What is the relevance of obtaining multiple blood samples for culture? A comprehensive model to optimize the strategy for diagnosing bacteremia

The clinical application value of multi-site mNGS detection of patients with sepsis in intensive care units

BACKGROUND

Sepsis remains a leading cause of mortality in intensive care units, and rapid and accurate pathogen detection is crucial for effective treatment. This study evaluated the clinical application of multi-site metagenomic next-generation sequencing (mNGS) for the diagnosis of sepsis, comparing its performance against conventional methods.

METHODS

A retrospective analysis was conducted on 69 patients with sepsis consecutively admitted to the Department of Intensive Care Medicine, Meizhou People's Hospital. Samples of peripheral blood and infection sites were collected for mNGS and conventional method tests to compare the positive rate of mNGS and traditional pathogen detection methods and the distribution of pathogens. The methods used in this study included a comprehensive analysis of pathogen consistency between peripheral blood and infection site samples. Additionally, the correlation between the pathogens detected and clinical outcomes was investigated.

RESULTS

Of the patients with sepsis, 57.97% experienced dyspnea, and 65.2% had underlying diseases, with hypertension being the most common. mNGS demonstrated a significantly higher pathogen detection rate (88%) compared to the conventional method tests (26%). The pathogen consistency rate was 60% between plasma and bronchoalveolar lavage fluid samples, and that of plasma and local body fluid samples was 63%. The most frequently detected pathogens were gram-negative bacteria, and Klebsiella pneumonia. There were no significant differences in the clinical features between the pathogens.

CONCLUSION

mNGS is significantly superior to conventional methods in pathogen detection. There was a notable high pathogen consistency detection between blood and local body fluid samples, supporting the clinical relevance of mNGS. This study highlights the superiority of mNGS in detecting a broad spectrum of pathogens quickly and accurately.

TRIAL REGISTRATION

Not applicable.

The Yield of One vs. Two Blood Cultures in Children: Under-Detection and Over-Testing

We aimed to determine whether obtaining two blood cultures (BCs) instead of one improved the detection of bloodstream infections (BSIs) in children. For this descriptive study, we used surveillance data collected in 2019-2021 from all Israeli hospitals serving children. The sample included 178,702 culturing episodes. One BC was taken in 90.1% of all episodes and 98.2% of episodes in the emergency department. A true pathogen was detected in 1687/160,964 (1.0%) of single-culture episodes and 1567/17,738 (8.9%) of two-culture episodes (p < 0.001). The yield was significantly different even when considering only the first BC in two-culture episodes: 1.0% vs. 7.5%. Among 1576 two-culture episodes that were positive for a true pathogen, the pathogen was detected only in the second culture in 252 (16.0%). We estimated that if a second culture had been taken in all episodes, an additional 343 BSIs by a true pathogen would have been detected. Among 1086 two-culture episodes with commensal bacteria, the second BC was sterile in 530 (48.8%), suggesting contamination. A commensal was isolated in 3094/4781 (64.7%) positive single-culture episodes, which could represent BSI or contamination. The yield of a single BC bottle was low, reflecting both lower sensitivity of a single bottle and the taking of single bottles in patients with a low probability of BSI.

The microbial pathology of maternal perinatal sepsis: A single-institution retrospective five-year review

INTRODUCTION

Greater than half of in-hospital maternal deaths are caused by sepsis, a condition that occurs when infection exceeds local tissue containment and results in organ dysfunction. Determining the source of infection can be challenging. Microbiological cultures of the uterine cavity are often difficult to obtain, so antimicrobial susceptibility results may not be available to guide treatment. The aim of this retrospective study was to assess the potential clinical value of microbiology samples used in the maternal "septic screen" of patients in an Irish maternity hospital.

METHODS

A review was completed of all maternal "septic screen" (i.e., high vaginal swabs, placenta swabs, blood cultures, throat swabs and urine samples) microbiology results from July 2016 to December 2021.

RESULTS

In the relevant period, 845 patients were subject to a "septic screen", of whom 430 also had a placental swab collected. These 430 patients comprise our study population. 2% of blood cultures yielded potential pathogens, compared with 37%, 33%, 9% and 7% respectively for placental swabs, high vaginal swabs, throat swabs and urine specimens. 95% of blood cultures were sterile, compared with 52%, 0%, 0% and 53% respectively for placental swabs, high vaginal swabs, throat swabs and urine specimens.

CONCLUSION

Of the five microbiological specimen types examined, placental swabs yielded the highest number of potential pathogens. Our results suggest that placental swabs are useful specimens for detecting potential pathogens from the uterine cavity, the most common source of perinatal infections.

Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults

We carried out integrated host and pathogen metagenomic RNA and DNA next generation sequencing (mNGS) of whole blood (n = 221) and plasma (n = 138) from critically ill patients following hospital admission. We assigned patients into sepsis groups on the basis of clinical and microbiological criteria. From whole-blood gene expression data, we distinguished patients with sepsis from patients with non-infectious systemic inflammatory conditions using a trained bagged support vector machine (bSVM) classifier (area under the receiver operating characteristic curve (AUC) = 0.81 in the training set; AUC = 0.82 in a held-out validation set). Plasma RNA also yielded a transcriptional signature of sepsis with several genes previously reported as sepsis biomarkers, and a bSVM sepsis diagnostic classifier (AUC = 0.97 training set; AUC = 0.77 validation set). Pathogen detection performance of plasma mNGS varied on the basis of pathogen and site of infection. To improve detection of virus, we developed a secondary transcriptomic classifier (AUC = 0.94 training set; AUC = 0.96 validation set). We combined host and microbial features to develop an integrated sepsis diagnostic model that identified 99% of microbiologically confirmed sepsis cases, and predicted sepsis in 74% of suspected and 89% of indeterminate sepsis cases. In summary, we suggest that integrating host transcriptional profiling and broad-range metagenomic pathogen detection from nucleic acid is a promising tool for sepsis diagnosis.

Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units

The performance of metagenomic next-generation sequencing (mNGS) was evaluated and compared with that of conventional culture testing in patients with sepsis. Prospective blood and bronchoalveolar lavage fluid (BALF) samples from 50 patients with sepsis were tested using cultures (bacterial, fungal, and viral) and mNGS of microbial DNA (blood and BALF) and RNA (BALF). mNGS had higher detection rates than blood culture (88.0% versus 26.0%, P < 0.001) and BALF culture (92.0% versus 76.0%, P = 0.054). RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. The number of multiple detections per specimen was higher in BALF (92.0%) than in blood (78.0%) samples, and the highest number of pathogens detected in a single specimen was 32. Among blood samples, compared to cultures, mNGS detected significantly more bacteria (P < 0.001), fungi (P = 0.012), and viruses (P < 0.001), whereas BALF mNGS had a higher detection rate for bacteria (P < 0.001) and viruses (P < 0.001). The percentage of mNGS-positive samples was significantly higher than that of culture-positive samples for several Gram-negative bacteria, some Gram-positive bacteria, and viruses, but not fungi. Mycobacteria had a higher detection rate by culture than by mNGS, but the difference was not significant due to the small sample size. The positive and negative agreements with 95% confidence intervals of mNGS and culture were 62.0% (50.4 to 72.7) and 96.8% (96.5 to 97.1), respectively. mNGS offers a sensitive diagnostic method for patients with sepsis and is promising for the detection of multipathogen infections. Clinical correlation is advised to interpret mNGS data due to the lack of unified diagnostic criteria.

IMPORTANCE Delays in effective antimicrobial therapy have resulted in decreased survival rates among patients with sepsis. However, current culture-based diagnostic methods have low sensitivity because of concurrent antibiotic exposure and fastidious and atypical causative organisms. Among patients with sepsis, we showed that mNGS methods had higher positive rates than culture methods, especially for bacteria, viruses, and multipathogen infections, which are difficult to culture and detect in patients treated with antibiotics. RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. mNGS also showed a high negative percent agreement with cultures. However, the interpretation of mNGS data should be combined with clinical data and conventional methods considering the lack of unified diagnostic criteria.

Accuracy of procalcitonin for diagnosing peripheral blood culture contamination among patients with positive blood culture for potential contaminants

PURPOSE

Blood culture contamination is still a frequently observed event and may lead to unnecessary antibiotic prescriptions and additional hazards and costs. However, in patients hospitalized in tertiary care, true bacteremias for pathogens that are classically considered as contaminants can be observed. We assessed the diagnostic accuracy of procalcitonin for differentiating blood culture contamination from bacteremia in patients with positive blood cultures for potential contaminants.

METHODS

We carried out a retrospective, cross-sectional, observational study on consecutive patients hospitalized between January 2016 and May 2019 at the University Hospital of Nancy and who had a positive peripheral blood culture for a pathogen classically considered as a potential contaminant.

RESULTS

During the study period, 156 patients were screened, and 154 were retained in the analysis. Among the variables that were significantly associated with a diagnosis of blood culture contamination in univariate analyses, four were maintained in multivariate logistic regression analysis: a number of positive blood culture bottles ≤ 2 (OR 23.76; 95% CI 1.94-291.12; P = 0.01), procalcitonin < 0.1 ng/mL (OR 14.88; 95% CI 1.62-136.47; P = 0.02), non-infection-related admission (OR 13.00; 95% CI 2.17-77.73; P = 0.005), and a percentage of positive blood culture bottles ≤ 25% (OR 12.15; 95% CI 2.02-73.15; P = 0.006).

CONCLUSIONS

These data provide new evidence on the usefulness of plasma procalcitonin as a reliable diagnostic biomarker in the diagnostic algorithm of peripheral blood culture contamination among patients hospitalized in tertiary care.

CLINICAL TRIAL

ClinicalTrials.gov #NCT04573894.

