Diagnostic performance and clinical impact of blood metagenomic next-generation sequencing in ICU patients suspected monomicrobial and polymicrobial bloodstream infections

Early Diagnosis of Bloodstream Infections Using Serum Metabolomic Analysis

BACKGROUND

Bloodstream infections (BSIs) pose a great challenge to treating patients, especially those with underlying diseases, such as immunodeficiency diseases. Early diagnosis helps to direct precise empirical antibiotic administration and proper clinical management. This study carried out a serum metabolomic analysis using blood specimens sampled from patients with a suspected infection whose routine culture results were later demonstrated to be positive.

METHODS

A liquid chromatograph-mass spectrometry-based metabolomic analysis was carried out to profile the BSI serum samples. The serum metabolomics data could be used to successfully differentiate BSIs from non-BSIs.

RESULTS

The major classes of the isolated pathogens (e.g., Gram-positive and Gram-negative bacteria) could be differentiated using our optimized statistical algorithms. In addition, by using different machine-learning algorithms, the isolated pathogens could also be classified at the species levels (e.g., Escherichia coli and Klebsiella pneumoniae) or according to their specific antibiotic-resistant phenotypes (e.g., extended-spectrum β-lactamase-producing and non-producing phenotypes) if needed.

CONCLUSIONS

This study provides an early diagnosis method that could be an alternative to the traditional time-consuming culture process to identify BSIs. Moreover, this metabolomics strategy was less affected by several risk factors (e.g., antibiotics administration) that could produce false culture results.

Gram-Negative Bloodstream Infections in a Medical Intensive Care Unit: Epidemiology, Antibiotic Susceptibilities, and Risk Factors for in-Hospital Death

Purpose

Gram-negative bloodstream infection (GNBI) poses a serious threat to critically ill patients. This retrospective study aimed to uncover drug resistance of pathogens and the GNBI effect on in-hospital death and distinguish death risk factors in a medical intensive care unit (ICU).

Patients and Methods

A retrospective study of all GNBI patients in the medical ICU of the Third Xiangya Hospital over 9 nine years was conducted. Blood samples were performed by a BACTEC 9240 system, MALDI-TOF MS, Bruker and Vitek-2 system. Logistic regression was used for analyzing risk factors for death.

Results

Seventy-five episodes of GNBI developed in 68 (1.4%) out of 4954 patients over a span of 9 years. The most frequently isolated bacterium was Klebsiella pneumoniae, with the lungs as the predominant source of GNBI. The resistance rate of Gram-negative bacteria to polymyxin B was 11.6% after excluding those intrinsically resistant non-fermentative bacteria. All Enterobacter spp. were susceptible to ceftazidime/avibactam. Thirty-three (48.5%) patients underwent inappropriate empirical antibiotic treatment and 48 (70.6%) patients died during the hospitalization. Multivariate logistic regression analysis identified that lymphocyte count at GNBI onset ≤0.5×109/L, invasive mechanical ventilation, and septic shock were related to in-hospital death. Body mass index ≥23 and appropriate empirical antibiotic use after GNBI were negatively associated with in-hospital death.

Conclusion

GNBI was a frequent complication among patients in the medical ICU. This study underscored the presence of diverse factors that either heightened or attenuated the risk of in-hospital death.

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.

Rapid and precise identification of cervicothoracic necrotizing fasciitis caused by Prevotella and Streptococcus constellatus by using Nanopore sequencing technology: a case report

Introduction

Cervicothoracic necrotizing fasciitis (CNF) is one form of necrotizing soft-tissue infections, which could lead to patient demise during short course. Therefore, early recognition and immediate treatment contribute to promising prognosis of patients.

