Bloodstream infections – Standard and progress in pathogen diagnostics

Rapid and receptor-free Prussian blue electrochemical sensor for the detection of pathogenic bacteria in blood

Bloodstream bacterial infections, a major health concern due to rising sepsis rates, require prompt, cost-effective diagnostics. Conventional methods, like CO2-based transduction, face challenges such as volatile metabolites, delayed gas-phase signaling, and the need for additional instruments, whereas electrochemical sensors provide rapid, sensitive, and efficient real-time detection. In this study, we developed a bioreceptor-free Prussian blue (PB) sensor platform for real-time bacterial growth monitoring in blood culture. PB thin films were electrodeposited onto a screen-printed carbon electrode (SPCE) via cyclic voltammetry (CV) technique under optimal conditions. The electrochemical performance of PB/SPCE was assessed using differential pulse voltammetry (DPV) against exoelectrogenic bacteria, including E. coli, P. aeruginosa, S. aureus, and E. faecalis. The proposed sensor exhibited surface-controlled electrochemical kinetics and bacteria-driven metal reduction from PB to Prussian white (PW), facilitated by extracellular electron transfer (EET). It showed significant sensitivity with an extensive detection range of 102-108 CFU/mL for E. coli and S. aureus, and 103-108 CFU/mL for P. aeruginosa and E. faecalis, with reliable detection limits. The sensor accessed the viability of the pathogen within 3 hrs, offering a rapid, efficient alternative to traditional, labor-intensive methods for blood-based diagnostics.

Development and application of an early prediction model for risk of bloodstream infection based on real-world study

BACKGROUND

Bloodstream Infection (BSI) is a severe systemic infectious disease that can lead to sepsis and Multiple Organ Dysfunction Syndrome (MODS), resulting in high mortality rates and posing a major public health burden globally. Early identification of BSI is crucial for effective intervention, reducing mortality, and improving patient outcomes. However, existing diagnostic methods are flawed by low specificity, long detection times and high demands on testing platforms. The development of artificial intelligence provides a new approach for early disease identification. This study aims to explore the optimal combination of routine laboratory data and clinical monitoring indicators, and to utilize machine learning algorithms to construct an early, rapid, and universally applicable BSI risk prediction model, to assist in the early diagnosis of BSI in clinical practice.

METHODS

Clinical data of 2582 suspected BSI patients admitted to the Chongqing University Central Hospital, from January 1, 2021 to December 31, 2023 were collected for this study. The data were divided into a modeling dataset and an external validation dataset based on chronological order, while the modeling dataset was further divided into a training set and an internal validation set. The occurrence rate of BSI, distribution of pathogens, and microbial primary reporting time were analyzed within the training set. During the feature selection stage, univariate regression and ML algorithms were applied. First, Univariate logistic regression was used to screen for predictive factors of BSI. Then, the Boruta algorithm, Lasso regression, and Recursive Feature Elimination with Cross-validation (RFE-CV) were employed to determine the optimal combination of predictors for predicting BSI. Based on the optimal combination, six machine learning algorithms were used to construct an early BSI risk prediction model. The best model was selected by models' performance, and the Shapley Additive Explanations (SHAP) method was used to explain the model. The external validation set was used to evaluate the predictive performance and generalizability of the selected model, and the research findings were ultimately applied in clinical practice.

RESULTS

The incidence of BSI among inpatients at the Chongqing University Central Hospital was 12.91%. Following further feature selection, a set of 5 variables was determined, including white blood cell count, standard bicarbonate, base excess of extracellular fluid, interleukin-6, and body temperature. BSI early risk prediction models were constructed using six machine learning algorithms, with the XGBoost model demonstrating the best performance, achieving an AUC value of 0.782 in the internal validation set and an AUC value of 0.776 in the external validation set. This model is made publicly available as an online webpage tool for clinical use.

CONCLUSIONS

This study successfully identified a set of 5 features by analyzing routine laboratory data clinical monitoring indicators among hospitalized patients. Based on this set, a machine learning-based early risk prediction model for BSI was constructed. The model is capable of early and rapid differentiation between BSI and non-BSI patients. The inclusion of minimal risk prediction factors enhances its applicability in clinical settings, particularly at the primary care level. To further improve the model's real-world applicability and more convenient for clinical use, the online application of the model could greatly improve the efficiency of BSI diagnosis and reducing patients' mortality.

Lighting up Resistance: Rapid Antimicrobial Susceptibility Testing of Gram-Negative Bacteria in Bloodstream Infections Using an Aggregation-Induced Emission Bioprobe

Rapid and accurate antimicrobial susceptibility testing (AST) is crucial for guiding treatment and combating resistance. However, conventional ASTs are time-consuming and require pure colonies, delaying the initiation of targeted antimicrobial therapy. Herein, a novel AST based on an aggregation-induced emission luminogen (AIEgen), DATVP, which can directly assess the antimicrobial susceptibility of Gram-negative bacteria in positive blood cultures, is reported. DATVP specifically lights up Gram-negative bacteria with damaged cell membranes while showing no fluorescence in intact bacteria. The antimicrobial-induced fluorescence turn-on of DATVP is found to be fast (within 6 h) and sensitive, allowing for reliable determination of antimicrobial susceptibility. Using DATVP, a wash-free AST is developed and its performance was validated on clinical isolates. The DATVP-based AST showed high categorical agreement (84-95%) with the standard method while shortening the time-to-result from days to hours. This method represents a new paradigm in phenotypic AST, offering speed, simplicity, and direct applicability to patient samples, with the potential to enable timely and targeted antimicrobial treatment.

Nanomaterials for bacterial enrichment and detection in healthcare

Bacterial infections in the blood (sepsis) have been recognized as a leading cause of mortality in the clinical field due to limitations in the detection of bacteria at low concentration and their resistance to antibiotics by excessive misuse. Some of the common symptoms are fever, chills, rapid heartbeat, difficulty breathing, confusion, and changes in mental status with occasionally pale, clammy, and mottled skin. Early diagnosis and identification are the keys to a successful treatment for sepsis patients. Researchers have developed nanoparticles to enrich bacterial populations followed by detection and applied them to conventional methods such as phenotypic and molecular diagnostics to enhance different detectors' responses toward pathogens. This short review systematically overviews steps that are followed in clinical labs for bacterial detection, identification, and their drawbacks. In this context, we discuss the role that nanoparticles can play in overcoming the limits of traditional microbiology methods in terms of turnaround times (TATs) and accuracy. We believe that this short review will provide up-to-date information about the applications of nanoparticles in the enrichment, separation, and identification of bacterial infection in the clinical field and, therefore, a way of rapid treatment.

Bacterial Specific Recognition of Sulfonium Poly(Amino Acid) Adsorbents for Ultrafast MRSA Capture Against Bloodstream Infection

Methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections pose significant health risks, potentially leading to severe conditions such as bacteremia. Developing effective treatments to eliminate resistant bacteria from the bloodstream, simultaneously mitigate infection-related complications, and reduce mortality remains challenging. Herein, microspheres are synthesized with bacterial elimination and inflammation prevention by crosslinked sulfonium poly(amino acids). As-synthesized microsphere, PM1 0.6B MS, exhibits an ultrafast adsorption efficiency of 0.41 × 108 CFU mg-1 min-1 for MRSA, which positions the highest index among the reported resin and inorganic adsorptions. This bacterial-specific and efficient capture of PM1 0.6B MS is attributed to its strong interactions with teichoic acids in MRSA (Ka: 1.8 × 105 M-1) rather than acting with phospholipids of mammalian cells. Unlike the present resin-based adsorbent, for example, heparin-modified polyethylene in the only commercial Seraph® 100, PM1 0.6B MS kills adsorbed bacteria within 1 h and can be reused by simple treatment. Meanwhile, PM1 0.6B MS also shows good hemocompatibility and longer thrombin activation time to reduce the risk of thrombosis and hemolysis. In vivo experiments further confirm the abilities of PM1 0.6B MS to prevent inflammation by removing bacteria. This adsorbent is a promising candidate for early treating life-threatening bloodstream infections, potentially preventing bacteremia and subsequent organ damage.

A case of bloodstream infection caused by Neisseria gonorrhoeae

Neisseria gonorrhoeae is fastidious, visual etiological evidence is extremely difficult to obtain, and positive results from blood cultures are even rarer. A 51-year-old female patient was admitted to our hospital for 3 days with fever, and polyarticular pain was diagnosed as infectious fever by a series of examinations, but the pathogen could not be determined. N. gonorrhoeae was identified by blood culture and mass spectrometry. Combined with the drug sensitivity test results, ceftriaxone was given and she recovered. This case is extremely rare, underlining the importance of standardized timely testing and collaboration between clinical and microbiology laboratories.

Next-generation diagnostics of bloodstream infections enabled by rapid whole-genome sequencing of bacterial cells purified from blood cultures

BACKGROUND

Blood culture (BC) remains the cornerstone for diagnosis of bloodstream infections (BSI), but the long turn-around time (TAT) hampers timely selection of appropriate chemotherapy. Novel molecular approaches have been developed to provide faster results but are also affected by limitations. We developed a analytical workflow named LC-WGS (Whole-Genome Sequencing of Liquid Colony) for rapid whole-genome sequencing-based diagnosis of BSI, evaluating its accuracy performance over standard of care (SoC) diagnostic procedures.