Optimized blood culture strategy to document febrile neutropenia

BACKGROUND

Poor and delayed microbiological documentation of episodes of febrile neutropenia (EFN) deserves improvement. We assessed the impact of a new blood culture (BC) sampling protocol to optimize the diagnosis of bloodstream infection during EFN, compared with standard of care protocol.

METHODS

This pre/post intervention included patients who presented an EFN in a pediatric hematology-oncology center. Data were compared between 1-year periods P1 (110 EFN, 53 patients) and P2 (124 EFN, 53 patients). Pre-intervention settings were 1-2 mL of blood cultured per BC set and several samplings over days (multisampling strategy) during period P1 vs. one unique early sampling of a large volume of blood (0.5-60 mL) depending on patient weight during period P2 (single-sampling weight-adapted strategy). Microbial detection and time-to-diagnosis were evaluated.

RESULTS

Seventeen EFNs were microbiologically documented in P1 (15.5%) and 26 in P2 (21%). The rate of positive BC sets increased during P2 (10.4% vs. 5.8%). All cases of bacteremia were documented by BC drawn during the first 4 days of fever, and during P2 by samples obtained on the first day of fever.

CONCLUSIONS

Bacteremia detection was improved. This proof-of-concept study shows benefits of combining the single-sampling strategy with large weight-adapted blood sampling strategy during EFN.

IMPACT

Combination of single-sampling and weight-adapted blood culture strategies showed benefits in the documentation of bloodstream infections during febrile neutropenia. Bacteremia detection was improved in this preliminary study and this warrants further evaluation in the overall pediatric population. We observed no adverse effects associated with the new strategy while overall blood sparing was improved and handling of intravascular devices was reduced. The good tolerance of the blood sampling suggests that the recommended 1% volume limitation in children could be reconsidered. A similar evaluation is justified in the overall pediatric population suspected for bloodstream infection.

Collection, transport and storage procedures for blood culture specimens in adult patients: recommendations from a board of Italian experts

Bloodstream infections (BSIs) remain a potentially life-threatening condition. The gold standard for the diagnosis of BSI is still blood cultures (BCs), and the diagnostic yield depends on clinical and technical factors that have an impact on collection and transportation. Hence, monitoring of the entire pre-analytical process from blood collection to transportation to the microbiology laboratory is critical. To optimize the clinical impact of the diagnostic and therapeutic procedures, a multidisciplinary approach and univocal protocols are mandatory. A board of specialists discussed the available evidence on the pre-analytical process and produced the present document to guide physicians and nurses on the ideal execution of BC: (1) timing and preparation for blood collection; (2) skin antisepsis; (3) blood volume; (4) sampling method and safety; (5) medium to be used; (6) time to BC transportation; and (7) quality assurance and quality management.

Single-Sampling Strategy vs. Multi-Sampling Strategy for Blood Cultures in Sepsis: A Prospective Non-inferiority Study

Background

Optimal sampling is critical for the performance of blood cultures (BCs). Most guidelines recommend collecting 40 ml of blood, divided between two venipuncture sites, i.e., multi-sampling strategy (MSS). Sampling through a single venipuncture site, i.e., single-sampling strategy (SSS) is easier; however, the diagnostic performance of SSS compared to MSS remains unknown. Thus, we aimed to study if SSS is non-inferior to MSS for detection of pathogenic microorganisms.

Methods

A prospective, paired, non-inferiority design was used. Patients with clinically suspected sepsis admitted to an Emergency Department were included. Six BC bottles were simultaneously collected, consisting of four BC bottles from the first arm and two from the other arm. SSS consisted of BC bottles 1, 2, 3, and 4, and MSS consisted of BC bottles 1, 2, 5, and 6. Samples were incubated in a BacT/ALERT BC system.

Results

The final analysis included 549 episodes. Pathogenic microorganisms were detected in 162 cases (29.5%) with MSS and 160 cases (29.1%) with SSS, yielding an absolute difference of 0.36%, with a 95% confidence interval of -1.33 to 2.06%, which did not exceed the predefined non-inferiority margin of 5%. MSS tended to produce more contaminant growth (7.3% of cases) than SSS (5.3% of cases; p = 0.072).

Conclusion

The study showed that SSS was non-inferior to MSS in detecting pathogenic microorganisms and supports the use of SSS as a routine method.

