Evaluation of Optimal Blood Culture Incubation Time To Maximize Clinically Relevant Results from a Contemporary Blood Culture Instrument and Media System

Evaluation of a four-day incubation protocol for blood cultures: a quality improvement project

Blood cultures are critical in diagnosing bloodstream infections and guiding the treatment of sepsis, which carries a significant mortality risk. Traditional blood culture protocols often recommend a five-day incubation period to ensure the recovery of clinically significant pathogens. However, recent evidence suggests that a shorter incubation period may be sufficient, potentially reducing laboratory workload and the recovery of contaminants.

METHODS

This quality improvement project was conducted to evaluate the performance of a four-day incubation protocol using the BD BACTEC automated blood culture system in a large academic center with over 1,000 beds, processing more than 70,000 blood culture requests annually. A retrospective analysis was performed on 71,862 blood cultures processed in 2022.

RESULTS

Results indicated that 99.2% of all positive cultures, including those in pediatric cases, were detected within four days, with a mean time to positivity of 23.97 h. Only 0.8% of blood cultures flagged positive after the four-day mark, and these were predominantly cases with previous positive cultures or repeat cultures that did not alter patient management.

CONCLUSION

We conclude that a four-day incubation period is sufficient for the detection of clinically significant pathogens using the BD BACTEC system. This change not only optimizes laboratory operations by increasing capacity and reducing waste but also supports timely clinical decision-making.

Review on biphasic blood drying method for rapid pathogen detection in bloodstream infections

Rapid and accurate detection of pathogenic microorganisms in blood is critical for diagnosing life-threatening conditions such as bloodstream infections (BSIs). Current methods for the detection and identification of bacteria from large volumes of blood (5 mL) involve culture steps followed by DNA extraction/purification/concentration and Polymerase Chain Reaction (PCR)-based nucleic acid amplification. DNA extraction and amplification directly from blood samples is hampered by the complexity of the blood matrix, resulting in time-consuming and labor-intensive processes. This review delves into recent advancements in molecular diagnostics based on blood drying, coined as 'biphasic reaction', and highlights this new technique that attempts to overcome the limitations of traditional sample preparation and amplification processes. The biphasic blood drying method, in combination with isothermal amplification methods such as loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA), has recently been shown to improve the sensitivity of detection of bacterial, viral, and fungal pathogens from ∼1 mL of whole blood, while minimizing DNA loss and avoiding the use of extraction/purification/concentration kits. Furthermore, the biphasic approach in combination with LAMP has been shown to be a culture-free method capable of detecting bacteria in clinical samples with a sensitivity of ∼1 CFU/mL in ∼2.5 h. This represents a significant reduction in detection and identification time compared to current clinical procedures based on bacterial culture prior to PCR amplification. This review paper aims to be a guide to identify new opportunities for future advancements and applications of the biphasic technology.

Rapid and sensitive identification of Candida in blood based on M1 beads enrichment combined with multiple recombinase-aided PCR: a culture-independent approach

Introduction

Clinically, timely diagnosis and effective treatment of Candida bloodstream infections rely on rapid and sensitive detection methods. However, the long turn-around time and low detection rate of blood culture (the gold standard) make rapid diagnosis of Candida challenging. This study develops a novel molecular assay (M1-mRAP) designed for the rapid and sensitive detection of three Candida species in blood samples: Candida albicans(CA), Candida tropicalis(CT), and Candida glabrata(CG).

Methods

We used the M1-mRAP method aimed at detecting Candida DNA in blood samples, in which we developed a novel multiplex recombinase-aided PCR (mRAP) assay for sensitive amplification of Candida DNA and used a self-developed recombinant human mannan-binding lectin beads (M1 beads)method for enrichment of Candida in blood. The analytical sensitivity of mRAP was evaluated using Candida recombinant plasmids. The analytical sensitivity of the M1-mRAP method for blood sample detection was assessed using quantitative Candida simulated blood samples. The clinical performance of the mRAP and M1-mRAP methods was evaluated in 120 non-blood samples and 9 blood samples and compared with conventional qPCR methods.

Results

The limit of detection(LOD) for CA, CT, and CG by the mRAP method were 4, 4, and 3 copies/μL, respectively. The LOD for CA, CT, and CG simulated blood samples by the M1-mRAP were 2, 2, and 1 CFU/mL, and the overall detection time was about 3.5 h. Clinical assays of mRAP and M1-mRAP showed that these two methods were consistent with qPCR (P<0.05), but had better clinical detection ability than qPCR. Specifically, the mRAP method identified 5 (4.2%) qPCR-negative samples, while M1-mRAP detected 1 (11.1%) classified as the qPCR grey zone sample.

Conclusion

The M1-mRAP method provides rapid and sensitive detection of low concentrations of CA, CT, and CG blood samples and has the potential to emerge as an important tool for the early detection of Candida bloodstream infections in clinical settings.

Validity of reducing blood culture incubation time for the BD BACTEC FX blood culture system considering microbiological and clinical aspects

INTRODUCTION

A blood culture (BC) test is vital for diagnosing bacteremia in clinical practice. Although incubation time varies among automated BC systems, 4-5 days is deemed to be sufficient time for the BD BACTEC FX blood culture system. This study compared the clinical and microbiological characteristics of true-positive BC samples on day 5 with those within 4 days to reduce missed true bacteremia cases.

METHODS

We conducted a retrospective study of blood cultures from hospitalized patients between April 2020 and April 2023 at a tertiary care hospital in Japan.