METHODS

A total of 85 prospectively collected positive BC were processed in parallel with SoC (subculturing, identification by MALDI-ToF, antimicrobial susceptibility testing by reference broth microdilution, usage of syndromic panels) and LC-WGS, which relied on automated purification of microbial cells (Qvella FAST system, Qvella Corp.), DNA purification, and real-time sequencing with the Oxford Nanopore MinION. A streamlined analysis pipeline was designed for pathogen identification (Kraken2), detection of resistance markers (KmerResistance, AMRFinderPlus), virulome profiling (abricate, VFDB), phylogenetic analysis (snippy, IQ-TREE), and pathogen subtyping (Meningotype).

FINDINGS

Compared with SoC, LC-WGS returned accurate species-level identification for 98% (65/66) of monomicrobial and 88% (14/16) of polymicrobial BCs, with a TAT as short as ∼2·6 h. Accurate resistome profiling (allelic variants) was achieved for 94% (58/62) of the most clinically-relevant resistance profiles in ∼4·2 h. In silico serotying (Neisseria meningitidis), virulotyping (Escherichia coli, Klebsiella pneumoniae) and comparative phylogenomics for outbreak investigation (K. pneumoniae) proved also feasible.

INTERPRETATION

In this proof-of-concept study, we proved that diagnosis of BSI can be significantly shortened using an optimised workflow based on real-time sequencing, providing rapid, actionable clinical microbiological data in support of timely selection of appropriate chemotherapy. LC-WGS proved also useful as molecular epidemiology tool for public health and infection control applications.

FUNDING

This study was partially supported by an investigator-initiated grant from Qvella Corporation.

Epidemiology and Outcomes of Bloodstream Infections in Patients in a Burns Intensive Care Unit: An 8-Year Retrospective Study

Background

Burns intensive care units (BICUs) have reduced mortality in patients with burns, but infections and sepsis remain the leading causes of death. Infections with multidrug-resistant (MDR) bacteria increase the risk of death in patients with burns, whose risk of acquiring such infections is higher due to various factors, including prolonged hospitalization and invasive procedures.

Methods

A retrospective study was performed in a French BICU over 8 years to analyze the epidemiology and risk factors for bloodstream infections (BSIs).

Results

In total, 1402 patients were admitted to the BICU. Thermal burns were the most common cause of injury, and the median total body surface area burned was 10%. Patients had various comorbid conditions, particularly smoking and hypertension. BSI occurred in 303 (21%) patients. When compared with patients without BSI, patients with BSI were older, had higher severity scores and a larger total body surface area burned, and were more likely to develop complications. The prevalence of monomicrobial and polymicrobial BSI remained stable during hospitalization, with gram-positive pathogens such as Staphylococcus aureus most common during the first week but with gram-negative pathogens, particularly MDR Pseudomonas aeruginosa, becoming more prevalent after 15 days. The distribution of microorganisms remained stable throughout the study, except for a significant decrease in Acinetobacter baumannii rates and an increase in MDR P aeruginosa rates after 2015.

Conclusions

An understanding of the epidemiology of BSI-causing microorganisms over time is crucial for sepsis management to ensure the selection of appropriate empirical antimicrobial therapy and to highlight the need for infection prevention and antimicrobial stewardship.

The Relationship Between the Type of Microorganisms Isolated in Cultures and Outcomes in Children on Extracorporeal Membrane Oxygenation Support Following Corrective Surgery for Congenital Heart Disease

ObjetivesExtracorporeal membrane oxygenation (ECMO) after surgery for congenital heart disease (CHD) provides hemodynamic support to patients when their myocardial function is temporarily affected. Postoperative infections in children with CHD on ECMO are a significant challenge, as they complicate recovery and affect outcomes during this critical period of hemodynamic support. The objective of this study was to analyze the mortality related to the micro-organism isolated in children with ECMO after surgery for CHD.MethodsRetrospective cohort study from January 2014 to December 2021 at a university hospital in Colombia. The primary outcome was the infection-related inpatient mortality of children undergoing surgery for CHD who received ECMO support, according to the type of microorganisms isolated in cultures.ResultsA total of 3307 surgeries for CHD were performed during the study period. Of these, 108 (3.3%) required veno-arterial ECMO after surgery. We found positive cultures in 35% of these patients. The incidence of infection was 14.5 cases per 1000 days of ECMO. The overall mortality of infected patients was 54.1%. Isolation of Gram-negative bacteria in cultures was associated with higher odds of dying compared with other isolations, regardless of age and type of CHD (aOR 6.92 95% CI 1.91-25.02; p < .01). We found no differences in hospital length of stay or PICU stay based on the type of bacteria isolated. The most commonly isolated Gram-negative bacteria was Klebsiella pneumoniae, which was associated with longer mechanical ventilation [26 (IQR 18.2-31.0) versus 11 (IQR 8.0-15.0) days; p < .01].ConclusionsThe presence of a Gram-negative bacterium as the cause of infection in any sample was associated with increased odds of mortality in children receiving ECMO support in the postoperative period following corrective surgery for congenital heart disease. Infections occurred in 1 out of 3 children on ECMO following surgery for CHD.

Emilia sonchifolia (L.) DC. inhibits the growth of Methicillin-Resistant Staphylococcus epidermidis by modulating its physiology through multiple mechanisms

Bloodstream infections (BSIs) are a public health concern, causing substantial morbidity and mortality. Staphylococcus epidermidis (S. epidermidis) is a leading cause BSIs. Antibiotics targeting S. epidermidis have been the mainstay of treatment for BSIs, however their efficacy is diminishing in combating with drug-resistant bacteria. Therefore, alternative treatments for antibiotic-resistant infections are urgently required. Studies have demonstrated that certain traditional Chinese medicine (TCM) exhibit notable antimicrobial activity and can help mitigate bacterial resistance. Among these, The ethanol extract of Emilia sonchifolia (L.) DC (E. sonchifolia) (10 g crude drug/1 g extract ) exhibits a noteworthy anti-methicillin-resistant S. epidermidis (MRSE) effect. This study explores antibacterial activity and underlying mechanisms of E. sonchifolia against MRSE. The antibacterial activity of E. sonchifolia against MRSE was assessed in vitro by measuring the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The MRSE-induced mouse BSIs model was used to evaluate the antibacterial activity of E. sonchifolia in vivo. Proteomic and transcriptomic analyses were performed to elucidate the underlying antibacterial mechanisms. The MIC and MBC values of E. sonchifolia against MRSE were 5 mg/mL and 20 mg/mL, respectively. In vivo, E. sonchifolia effectively treated MRSE-induced BSIs. Additionally, proteomic and transcriptomic analyses revealed considerable down-regulation of purine metabolism, that were associated with oxidative stress and cell wall synthesis. The enzyme linked immunosorbent assay(ELISA) results showed decreased levels of inosine monophosphate (IMP), Adenosine monophosphate(AMP) and guanine monophosphate (GMP), indicating inhibited purine metabolism. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis confirmed bacterial cell wall damage. E. sonchifolia exerts antibacterial effects by inhibiting purine metabolism, promoting bacterial oxidative stress, and impairing cell wall synthesis. These findings provide novel insights into the mechanistic understanding of E. sonchifolia's efficacy against MRSE, offering potential strategies for managing MRSE infections.

Temporal Shifts in Etiological Agents and Trends in Antimicrobial Resistance of Bloodstream Infection in Southwest China from 2016 to 2023

Objective

The purpose of this study was to assess the frequency distribution of bacterial pathogens causing bloodstream infections (BSIs) as well as the characteristics of antibiotic susceptibility and resistance to gain a deeper understanding of the drug resistance situation in the southwest China.

Methods

Non-duplicate pathogenic bacteria according to the American Clinical and Laboratory Standards Institute (CLSI) M100 and analyzed using WHONET 5.6 software.

Results

A total of 170,246 non-duplicated pathogenic bacteria were isolated from blood from 2016 to 2023. Gram-negative bacteria accounted for 59.5% and Gram-positive bacteria accounted for 40.5%. The top five detection rates were Escherichia coli (33.9%), coagulase-negative staphylococci (21.7%), Klebsiella pneumoniae (11.5%), Staphylococcus aureus (7.0%), and Enterococcus spp (5.4%). Streptococcus pneumoniae, Salmonella spp and β-Hemolytic Streptococcus were significantly more frequently isolated in pediatric patients than in adult patients. The rate of resistance to carbapenems was less than 1.2% in the Escherichia coli over the 8-year period, with a significant upward trend in the Klebsiella pneumoniae. The overall resistance rate of Pseudomonas aeruginosa to imipenem and meropenem had a slow decreasing trend. The resistance rate of Acinetobacter baumannii to imipenem and meropenem has been maintained at a high level, which is greater than 50%. The detection rate of MRSA was 27.70% and vancomycin- and linezolid-resistant strains were not found. The resistance rates of Enterococcus faecium and Enterococcus faecalis to vancomycin, linezolid and teicoplanin were less than 2.1%.