Best Practices of Blood Cultures in Low- and Middle-Income Countries

Bloodstream infections (BSI) have a substantial impact on morbidity and mortality worldwide. Despite scarcity of data from many low- and middle-income countries (LMICs), there is increasing awareness of the importance of BSI in these countries. For example, it is estimated that the global mortality of non-typhoidal Salmonella bloodstream infection in children under 5 already exceeds that of malaria. Reliable and accurate diagnosis of these infections is therefore of utmost importance. Blood cultures are the reference method for diagnosis of BSI. LMICs face many challenges when implementing blood cultures, due to financial, logistical, and infrastructure-related constraints. This review aims to provide an overview of the state-of-the-art of sampling and processing of blood cultures, with emphasis on its use in LMICs. Laboratory processing of blood cultures is relatively straightforward and can be done without the need for expensive and complicated equipment. Automates for incubation and growth monitoring have become the standard in high-income countries (HICs), but they are still too expensive and not sufficiently robust for imminent implementation in most LMICs. Therefore, this review focuses on "manual" methods of blood culture, not involving automated equipment. In manual blood cultures, a bottle consisting of a broth medium supporting bacterial growth is incubated in a normal incubator and inspected daily for signs of growth. The collection of blood for blood culture is a crucial step in the process, as the sensitivity of blood cultures depends on the volume sampled; furthermore, contamination of the blood culture (accidental inoculation of environmental and skin bacteria) can be avoided by appropriate antisepsis. In this review, we give recommendations regarding appropriate blood culture sampling and processing in LMICs. We present feasible methods to detect and speed up growth and discuss some challenges in implementing blood cultures in LMICs, such as the biosafety aspects, supply chain and waste management.

Procalcitonin: A Marker of Bacteraemia in SIRS

A number of European studies have documented the ability of procalcitonin (PCT), a novel inflammatory marker, to discriminate patients with sepsis from those with other causes of systemic inflammatory response syndrome (SIRS). The aim of this study was to assess procalcitonin's performance in an Australian intensive care unit (ICU) setting to examine whether it could discriminate between these two conditions.

One hundred and twenty-three consecutive adult ICU patients fulfilling criteria for SIRS were enlisted in the study. Over a period of five days, daily serum PCT and C-reactive protein (CRP) levels were measured. At least two sets of cultures were taken of blood, sputum/broncho-alveolar lavage (BAL) and urine. Other cultures were taken as clinically indicated. Questionnaires to ascertain clinical suspicion of sepsis were prospectively answered by the ICU senior registrars.

PCT values were ten times higher in patients with positive blood cultures; CRP values were also significantly higher in the bacteraemic patients. Both PCT and CRP had a good ability to discriminate bacteraemia from non-infectious SIRS, with the area under receiver operating characteristics (ROC) curves for PCT being 0.8 and for CRP being 0.82. However neither PCT or CRP was able to discriminate patients with localized sepsis from those without. Utilizing both tests resulted in a more sensitive screen than either one alone, while PCT was a more accurate diagnostic test for bacteraemia than CRP. The PCT value also differed between those who died in hospital and those who survived.

Measurement of PCT alone or in combination with CRP can aid discrimination of septicaemia/bacteraemia with associated SIRS from non-infectious SIRS in an Australian ICU setting.

How to: accreditation of blood cultures' proceedings. A clinical microbiology approach for adding value to patient care

BACKGROUND

Quality assurance and quality management are driving forces for controlling blood culture best practices but should not be disconnected from the end-point target, i.e. patient value.

AIMS

This article is intended to help microbiologists implement blood culture accreditation that is actually beneficial to patient management.

SOURCES

Experience from a nationwide taskforce for promoting quality assurance and competence in clinical microbiology laboratories, guidelines on blood culture.

CONTENT

Experience in blood culture accreditation according to International standard ISO 15189 standards is provided in this review, with a particular focus on critical points that are specific to blood culture (e.g. excluding strain identification or antimicrobial susceptibility testing). Blood culture test method verification is based on risk analysis, and evaluation of the test method's performance is based on the literature review and suppliers' data. In addition, blood culture performance relies largely on the quality of its pre-analytical phase, and the test method should be monitored based on key performance indicators such as the volume of blood cultured, the contamination rate and time to transportation. Other critical key indicators include the rate of false-positive signals, the rate of positive blood cultures, the ecology associated with positive results, and the timely communication of the results to the ward during the post-analytical phase. Finally, a critical analysis of quality controls and of the tools needed to improve blood culture monitoring in the future is provided.

IMPLICATION

Appropriate quality assurance should focus on patient value rather than technical details to provide an appropriate clinical service.

Rapid Detection and Differentiation of Clinically Relevant Candida Species Simultaneously from Blood Culture by Use of a Novel Signal Amplification Approach

Fungal bloodstream infections are a significant problem in the United States, with an attributable mortality rate of up to 40%. An early diagnosis to direct appropriate therapy has been shown to be critical to reduce mortality rates. Conventional phenotypic methods for fungal detection take several days, which is often too late to impact outcomes. Herein, we describe a cost-effective multiplex assay platform for the rapid detection and differentiation of major clinically relevant Candida species directly from blood culture. This approach utilizes a novel biotin-labeled polymer-mediated signal amplification process combined with targeting rRNA to exploit phylogenetic differences for sensitive and unambiguous species identification; this assay detects seven pathogenic Candida species (C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, C. lusitaniae, and C. guilliermondii) simultaneously with very high specificity to the species level in less than 80 min with the limits of detection at 1 × 10³ to 10 × 10³ CFU/ml or as few as 50 CFU per assay. The performance of the described assay was verified with 67 clinical samples (including mixed multiple-species infections as well), with an overall 100% agreement with matrix-assisted laser desorption ionization (MALDI) mass spectrometry-based reference results. By providing a species identity rapidly, the clinician is aided with information that may direct appropriate therapy sooner and more accurately than current approaches, including PCR-based tests.