RESULTS

In total, 12,342 BC sets were collected from 6,567 patients. Gram-positive bacilli other than Bacillus spp. and Corynebacterium spp., non-albicans Candida, and yeasts other than Candida spp. were detected more frequently in BC-positive patients on day 5 than in those within 4 days. The gastrointestinal tract was the portal of entry more frequently on day 5 than within 4 days (25 % vs. 4 %, p = 0.006).

CONCLUSION

A 4-day incubation period is sufficient for the BD BACTEC FX blood culture system under routine conditions. However, a 5-day incubation period may be warranted when low pathogenicity is suspected or the gastrointestinal tract is suspected as the portal of entry.

Development of molecular sterility assay for rapid quality release of cord blood erythrocytes units for transfusion

BACKGROUND

Umbilical cord blood (CB) units stored in banks are an important source of hematopoietic stem cells for transplantation and other cell therapies. New applications, such as their use in transfusions, require rapid quality release as cord blood red blood cells (CB-RBC) have a shorter shelf life.

STUDY DESIGN AND METHODS

This project aims to investigate the most prevalent microbial contaminants in CB preparations and validate a rapid sterility testing strategy for CB-RBC based on an automated system (BACT/ALERT®) in tandem with a molecular assay (real-time PCR) capable of detecting at least 100 CFU/mL of Cutibacterium acnes in CB-RBC to accelerate the detection of the most common slow-growing bacteria.

RESULTS

Microbial contamination incidence was assessed by reviewing 4696 CB sterility tests, revealing a positivity rate of 3.4%, with C. acnes being the most common slow-growing pathogen. The BACT/ALERT® system, which was validated according to European Pharmacopeia guidelines, was an appropriate method for sterility testing of CB-RBC, although it required up to 14 days of culture to detect C. acnes when iFAPlus and iFNPlus bottles were used to neutralize antimicrobials. Interestingly, the BACT/ALERT® method detected C. acnes at 30 CFU/mL within 14 days, while real-time PCR identified concentrations ≥65 CFU/mL by Day 4.

DISCUSSION

In conclusion, we developed a rapid sterility testing strategy that combines automated culture systems and real-time PCR for early microbial contamination, enhancing CB-RBC shelf life for transfusion and emphasizing the importance of combining detection methods.

Machine learning algorithms for the early detection of bloodstream infection in children with osteoarticular infections

Background

Bloodstream infection (BSI) poses a significant life-threatening risk in pediatric patients with osteoarticular infections. Timely identification of BSI is crucial for effective management and improved patient outcomes. This study aimed to develop a machine learning (ML) model for the early identification of BSI in children with osteoarticular infections.

Materials and methods

A retrospective analysis was conducted on pediatric patients diagnosed with osteoarticular infections admitted to three hospitals in China between January 2012 and January 2023. All patients underwent blood and puncture fluid bacterial cultures. Sixteen early available variables were selected, and eight different ML algorithms were applied to construct the model by training on these data. The accuracy and the area under the receiver operating characteristic (ROC) curve (AUC) were used to evaluate the performance of these models. The Shapley Additive Explanation (SHAP) values were utilized to explain the predictive value of each variable on the output of the model.

Results

The study comprised 181 patients in the BSI group and 420 in the non-BSI group. Random Forest exhibited the best performance, with an AUC of 0.947 ± 0.016. The model demonstrated an accuracy of 0.895 ± 0.023, a sensitivity of 0.847 ± 0.071, a specificity of 0.917 ± 0.007, a precision of 0.813 ± 0.023, and an F1 score of 0.828 ± 0.040. The four most significant variables in both the feature importance matrix plot of the Random Forest model and the SHAP summary plot were procalcitonin (PCT), neutrophil count (N), leukocyte count (WBC), and fever days.

Conclusions

The Random Forest model proved to be effective in early and timely identification of BSI in children with osteoarticular infections. Its application could aid in clinical decision-making and potentially mitigate the risk associated with delayed or inaccurate blood culture results.

An Update on Recent Clinical Trial Data in Bloodstream Infection

Bloodstream infections (BSIs) remain a significant source of morbidity and mortality globally, exacerbated by an ageing population and rising antimicrobial resistance (AMR). This review offers an updated evaluation of randomized clinical trials (RCTs) in BSI management from 2018 onwards, focusing on the evolving landscape of diagnostics and treatment. New rapid diagnostic technologies and shorter antimicrobial courses have transformed clinical practice, reducing the time to appropriate therapy and hospital stays. Several RCTs demonstrated that rapid phenotypic and genotypic tests shorten the time to optimal therapy, especially when paired with antimicrobial stewardship. Ongoing trials are investigating novel antimicrobial regimens and the safety of early oral switch strategies, particularly for Gram-positive and Gram-negative BSIs. Recent RCTs on Staphylococcus aureus BSI (SAB) and multidrug-resistant Gram-negative bacteria highlight advances in treatment but emphasize the need for further study into the efficacy of combination therapies and the utility of rapid diagnostics in different healthcare settings. The review also explores challenges in trail design, with adaptive and pragmatic appropriates improving the efficacy of clinical trials. Finally, this paper identifies gaps in the research, including the need for further investigation into oral step-down therapy, optimal durations, and the role of rapid diagnostics in resource-limited settings.

