SepsiTest only. In vitro spiking experiments suggested equal sensitivity of SepsiTest and IHP. A diagnostic algorithm using CD64 index as a decision maker to perform SepsiTest shows improved detection of pathogens in patients with suspected blood stream infection and may enable earlier targeted antibiotic therapy.

Evaluation of an automated rapid diagnostic assay for detection of Gram-negative bacteria and their drug-resistance genes in positive blood cultures

We evaluated the performance of the Verigene Gram-Negative Blood Culture Nucleic Acid Test (BC-GN; Nanosphere, Northbrook, IL, USA), an automated multiplex assay for rapid identification of positive blood cultures caused by 9 Gram-negative bacteria (GNB) and for detection of 9 genes associated with β-lactam resistance. The BC-GN assay can be performed directly from positive blood cultures with 5 minutes of hands-on and 2 hours of run time per sample. A total of 397 GNB positive blood cultures were analyzed using the BC-GN assay. Of the 397 samples, 295 were simulated samples prepared by inoculating GNB into blood culture bottles, and the remaining were clinical samples from 102 patients with positive blood cultures. Aliquots of the positive blood cultures were tested by the BC-GN assay. The results of bacterial identification between the BC-GN assay and standard laboratory methods were as follows: Acinetobacter spp. (39 isolates for the BC-GN assay/39 for the standard methods), Citrobacter spp. (7/7), Escherichia coli (87/87), Klebsiella oxytoca (13/13), and Proteus spp. (11/11); Enterobacter spp. (29/30); Klebsiella pneumoniae (62/72); Pseudomonas aeruginosa (124/125); and Serratia marcescens (18/21); respectively. From the 102 clinical samples, 104 bacterial species were identified with the BC-GN assay, whereas 110 were identified with the standard methods. The BC-GN assay also detected all β-lactam resistance genes tested (233 genes), including 54 bla_CTX-M, 119 bla_IMP, 8 bla_KPC, 16 bla_NDM, 24 bla_OXA-23, 1 bla_OXA-24/40, 1 bla_OXA-48, 4 bla_OXA-58, and 6 bla_VIM. The data shows that the BC-GN assay provides rapid detection of GNB and β-lactam resistance genes in positive blood cultures and has the potential to contributing to optimal patient management by earlier detection of major antimicrobial resistance genes.

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.

A novel, multiplex, real-time PCR-based approach for the detection of the commonly occurring pathogenic fungi and bacteria

Background

Polymerase chain reaction (PCR)-based techniques are widely used to identify fungal and bacterial infections. There have been numerous reports of different, new, real-time PCR-based pathogen identification methods although the clinical practicability of such techniques is not yet fully clarified.

The present study focuses on a novel, multiplex, real-time PCR-based pathogen identification system developed for rapid differentiation of the commonly occurring bacterial and fungal causative pathogens of bloodstream infections.

Results

A multiplex, real-time PCR approach is introduced for the detection and differentiation of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. The Gram classification is performed with the specific fluorescence resonance energy transfer (FRET) probes recommended for LightCycler capillary real-time PCR. The novelty of our system is the use of a non-specific SYBR Green dye instead of labelled anchor probes or primers, to excite the acceptor dyes on the FRET probes. In conjunction with this, the use of an intercalating dye allows the detection of fungal amplicons.

With the novel pathogen detection system, fungi, G + and G- bacteria in the same reaction tube can be differentiated within an hour after the DNA preparation via the melting temperatures of the amplicons and probes in the same tube.

Conclusions

This modified FRET technique is specific and more rapid than the gold-standard culture-based methods. The fact that fungi, G + and G- bacteria were successfully identified in the same tube within an hour after the DNA preparation permits rapid and early evidence-based management of bloodstream infections in clinical practice.

Pathogen-specific local immune fingerprints diagnose bacterial infection in peritoneal dialysis patients

Accurate and timely diagnosis of bacterial infection is crucial for effective and targeted treatment, yet routine microbiological identification is inefficient and often delayed to an extent that makes it clinically unhelpful. The immune system is capable of a rapid, sensitive and specific detection of a broad spectrum of microbes, which has been optimized over millions of years of evolution. A patient's early immune response is therefore likely to provide far better insight into the true nature and severity of microbial infections than conventional tests. To assess the diagnostic potential of pathogen-specific immune responses, we characterized the local responses of 52 adult patients during episodes of acute peritoneal dialysis (PD)-associated peritonitis by multicolor flow cytometry and multiplex ELISA, and defined the immunologic signatures in relation to standard microbiological culture results and to clinical outcomes. We provide evidence that unique local "immune fingerprints" characteristic of individual organisms are evident in PD patients on the day of presentation with acute peritonitis and discriminate between culture-negative, Gram-positive, and Gram-negative episodes of infection. Those humoral and cellular parameters with the most promise for defining disease-specific immune fingerprints include the local levels of IL-1β, IL-10, IL-22, TNF-α, and CXCL10, as well as the frequency of local γδ T cells and the relative proportion of neutrophils and monocytes/macrophages among total peritoneal cells. Our data provide proof of concept for the feasibility of using immune fingerprints to inform the design of point-of-care tests that will allow rapid and accurate infection identification and facilitate targeted antibiotic prescription and improved patient management.