A Quality Improvement Initiative to Decrease the Rate of Solitary Blood Cultures in the Emergency Department

OBJECTIVES

Best practice guidelines recommend that at least two sets of blood cultures (BCs) be sent when blood cultures are required. However, high rates of solitary BCs are still common in the emergency department (ED). The aim of this study was to evaluate the efficacy of different quality improvement initiatives aimed at reducing the rate of solitary blood cultures being sent to the laboratory on patients ultimately discharged from our ED.

METHODS

This was a multicenter, multiphase, prospective study evaluating a comprehensive education-based intervention and a second intervention that combined a computerized forcing function (FF) along with a brief education-based intervention. The results were analyzed using segmented regression analysis, as well as statistical process control charts.

RESULTS

The baseline rate of solitary sets of BCs was 41.1%. The education intervention reduced this rate to 30.3%. The introduction of a FF with a brief educational intervention further reduced the rate to 11.6%. This represents an absolute reduction of 29.5% from baseline (relative reduction of 71.8%). According to segmental regression analyses, the education intervention alone did not produce a statistically significant change when factoring possible background time-related trends (p = 0.071). However, the FF produced a statistically significant improvement (p < 0.0005), which was maintained for 6 months.

CONCLUSION

The combination of a brief education-based intervention and a computerized FF was more effective than education alone in reducing solitary BC collection in our ED in this time series study. FFs can be a powerful tool in modifying behaviors and processes in the clinical setting.

Comparative evaluation of the role of single and multiple blood specimens in the outcome of blood cultures using BacT/ALERT 3D (automated) blood culture system in a tertiary care hospital

Introduction:

Bloodstream infection (BSI) is a leading cause of mortality in critically ill patients. The mortality directly attributable to BSI has been estimated to be around 16% and 40% in general hospital population and Intensive Care Unit (ICU) population, respectively. The detection rate of these infections increases with the number of blood samples obtained for culture. The newer continuous monitoring automated blood culture systems with enhanced culture media show increased yield and sensitivity. Hence, we aimed at studying the role of single and multiple blood specimens from different sites at the same time in the outcome of automated blood culture system.

Materials and Methods and Results:

A total of 1054 blood culture sets were analyzed over 1 year, the sensitivity of one, two, and three samples in a set was found to be 85.67%, 96.59%, and 100%, respectively, which showed a statistically significant difference (P < 0.0001). Similar findings were seen in few more studies, however, among individual organisms in contrast to other studies, the isolation rates of Gram-positive bacteria were less than that of Gram-negative Bacilli with one (or first) sample in a blood culture set. In our study, despite using BacT/ALERT three-dimensional continuous culture monitoring system with FAN plus culture bottles, 15% of positive cultures would have been missed if only a single sample was collected in a blood culture set.

Conclusion:

The variables like the volume of blood and number of samples collected from different sites still play a major role in the outcome of these automated blood culture systems.

The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood

Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States.

How to Optimize the Use of Blood Cultures for the Diagnosis of Bloodstream Infections? A State-of-the Art

Bloodstream infection (BSI) is a major cause of death in developed countries and the detection of microorganisms is essential in managing patients. Despite major progress has been made to improve identification of microorganisms, blood culture (BC) remains the gold standard and the first line tool for detecting BSIs. Consensus guidelines are available to ensure optimal BSI procedures, but BC practices often deviate from the recommendations. This review provides an update on clinical and technical issues related to blood collection and to BC performance, with a special focus on the blood sample strategy to optimize the sensitivity and specificity of BCs.

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.

Personalised beta-lactam therapy: basic principles and practical approach

Bacterial infections are potentially life-threatening diseases requiring effective antibiotic treatment right from the outset to achieve a favourable prognosis. Therapeutic success depends on the susceptibility of the bacterial pathogen, determined by the minimum inhibitory concentration (MIC), and the concentration of the antibiotic at the focus of infection, which is influenced by drug metabolism and pharmacokinetic (PK) factors. Beta-lactams are time-dependent antibiotics. Bacterial killing correlates with the duration of the drug concentration above the MIC of the pathogen. Critical illness is associated with major PK changes. This may lead to unexpected drug concentrations and unpredictable dose requirements differing significantly from standard dosages. Emerging dosing strategies are therefore based on PK/pharmacodynamic (PD) principles. Therapeutic drug monitoring (TDM) is increasingly playing a key role in antibiotic treatment optimisation in general and in beta-lactam therapy, in particular, notably in severely ill patients. Furthermore, evidence of the superiority of continuous beta-lactam infusions over shorter administration regimens is growing. Target drug concentrations have to be defined, considering MIC values especially in pathogens with limited susceptibility. For reliable TDM results, correct pre-analytical sample handling is indispensable. Personalised, TDM-guided therapy currently offers the most promising approach to assuring that beta-lactam treatment is effective, especially in critically ill patients.