Integrating Genomic Data with the Development of CRISPR-Based Point-of-Care-Testing for Bacterial Infections

Purpose of Review

Bacterial infections and antibiotic resistance contribute to global mortality. Despite many infections being preventable and treatable, the lack of reliable and accessible diagnostic tools exacerbates these issues. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based diagnostics has emerged as a promising solution. However, the development of CRISPR diagnostics has often occurred in isolation, with limited integration of genomic data to guide target selection. In this review, we explore the synergy between bacterial genomics and CRISPR-based point-of-care tests (POCT), highlighting how genomic insights can inform target selection and enhance diagnostic accuracy.

Recent Findings

We review recent advances in CRISPR-based technologies, focusing on the critical role of target sequence selection in improving the sensitivity of CRISPR-based diagnostics. Additionally, we examine the implementation of these technologies in resource-limited settings across Asia and Africa, presenting successful case studies that demonstrate their potential.

Summary

The integration of bacterial genomics with CRISPR technology offers significant promise for the development of effective point-of-care diagnostics.

Antibiotic utilization trends in Veterans Affairs patients with Stenotrophomonas maltophilia bloodstream infections

Objective

Stenotrophomonas maltophilia is a multidrug-resistant gram-negative bacillus that can cause serious infections but has limited treatment options. This study aims to establish trends in the treatment of S. maltophilia bloodstream infections (BSI) across the United States in Department of Veterans Affairs (VA) facilities.

Methods

Data was evaluated over a 10-year timeframe (2012 to 2021) in this retrospective cohort study. Veterans with ≥ 1 blood culture with S. maltophilia within a VA medical encounter were included. Microbiology, pharmacy, and patient information were collected through national VA data sources and chart review. Descriptive statistics and Poisson regression were used to summarize patient demographics, facility characteristics, microbiologic data, and treatment trends.

Results

A total of 374 blood cultures positive for S. maltophilia were identified across 75 VA facilities. Of 282 unique patients with BSI, the majority were male (93.6%), white (67.4%), with a mean age of 64 ± 13.1 years. Of those patients, 78% received treatment, 12.8% had a polymicrobial blood culture, and 5.3% had a documented sulfa allergy. Susceptibility results were most reported for trimethoprim-sulfamethoxazole (TMP-SMX), levofloxacin, and ceftazidime, with 4.5%, 4.3%, and 44.4% resistant isolates, respectively. Antibiotics most prescribed included TMP-SMX (41.5%) and levofloxacin (39.4%), followed by ciprofloxacin (13.8%) and ceftazidime (12.4%). Combination therapy was prescribed in 33% of patients. No significant trends were found with antibiotic utilization over time.

Conclusions

TMP-SMX and levofloxacin were the most prescribed antibiotics for S. maltophilia BSI treatment. No significant changes were seen with antibiotic prescribing trends in Veterans from 2012 to 2021.

Infective endocarditis

First described more than 350 years ago, infective endocarditis represents a global health concern characterised by infections affecting the native or prosthetic heart valves, the mural endocardium, a septal defect, or an indwelling cardiac device. Over recent decades, shifts in causation and epidemiology have been observed. Echocardiography remains pivotal in the diagnosis of infective endocarditis, with alternative imaging modalities gaining significance. Multidisciplinary management requiring expertise of cardiologists, cardiovascular surgeons, infectious disease specialists, microbiologists, radiologists and neurologists, is imperative. Current recommendations for clinical management often rely on observational studies, given the limited number of well conducted randomised controlled trials studying infective endocarditis due to the rarity of the disease. In this Seminar, we provide a comprehensive overview of optimal clinical practices in infective endocarditis, highlighting key aspects of pathophysiology, pathogens, diagnosis, management, prevention, and multidisciplinary approaches, providing updates on recent research findings and addressing remaining controversies in diagnostic accuracy, prevention strategies, and optimal treatment.

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.

Prediction of carbapenem-resistant gram-negative bacterial bloodstream infection in intensive care unit based on machine learning

BACKGROUND

Predicting whether Carbapenem-Resistant Gram-Negative Bacterial (CRGNB) cause bloodstream infection when giving advice may guide the use of antibiotics because it takes 2-5 days conventionally to return the results from doctor's order.

METHODS

It is a regional multi-center retrospective study in which patients with suspected bloodstream infections were divided into a positive and negative culture group. According to the positive results, patients were divided into the CRGNB group and other groups. We used the machine learning algorithm to predict whether the blood culture was positive and whether the pathogen was CRGNB once giving the order of blood culture.

RESULTS

There were 952 patients with positive blood cultures, 418 patients in the CRGNB group, 534 in the non-CRGNB group, and 1422 with negative blood cultures. Mechanical ventilation, invasive catheterization, and carbapenem use history were the main high-risk factors for CRGNB bloodstream infection. The random forest model has the best prediction ability, with AUROC being 0.86, followed by the XGBoost prediction model in bloodstream infection prediction. In the CRGNB prediction model analysis, the SVM and random forest model have higher area under the receiver operating characteristic curves, which are 0.88 and 0.87, respectively.

CONCLUSIONS

The machine learning algorithm can accurately predict the occurrence of ICU-acquired bloodstream infection and identify whether CRGNB causes it once giving the order of blood culture.

Diagnostic performance of the time to positivity of blood cultures to distinguish true bacteremia from contaminants based on an automated system

OBJECTIVE.

To determine the diagnostic performance of blood culture positivity times for distinguishing true bacteremia from contaminants in the automated "BACT/ALERT®" system.

MATERIALS AND METHODS.