Bench-to-bedside review: Challenges of diagnosis, care and prevention of central catheter-related bloodstream infections in children

Central venous catheters (CVCs) are indispensable in modern pediatric medicine. CVCs provide secure vascular access, but are associated with a risk of severe complications, in particular bloodstream infection. We provide a review of the recent literature about the diagnostic and therapeutic challenges of catheter-related bloodstream infection (CRBSI) in children and its prevention. Variations in blood sampling and limitations in blood culturing interfere with accurate and timely diagnosis of CRBSI. Although novel molecular testing methods appear promising in overcoming some of the present diagnostic limitations of conventional blood sampling in children, they still need to solidly prove their accuracy and reliability in clinical practice. Standardized practices of catheter insertion and care remain the cornerstone of CRBSI prevention although their implementation in daily practice may be difficult. Technology such as CVC impregnation or catheter locking with antimicrobial substances has been shown less effective than anticipated. Despite encouraging results in CRBSI prevention among adults, the goal of zero infection in children is still not in range. More high-quality research is needed in the field of prevention, accurate and reliable diagnostic measures and effective treatment of CRBSI in children.

Accurate and rapid identification of Candida spp. frequently associated with fungemia by using PCR and the microarray-based Prove-it Sepsis assay

The rapid identification of microbes responsible for bloodstream infections (BSIs) allows more focused and effective therapies and outcomes. DNA sequence-based methods offer an opportunity for faster, accurate diagnosis and for effective therapy. As our objective of the study, the ability of the Prove-it Sepsis platform, already proven as a rapid PCR- and microarray-based assay for the majority of sepsis-causing bacteria, was extended to also rapidly identify clinically relevant yeasts in blood culture. The performance characteristics of this extended platform are described. We found that the extended diagnostic Prove-it Sepsis platform was found to be highly accurate when analyzing primary isolates, spiked blood cultures, nucleic acid extracts from a retrospective blood culture data set, and primary blood cultures. Comparison of the blood culture results from the Prove-it Sepsis platform with those from conventional culture-based methods or by gene sequencing demonstrated a sensitivity of 99% and a specificity of 98% for fungal targets (based on analysis of a total of 388 specimens). Total assay time was 3 h from DNA extraction to BSI diagnosis. These results extend the performance characteristics of the Prove-it platform for bacteria to the easy, rapid, and accurate detection and species identification of yeasts in positive blood cultures. Incorporation of this extended and rapid diagnostic platform into the tools for clinical patient management would allow possibly faster identification and more focused therapies for BSIs.

Bench-to-bedside review: Rapid molecular diagnostics for bloodstream infection--a new frontier?

Among critically ill patients, the diagnosis of bloodstream infection poses a major challenge. Current standard bacterial identification based on blood culture platforms is intrinsically time-consuming and slow. The continuous evolvement of molecular techniques has the potential of providing a faster, more sensitive and direct identification of causative pathogens without prior need for cultivation. This may ultimately impact clinical decision-making and antimicrobial treatment. This review summarises the currently available technologies, their strengths and limitations and the obstacles that have to be overcome in order to develop a satisfactory bedside point-of-care diagnostic tool for detection of bloodstream infection.

Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies

Infectious disease management essentially consists in identifying the microbial cause(s) of an infection, initiating if necessary antimicrobial therapy against microbes, and controlling host reactions to infection. In clinical microbiology, the turnaround time of the diagnostic cycle (>24 hours) often leads to unnecessary suffering and deaths; approaches to relieve this burden include rapid diagnostic procedures and more efficient transmission or interpretation of molecular microbiology results. Although rapid nucleic acid-based diagnostic testing has demonstrated that it can impact on the transmission of hospital-acquired infections, we believe that such life-saving procedures should be performed closer to the patient, in dedicated 24/7 laboratories of healthcare institutions, or ideally at point of care. While personalized medicine generally aims at interrogating the genomic information of a patient, drug metabolism polymorphisms, for example, to guide drug choice and dosage, personalized medicine concepts are applicable in infectious diseases for the (rapid) identification of a disease-causing microbe and determination of its antimicrobial resistance profile, to guide an appropriate antimicrobial treatment for the proper management of the patient. The implementation of point-of-care testing for infectious diseases will require acceptance by medical authorities, new technological and communication platforms, as well as reimbursement practices such that time- and life-saving procedures become available to the largest number of patients.