A Molecular Host Response Assay to Discriminate Between Sepsis and Infection-Negative Systemic Inflammation in Critically Ill Patients: Discovery and Validation in Independent Cohorts

BACKGROUND

Systemic inflammation is a whole body reaction having an infection-positive (i.e., sepsis) or infection-negative origin. It is important to distinguish between these two etiologies early and accurately because this has significant therapeutic implications for critically ill patients. We hypothesized that a molecular classifier based on peripheral blood RNAs could be discovered that would (1) determine which patients with systemic inflammation had sepsis, (2) be robust across independent patient cohorts, (3) be insensitive to disease severity, and (4) provide diagnostic utility. The goal of this study was to identify and validate such a molecular classifier.

METHODS AND FINDINGS

We conducted an observational, non-interventional study of adult patients recruited from tertiary intensive care units (ICUs). Biomarker discovery utilized an Australian cohort (n = 105) consisting of 74 cases (sepsis patients) and 31 controls (post-surgical patients with infection-negative systemic inflammation) recruited at five tertiary care settings in Brisbane, Australia, from June 3, 2008, to December 22, 2011. A four-gene classifier combining CEACAM4, LAMP1, PLA2G7, and PLAC8 RNA biomarkers was identified. This classifier, designated SeptiCyte Lab, was validated using reverse transcription quantitative PCR and receiver operating characteristic (ROC) curve analysis in five cohorts (n = 345) from the Netherlands. Patients for validation were selected from the Molecular Diagnosis and Risk Stratification of Sepsis study (ClinicalTrials.gov, NCT01905033), which recruited ICU patients from the Academic Medical Center in Amsterdam and the University Medical Center Utrecht. Patients recruited from November 30, 2012, to August 5, 2013, were eligible for inclusion in the present study. Validation cohort 1 (n = 59) consisted entirely of unambiguous cases and controls; SeptiCyte Lab gave an area under curve (AUC) of 0.95 (95% CI 0.91-1.00) in this cohort. ROC curve analysis of an independent, more heterogeneous group of patients (validation cohorts 2-5; 249 patients after excluding 37 patients with an infection likelihood of "possible") gave an AUC of 0.89 (95% CI 0.85-0.93). Disease severity, as measured by Sequential Organ Failure Assessment (SOFA) score or Acute Physiology and Chronic Health Evaluation (APACHE) IV score, was not a significant confounding variable. The diagnostic utility of SeptiCyte Lab was evaluated by comparison to various clinical and laboratory parameters available to a clinician within 24 h of ICU admission. SeptiCyte Lab was significantly better at differentiating cases from controls than all tested parameters, both singly and in various logistic combinations, and more than halved the diagnostic error rate compared to procalcitonin in all tested cohorts and cohort combinations. Limitations of this study relate to (1) cohort compositions that do not perfectly reflect the composition of the intended use population, (2) potential biases that could be introduced as a result of the current lack of a gold standard for diagnosing sepsis, and (3) lack of a complete, unbiased comparison to C-reactive protein.

CONCLUSIONS

SeptiCyte Lab is a rapid molecular assay that may be clinically useful in managing ICU patients with systemic inflammation. Further study in population-based cohorts is needed to validate this assay for clinical use.

The potential of whole genome NGS for infectious disease diagnosis

Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.

Improved sensitivity for molecular detection of bacterial and Candida infections in blood

The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections.

Comparison of two molecular assays with conventional blood culture for diagnosis of sepsis

In this small study, the LightCycler® SeptiFast, and the SepsiTest™ were compared with blood culture. The SeptiFast showed a higher sensitivity (42.9%) and specificity (88.2%) when compared to blood culture than the SepsiTest™ (28.6 and 85.3%). The SeptiFast provides more species specific results, although the identification panel is smaller.

Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture

The purpose of this paper is to define guidelines to interpret positive blood cultures (BCs) to distinguish bloodstream infection (BSI) from contamination in BCs drawn with a single venipuncture. During a 2-year period, each positive BC set (comprising six bottles from a single venipuncture) was prospectively categorised by clinicians, bacteriologists and hospital epidemiologists as BSI or contamination. For each case, the number of positive bottles per set, results from Gram staining and microorganism identification were analysed in order to define interpretation guidelines. We analysed 940 positive BC sets. The BSI rate in monomicrobial BC sets was positively correlated with the number of positive bottles. The positive predictive value was 88% with one and 100% with ≥2 positive bottles for Escherichia coli; 100% for Staphylococcus aureus, Pseudomonas and Candida spp., regardless of the number of positive bottles; 3.5%, 61.1%, 78.9% and 100% for coagulase-negative staphylococci (CoNS) with one, two, three and ≥4 positive bottles, respectively. Using a single-sampling strategy, interpretation guidelines for monomicrobial positive BCs are based on the number of positive bottles per set, results from Gram staining and microorganism identification: ≥4 positive bottles (≥2 with Gram-negative bacilli) always led to a diagnosis of BSI. The CoNS BSI rate positively correlates with the number of positive bottles.