A cross-sectional, diagnostic test-type study was conducted from a database of blood culture samples processed between January 2016 and August 2021. All blood culture samples from patients with suspected bacteremia were included; blood culture samples were entered into the "BACT/ALERT®" system to differentiate true bacteremia from contaminants.

RESULTS.

We obtained 33,951 blood cultures samples, of which 3875 were positive. Of the total number of positive blood cultures, 75.2% (n=2913) were true bacteremia and 24.8% (n=962) were contaminants. The median time to positivity in blood cultures with true bacteremia was significantly shorter (16.3 hours; IQR: 11.2 - 24.9) than the median time to positivity of blood cultures with contaminants (22.5 hours; IQR: 18.4 - 31.8; p<0.001). The positivity time showed the capacity to differentiate true bacteremia from contaminants, with an AUC-ROC of 0.73 (95%CI: 0.71 - 0.75), with 85% and 63% sensitivity and specificity respectively for the diagnosis of contaminants when the positivity time exceeds 16.5 hours. The use of antibiotics prior to sampling delayed the time to positivity, while having fever before sampling shortened the time to positivity.

CONCLUSIONS.

Our results show good diagnostic performance of blood culture positivity times to differentiate true bacteremia from contaminants using the "BACT/ALERT®" system when the positivity time was longer than 16.5 hours.

Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing

Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2-4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102-104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103-107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.

The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids

The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.

Metagenomic identification of pathogens and antimicrobial-resistant genes in bacterial positive blood cultures by nanopore sequencing

Nanopore sequencing workflows have attracted increasing attention owing to their fast, real-time, and convenient portability. Positive blood culture samples were collected from patients with bacterial bloodstream infection and tested by nanopore sequencing. This study compared the sequencing results for pathogen taxonomic profiling and antimicrobial resistance genes to those of species identification and phenotypic drug susceptibility using traditional microbiology testing. A total of 37 bacterial positive blood culture results of strain genotyping by nanopore sequencing were consistent with those of mass spectrometry. Among them, one mixed infection of bacteria and fungi was identified using nanopore sequencing and confirmatory quantitative polymerase chain reaction. The amount of sequencing data was 21.89 ± 8.46 MB for species identification, and 1.0 MB microbial strain data enabled accurate determination. Data volumes greater than or equal to 94.6 MB nearly covered all the antimicrobial resistance genes of the bacteria in our study. In addition, the results of the antimicrobial resistance genes were compared with those of phenotypic drug susceptibility testing for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Therefore, the nanopore sequencing platform for rapid identification of causing pathogens and relevant antimicrobial resistance genes complementary to conventional blood culture outcomes may optimize antimicrobial stewardship management for patients with bacterial bloodstream infection.

A PCR-Reverse Dot Blot Hybridization Based Microfluidics Detection System for the Rapid Identification of 13 Fungal Pathogens Directly After Blood Cultures Over a Period of Time

Introduction

It is time-consuming to identify fungal pathogens from positive blood cultures using the standard culture-based method. And delayed diagnosis of bloodstream infection leads to significantly increased mortality.

Methods

We developed a PCR-reverse dot blot hybridization combined with microfluidic chip techniques to rapidly identify 13 fungal pathogens within 3-4 h using the sample of blood cultured over a period of time.

Results

We performed clinical validation using 43 blood culture-positive samples with a sensitivity of 96.7%, a specificity of 100%, and a concordance rate of 97.7%. Samples with different culture durations were evaluated using our approach, showing a detection rate of 85.2% at 16 h and 96.3% at 24 h; the platform could reach a detection limit of 103cfu/mL for the Candida spp. and 103 copies/mL for Aspergillus spp.

Discussion

The detection rate of the platform is much higher than the positive rates of concurrent blood cultures. This method bears substantial clinical application potential as it incorporates the microfluidic platform with low reagent consumption, automation, and low cost (about 10 dollars).

Infective Endocarditis Due to Haemophilus parainfluenzae: A Case Report and Review of the Literature

We present a 20-year-old male who was admitted with recurrent fevers. He was diagnosed with Haemophilus parainfluenzae mitral valve endocarditis with severe regurgitation and perforated leaflet. H. parainfluenzae was resistant to ceftriaxone but repeated sensitivities showed a sensitive organism. Despite endocarditis caused by H. parainfluenzae is rare, physicians should be vigilant of such diagnosis. Antibiotics sensitivity may be questioned if shows a resistant organism.

Safety and Efficacy of a Single Procedure of Extraction and Reimplantation of Infected Cardiovascular Implantable Electronic Device (CIED) in Comparison with Deferral Timing: An Observational Retrospective Multicentric Study

(1) Background: Infections are among the most frequent and life-threatening complications of cardiovascular implantable electronic device (CIED) implantation. The aim of this study is to compare the outcome and safety of a single-procedure device extraction and contralateral implantation versus the standard-of-care (SoC) two-stage replacement for infected CIEDs. (2) Methods: We retrospectively included 66 patients with CIED infections who were treated at two Italian hospitals. Of the 66 patients enrolled in the study, 27 underwent a single procedure, whereas 39 received SoC treatment. All patients were followed up for 12 months after the procedure. (3) Results: Considering those lost to follow-up, there were no differences in the mortality rates between the two cohorts, with survival rates of 81.5% in the single-procedure group and 84.6% in the SoC group (p = 0.075). (4) Conclusions: Single-procedure reimplantation associated with an active antibiofilm therapy may be a feasible and effective therapeutic option in CIED-dependent and frail patients. Further studies are warranted to define the best treatment regimen and strategies to select patients suitable for the single-procedure reimplantation.