Conclusion

The pathogenic bacteria of bloodstream infection in southwest China were diversified, and the multi-drug resistant bacteria, especially Carbapenem-resistant Klebsiella pneumoniae (CRKP), had increased significantly, posing a serious challenge to clinical treatment. Additionally, the situation of Methicillin-resistant Staphylococcus aureus (MRSA) and Vancomycin-resistant Enterococcus (VRE) also required close attention.

Dielectrophoretic Microfluidic Designs for Precision Cell Enrichments and Highly Viable Label-Free Bacteria Recovery from Blood

Conducting detailed cellular analysis of complex biological samples poses challenges in cell sorting and recovery for downstream analysis. Label-free microfluidics provide a promising solution for these complex applications. In this work, we investigate particle manipulation on two label-free microdevice designs using cDEP to enrich E. coli from whole human blood to mimic infection workflows. E. coli is still a growing source of bacteremia, sepsis, and other infections in modern countries, affecting millions of patients globally. The two microfluidic designs were evaluated for throughput, scaling, precision targeting, and high-viability recovery. While CytoChip D had the potential for higher throughput, given its continuous method of DEP-based sorting to accommodate larger clinical samples like a 10 mL blood draw, it could not effectively recover the bacteria. CytoChip B achieved a high-purity recovery of over 98% of bacteria from whole human blood, even in concentrations on the order of <100 CFU/mL, demonstrating the feasibility of processing and recovering ultra-low concentrations of bacteria for downstream analysis, culture, and drug testing. Future work will aim to scale CytoChip B for larger volume throughput while still achieving high bacteria recovery.

Detection of clinically relevant Candida species from positive blood cultures using a novel sample-to-answer molecular assay

We evaluated the diagnostic performance of the newly developed MoiM Dx Candida 9-plex (MoiM) assay for the detection of Candida species from positive blood cultures and compared the results with those obtained from the BIOFIRE Blood Culture Identification 2 (BCID2) Panel. This study included 39 candidaemia cases and 40 cases of non-Candida bloodstream infections as negative controls. Routine culture results, which were identified via matrix-assisted laser desorption/ionization time‒of‒flight mass spectrometry (MALDI‒TOF MS), were used as the reference standard for analysis. The performance of the MoiM assay was evaluated using positive percent agreement (PPA) and negative percent agreement (NPA). The MoiM assay demonstrated a PPA of 97.1% and an NPA of 100% for detecting the five most common Candida species (C. albicans, C. glabrata, C. tropicalis, C. parapsilosis, and C. krusei) in candidaemia cases. In comparison, the BCID2 panel yielded a PPA of 67.6% and an NPA of 100.0% (P = 0.001). Additionally, the MoiM assay correctly identified C. guilliermondii and C. lusitaniae, not covered by the BCID2 panel. Among the 10 discrepant results between the two assays, all 10 cases were incompletely identified by the BCID2 panel, but the results from the MoiM assay were identical to the culture results. The MoiM assay was designed as an automated sample-to-answer molecular assay for the detection of Candida species from positive blood cultures. Our study revealed that this assay shows good overall agreement with routine culture and is comparable to the BCID2 panel.

Predictive value of serum procalcitonin level for the diagnosis of bloodstream infections in hematological patients

OBJECTIVES

Procalcitonin (PCT) is a critical diagnostic biomarker for bacterial infections in patients. Numerous studies have shown that PCT have high sensitivity and specificity for diagnosing bloodstream infection. However, the cut-off value of PCT for the diagnosis of bloodstream infections in patients with hematolgic diseases is still unclear and unreliable.

METHODS

We conducted a retrospective study involving 2299 cases with hematological diseases and who had been performed blood culture and PCT test within 24 h.

RESULTS

For patients with hematological diseases, the serum PCT was slightly elevated in the BSI group. We found that most hematological patients with bloodstream infection were in the stage of severe neutropenia. The main infected strains were Escherichia coli (n = 84, 21%), Klebsiella pneumoniae (n = 61, 15.25%) and Pseudomonas aeruginosa (n = 65, 16.25%), and the increasing trend of PCT level was more obvious in patients infected with Gram-negative bacteria. ROC analysis results showed that the area under the receiver operating characteristic curve for distinguishing bacterial infection from non-bacterial infection was 0.554 (95%CI: 0.522-0.585) with the diagnostic threshold of BSI (PCT > 0.5ng/mL).

CONCLUSIONS

In our study, low PCT levels were found in patients with hematological diseases, and a better cut-off value may be necessary to determine infection in hematology patients.

The trends of blood culture contamination and utilization rates in an LMIC tertiary care center from 2010 to 2022: a call for diagnostic stewardship?

Objective

At Saint George Hospital University Medical Center in Beirut, Lebanon, we determine (1) annual blood culture (BC) contamination (BCC) and utilization (BCU) rates vs international benchmarks, (2) identify blood culture contaminants, (3) bloodstream infections episodes in patients with and without COVID-19 after the pandemic onset, and (4) any epidemiologic trends in BCC and BCU.

Design

Retrospective observational study.

Setting

Private tertiary referral center, from January 1, 2010, to December 31, 2022.

Methods

We define a contaminated BC as the growth of a typical contaminant/skin flora in 1-2/4 BC bottles. We calculate BCC rates as a percentage of the contaminated BC/total BC during the period and BCU rates as the number of BC/1000 patient days (PD).

Results

The average BCU rate of 85.9/1000 PD in 2010-2019 increased to 106.6/1000 PD in 2020-2022. On average, patients with COVID-19 had a higher BCU rate of 185.9/1000 PD, corresponding to an additional 100 blood cultures/1000 PD. The average BCC rate was 7%, ranging from 6% in 2010-2019 to 8% in 2020-2022. We observed the highest BCC rate of 9% in patients with COVID-19, likely due to the higher BCU. The most frequently isolated contaminants were coagulase-negative Staphylococcus (96%), of which 65% were Staphylococcus epidermidis.

Conclusion

We saw a multifactorial, persistently elevated rate of BCC over 13 years as unaffected by strict infection control practices. We think that further research targeting a standardized, low BCU rather than inevitable BCC while advocating for diagnostic stewardship of low-middle-income countries is essential, especially where the lack of appropriate resource allocation and awareness are problematic.

Clinical evaluation of a multiplex droplet digital PCR for diagnosing suspected bloodstream infections: a prospective study

Background

Though droplet digital PCR (ddPCR) has emerged as a promising tool for early pathogen detection in bloodstream infections (BSIs), more studies are needed to support its clinical application widely due to different ddPCR platforms with discrepant diagnostic performance. Additionally, there is still a lack of clinical data to reveal the association between pathogen loads detected by ddPCR and corresponding BSIs.

Methods

In this prospective study, 173 patients with suspected BSIs were enrolled. A multiplex ddPCR assay was used to detect 18 pathogens. The results of ddPCR testing were evaluated in comparison with blood cultures (BCs) and clinical diagnosis. Taking BC as the gold standard, receiver operating characteristic curve and Cohen's kappa agreement were used to investigate whether the pathogen load could predict a corresponding culture-proven BSI for the top five microorganisms detected by ddPCR.

Results

Of the 173 blood samples collected, BC and ddPCR were positive in 48 (27.7%) and 92 (53.2%) cases, respectively. Compared to BC, the aggregate sensitivity and specificity for ddPCR were 81.3% and 63.2%, respectively. After clinical adjudication, the sensitivity and specificity of ddPCR increased to 88.8% and 86.0%, respectively. There were 143 microorganisms detected by ddPCR. The DNA loads of these microorganisms ranged from 30.0 to 3.2×105 copies/mL (median level: 158.0 copies/mL), 72.7% (104/143) of which were below 1,000 copies/mL. Further, statistical analysis showed the DNA loads of Escherichia coli (AUC: 0.954, 95% CI: 0.898-1.000, κ=0.731, cut-off values: 93.0 copies/mL) and Klebsiella pneumoniae (AUC: 0.994, 95% CI: 0.986-1.000, κ=0.834, cut-off values: 196.5 copies/mL) were excellent predictors for the corresponding BSIs. The DNA loads of Pseudomonas aeruginosa (AUC: 0.816, 95% CI: 0.560-1.000, κ=0.167), Acinetobacter baumannii (AUC: 0.728, 95% CI: 0.195-1.000), and Enterococcus spp. (AUC: 0.282, 95% CI: 0.000-0.778) had little predictive value for the corresponding culture-proven BSIs.

Conclusion

Our results indicate that the multiplex ddPCR is a promising platform as a complementary add-on to conventional BC. The DNA loads of E. coli and K. pneumoniae present excellent predictive value for the corresponding BSIs. Further research is needed to explore the predictive potential of ddPCR for other microorganisms.