Case presentation

A 58-year-old diabetic patient presented with a sore throat and progressive irritation of the neck and chest for 4 days. The initial diagnosis was considered to be soft-tissue infection and the clinician gave empirical anti-infectious medication for expectant treatment. During the course of disease, surgical incision was performed to relieve suffocation and shortness of breath. The drainage fluids were detected with microbiological culture and molecular sequencing. Nanopore sequencing technology (NST) helped to identify the coinfection of Streptococcus constellatus and Prevotella spp., which was not recognized during the original period of 15 days. The precise identification of pathogen supported to guide the pharmacologic treatment with meropenem and linezolid. Ultimately, combined with the surgical observation and post-surgical pathological examination, the patient was diagnosed as CNF, which could be much more acute and serious than normal soft-tissue infections. The patient has been successfully treated with prompt antimicrobial medication and appropriate surgical debridement.

Conclusion

This case presented a CNF patient with type 2 diabetes, successfully recovered after prompt microbial detection, precise anti-infectious treatment, and appropriate surgical intervention. It highlights the importance of recognizing pathogen by applying rapid microbiological detection, including NST, in acute and serious infectious disease.

Diagnostic performance of metagenomic sequencing in patients with suspected infection: a large-scale retrospective study

Background

Metagenomic next-generation sequencing (mNGS) has been widely reported to identify pathogens in infectious diseases (IDs). In this work, we intended to investigate the diagnostic value and clinical acceptance of paired-samples mNGS as compared to the culture method.

Methods

A total of 361 patients with suspected infection were retrospectively included. With reference to the clinical diagnosis, we compared the diagnostic performance and clinical acceptance in pathogen detection between mNGS and culture tests. Moreover, the pathogen concordance of paired blood and respiratory tract (RT) samples in mNGS assay was investigated.

Results

Among 511 samples, 62.04% were shown to be pathogen positive by mNGS, and that for clinical diagnosis was 51.86% (265/511). When compared to culture assay (n = 428), mNGS had a significantly higher positivity rate (51.87% vs. 33.18%). With reference to the clinical diagnosis, the sensitivity of mNGS outperformed that of culture (89.08% vs. 56.72%). Importantly, mNGS exhibited a clinically accepted rate significantly superior to that of culture. In addition, the mNGS result from 53 paired blood and RT samples showed that most pairs were pathogen positive by both blood and RT, with pathogens largely being partially matched.

Conclusion

Through this large-scale study, we further illustrated that mNGS had a clinically accepted rate and sensitivity superior to those of the traditional culture method in diagnosing infections. Moreover, blood and paired RT samples mostly shared partial-matched positive pathogens, especially for pathogens with abundant read numbers in RT, indicating that both blood and RT mNGS can aid the identification of pathogens for respiratory system infection.

Using cerebrospinal fluid nanopore sequencing assay to diagnose tuberculous meningitis: a retrospective cohort study in China

OBJECTIVE

This study aimed to evaluate the efficiency of nanopore sequencing for the early diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid and compared it with acid-fast bacilli (AFB) smear, mycobacterial growth indicator tube culture and Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF).

DESIGN

Single-centre retrospective study.

SETTING

The Tuberculosis Diagnosis and Treatment Center of Zhejiang Chinese and Western Medicine Integrated Hospital.

PARTICIPANTS

We enrolled 64 adult patients with presumptive TBM admitted to our hospital from August 2021 to August 2023.

METHODS

We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of AFB smear, culture, Xpert MTB/RIF and nanopore sequencing to evaluate their diagnostic efficacy compared with a composite reference standard for TBM.

RESULTS

Among these 64 patients, all tested negative for TBM by AFB smear. The sensitivity, specificity, PPV and NPV were 11.11%, 100%, 100% and 32.2% for culture, 13.33%, 100%, 100% and 2.76% for Xpert MTB/RIF, and 77.78%, 100%, 100% and 65.52% for nanopore sequencing, respectively.

CONCLUSION

The diagnostic accuracy of the nanopore sequencing test was significantly higher than that of conventional testing methods used to detect TBM.

Antimicrobial Tolerance in Cross-Kingdom Dual-Species Biofilms Formed by Fungi and Bacteria

Candida albicans, the most common pathogenic fungus, can form biofilms on the surface of medical devices and often causes bloodstream infections. Biofilms have a complex structure composed of microorganisms and a surrounding extracellular matrix. Biofilms are difficult to treat because they are resistant to antifungal drugs and the host environment. Nearly one in four patients with candidemia have a polymicrobial infection. These polymicrobial biofilms, especially those comprising cross-kingdom species of fungi and bacteria, can lead to long hospital stays and high mortality rates. This review outlines the unique interactions of dual-species biofilms with Candida albicans and the clinically important bacteria Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli.