Subculturing and Gram staining of blood cultures flagged negative by the BACTEC™ FX system: Optimizing the workflow for detection of Cryptococcus neoformans in clinical specimens

Objective

To investigate whether an incubation time of 5 days (Aerobic/F, Anaerobic/F) and 14 days (Myco/F) blood culture bottles is sufficient to prevent false-negative results.

Methods

We evaluated 1,244 blood bottles (344 patients) defined as negative by the BACTEC™ FX system. We also reviewed published cases and our own cases of bloodstream infection caused by Cryptococcus neoformans and simulated different scenarios, including different inoculation concentrations, bottle types, and clinical isolates.

Results

Two bottles (0.16%) were found to contain C. neoformans when subcultured and Gram stained. A 5-day protocol with Aerobic/F bottles was insufficient for the growth of C. neoformans in some cases, and C. neoformans grew better in Myco/F bottles than in Aerobic/F bottles.

Conclusion

Subculturing and Gram staining after a 5-day protocol were important for the detection of C. neoformans, and Myco/F bottles should be collected for the blood culture of C. neoformans.

Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods

Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.

Examining the Composition of the Oral Microbiota as a Tool to Identify Responders to Dietary Changes

BACKGROUND

The role of diet and nutrition in the prevention of oral diseases has recently gained increasing attention. Understanding the influence of diet on oral microbiota is essential for developing meaningful prevention approaches to oral diseases, and the identification of typical and atypical responders may contribute to this.

METHODS

We used data from an experimental clinical study in which 11 participants were exposed to different dietary regimens in five consecutive phases. To analyse the influence of additional nutritional components, we examined changes in bacterial concentrations measured by culture techniques compared to a run-in phase. A measure of correspondence between the mean and individual patterns of the bacterial composition is introduced.

RESULTS

The distance measures introduced showed clear differences between the subjects. In our data, two typical and three atypical responders appear to have been identified.

CONCLUSIONS

The proposed method is suitable to identify typical and atypical responders, even in small datasets. We recommend routinely performing such analyses.

The Past, Present, and Future of Kingella kingae Detection in Pediatric Osteoarthritis

As a result of the increasing use of improved detection methods, Kingella kingae, a Gram-negative component of the pediatric oropharyngeal microbiota, is increasingly appreciated as the prime etiology of septic arthritis, osteomyelitis, and spondylodiscitis in children aged 6 to 48 months. The medical literature was reviewed to summarize the laboratory methods required for detecting the organism. Kingella kingae is notoriously fastidious, and seeding skeletal system samples onto solid culture media usually fails to isolate it. Inoculation of synovial fluid aspirates and bone exudates into blood culture vials enhances Kingella kingae recovery by diluting detrimental factors in the specimen. The detection of the species has been further improved by nucleic acid amplification tests, especially by using species-specific primers targeting Kingella kingae's rtxA, groEL, and mdh genes in a real-time PCR platform. Although novel metagenomic next-generation technology performed in the patient's plasma sample (liquid biopsy) has not yet reached its full potential, improvements in the sensitivity and specificity of the method will probably make this approach the primary means of diagnosing Kingella kingae infections in the future.

Routine Use of Anaerobic Blood Culture Bottles for Specimens Collected from Adults and Children Enhances Microorganism Recovery and Improves Time to Positivity

The utility of anaerobic blood culture bottles remains controversial, especially for specimens from children. Data are limited on the inclusion of an anaerobic bottle as part of a blood culture "set" when using contemporary blood culture instruments and media. Here, we evaluated the clinical utility of anaerobic blood culture bottles (FN Plus) and aerobic bottles (FA Plus) for the BacT/Alert Virtuo blood culture system (bioMérieux). A total of 158,710 bottles collected between November 2018 and October 2019 were evaluated. There were 6,652 positive anaerobic bottles, of which 384 (5.8%) contained 403 obligate anaerobes. In patients <19 years old, there were 389 positive anaerobic bottles, with 15 (1.8%) containing 16 obligate anaerobes. If not for anaerobic bottles, all but 8 obligate anaerobes would have gone undetected. Furthermore, anaerobic bottles were advantageous for some facultative anaerobes. Staphylococcus aureus from anaerobic bottles demonstrated statistically significant increased recovery (1,992 anaerobic versus 1,901 aerobic bottles, P = 0.009) and faster mean time to positivity (1,138 versus 1,174 min, P = 0.027). Only 25 microorganisms had statistically significant improved recovery and/or faster time to positivity from aerobic versus anaerobic bottles, suggesting anaerobic bottles offer comparable growth for most species. Finally, if only an aerobic bottle had been collected, 2,027 fewer positive cultures would have been detected and 7,452 fewer isolates would have been reported, including cultures with S. aureus (413 isolates, 10.6% less), Pseudomonas aeruginosa (9 isolates, 3.1% less) and Escherichia coli (193 isolates, 14.0% less). Taken together, these findings support the practice of routinely including an anaerobic bottle for blood culture collection.

The diagnostic value of next-generation sequencing technology in sepsis

Objective

This study aims to assess the clinical utility of next-generation sequencing (NGS) in sepsis diagnosis.

Methods

A prospective study was conducted on patients with a high suspicion of sepsis by unknown pathogens from January 2017 to December 2021. Blood samples were taken from patients to perform NGS, blood culture (BC), leucocyte (WBC), procalcitonin (PCT), creatinine (CREA), Albumin (ALB) and C-reactive protein (CRP) tests.