The role of metagenomic next-generation sequencing in diagnosing and managing post-kidney transplantation infections

Kidney transplantation (KT) is a life-saving treatment for patients with end-stage renal disease, but post-transplant infections remain one of the most significant challenges. These infections, caused by a variety of pathogens, can lead to prolonged hospitalization, graft dysfunction, and even mortality, particularly in immunocompromised patients. Traditional diagnostic methods often fail to identify the causative organisms in a timely manner, leading to delays in treatment and poorer patient outcomes. This review explores the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of post-KT infections. mNGS allows for the rapid, comprehensive detection of a wide range of pathogens, including bacteria, viruses, fungi, and parasites, without the need for culture-based techniques. We discuss the advantages of mNGS in early and accurate pathogen identification, its role in improving patient management, and the potential challenges in its clinical implementation. Additionally, we consider the future prospects of mNGS in overcoming current diagnostic limitations and its potential for guiding targeted therapies, particularly in detecting antimicrobial resistance and emerging pathogens. This review emphasizes the promise of mNGS as an essential tool in improving the diagnosis and treatment of infections in KT recipients.

Clinical diagnostic performance of droplet digital PCR for pathogen detection in patients with Escherichia coli bloodstream infection: a prospective observational study

BACKGROUND

Droplet digital PCR (ddPCR) is a highly sensitive tool for detecting bacterial DNA in bacterial bloodstream infections (BSI). This study aimed to examine the sensitivity and specificity of ddPCR and the association between bacterial DNA load in whole blood and the time-to-positivity (TTP) of blood culture (BC) in patients with Escherichia coli BSI.

METHODS

This prospective study enrolled patients with E. coli BSI confirmed via BC at the Hiroshima University Hospital from June 2023 to August 2024. The E. coli DNA load in whole blood, which was simultaneously obtained from two BC sets, was measured using ddPCR with E. coli specific primer and probe. Whole blood samples from 50 patients with BC positive for pathogens other than E. coli (n = 25) and BC negative (n = 25) were also evaluated using ddPCR.

RESULTS

A total of 131 patient samples were analyzed in this study. Of the 81 patients with E. coli BSI, ddPCR detected E. coli DNA in 67 (82.7%). The results of ddPCR for E. coli had a sensitivity of 82.7% (95% CI: 73.1-89.4%), specificity 100% (95% CI: 93.0-100%). Patients with positive ddPCR results had significantly shorter TTP than those with negative results (median, 8.8 h vs. 10.7 h, p < 0.001). The positivity rate for both BC sets was significantly higher in patients with positive ddPCR results than in those with negative results (89.6% vs. 35.1%, p < 0.001). Among ddPCR-positive patients, septic shock was significantly associated with intestinal perforation, higher E. coli DNA load, higher 28-d mortality, shorter TTP, and higher positivity rate for four bottles of BC than those without septic shock. The E. coli DNA load in whole blood negatively correlated with TTP (p < 0.001, R2 = 0.38).

CONCLUSION

The E. coli DNA load in whole blood is inversely correlated with TTP. Notably, a higher E. coli DNA load is associated with septic shock.

Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing

Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation. Results showed that bacterial reads were higher in WB than plasma. Differences for Staphylococcus aureus and Streptococcus pneumoniae were more pronounced compared to Escherichia coli. Plasma samples exhibited better method reproducibility, with more consistent droplet digital PCR results for human DNA. The study found that extraction was more efficient for Gram-positive bacteria than Gram-negative, suggesting that the human DNA depletion exerts a negative effect on Gram-negative bacteria. Overall, shotgun metagenomics needs further optimisation to improve bacterial DNA recovery and enhance pathogen detection sensitivity. This study highlights some critical steps in the methodology of shotgun metagenomic-based diagnosis of blood stream infections using Nanopore sequencing.

Molecular detection of Staphylococcus aureus in urine in patients with S. aureus bacteremia: an exploratory study

PURPOSE

Staphylococcus aureus bacteremia (SAB) is associated with a 90-day mortality of 28-34%. Many SAB-patients (7.8-39%) have a secondary S. aureus bacteriuria (SABU) mainly without symptoms of a urinary tract infection. Due to high morbidity and mortality, there is an interest in rapid detection of S. aureus bacteremia. Here, we compared a rapid nucleic acid amplification test (NAAT) with conventional culture to detect S. aureus in urine and to identify cases with increased risk for SAB.

METHODS

In a cross-sectional study, we assessed urine samples (mid-stream, clean catch and catheter urine) of patients with SAB and bacteremia other than SAB (non-SAB). Urine samples were collected ± 3 days to the collection of the positive blood culture and were cultured on a set of selective and non-selective agar plates. NAAT was performed using a commercial test (Xpert® SA Nasal Complete G3, Cepheid) from a sterile swab soaked in urine.

RESULTS

We included samples from 100 patients (68% male, median age: 67.4 years) with SAB and 20 patients (75% male, median age: 65.84 years) with non-SAB. The sensitivity of detecting SAB from urine samples was 47% (specificity: 90%) for NAAT, when applying a Ct-value of ≤ 37.4 for positive results. Urine culture had a sensitivity of 25% and a specificity of 95%. Molecular and culture methods showed a moderate agreement (80%, Cohens kappa: 0.55).

CONCLUSION

NAAT from urine has a higher sensitivity than culture in patients with SAB and could potentially identify cases with increased risk for SAB. Future studies should investigate whether this characteristic could translate into a clinical benefit through rapid detection of SAB.

Simulating the clinical manifestations and disease progression of human sepsis: A monobacterial injection approach for animal modeling

Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection, with great clinical heterogeneity, high morbidity, and high mortality. At the same time, there are many kinds of infection sources, the pathophysiology is very complex, and the pathogenesis has not been fully elucidated. An ideal animal model of sepsis can accurately simulate clinical sepsis and promote the development of sepsis-related pathogenesis, treatment methods, and prognosis. The existing sepsis model still uses the previous Sepsis 2.0 modelling standard, which has some problems, such as many kinds of infection sources, poor repeatability, inability to take into account single-factor studies, and large differences from clinical sepsis patients. To solve these problems, this study established a new animal model of sepsis. The model uses intravenous tail injection of a single bacterial strain, simplifying the complexity of multibacterial infection, and effectively solving the above problems.

Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy platform: Characterization of ESBL-producing Enterobacterales from bloodstream infections

OBJECTIVES

Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia.

METHODS

We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed.

RESULTS

The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were blaCTX-M-15 (62.1%) and blaCTX-M-27 (13.6%).

CONCLUSIONS

The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.

Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections

Background

Determining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses.

Methods

In this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology.

Results

A total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p < 0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively.

Conclusion

Our study demonstrates the high accuracy of probe capture sequencing technology compared to blood cultures in the identification of pathogenic microorganisms in BSI upon final clinical diagnosis. Among the different sample types, white blood cell samples had a lower clinical compliance rate compared to plasma samples, possibly due to the higher host rate in cell samples, which impairs the sensitivity of pathogen detection.

Epidemiological characteristics and impact of sepsis on survival after osteoporotic pelvic fracture in Austria

We performed a retrospective nationwide register-based cohort study which included all in-hospital patients aged ≥ 50 with pelvic fracture (PF) between 2010 and 2018 in Austria. We identified patients who were hospitalized with sepsis within 180 days following a PF event. Aetiology of sepsis was divided by unspecified, gram positive, gram negative and other. Among 59,081 patients hospitalized with PF between 2010 and 2018 we identified 619 (1.05%) patients who were hospitalized with sepsis within 180 days following PF. The cumulative incidence risk of sepsis within 180 days after PF was significantly higher in males (1.4%, 95% CI 1.2%-1.5%) as compared to females (0.92%, 95% CI 0.83%-1.0%), p < 0.001. In the cohort of patients with sepsis, the one-year mortality was 50.4%. Mortality risk was greater for patients who developed sepsis, independently of age, sex and comorbidity status (HR 3.12, 95% CI 2.83-3.44, p < 0.001) as compared to patients without sepsis. With a very high one-year mortality risk among those who develop sepsis, our study emphasizes the substantial impact of sepsis on long term survival in fractured patients. These findings underscore the critical need for sepsis prevention and early detection and management to mitigate its detrimental effects on patient outcomes.

MALDI-TOF direct identification of positive blood cultures: A four-year analytical evaluation of A Triton based workflow

Rapid and reliable identification of the causal organism in bloodstream infections and sepsis is crucial for both individual patient care and public health. We have implemented a rapid in-house identification protocol (with 10 % Triton) using MALDI-TOF MS for identifying the causative organism in positive blood cultures without prior culture. Our objective was to retrospectively analyze data collected over a four-year period while implementing this rapid in-house identification protocol and to develop a guide for evaluating and reporting the obtained results. Overall, our method utilizing MALDI-TOF MS for rapid in-house identification, demonstrated comparable results to other commercially available and in-house methods reported in the literature. Over the past four years, direct identification has facilitated the distinction between clinically relevant positive blood cultures and irrelevant ones, guiding rapid focus control and appropriate antibiotic treatment. The established guide can serve as a valuable tool in reporting positive blood cultures and associated antibiotic treatments.

