Optimal specimen type for accurate diagnosis of infectious peripheral pulmonary lesions by mNGS

Metagenomic next-generation sequencing for etiological diagnosis of an unexpected rabies case with unclear exposure history

BACKGROUND

Rabies is an acute and lethal zoonotic disease caused by the rabies virus (RABV). After onset, there are no effective drugs or treatment methods.

CASE PRESENTATION

A 49-year-old female from Hefei, Anhui Province, China, presented to a local hospital with fever, pruritus, chest distress, and shortness of breath. During the consultation, the patient exhibited agitation and was later admitted to the intensive care unit (ICU) in the local hospital for endotracheal intubation and mechanical ventilation due to worsened agitation and dyspnea. Cerebrospinal fluid (CSF) and blood samples were collected and pathogenic microorganism identification was performed by culture and mNGS. However, all results were negative. In addition, the patient did not display typical rabies-specific symptoms such as aerophobia, hydrophobia or photophobia from onset to admission. Subsequently, saliva samples were collected for mNGS detection following consultation with experts at our hospital. Nucleic acid sequences uniquely aligned to the rabies virus (RABV) were identified in these samples. The result was further confirmed by local Center for Disease Control and Prevention (CDC) through RT-qPCR which detected part of the N gene of RABV in the saliva sample. The patient was then transferred to the ICU for isolation. Unfortunately, the patient died on the 10th day of admission due to multiple organ failure. The detection of human rabies virus IgG antibodies reported positive during the advanced stage of the disease during the hospitalization. We consistently verified with the patient's family member that there was no clear history of animal bites and no history of RABV vaccination. Furthermore, we performed phylogenetic analysis of partial L and G gene sequences of RABV obtained by mNGS (designated HFG23-L and HFG23-G, respectively), the results showed that both HFG23-L and HFG23-G belonged to the China I lineage, and shared 99.7% similarity with the Fengtai strain isolated from dogs in Beijing.

CONCLUSIONS

The identification of unique RABV sequence through mNGS in the patient's saliva sample suggested that mNGS could serve as a valuable screening tool for the etiological diagnosis of rabies, especially when timely laboratory testing was unavailable or when patients lacked non-specific prodromal symptom and clear exposure history.

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.

Bronchoalveolar lavage fluid and lung biopsy tissue metagenomic next-generation sequencing in the diagnosis of pulmonary cryptococcosis

Objective

To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens.

Methods

In this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. Individuals were classified into PC and non-PC groups according to the diagnostic criteria for PC, and conventional fungal cultures were performed. A serum/BALF cryptococcal antigen (CrAg) test was performed in some patients with PC. The diagnostic efficiencies of three methods for PC (mNGS, conventional culture, and CrAg) were compared. Additionally, two mNGS methods were used in this study: original mNGS (OmNGS, testing time from January 2021 to December 2022) and modified mNGS (MmNGS, testing time from January to December 2023). The diagnostic efficiency of the two mNGS methods on PC was simultaneously compared.

Results

Among the 321 patients, 23 (7.2%) had PC and 298 (92.8%) did not. Compared with the composite reference standard for PC diagnosis, the sensitivity, specificity, and accuracy of mNGS for PC were 78.3% (95% confidence interval [CI], 55.8%-91.7%), 98.7% (95% CI, 96.4%-99.6%), and 97.2% (95% CI, 94.7%-98.7%), respectively. The sensitivity of mNGS was similar to that of CrAg (80.0%, 12/15) (P > 0.05). The diagnostic sensitivity of both mNGS and CrAg was higher than that of conventional culture (35.0%, 7/20) (P = 0.006, P = 0.016), and the combined detection of mNGS and CrAg further improved the diagnostic sensitivity of PC (93.3%, 14/15). The area under the receiver operating characteristic curve of mNGS was superior to that of conventional culture (0.885 vs. 0.675). In addition, the diagnostic sensitivity of PC was higher than that of OmNGS (P = 0.046).

Conclusion

The sensitivity of mNGS is better than that of conventional culture. The combination of mNGS and CrAg improves the testing sensitivity of Cryptococcus. MmNGS could further improve the detection of Cryptococcus. Conventional PC detection methods are indispensable and mNGS can be used as a rapid and accurate auxiliary diagnostic method for PC.

Disseminated nocardiosis caused by Nocardia otitidiscaviarum-A case report

In this article we report a case of disseminated nocardiosis caused by Nocardia otitidiscaviarum in an immunocompetent patient with chronic obstructive pulmonary disease (COPD) who complained of a cough, followed by skin and intracranial lesions. On metagenomic next-generation sequencing (mNGS) technology of respiratory samples (bronchoalveolar lavage fluid, BALF) Nocardia otitidiscaviarum was identified. The patient was treated with therapy combined with a low dose of TMP-SMX and imipenem cilastatin sodium and had a favorable outcome. The timely diagnosis of Nocardia with the help of mNGS technology and early rational treatment of TMP-SMX can help improve the prognosis.