Results

The feedback time for BC was 3~5 days for bacteria and 5~7 days for fungi, while the turnover time for NGS was only 24 h. The clinical diagnosis was considered the “gold standard”. 83 patients passed our inclusion criteria and were separated into two groups by clinical diagnosis. 62 met the clinical diagnosis criteria for sepsis and 21 were non-sepsis. The data from the two groups were retrospectively compared and analyzed. Of 62 sepsis in 83 patients, 8(9.64%) were diagnosed by both BC and NGS, 51 (61.45%) by NGS only, 1(1.20%) by BC and 2 (2.41%) by conventional testing only; PCT, CREA, CRP levels and the detection rate of NGS and BC were higher in the sepsis group than in the non-sepsis group, while ALB levels were lower (p&lt;0.05). The logistic regression results in our study revealed that NGS and ALB were independent prediction factors for sepsis (p&lt;0.05), the area under the receiver operating characteristic curve (AUC), sensitivity and specificity of NGS for diagnosing sepsis was 0.857, 95.16% and 76.19%, while ALB was 0.728, 58.06%, 80.95%, respectively. The combination’s sensitivity, specificity and AUC of NGS and ALB were 93.55%, 85.71% and 0.935, greater than that of Albumin or NGS only (both p&lt;0.05).

Conclusion

NGS can effectively and quickly identify pathogens, thereby emerges as a promising technology for sepsis diagnosis. Combination of NGS and ALB can be used for early screening and is more powerful than NGS or ALB only.

Plethora of Antibiotics Usage and Evaluation of Carbapenem Prescribing Pattern in Intensive Care Units: A Single-Center Experience of Malaysian Academic Hospital

Excessive antibiotic consumption is still common among critically ill patients admitted to intensive care units (ICU), especially during the coronavirus disease 2019 (COVID-19) period. Moreover, information regarding antimicrobial consumption among ICUs in South-East Asia remains scarce and limited. This study aims to determine antibiotics utilization in ICUs by measuring antibiotics consumption over the past six years (2016−2021) and specifically evaluating carbapenems prescribed in a COVID-19 ICU and a general intensive care unit (GICU) during the second year of the COVID-19 pandemic. (2) Methods: This is a retrospective cross-sectional observational analysis of antibiotics consumption and carbapenems prescriptions. Antibiotic utilization data were estimated using the WHO Defined Daily Doses (DDD). Carbapenems prescription information was extracted from the audits conducted by ward pharmacists. Patients who were prescribed carbapenems during their admission to COVID-19 ICU and GICU were included. Patients who passed away before being reviewed by the pharmacists were excluded. (3) Results: In general, antibiotics consumption increased markedly in the year 2021 when compared to previous years. Majority of carbapenems were prescribed empirically (86.8%). Comparing COVID-19 ICU and GICU, the reasons for empirical carbapenems therapy in COVID-19 ICU was predominantly for therapy escalation (64.7% COVID-19 ICU vs. 34% GICU, p < 0.001), whereas empirical prescription in GICU was for coverage of extended-spectrum beta-lactamases (ESBL) gram-negative bacteria (GNB) (45.3% GICU vs. 22.4% COVID-19 ICU, p = 0.005). Despite microbiological evidence, the empirical carbapenems were continued for a median (interquartile range (IQR)) of seven (5−8) days. This implies the need for a rapid diagnostic assay on direct specimens, together with comprehensive antimicrobial stewardship (AMS) discourse with intensivists to address this issue.

Clinical Significance of BD Bactec FX Blood Culture Incubation Beyond 96 Hours (4 Days)

Blood cultures (BC) for bacteria and yeast have traditionally been incubated for 5 days using modern instruments. Many organisms may grow sooner, and the need for the full 5-day incubation period has been questioned. This study evaluated the clinical significance of isolates recovered beyond 96 h. A retrospective chart review was conducted on all positive BC (+BC) performed via BD Bactec FX with >96 h of incubation from 5/2019 to 1/2022 at the UW Health University Hospital clinical microbiology laboratory. A total of 59,958 BC were performed; 6,031 (10%) were +BC. Of +BC, 104 (2%) demonstrated growth >96 h. The 104 cultures were from 89 patients and included 12 (12%) Staphylococcus aureus (1 MRSA), 9 (9%) yeast (8 Candida sp.), 8 (8%) Escherichia coli and 7 (7%) Enterococcus sp. (1 VRE) isolates. Fifty-six percent (n = 50) of the 89 +BC >96 h cases were clinically significant, and 26% (n = 13) resulted in antibiotic adjustments based on the +BC; 4 of these had previous positive cultures. Of the remaining 37 clinically significant +BC >96 h for which no antibiotic changes were made, 32 patients had previous positive cultures. The majority (98%) of BC bottles were positive before 96 h. For isolates that required >96 h, most (56%) were considered clinically significant, including S. aureus and E. coli cultures. Changes to antibiotic therapy were made in a minority (26%) of clinically significant cases. Based on these findings, under routine conditions, laboratories using BD Bactec FX should maintain a 120 h incubation period.

Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group

Bacteroides fragilis group (BFG) species are common members of the human microbiota that provide several benefits to healthy hosts, yet BFG are also the most common anaerobes isolated from human infections, including intra-abdominal infections, abscesses, and bloodstream infection. Compared to many other anaerobes associated with disease, members of the BFG are more likely to be resistant to commonly used antimicrobials, including penicillin (>90% resistant), carbapenems (2 to 20% resistant), and metronidazole (0.2 to 4% resistant). As a result, infection with BFG bacteria can be associated with poor clinical outcomes. Here, we discuss the role of BFG in human health and disease, proposed taxonomic reclassifications within the BFG, and updates in methods for species-level identification. The increasing availability of whole-genome sequencing (WGS) supports recent proposals that the BFG now span two families (Bacteroidaceae and "Tannerellaceae") and multiple genera (Bacteroides, Parabacteroides, and Phocaeicola) within the phylum Bacteroidota. While members of the BFG are often reported to "group" rather than "species" level in many clinical settings, new reports of species-specific trends in antimicrobial resistance profiles and improved resolution of identification tools support routine species-level reporting in clinical practice. Empirical therapy may not be adequate for treatment of serious infections with BFG, warranting susceptibility testing for serious infections. We summarize methods for antimicrobial susceptibility testing and resistance prediction for BFG, including broth microdilution, agar dilution, WGS, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We examine global trends in BFG antimicrobial resistance and review genomics of BFG, revealing insights into rapid activation and dissemination of numerous antimicrobial resistance mechanisms.

Evaluation of the EUCAST Rapid Antimicrobial Susceptibility Test for Enterobacterales-Containing Blood Cultures in China

Bloodstream infection (BSI) is defined by the presence of microbes in the bloodstream and has high mortality. Early antimicrobial therapy is key to treating BSI patients. Because of potential antimicrobial resistance, rapid evaluation for the most suitable antimicrobial therapy is important for appropriate treatment. In China, the current workflow of microbiological diagnosis in BSI involves blood culture, species identification, and antimicrobial susceptibility testing, which takes around 3 days. However, this delay could lead to worse symptoms. To rapidly and accurately assess antimicrobial susceptibility, in this study, we applied EUCAST rapid antimicrobial susceptibility testing (RAST) to determine the antimicrobial susceptibilities of the most frequently detected Enterobacterales sampled in China, including Escherichia coli and Klebsiella pneumoniae. Based on EUCAST guidelines, we evaluated its efficiencies with six commercially available antimicrobials, including imipenem (10 μg), meropenem (10 μg), ciprofloxacin (5 μg), levofloxacin (5 μg), amikacin (30 μg), and trimethoprim-sulfamethoxazole (1.25/23.75 μg), with bacterium-spiked blood cultures. In addition, we developed potential breakpoints for a recently introduced antimicrobial, 30/20 μg ceftazidime-avibactam, which has high potential for treating multidrug-resistant Enterobacterales. Our results showed that EUCAST RAST is a reliable method for rapidly determining the antimicrobial susceptibilities of BSI-causing bacteria in China, with an overall categorical agreement rate at 8 h of ≥90%. The breakpoints developed in this study can categorize the isolates sampled in this study with an accuracy of 93%. Results from our experiments can be applied to clinically determine the microbial susceptibility of BSI-causing bacteria within 8 h and benefit clinical diagnostics for BSI patients.

The Impact of Implementing the Virtuo Blood Culture System on the Characteristics and Management of Patients with Staphylococcus aureus Bacteremia

Persistent Staphylococcus aureus bacteremia (SAB) has been associated with increased mortality. Enhanced microbial detection with new blood culture technology may improve detection of S. aureus in patients with SAB. We performed a 24-month retrospective study of hospitalized adults with SAB and an infectious diseases consult comparing two time periods pre- (January to December 2018) and postimplementation (January to December 2019) in which the VersaTREK and BacT/Alert Virtuo blood culture systems were used, respectively. Measurements included SAB duration, time to positivity, source of bacteremia, antimicrobial therapy, and mortality. A total of 416 episodes of SAB occurred during the study period: 176 (42%) pre- and 240 (58%) postimplementation. Patients in both periods had similar clinical characteristics; however, patients in the postimplementation period were more likely to have intermediate (3 to 6 days; 23% versus 40%; P < 0.001) and prolonged SAB duration (>7 days; 4% versus 14%; P < 0.001). Combination antistaphylococcal therapy was more frequent postimplementation (6.3% pre- versus 15.8% postimplementation; P = 0.003), and the median time to source control was shorter (4 versus 2 days; P = 0.02). Median time to positivity for the index blood culture was shorter postimplementation (17.8 h pre- versus 13.3 h postimplementation; P < 0.001). There was no difference in 90-day all-cause readmissions (51% versus 44%; P = 0.11) or mortality (32% versus 32%; P = 0.95). An increased frequency of prolonged SAB with increased use of combination antistaphylococcal therapy was noted with implementation of a new blood culture system, likely secondary to the blood culture media; however, no differences on adverse outcomes were noted.

Unresolved issues in the epidemiology and diagnosis of bacteremia: an opinion paper

Bacteremia is an important cause of morbidity and mortality worldwide and, despite the diagnostic and therapeutic advances of the last decades, the evidence supporting many diagnostic aspects of bacteremia is scarce. Information on the epidemiological evolution of this entity is limited and many methodological aspects of blood culture collection and analysis are under discussion. Furthermore, the recommendations of the main scientific societies on many of these aspects are variable and, in many cases, have not been updated recently. In this scenario, we have arranged a series of questions on different aspects of bacteremia and reviewed the literature trying to find proper answers for them. We offer our opinion on the topics where the evidence was weak. The topics covered include epidemiological aspects of bacteremia, indications for blood culture extraction, methods for obtaining and incubating samples, or ways of transmitting results from the microbiology laboratory. We do not intend to summarize the current clinical practice guidelines, nor will we deal with the therapeutic management of this entity. The aim of this paper is to review the current perspective on the diagnosis of bacteremia with a critical approach, to point out the gaps in the literature, to offer the opinion of a team dedicated to infectious diseases and clinical microbiology, and to identify some areas of knowledge on which future studies should focus.