Comparison of Zybio Kit and saponin in-house method in rapid identification of bacteria from positive blood cultures by EXS2600 matrix-assisted laser desorption ionization time-of-flight mass spectrometry system

We evaluated the performance of Zybio EXS2600 matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) (Zybio Inc., Chongqing, China) for the identification of bacteria from positive blood culture (BC) bottles using Blood Culture Positive Sample Pretreatment Kit (Zybio Inc., Chongqing, China) in comparison to an in-house saponin method. Following a positive signal by the BACTEC™ FX system, confirmation of identification was achieved using subcultured growing biomass used for MALDI-TOF MS analysis. A total of 94 positive BC bottles with 97 bacterial isolates were analyzed. The overall identification rates at the genus and species levels for the saponin method were 89.7% (87/97) and 74.2% (72/97), respectively. With the Zybio Kit, 88.7% (86/97) and 80.4% (78/97) of microorganisms were correctly identified to the genus and species levels, respectively. The saponin method identified 65.3% (32/49) of Gram-positive bacteria at the species level, whereas the Zybio Kit achieved a higher species-level identification rate of 79.6% (39/49) (p = 0.1153). The saponin method with additional on-plate formic acid extraction showed a significantly higher overall identification rate in comparison to the saponin method without that step for both genus (87.6% [85/97] vs. 70.1% [68/97], p = 0.0029) and species level (70.1% [68/97] vs. 46.4% [45/97], p = 0.0008). Identification rates of Gram-negative bacteria showed a higher identification rate, however, not statistically significant with additional Zybio Kit protocol step on both genus (85.4% [41/48] vs. 81.3% [39/48], p = 0.5858) and species level (77.1% [37/48] vs. 75% [36/48], p = 0.8120). Zybio Kit could offer an advantage in species-level identification, particularly for Gram-positive bacteria. The inclusion of on-plate formic acid extraction in the saponin method notably enhanced identification at both genus and species levels for Gram-positive bacteria. The extended protocol provided by the Zybio Kit could potentially offer an advantage in the identification of Gram-negative bacteria at both genus and species levels. Enhancements to the Zybio EXS2600 MALDI-TOF instrument software database are necessary.

Early detection of bacteremia pathogens with rapid molecular diagnostic tests and evaluation of effect on intensive care patient management

İNTRODUCTION: The BioFire FilmArray Blood Culture Identification panel (BCID2), a rapid molecular blood culture identification test based on multiplex nested polymerase chain reaction. The aim of this study was to evaluate clinical outcomes between the period before (pre-BCID2 group) and after (post-BCID2 group) the introduction of the BCID2 panel into our routine practice.

METHODS

The primary endpoint was time to optimal antibiotherapy, and the secondary endpoints were duration of hospital and intensive care unit stay, 7-day, 14-day and 28-day mortality rates after bacteremia.

RESULTS

The median time from empirical antibiotherapy to optimal antimicrobial therapy was 4560 (IQR;3060-7140) minutes in the pre-BCID2 group and 1715 (IQR;1362- 2776.25) minutes (in the post-BCID2 group (p<0.05).

CONCLUSION

Adding the BCID2 panel may improve antibiotic management in critically ill bacteremia patients.

Rapid Diagnostic Tests and Antimicrobial Stewardship Programs for the Management of Bloodstream Infection: What Is Their Relative Contribution to Improving Clinical Outcomes? A Systematic Review and Network Meta-analysis

BACKGROUND

Evidence about the clinical impact of rapid diagnostic tests (RDTs) for the diagnosis of bloodstream infections is limited, and whether RDT are superior to conventional blood cultures (BCs) embedded within antimicrobial stewardship programs (ASPs) is unknown.

METHODS

We performed network meta-analyses using results from studies of patients with bloodstream infection with the aim of comparing the clinical impact of RDT (applied on positive BC broth or whole blood) to conventional BC, both assessed with and without ASP with respect to mortality, length of stay (LOS), and time to optimal therapy.

RESULTS

Eighty-eight papers were selected, including 25 682 patient encounters. There was an appreciable amount of statistical heterogeneity within each meta-analysis. The network meta-analyses showed a significant reduction in mortality associated with the use of RDT + ASP versus BC alone (odds ratio [OR], 0.72; 95% confidence interval [CI], .59-.87) and with the use of RDT + ASP versus BC + ASP (OR, 0.78; 95% CI, .63-.96). No benefit in survival was found associated with the use of RDT alone nor with BC + ASP compared to BC alone. A reduction in LOS was associated with RDT + ASP versus BC alone (OR, 0.91; 95% CI, .84-.98) whereas no difference in LOS was shown between any other groups. A reduced time to optimal therapy was shown when RDT + ASP was compared to BC alone (-29 hours; 95% CI, -35 to -23), BC + ASP (-18 hours; 95% CI, -27 to -10), and to RDT alone (-12 hours; 95% CI, -20 to -3).

CONCLUSIONS

The use of RDT + ASP may lead to a survival benefit even when introduced in settings already adopting effective ASP in association with conventional BC.

Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: Three case reports

BACKGROUND

Infectious diseases are still one of the greatest threats to human health, and the etiology of 20% of cases of clinical fever is unknown; therefore, rapid identification of pathogens is highly important. Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming; serologic detection has window periods, false-positive and false-negative problems; and nucleic acid molecular detection methods can detect several known pathogens only once. Three-generation nanopore sequencing technology provides new options for identifying pathogens.

CASE SUMMARY

Case 1: The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days, accompanied by cough and sputum. Nanopore sequencing of the drainage fluid revealed the presence of oral-like bacteria, leading to a clinical diagnosis of bronchopleural fistula. Cefoperazone sodium sulbactam treatment was effective. Case 2: The patient was admitted to the hospital with fever and headache, and CT revealed lung inflammation. Antibiotic treatment for Streptococcus pneumoniae, identified through nanopore sequencing of cerebrospinal fluid, was effective. Case 3: The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months. Despite antibacterial treatment, her symptoms worsened. The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii. The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.

CONCLUSION

Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.

Integrated decentralized blood culture incubation: A step towards a 24/7 microbiology service?

To have an impact on the mortality of bloodstream infections, microbiological diagnostics of blood cultures (BC) should provide first results within 12 h. Here, we show how a decentralized BC incubation connected to the central BC incubators via a browser-based application significantly reduces turnaround times.

Multiplex microarray PCR Unyvero BCU system to accelerate relevant antimicrobial treatment in polymicrobial bloodstream infection

PURPOSE

To evaluate the performance of a rapid multiplex microarray-based method (Unyvero BCU system, BCU) to identify microorganisms and detect antimicrobial resistance directly from positive blood culture (BC) bottles with polymicrobial growth, and to assess relevance of information provided for timely guidance of polymicrobial bloodstream infection treatment.

METHODS

Accuracy, time-to-actionable results and potential impact of BCU on antimicrobial treatment were compared with those of standard of care during a prospective study for the sample analysis (November 2017-November 2018) and a retrospective study for the clinical data analysis and the time-to-result analysis. The study was complemented with an experimental study, based on spiked blood cultures to assess the ability of the method to detect antimicrobial resistance genes.

RESULTS

Sixty-five clinical polymicrobial BC samples (163 total microorganisms) and 30 simulated polymicrobial BC samples (60 strains) were included. BCU reported 84.6% samples as polymicrobial, correctly identified all the bacteria of the mix for 72.3% samples (47/65) and detected bacteria that were missed by the conventional culture for 13.8% samples. All identifications and antimicrobial resistances were accurately detected for 61.5% (40/65) samples. Limitations concerned the detection of anaerobes, enterococci and enterobacterial susceptibility to third generation cephalosporins. BCU results would have guided antimicrobial treatment for 50.8% of the cases (33/65) in a timely and relevant manner, had no impact for 27.7% (18/65) and been misleading for 18.5% (12/65).

CONCLUSIONS

Despite some limitations, the Unyvero BCU system is a rapid and reliable method for polymicrobial BC sample analysis.

Risk factors of bloodstream infection in erythroderma from atopic dermatitis, psoriasis, and drug reactions: a retrospective observational cohort study

Background

Atopic dermatitis (AD), psoriasis, and drug reactions associated with erythroderma are frequently complicated by infections. However, bloodstream infection (BSI) have received less research attention.

Objectives

This study aimed to investigate the clinical characteristics and risk factors associated with BSI in patients with erythroderma.

Methods

A retrospective analysis was conducted on 141 erythroderma cases. Eleven cases were identified as having BSI. Clinical records of both BSI and non-BSI groups were reviewed and compared.

Results

BSI was diagnosed in 7.80% (11/141) of erythroderma cases, with a breakdown of 7.14% in AD, 2.00% in psoriasis, and 17.14% in drug reactions. Notably, all positive skin cultures (7/7) showed bacterial isolates concordant with blood cultures. Univariate logistic regression analysis revealed several significant associations with BSI, including temperature (≤36.0 or ≥38.5 °C; odds ratio (OR) = 28.06; p < 0.001), chilling (OR = 22.10; p < 0.001), kidney disease (OR = 14.64; p < 0.001), etiology of drug reactions (OR = 4.18; p = 0.03), albumin (ALB) (OR = 0.86; p < 0.01), C-reaction protein (CRP) (OR = 1.01; p = 0.02), interleukin 6 (IL-6) (OR = 1.02; p = 0.02), and procalcitonin (PCT) (OR = 1.07; p = 0.03). Receiver operating characteristic (ROC) curves demonstrated significant associations with ALB (p < 0.001; the area under curve (AUC) = 0.80), PCT (p = 0.009; AUC = 0.74), and CRP (p = 0.02; AUC = 0.71).