Year in review 2010: Critical Care--Infection

Infections remain among the most important concerns in critically ill patients. Early and reliable diagnosis of infection still poses difficulties in this setting but also represents a crucial step toward appropriate antimicrobial therapy. Increasing antimicrobial resistance challenges established approaches to the optimal management of infections in the intensive care unit. Rapid infection diagnosis, antibiotic dosing and optimization through pharmacologic indices, progress in the implementation of effective antimicrobial stewardship and infection control programs, and management of fungal infections are some of the most relevant issues in this special patient population. During the last 18 months, Critical Care and other journals have provided a wide array of descriptive and interventional clinical studies and scientific reports helping clinical investigators and critical care physicians to improve diagnosis, management, and therapy of infections in critically ill patients.

Evaluation of high-throughput PCR and microarray-based assay in conjunction with automated DNA extraction instruments for diagnosis of sepsis

BACKGROUND

High incidence of septic patients increases the pressure of faster and more reliable bacterial identification methods to adapt patient management towards focused and effective treatment options. The aim of this study was to assess two automated DNA extraction solutions with the PCR and microarray-based assay to enable rapid and reliable detection and speciation of causative agents in the diagnosis of sepsis.

METHODOLOGY/PRINCIPAL FINDINGS

We evaluated two automated DNA instruments NucliSENS® easyMAG® and NorDiag Arrow for the preparation of blood culture samples. A set of 91 samples flagged as positive during incubation was analyzed prospectively with the high-throughput generation of Prove-it™ Sepsis assay designed to identify over 60 gram-negative and gram-positive bacterial species as well as methicillin resistance marker from a blood culture. Bacterial findings were accurately reported from 77 blood culture samples, whereas 14 samples were reported as negative, containing bacteria not belonging to the pathogen panel of the assay. No difference was observed between the performance of NorDiag Arrow or NucliSENS® easyMAG® with regard to the result reporting of Prove-it™ Sepsis. In addition, we also assessed the quality and quantity of DNA extracted from the clinical Escherichia coli isolate with DNA extraction instruments. We observed only minor differences between the two instruments.

CONCLUSIONS

Use of automated and standardized sample preparation methods together with rapid, multiplex pathogen detection offers a strategy to speed up reliably the diagnostics of septic patients. Both tested DNA extraction devices were shown to be feasible for blood culture samples and the Prove-it™ Sepsis assay, providing an accurate identification of pathogen within 4.5 hours when the detected pathogen was in the repertoire of the test.

New concepts in the pathogenesis, diagnosis and treatment of bacteremia and sepsis

Bacteremia and sepsis are major health concerns. Despite intensive research, there are only a limited number of successful treatment options, and it is difficult to see the forest for the trees when considering the pathogenesis of this condition. Studies in the last decade have shown that a major pathophysiologic event in sepsis is the progression from proinflammation to an immunosuppressive state. However, recent genome-based data indicate that sepsis-related inflammatory responses are highly variable, which calls in question the classic two-phase model of sepsis. Adequate and timely antimicrobial treatment is a cornerstone for survival in patients with bacteremia and sepsis. However, microbial resistance has emerged as an increasing challenge for clinicians and with an increasing number of resistant pathogens causing infections, selection of empiric antimicrobial treatment has become difficult. Treatment options currently under way are targeted to enhance immune responses, rebalance the regulation of the dysregulated immune system, remove endotoxin and block/inhibit apoptosis.

Guidelines for hospital-acquired pneumonia and health-care-associated pneumonia: a vulnerability, a pitfall, and a fatal flaw

The 2005 American Thoracic Society and Infectious Disease Society of America's guidelines for pneumonia introduced the new category of health-care-associated pneumonia, which increased the number of people to whom the guidelines for multidrug-resistant pathogens applied. Three fundamental issues inherent in the definition of hospital-acquired pneumonia and health-care-associated pneumonia undermined the credibility of these guidelines and the applicability of their recommendations: a vulnerability, a pitfall, and a fatal flaw. The vulnerability is the extreme heterogeneity of the population of patients. The fatal flaw is the failure to accurately diagnose hospital-acquired pneumonia and ventilator-associated pneumonia; inability to distinguish colonisation from infection in respiratory-tract cultures renders the guidelines inherently unstable. The pitfall is spiralling empiricism of antibiotic use for severely ill patients in whom infection might not be present. A vicious circle of antibiotic overuse leading to emergence of resistant microflora can become established, leading to unnecessary use of empirical broad-spectrum combination antibiotics and increased mortality. Controlled studies now show that administration of broad-spectrum combination antibiotic therapy can lead to increased mortality in uninfected patients. Proposed solutions include the use of individualised assessment of patients. Health-care-associated pneumonia should be broken down into several distinct subgroups so narrow-spectrum antibiotic therapy can be used. Emphasis should be placed on defining the microbial cause of the pneumonia rather than reflex administration of empirical combination therapy.