Gram-negative endocarditis: disease presentation, diagnosis and treatment

PURPOSE OF REVIEW

Gram-negative bacilli (GNB) cause between 1% and 10% of infective endocarditis (IE). Most episodes are caused by microorganisms of the Haemophilus spp., Aggregatibacter spp. Cardiobacterium spp., Eikenella spp., and Kingella spp (HACEK) group. The frequency of IE caused by non-HACEK (GNB-IE) has increased in recent years. Uncertainties persist regarding its best medical treatment and the appropriateness and timing of surgical treatment. In addition, there are new drugs with activity against multiresistant microorganisms, of which there is little experience in this disease. We review this topic by answering the most frequently asked questions that arise among our colleagues.

RECENT FINDINGS

HACEK microorganisms cause 1.5-2% of IE with only a 2% mortality. In contrast, non-HACEK GNB-IE accounts for 2.5-3% of all IE cases and is associated with nosocomial acquisition, advanced age, solid organ transplantation and 20-30% mortality. Drug addiction is important in areas with epidemic opioid abuse.

SUMMARY

The frequency of IE caused by GNB has been modified in recent years. HACEK episodes are no longer treated with ampicillin and aminoglycosides. In non-HACEK GNB-IE, combination therapy with a beta-lactam and a quinolone or aminoglycoside is recommended. The surgical indication and its value are evident in many patients. Management should rely on a collaborative group with experience in this disease.

Real World Evaluation of the Impact of Implementation of the VIRTUO Blood Culture System in a Tertiary Care Hospital

The bioMerieux BACT/ALERT VIRTUO (VIRTUO) blood culture system used in combination with resin-containing media may enhance the growth of microorganisms. Our objective was to assess the impact of transitioning to the VIRTUO system in comparison to the VersaTREK blood culture system at a tertiary care medical center. We retrospectively reviewed all blood cultures performed at a 1250-bed academic medical center between January-December 2018 (VersaTREK) and January-December 2019 (VIRTUO). Blood culture positivity rates and contamination rates were compared pre- versus post-VIRTUO implementation. Of 101,438 blood cultures performed during the study period, 48,839 (48.1%) were processed pre-implementation and 52,599 (51.9%) post-implementation. The blood culture positivity rate increased from 8.1% pre-implementation to 11.7% post-implementation (p<0.001). Staphylococcus aureus was the most frequently isolated species in both time periods and had higher recovery rate post-implementation (1.5% of all blood cultures obtained pre- vs. 3.4% post-implementation, p<0.001). A higher recovery rate in the post-implementation period was also noted for coagulase-negative staphylococci (1.9% pre- vs. 2.7% post-implementation, p<0.001), as well as modest but statistically significant changes for E. coli (0.8% vs. 1.0%, p<0.001), K. pneumoniae (0.4% vs. 0.5%, p=0.005) and Candida albicans. (0.1% vs. 0.2%, p=0.038). The inpatient blood culture contamination rate was higher post-implementation (1.5% pre- vs. 1.9% post-implementation, p<0.001). The VIRTUO blood culture system was associated with a higher observed proportion of positive blood cultures compared to the previous VersaTREK system. Future studies are needed to assess whether an increased rate of positive blood cultures is associated with changes in clinical outcomes.

Comparison of Microorganism Detection and Time to Positivity in Pediatric and Standard Media from Three Major Commercial Continuously Monitored Blood Culture Systems

New blood culture instrumentation and medium formulations have led to improved time to positivity (TTP) for positive blood cultures. Data regarding the necessity of pediatric blood culture bottles with contemporary blood culture systems are sparse. We compared performance of three commercial blood culture systems, evaluating impact of blood volumes in standard and pediatric blood culture media across systems. Simulated blood cultures with packed red blood cells (PRBCs) and three Gram-positive, four Gram-negative, and one anaerobic organism (final concentrations ranging from 0.5 to 19 CFU/ml blood) on the Virtuo, VersaTrek, and Bactec FX instruments were evaluated with FAN Plus, Redox, and Bactec Plus media, respectively. For each medium/instrument/organism combination, 1-, 3-, 5-, and 10-ml blood volumes were evaluated in triplicate. Detection rate was not affected by blood volume. Aerobic organisms that demonstrated variable rates of detection were Kingella kingae, Haemophilus influenzae, and Neisseria meningitidis. Bacteroides fragilis was detected in 83%, 100%, and 100% of Virtuo, VersaTrek, and Bactec anaerobic bottles, respectively. The average TTP of standard medium for aerobic organisms detected on Virtuo was decreased compared to those for VersaTrek (-2.3 h) and Bactec (-4.9 h). Compared to standard medium, detection rate and TTP were unchanged on Virtuo, while TTP was reduced with pediatric medium for 2/8 organisms tested on Bactec and 7/8 organisms on VersaTrek, illustrating the potential benefit of pediatric medium on VersaTrek or Bactec when low blood volumes (<5 ml) are collected. These results demonstrate that TTP is decreased on the Virtuo compared to VersaTrek and Bactec for many microorganisms associated with bloodstream infection (BSI) but may have species-specific limitations.