Conclusions

Increased awareness of BSI risk is essential in erythroderma management. Patients with specific risk factors, such as abnormal body temperature (≤36.0 or ≥38.5 °C), chilling sensations, kidney disease, a history of drug reactions, elevated CRP (≥32 mg/L), elevated PCT (≥1.00 ng/ml), and low albumin (≤31.0 g/L), require close monitoring for BSI development.

Time Is of the Essence: Achieving Prompt and Effective Antimicrobial Therapy of Bloodstream Infection With Advanced Hospital Information Systems

The early administration of appropriate antibiotic therapy is crucial for the survival of patients with bacteremia. Current research focuses on improving analytical times through technology, whereas there have been very few efforts to improve postanalytical times even though they represent 40% of the time between blood taking and appropriate treatment administration. One of the clues is the efficiency and appropriateness of the result communication system. Here, we review all delays in the entire process with the aim of improving time to appropriate treatment administration. We discuss causes for long times to adjust treatment once microbiological results are released. We argue that the pervasive health information system in this organization serves as both a bottleneck and a rigid framework. Finally, we explore how next-generation hospital information systems should be designed to effectively assist the doctors in treating patients with bacteremia.

Clinical evaluation of droplet digital PCR in the early identification of suspected sepsis patients in the emergency department: a prospective observational study

Background

Rapid and accurate diagnosis of the causative agents is essential for clinical management of bloodstream infections (BSIs) that might induce sepsis/septic shock. A considerable number of suspected sepsis patients initially enter the health-care system through an emergency department (ED), hence it is vital to establish an early strategy to recognize sepsis and initiate prompt care in ED. This study aimed to evaluate the diagnostic performance and clinical value of droplet digital PCR (ddPCR) assay in suspected sepsis patients in the ED.

Methods

This was a prospective single-centered observational study including patients admitted to the ED from 25 October 2022 to 3 June 2023 with suspected BSIs screened by Modified Shapiro Score (MSS) score. The comparison between ddPCR and blood culture (BC) was performed to evaluate the diagnostic performance of ddPCR for BSIs. Meanwhile, correlative analysis between ddPCR and the inflammatory and prognostic-related biomarkers were conducted to explore the relevance. Further, the health economic evaluation of the ddPCR was analyzed.

Results

258 samples from 228 patients, with BC and ddPCR performed simultaneously, were included in this study. We found that ddPCR results were positive in 48.13% (103 of 214) of episodes, with identification of 132 pathogens. In contrast, BC only detected 18 positives, 88.89% of which were identified by ddPCR. When considering culture-proven BSIs, ddPCR shows an overall sensitivity of 88.89% and specificity of 55.61%, the optimal diagnostic power for quantifying BSI through ddPCR is achieved with a copy cutoff of 155.5. We further found that ddPCR exhibited a high accuracy especially in liver abscess patients. Among all the identified virus by ddPCR, EBV has a substantially higher positive rate with a link to immunosuppression. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity as well as prognosis. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs.

Conclusions

The multiplexed ddPCR delivers precise and quantitative load data on the causal pathogen, offers the ability to monitor the patient's condition and may serve as early warning of sepsis in time-urgent clinical situations as ED.

Importance

Early detection and effective administration of antibiotics are essential to improve clinical outcomes for those with life-threatening infection in the emergency department. ddPCR, an emerging tool for rapid and sensitive pathogen identification used as a precise bedside test, has developed to address the current challenges of BSI diagnosis and precise treatment. It characterizes sensitivity, specificity, reproducibility, and absolute quantifications without a standard curve. ddPCR can detect causative pathogens and related resistance genes in patients with suspected BSIs within a span of three hours. In addition, it can identify polymicrobial BSIs and dynamically monitor changes in pathogenic microorganisms in the blood and can be used to evaluate antibiotic efficacy and survival prognosis. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs.

Clinical and economic evaluation of blood culture whole process optimisation in critically ill adult patients with positive blood cultures

OBJECTIVES

Optimising blood culture processing is important to ensure that bloodstream infections are accurately diagnosed while minimising adverse events caused by antibiotic abuse. This study aimed to evaluate the impact of optimised blood culture processes on antibiotic use, clinical outcomes and economics in intensive care unit (ICU) patients with positive blood cultures.

METHODS

From March 2020 to October 2021, this microbiology laboratory implemented a series of improvement measures, including the clinical utility of Fastidious Antimicrobial Neutralization (FAN® PLUS) bottles for the BacT/Alert Virtuo blood culture system, optimisation of bottle reception, graded reports and an upgraded laboratory information system. A total of 122 ICU patients were included in the pre-optimisation group from March 2019 to February 2020, while 179 ICU patients were included in the post-optimisation group from November 2021 to October 2022.

RESULTS

Compared with the pre-optimisation group, the average reporting time of identification and antimicrobial sensitivity was reduced by 16.72 hours in the optimised group. The time from admission to targeted antibiotic therapy within 24 hours after receiving both the Gram stain report and the final report were both significantly less in the post-optimisation group compared with the pre-optimisation group. The average hospitalisation time was reduced by 6.49 days, the average antimicrobial drug cost lowered by $1720.85 and the average hospitalisation cost by $9514.17 in the post-optimisation group.

CONCLUSIONS

Optimising blood culture processing was associated with a significantly increased positive detection rate, a remarkable reduction in the length of hospital stay and in hospital costs for ICU patients with bloodstream infections.

Clinical impact and cost-consequence analysis of ePlex® blood culture identification panels for the rapid diagnosis of bloodstream infections: a single-center randomized controlled trial

To assess clinical impact and perform cost-consequence analysis of the broadest multiplex PCR panels available for the rapid diagnosis of bloodstream infections (BSI). Single-center, randomized controlled trial conducted from June 2019 to February 2021 at a French University hospital with an institutional antimicrobial stewardship program. Primary endpoint was the percentage of patients with optimized antimicrobial treatment 12 h after transmission of positivity and Gram stain results from the first positive BC. This percentage was significantly higher in the multiplex PCR (mPCR) group (90/105 = 85.7% %, CI95% [77.5 ; 91.8] vs. 68/107 = 63.6%, CI95% [53.7 ; 72.6]; p < 10- 3) at interim analysis, resulting in the early termination of the study after the inclusion of 309 patients. For patients not optimized at baseline, the median time to obtain an optimized therapy was much shorter in the mPCR group than in the control group (6.9 h, IQR [2.9; 17.8] vs. 26.4 h, IQR [3.4; 47.5]; p = 0.001). Early optimization of antibiotic therapy resulted in a non-statistically significant decrease in mortality from 12.4 to 8.8% (p = 0.306), with a trend towards a shorter median length of stay (18 vs. 20 days; p = 0.064) and a non-significant reduction in the average cost per patient of €3,065 (p = 0.15). mPCR identified all the bacteria present in 88% of the samples. Despite its higher laboratory cost, the use of multiplex PCR for BSI diagnosis leads to early-optimised therapy, seems cost-effective and could reduce mortality and length of stay. Their impact could probably be improved if implemented 24/7.

The Impact of Reporting the Same-Day Identification and Antibiotic Susceptibility Test Results on the Treatment of Bloodstream Infections

Objective

The rise of antibiotic-resistant organisms necessitates the implementation of rapid identification (ID) and antibiotic susceptibility testing (AST) methods for patient management. We aimed to analyze how rapid ID and AST reporting influenced clinicians' treatment decisions.

Materials and Methods

Bacteria were identified directly from positive blood cultures (BC) using serum separator tubes and MALDI-TOF MS. EUCAST rapid antibiotic susceptibility testing (RAST) method was performed for AST. The impact of rapid ID and AST reports on clinician treatment decisions was evaluated through clinical documentation. The appropriateness of antimicrobial therapy and interventions was assessed according to institutional antimicrobial prescribing guidelines, AST results, and clinical data.

Results

A total of 128 BC bottles from 86 patients underwent processing. The rapid ID method was successful in 105 (82.1%) bottles obtained from 76 patients. The rapid ID results were reviewed by the Infectious Diseases Team on the same day for 55 (72.4%) of the 76 patients. Following the evaluation, new treatments or interventions were recommended for 28 (36.8%) patients. RAST results were available for 24 patients. The susceptibility profile of seven patients was assessed by the Infectious Diseases Team on the same day. Antimicrobial treatment was escalated in four cases, and de-escalation was made in two based on RAST results. If all rapid results had been assessed, adjustments could have been made for eight (10.5%) and eleven (14.5%) more patients, according to ID and RAST results, respectively.

Conclusion

Implementation of rapid ID and AST may contribute to patient management. Although rapid reporting was made, some results were not evaluated by the clinician on the same day, indicating that communication between the clinician and the laboratory needs to be strengthened.