Update on the management of infection in patients with severe sepsis

Morbidity and mortality associated with the development of severe sepsis remain unacceptably high. However, with the introduction of a protocol called early goal-directed therapy, significant benefits in terms of patient's outcome have been demonstrated. In an aim to improve outcome and to increase awareness, practical evidence-based guidelines for the management of severe sepsis and septic shock were developed under the auspices of the Sepsis Surviving Campaign, easy to apply by the bedside medical and nursing staff. The treatment of severe sepsis includes 3 main essentials: (1) eradication of the inciting infection using source control measures and empiric antimicrobials, (2) hemodynamic resuscitation of tissue hypoperfusion using fluids and inotropic drugs to prevent life-threatening organ damage, and (3) sustained organ support using mechanical interventions to diminish organ injury. This review article highlights the anti-infective approach of the management of sepsis.

Severe sepsis and septic shock in the emergency department

Increased attention has focused recently on the acute management of severe sepsis and septic shock, conditions that represent the end-stage systemic deterioration of overwhelming infection. Clinical trials have identified new therapies and management approaches that, when applied early, appear to reduce mortality. Practice guidelines have been advanced by critical care societies, and many of the proposed interventions involve therapies other than antimicrobials directed at hemodynamic resuscitation or addressing adverse effects of the inflammatory cascade. Although many emergency departments (EDs) are now adopting treatment protocols for sepsis that are based on published treatment guidelines, recent research calls many of the initial recommendations into question, and validation trials of some of these approaches are ongoing. This article reviews the initial evaluation and treatment considerations of sepsis in the ED setting.

Dialysis Surveillance Report: National Healthcare Safety Network (NHSN)-data summary for 2006

Thirty-two outpatient hemodialysis providers in the United States voluntarily reported 3699 adverse events to the Centers for Disease Control and Prevention (CDC) National Healthcare Safety Network (NHSN) during 2006. These providers were previously enrolled in the Dialysis Surveillance Network. The pooled mean rates of hospitalization among patients with arteriovenous fistulas, grafts, permanent and temporary central venous catheters were 7.7, 9.2, 15.7, and 34.7 per 100 patient-months, respectively. For bloodstream infection the pooled mean rates were 0.5, 0.9, 4.2, and 27.1 per 100 patient-months in these groups. Among the 599 isolates reported, 461 (77%) represented access-associated blood stream infections in patients with central lines, and 138 (23%) were in patients with fistulas or grafts. The microorganisms most frequently identified were common skin contaminants (e.g., coagulase-negative staphylococci). In 2007, enrollment in NHSN opened to all providers of outpatient hemodialysis. Specific information is available at http://www.cdc.gov/ncidod/dhqp/nhsn_FAQenrollment.html.

[Influence of axillary temperature on blood culture yield in the emergency department]

OBJECTIVES

To determine the clinical and epidemiological characteristics of patients undergoing blood culture in the emergency department and to identify the relation between the results of blood culture and axillary temperature at blood extraction.

METHOD

We performed a prospective, observational study. All patients who underwent blood extraction by 2 emergency department nurses, as indicated by physicians, between January 2004 and December 2005 were included. The patients were stratified into subgroups according to their temperature on extraction and final diagnosis. Bivariate analysis was performed to compare the clinical and epidemiological characteristics of the patients in relation to the presence of bacteremia and the distinct subgroups established. Isolates of common contaminating microorganisms were discarded.

RESULTS

A total of 603 patients were included. The highest percentages of bacteremia were found in patients with high fever or hypothermia. Among the overall group of patients, a significant correlation was found between axillary temperature and bacteremia. However, when patients with a final diagnosis of a disease with a low probability of bacteremia were excluded, this correlation disappeared and no association was found between temperature and the risk of bacteremia in specific infectious processes (pneumonia, pyelonephritis, etc).

CONCLUSIONS

The main factor associated with bacteremia was the disease prompting blood culture rather than patient temperature.

Relevance of routine use of the anaerobic blood culture bottle

Using the BacT/Alert automated system, we conducted a 1-year retrospective study on blood cultures, focusing on the relevance of routine use of the anaerobic bottle. The rate of patients with positive blood cultures was 19.7%. Among these, 13.5% had a positive anaerobic bottle in the absence of any aerobic bottle, and 2/3 of these grew with nonobligate anaerobes. These patients were hospitalized in 20 out of 26 wards of the hospital group. For 65.4% of the monomicrobial-positive blood cultures growing Enterobacteriaceae, the anaerobic bottle detected growth earlier than the corresponding aerobic bottle. These data suggest that, in our institution, the use of an anaerobic bottle is still relevant.