Performance of next-generation sequencing for diagnosis of blood infections by Klebsiella pneumoniae

Objective

Klebsiella pneumoniae (Kp) bloodstream infections (BSI) can be a life-threatening opportunistic infection. We aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for Kp BSI.

Methods

We retrospectively analyzed 72 patients suspected with bloodstream infection and mNGS Kp positive in peripheral blood, who were hospitalized in our hospital from January 2022 to January 2023. Clinical data and laboratory parameters were collected. All patients had blood drawn and other samples for blood mNGS, blood cultures (BC) and other cultures (OC). The accuracy of mNGS results was analyzed according to infection site, clinical indicators, therapeutic effect and routine culture results. The detection of pathogenic microorganisms by blood mNGS and routine culture was compared.

Results

Among 72 infection patients, 29 cases (40.28%) were BC positive, 43 cases (59.72%) were other culture (OC) positive, 16 cases (22.22%) were both BC and OC positive, 56 cases were positive for both mNGS and routine culture. Among the 56 double-positive cases, mNGS and conventional cultures were completely consistent in 27 cases, partially consistent in 15 cases, and completely inconsistent in 14 cases. Using the clinical diagnosis as the reference standard, There were 51 cases consistent with the results of mNGS with Kp BSI, the clinical consistency was 70.83% (51/72). The coincidence rate of mNGS and clinical diagnosis was higher than that of BC (54.17%, 39/72), indicating a statistically significant difference between the two methods (P<0.01).

Conclusions

Current evidence indicates that mNGS exhibits excellent accuracy for the diagnosis of Kp BSI. Although it cannot replace blood culture detection technology, it can be used as a supplement to provide stronger diagnostic capabilities for BSI and optimize treatment.

Evaluation of Different Blood Culture Bottles for the Diagnosis of Bloodstream Infections in Patients with HIV

INTRODUCTION

Bloodstream infection (BSI) is a significant factor contributing to hospitalization and high mortality rates among human immunodeficiency virus(HIV)-positive patients. Therefore, the timely detection of this condition is of utmost importance. Blood culture is considered the gold standard for diagnosing BSIs. Currently, BD BACTEC™ Plus Aerobic/F culture bottles and the BD BACTEC™ Myco/F Lytic culture bottles can be used for blood culture. This study aimed to evaluate the efficacy of two different types of culture bottles in diagnosing BSIs in patients with HIV.

METHODS

A retrospective analysis was conducted on HIV-positive patients hospitalized in the Infection Department of Wenzhou Central Hospital between July 2019 and October 2021. A total of 246 pairs of blood samples were included, consisting of an aerobic culture vial and a Myco/F culture vial. Blood culture results and clinical diagnosis were utilized to identify the presence of BSI.

RESULTS

Out of 246 cases, 84 cases had positive blood cultures. Fungal BSIs, particularly Talaromyces marneffei BSIs, were the most prevalent among patients with HIV. The positive rate of Myco/F culture bottles (89.29%) was significantly higher compared with aerobic culture bottles (69.05%; P = 0.001). In the diagnosis of fungal BSIs, the positive rate of Myco/F culture bottles was 88.57%, which was significantly higher than that of aerobic culture bottles (72.86%; P = 0.018). The Myco/F culture bottle has more advantages in diagnosing Talaromyces marneffei BSIs (P=0.028). In addition, mycobacteria were exclusively detected in Myco/F culture bottles.

CONCLUSIONS

Fungal BSIs are the predominant type of infections in HIV-positive patients. Myco/F culture bottles exhibit noteworthy attributes of high positive rate in diagnosing HIV combined with BSI. These advantages are conducive to obtaining accurate culture results and minimizing missed diagnoses.