Molecular rapid diagnostic testing for bloodstream infections: Nanopore targeted sequencing with pathogen-specific primers

BACKGROUND

Nanopore sequencing, known for real-time analysis, shows promise for rapid clinical infection diagnosis but lacks effective assays for bloodstream infections (BSIs).

METHODS

We prospectively assessed the performance of a novel nanopore targeted sequencing (NTS) assay in identifying pathogens and predicting antibiotic resistance in BSIs, analyzing 387 blood samples from December 2021 to April 2023.

RESULTS

The positivity rate for NTS (69.5 %, 269/387) nearly matches that of metagenomic next-generation sequencing (mNGS) (74.7 %, 289/387; p = 0.128) and surpasses the positivity rate of conventional blood culture (BC) (33.9 %, 131/387; p < 0.01). Frequent pathogens detected by NTS included Klebsiella pneumoniae (n = 54), Pseudomonas aeruginosa (n = 36), Escherichia coli (n = 36), Enterococcus faecium(n = 30), Acinetobacter baumannii(n = 26), Staphylococcus aureus(n = 23), and Human cytomegalovirus (n = 37). Against a composite BSI diagnostic standard, NTS demonstrated a sensitivity and specificity of 84.0 % (95 % CI 79.5 %-87.7 %) and 90.1 % (95 % CI 81.7 %-88.5 %), respectively. The concordance between NTS and mNGS results (the percentage of total cases where both either detected BSI-related pathogens or were both negative) was 90.2 % (359/387), whereas the consistency between NTS and BC was only 60.2 % (233/387). In 80.6 % (50/62) of the samples with identical pathogens identified by both NTS tests and BCs, the genotypic resistance identified by NTS correlated with culture-confirmed phenotypic resistance. Using NTS, 95 % of samples can be tested and analyzed in approximately 7 h, allowing for early patient diagnosis.

CONCLUSIONS

NTS is rapid, sensitive, and efficient for detecting BSIs and drug-resistant genes, making it a potential preferred diagnostic tool for early infection identification in critically ill patients.

Prognostic value of poly-microorganisms detected by droplet digital PCR and pathogen load kinetics in sepsis patients: a multi-center prospective cohort study

This study aimed to investigate the prognostic value of a novel droplet digital polymerase chain reaction (DDPCR) assay in sepsis patients. In this prospective cohort study, univariable and multivariable Cox regressions were used to assess risk factors for 28-day mortality. We also monitored pathogen load together with clinical indicators in a subgroup of the cohort. A total of 107 sepsis patients with positive baseline DDPCR results were included. Detection of poly-microorganisms [adjusted hazard ratio (HR) = 3.19; 95% confidence interval (CI) = 1.34-7.62; P = 0.009], high Charlson Comorbidity Index (CCI) score (adjusted HR = 1.14; 95% CI = 1.01-1.29; P = 0.041), and Sequential Organ Failure Assessment (SOFA) score (adjusted HR = 1.18; 95% CI = 1.05-1.32; P = 0.005) at baseline were independent risk factors for 28-day mortality while initial pathogen load was not associated (adjusted HR = 1.17; 95% CI = 0.82-1.66; P = 0.385). Among 63 patients with serial DDPCR results, an increase in pathogen load at days 6-8 compared to baseline was a risk factor for 28-day mortality (P = 0.008). Also, pathogen load kinetics were significantly different between day-28 survivors and nonsurvivors (P = 0.022), with a decline overtime only in survivors and an increase from days 3 and 4 to days 6-8 in nonsurvivors. Using DDPCR technique, we found that poly-microorganisms detected and increased pathogen load a week after sepsis diagnosis were associated with poor prognosis.IMPORTANCEThis prospective study was initiated to explore the prognostic implications of a novel multiplex PCR assay in sepsis. Notably, our study was the largest cohort of sepsis with droplet digital polymerase chain reaction pathogen monitoring to date, allowing for a comprehensive evaluation of the prognostic significance of both pathogen species and load. We found that detection of poly-microorganisms was an independent risk factors for 28-day mortality. Also, pathogen load increase 1 week after sepsis diagnosis was a risk factor for 28-day mortality, and differential pathogen load kinetics were identified between day-28 survivors and nonsurvivors. Overall, this study demonstrated that pathogen species and load were highly correlated with sepsis prognosis. Patients exhibiting conditions mentioned above face a more adverse prognosis, suggesting the potential need for an escalation of antimicrobial therapy.Registered at ClinicalTrials.gov (NCT05190861).

Early assessment of blood culture negativity as a potential support tool for antimicrobial stewardship

Objective

To assess whether 48-h negative blood culture (BC) bottles are still negative at the classic 120-h incubation endpoint and whether 48 h might be the time to make antimicrobial therapy decisions.

Methods

Data from the first collected bottles from bloodstream infection (BSI) episodes of single patients were retrospectively analyzed. Probabilities of bottles being negative at the classic endpoint were calculated from 0 to 120 h of incubation.

Results

Among BC-negative episodes (4018/4901 [82.0%]), most (2097/4018 (52.2%) occurred in medicine patients. At 48 h, probability was 100.0% (95% CI, 99.9-100.0) for all 4018 patients. Of these, 1244 (31.0%) patients remained on antibiotics until 120 h. Excluding 401 (32.2%) patients who received antibiotics for another (non-bloodstream) infection, 843 (67.8%) of 1244 patients could have merited early (48-h) discontinuation of antibiotics. Stopping treatment in these patients would have led to saving 5201 days of access (943 [18.1%] days), watch (3624 [69.7%] days), or reserve (634 [12.2%]) AWaRe groups' antibiotics, which correspond to 65.6% (5201/7928) of days of administered antibiotics in all 1244 patients.

Conclusion

As an early indicator of BC negativity, the 48-h endpoint could reliably support antimicrobial stewardship, but the clinical judgment remains imperative especially when BSI is highly suspected.

Reliability of Droplet Digital PCR Alone and in Combination with Interleukin-6 and Procalcitonin for Prognosis of Bloodstream Infection

Purpose

Bloodstream infection(BSI) is linked with high mortality, underscoring the significance of prompt etiological diagnosis for timely and precise treatment. This study aims to investigate the diagnostic value of droplet digital polymerase chain reaction(ddPCR) in combination with conventional inflammatory markers [interleukin-6(IL-6) and procalcitonin(PCT)] concerning disease progression and treatment prognosis in BSI patients. Furthermore, the study aims to explore a more efficient clinical application strategy.

Patients and Methods

This prospective case seried study centers on 176 patients suspected of or confirmed with BSI. Blood samples were collected to extract nucleic acids for identifying pathogens (bacteria, fungi, and viruses) and determining copy loads via ddPCR.

Results

The sensitivity of ddPCR was markedly higher compared to the culture method (74.71% vs 31.03%). A positive correlation existed between bacterial load and levels of inflammatory markers [IL-6 (P=0.0182), PCT (P=0.0029), and CRP (P=0.0005)]. In suspected BSI cases, the combination of ddPCR and inflammatory markers could predict sepsis risk [ROC: Area under the curve(AUC)=0.6071, P=0.0383]. Within confirmed BSI patients, the ddPCR bacterial load of those with SOFA<7 was lower than that of the SOFA≥7 (P=0.0334). ddPCR (OR: 1.789, P=0.035) monitoring combined with PCT (OR: 1.787, P=0.035) holded predictive value for SOFA progression (AUC=0.7913, P=0.0003). Similarly, BSI survivors displayed a lower burden than non-survivors (P=0.0170). Additionally, ddPCR combinated with IL-6 provided a more accurate and expedited insight into clinical outcomes prediction for BSI confirmed patients (AUC=0.7352, P=0.0030). Serial monitoring of bacterial load by ddPCR effectively mirrored the clinical course of BSI in patients. Notably, patients with positive ddPCR virus infection exhibited significantly reduced lymphocyte counts (P=0.0003).

Conclusion

In a clinical context, qualitative ddPCR results and quantitative continuous monitoring can more precisely assess sepsis progression and treatment prognosis in BSI patients. Furthermore, ddPCR results offer quicker and more accurate reference points for clinical antibacterial and antiviral interventions.

Bacterial Infections in Intensive Care Units: Epidemiological and Microbiological Aspects

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

Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection

BACKGROUND

The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood.

METHODS

Blood samples from healthy donors were spiked with different concentrations of four prevalent causative species of BSI. All samples were then subjected to a modified saponin-based host DNA depletion protocol and optimised DNA extraction, whole genome amplification and debranching steps in preparation for sequencing, followed by bioinformatical analyses. Two related variants of the protocol are presented: 1mL of blood processed without bacterial enrichment, and 5mL of blood processed following a rapid bacterial enrichment protocol-SepsiPURE.

RESULTS

After first identifying that a large proportion of host mitochondrial DNA remained, the host depletion process was optimised by increasing saponin concentration to 3% and scaling the reaction to allow more sample volume. Compared to non-depleted controls, the 3% saponin-based depletion protocol reduced the presence of host chromosomal and mitochondrial DNA < 106 and < 103 fold respectively. When the modified depletion method was further combined with a rapid bacterial enrichment method (SepsiPURE; with 5mL blood samples) the depletion of mitochondrial DNA improved by a further > 10X while also increasing detectable bacteria by > 10X. Parameters during DNA extraction, whole genome amplification and long-read sequencing were also adjusted, and subsequently amplicons were detected for each input bacterial species at each of the spiked concentrations, ranging from 50-100 colony forming units (CFU)/mL to 1-5 CFU/mL.