Severe sepsis and septic shock: review of the literature and emergency department management guidelines

Severe sepsis and septic shock are as common and lethal as other acute life-threatening conditions that emergency physicians routinely confront such as acute myocardial infarction, stroke, and trauma. Recent studies have led to a better understanding of the pathogenic mechanisms and the development of new or newly applied therapies. These therapies place early and aggressive management of severe sepsis and septic shock as integral to improving outcome. This independent review of the literature examines the recent pathogenic, diagnostic, and therapeutic advances in severe sepsis and septic shock for adults, with particular relevance to emergency practice. Recommendations are provided for therapies that have been shown to improve outcomes, including early goal-directed therapy, early and appropriate antimicrobials, source control, recombinant human activated protein C, corticosteroids, and low tidal volume mechanical ventilation.

Opportunities to Replace the Use of Animals in Sepsis Research

Sepsis and multiple organ failure are common causes of death in patients admitted to intensive care units. The incidence of sepsis and associated mortalities has been steadily increasing over the past 20 years. Sepsis is a complex inflammatory condition, the precise causes of which are still poorly understood. Animal models of sepsis have the potential to cause substantial suffering, and many of them have been poorly representative of the human syndrome. However, a number of non-animal approaches, including in vitro, in silico and clinical studies, show promise for addressing this situation. This report is based on discussions held at an expert workshop convened by Focus on Alternatives and held in 2004 at the Wellcome Trust, London. It provides an overview of some non-animal approaches to sepsis research, including their strengths and weaknesses, and argues that they should be prioritised for further development.

Growth of Mycobacterium tuberculosis in conventional BacT/ALERT FA blood culture bottles allows reliable diagnosis of Mycobacteremia

The conventional BacT/ALERT FA blood cultures supported the ample growth of Mycobacterium tuberculosis in seeding experiments and appeared to perform as reliably as the BACTEC Myco/F-Lytic vials in the recovery of M. tuberculosis from blood in HIV-infected patients. Overall, blood cultures were positive in 39% of patients with tuberculosis.

[Infection-related emergencies in oncology]

Infections in immunosuppressed patients have always to be regarded as emergencies, as they have a high rate of complications and mortality. The most important risk factor is severity and duration of granulocytopenia. Risk scores help to identify patients who, despite their immune deficiency have a low risk of complications. Diagnostic measures to identify the causative microorganism and the source of infection is necessary. However, diagnostic investigation must not delay the immediate onset of antimicrobial treatment. Patients often have to be treated empirically as the identification of the causative microorganism or the source of infection are often unknown at the beginning of clinical symptoms. Empirical treatment has to be broad to cover possible microorganisms. Especially meningitis, abdominal infections, sepsis and pneumonia can be regarded as infectiological emergencies. Patients with these infections have to be treated with intensive antimicrobial treatment, taking into account the possible causative agents.

Repeating blood cultures during hospital stay: practice pattern at a teaching hospital and a proposal for guidelines

Guidelines for blood culture (BC) address the appropriate frequency, number and volume, but no guidelines exist for repeating BCs. The pattern of repeated BCs was studied in all patients hospitalised in December 2001 to determine the extent of and reasons for repeating cultures. BC was repeated in 127 (31.6%) of 405 adults with an initial BC during the study period. All patients with available records (n = 96; 75.6%) were included. The average patient age was 62.2 +/- 15.9 years. In total, 295 BC sets (one to four BCs/set) were obtained, comprising 96 initial and 199 repeats (one to nine repeats/patient). Sixty-nine (34.7%) repeats were taken within 24 h, and 89 (44.7%) within 2-4 days. The most common reason (32.2%) was persistent fever. The result of repeated cultures was: no growth (83.4%), same pathogen (9.1%), new pathogen (2.5%) or contamination (5.0%). Thus, BC repeats accounted for one-third of all BCs handled in the laboratory, with little additional yield. Guidelines for repeating BCs may decrease unnecessary testing.

Predictive Value of Blood Cultures Positive for Coagulase-Negative Staphylococci: Implications for Patient Care and Health Care Quality Assurance

Interpretation of blood cultures that are positive for coagulase-negative staphylococci (CoNS) is often difficult. Predictive values for blood cultures positive for CoNS in patients with a central vascular line in place were calculated using the following rates: true bacteremia, 3%; blood culture contamination, 2%; detection of bacteremia, 80%; and catheter colonization, 2% (for blood samples obtained through a central vascular line). Positive predictive values were 55% for 1 positive culture result of 1 culture performed, 20% for 1 positive result of 2 performed, and only 5% for 1 positive result of 3 performed. For 2 positive culture results of 2 cultures performed, the positive predictive value was 98% if both samples were obtained through the vein, 96% if one sample was obtained through a catheter and the other was obtained by vein, and only 50% if both samples were obtained through a catheter. Use of this model with institution-specific values for input parameters would assist in clinical decision-making as well as hospital quality assurance.