CONCLUSION

In this proof-of-concept study, four prevalent BSI causative species were detected in under 12 h to species level (with antimicrobial resistance determinants) at concentrations relevant to clinical blood samples. The use of a rapid and precise metagenomic protocols has the potential to advance the diagnosis of BSI.

Development and validation a nomogram prediction model for early diagnosis of bloodstream infections in the intensive care unit

Purpose

This study aims to develop and validate a nomogram for predicting the risk of bloodstream infections (BSI) in critically ill patients based on their admission status to the Intensive Care Unit (ICU).

Patients and methods

Patients' data were extracted from the Medical Information Mart for Intensive Care-IV (MIMIC-IV) database (training set), the Beijing Friendship Hospital (BFH) database (validation set) and the eICU Collaborative Research Database (eICU-CRD) (validation set). Univariate logistic regression analyses were used to analyze the influencing factors, and lasso regression was used to select the predictive factors. Model performance was assessed using area under receiver operating characteristic curve (AUROC) and Presented as a Nomogram. Various aspects of the established predictive nomogram were evaluated, including discrimination, calibration, and clinical utility.

Results

The model dataset consisted of 14930 patients (1444 BSI patients) from the MIMIC-IV database, divided into the training and internal validation datasets in a 7:3 ratio. The eICU dataset included 2100 patients (100 with BSI) as the eICU validation dataset, and the BFH dataset included 419 patients (21 with BSI) as the BFH validation dataset. The nomogram was constructed based on Glasgow Coma Scale (GCS), sepsis related organ failure assessment (SOFA) score, temperature, heart rate, respiratory rate, white blood cell (WBC), red width of distribution (RDW), renal replacement therapy and presence of liver disease on their admission status to the ICU. The AUROCs were 0.83 (CI 95%:0.81-0.84) in the training dataset, 0.88 (CI 95%:0.88-0.96) in the BFH validation dataset, and 0.75 (95%CI 0.70-0.79) in the eICU validation dataset. The clinical effect curve and decision curve showed that most areas of the decision curve of this model were greater than 0, indicating that this model has a certain clinical effectiveness.

Conclusion

The nomogram developed in this study provides a valuable tool for clinicians and nurses to assess individual risk, enabling them to identify patients at a high risk of bloodstream infections in the ICU.

An improved protocol for bacteria identification by MALDI-TOF MS directly from positive blood cultures

FASTinov® developed a rapid antimicrobial susceptibility test that includes the purification of a bacterial suspension directly from positive blood cultures (BC). In order to streamline laboratory workflow, the use of the bacterial suspension obtained through FASTinov® sample prep was tested for identification (ID) by matrix absorption laser deionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker) in 364 positive BC, and its accuracy assessed comparing with the MALDI-TOF MS ID of the next-day subcultured colonies. FASTinov sample prep was highly reliable for rapid ID directly from BC with proportion of agreement of 94.9% for Gram-positive and 96.3% for Gram-negative bacteria.

A multi-pronged approach to improve blood culture diagnostics in different clinical departments: a single-centre experience

PURPOSE

Blood culture (BC) diagnostics are influenced by many factors. We performed a targeted interdisciplinary analysis to analyse effects of various measures on BC diagnostics performance.

METHODS

A diagnostic stewardship initiative was conducted at two intervention and two control wards in a German tertiary level hospital. The initiative comprised staff training on the correct indications and sampling for BC, implementation of information cards, labels to identify the collection site, regular BC bottle feedback including the number of bottles, filling volumes and identified pathogens; and the use of a specific sampling device (BD Vacutainer®). Before and after the interventions, two three-month measurement periods were performed, as well as a one-month follow-up period to assess the sustainability of the conducted measures.

RESULTS

In total, 9362 BC bottles from 787 patients were included in the analysis. The number of BCs obtained from peripheral venous puncture could be increased at both intervention wards (44.0 vs. 22.2%, 58.3 vs. 34.4%), while arterial sampling could be reduced (30.6 vs. 4.9%). A total of 134 staff members were fully trained. The intervention led to a considerable increase in BC knowledge (from 62.4 to 79.8% correct answers) with differences between the individual professional groups. Relevant reduced contamination rates could be detected at both intervention wards.

CONCLUSIONS

As knowledge on the correct BC sampling and strategies to reduce contamination varies considerably between clinical departments and healthcare professionals, a targeted training should be adapted to the specific needs of the individual professional groups. An additional filling device is not necessary.

Identifying the need for infection-related consultations in intensive care patients using machine learning models

Infection-related consultations on intensive care units (ICU) have a positive impact on quality of care and clinical outcome. However, timing of these consultations is essential and to date they are typically event-triggered and reactive. Here, we investigate a proactive approach to identify patients in need for infection-related consultations by machine learning models using routine electronic health records. Data was retrieved from a mixed ICU at a large academic tertiary care hospital including 9684 admissions. Infection-related consultations were predicted using logistic regression, random forest, gradient boosting machines, and long short-term memory neural networks (LSTM). Overall, 7.8% of admitted patients received an infection-related consultation. Time-sensitive modelling approaches performed better than static approaches. Using LSTM resulted in the prediction of infection-related consultations in the next clinical shift (up to eight hours in advance) with an area under the receiver operating curve (AUROC) of 0.921 and an area under the precision recall curve (AUPRC) of 0.541. The successful prediction of infection-related consultations for ICU patients was done without the use of classical triggers, such as (interim) microbiology reports. Predicting this key event can potentially streamline ICU and consultant workflows and improve care as well as outcome for critically ill patients with (suspected) infections.

Comparison of metagenomic next-generation sequencing and blood culture for diagnosis of bloodstream infections

Objectives

This study aimed to evaluate the clinical performance of plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) for pathogen detection in patients with sepsis.

Methods

A total of 43 pairs of blood and plasma samples form 33 blood culture-positive patients were used as testing samples in metagenomic NGS (mNGS) and NGS of 16S ribosomal RNA gene amplicons (16S rRNA NGS). The results of routine tests, including microbial culture, complete blood count, and biochemical tests, were collected from electronic medical records.

Results

Using blood as an mNGS testing sample, the proportion of host DNA was 99.9%, with only three bacteria and no fungi detected. When using plasma in mNGS, the proportion of host DNA was approximately 97%, with 84 bacteria and two fungi detected. Notably, 16S rRNA NGS detected 15 and 16 bacteria in 43 pairs of blood and plasma samples, respectively. Blood culture detected 49 bacteria (23 gram-negative bacilli and 26 gram-positive cocci) and four fungi, with 14 bacteria considered contaminants by clinical microbiologists. For all blood cultures, plasma cfDNA mNGS detected 78.26% (19/23) gram-negative rods, 17% (2/12) gram-positive cocci, and no fungi. Compared to blood cultures, the sensitivity and specificity of plasma cfDNA mNGS for detecting bacteria and fungi were 62.07% and 57.14%, respectively.

Conclusion

Compared to blood, plasma is more suitable for the detection of bloodstream infections using mNGS and is less affected by host DNA. The positive detection rate of plasma cfDNA mNGS for bloodstream infections caused by gram-negative bacteria was higher than that caused by gram-positive cocci.

Blood culture quality and turnaround time of clinical microbiology laboratories in Chinese Teaching Hospitals: A multicenter study

PURPOSE

Blood culture (BC) remains the gold standard for the diagnosis of bloodstream infections. Improving the quality of clinical BC samples, optimizing BC performance, and accelerating antimicrobial susceptibility test (AST) results are essential for the early detection of bloodstream infections and specific treatments.

METHODS

We conducted a retrospective multicenter study using 450,845 BC specimens from clinical laboratories obtained from 19 teaching hospitals between 1 January 2021 and 31 December 2021. We evaluated key performance indicators (KPIs), turnaround times (TATs), and frequency distributions of processing in BC specimens. We also evaluated the AST results of clinically significant isolates for four different laboratory workflow styles.

RESULTS

Across the 10 common bacterial isolates (n = 16,865) and yeast isolates (n = 1011), the overall median (interquartile range) TATs of AST results were 2.67 (2.05-3.31) and 3.73 (2.98-4.64) days, respectively. The specimen collections mainly occurred between 06:00 and 24:00, and specimen reception and loadings mainly between 08:00 and 24:00. Based on the laboratory workflows of the BCs, 16 of the 19 hospitals were divided into four groups. Time to results (TTRs) from specimen collection to the AST reports were 2.35 (1.95-3.06), 2.61 (1.98-3.32), 2.99 (2.60-3.87), and 3.25 (2.80-3.98) days for groups I, II, III, and IV, respectively.

CONCLUSION

This study shows the related BC KPIs and workflows in different Chinese hospitals, suggesting that laboratory workflow optimization can play important roles in shortening time to AST reports and initiation of appropriate timely treatment.