A single-center, retrospective study of hospitalized patients with lower respiratory tract infections: clinical assessment of metagenomic next-generation sequencing and identification of risk factors in patients

INTRODUCTION

Lower respiratory tract infections(LRTIs) in adults are complicated by diverse pathogens that challenge traditional detection methods, which are often slow and insensitive. Metagenomic next-generation sequencing (mNGS) offers a comprehensive, high-throughput, and unbiased approach to pathogen identification. This retrospective study evaluates the diagnostic efficacy of mNGS compared to conventional microbiological testing (CMT) in LRTIs, aiming to enhance detection accuracy and enable early clinical prediction.

METHODS

In our retrospective single-center analysis, 451 patients with suspected LRTIs underwent mNGS testing from July 2020 to July 2023. We assessed the pathogen spectrum and compared the diagnostic efficacy of mNGS to CMT, with clinical comprehensive diagnosis serving as the reference standard. The study analyzed mNGS performance in lung tissue biopsies and bronchoalveolar lavage fluid (BALF) from cases suspected of lung infection. Patients were stratified into two groups based on clinical outcomes (improvement or mortality), and we compared clinical data and conventional laboratory indices between groups. A predictive model and nomogram for the prognosis of LRTIs were constructed using univariate followed by multivariate logistic regression, with model predictive accuracy evaluated by the area under the ROC curve (AUC).

RESULTS

(1) Comparative Analysis of mNGS versus CMT: In a comprehensive analysis of 510 specimens, where 59 cases were concurrently collected from lung tissue biopsies and BALF, the study highlights the diagnostic superiority of mNGS over CMT. Specifically, mNGS demonstrated significantly higher sensitivity and specificity in BALF samples (82.86% vs. 44.42% and 52.00% vs. 21.05%, respectively, p < 0.001) alongside greater positive and negative predictive values (96.71% vs. 79.55% and 15.12% vs. 5.19%, respectively, p < 0.01). Additionally, when comparing simultaneous testing of lung tissue biopsies and BALF, mNGS showed enhanced sensitivity in BALF (84.21% vs. 57.41%), whereas lung tissues offered higher specificity (80.00% vs. 50.00%). (2) Analysis of Infectious Species in Patients from This Study: The study also notes a concerning incidence of lung abscesses and identifies Epstein-Barr virus (EBV), Fusobacterium nucleatum, Mycoplasma pneumoniae, Chlamydia psittaci, and Haemophilus influenzae as the most common pathogens, with Klebsiella pneumoniae emerging as the predominant bacterial culprit. Among herpes viruses, EBV and herpes virus 7 (HHV-7) were most frequently detected, with HHV-7 more prevalent in immunocompromised individuals. (3) Risk Factors for Adverse Prognosis and a Mortality Risk Prediction Model in Patients with LRTIs: We identified key risk factors for poor prognosis in lower respiratory tract infection patients, with significant findings including delayed time to mNGS testing, low lymphocyte percentage, presence of chronic lung disease, multiple comorbidities, false-negative CMT results, and positive herpesvirus affecting patient outcomes. We also developed a nomogram model with good consistency and high accuracy (AUC of 0.825) for predicting mortality risk in these patients, offering a valuable clinical tool for assessing prognosis.

CONCLUSION

The study underscores mNGS as a superior tool for lower respiratory tract infection diagnosis, exhibiting higher sensitivity and specificity than traditional methods.

Application of metagenomic next-generation sequencing in the clinical diagnosis of infectious diseases after allo-HSCT: a single-center analysis

BACKGROUND

We investigated the value of metagenomic next-generation sequencing (mNGS) in diagnosing infectious diseases in patients receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT).

METHODS

Fifty-four patients who had fever following allo-HSCT from October 2019 to February 2022 were enrolled. Conventional microbiological tests (CMTs) and mNGS, along with imaging and clinical manifestations, were used to diagnose infection following allo-HSCT. The clinical diagnostic value of mNGS was evaluated.

RESULTS

A total of 61 mNGS tests were performed, resulting in the diagnosis of 46 cases of infectious diseases. Among these cases, there were 22 cases of viral infection, 13 cases of fungal infection, and 11 cases of bacterial infection. Moreover, 27 cases (58.7%) were classified as bloodstream infections, 15 (32.6%) as respiratory infections, 2 (4.3%) as digestive system infections, and 2 (4.3%) as central nervous system infections. Additionally, there were 8 cases with non-infectious diseases (8/54, 14.81%), including 2 cases of interstitial pneumonia, 2 cases of bronchiolitis obliterans, 2 cases of engraftment syndrome, and 2 cases of acute graft-versus-host disease. The positive detection rates of mNGS and CMT were 88.9% and 33.3%, respectively, with significant differences (P < 0.001). The sensitivity of mNGS was 97.82%, the specificity was 25%, the positive predictive value was 93.75%, and the negative predictive value was 50%. Following treatment, 51 patients showed improvement, and 3 cases succumbed to multidrug-resistant bacterial infections.

CONCLUSIONS

mNGS plays an important role in the early clinical diagnosis of infectious diseases after allo-HSCT, which is not affected by immunosuppression status, empiric antibiotic therapy, and multi-microbial mixed infection.

Clinical and diagnostic values of metagenomic next-generation sequencing for infection in hematology patients: a systematic review and meta-analysis

OBJECTIVES

This meta-analysis focused on systematically assessing the clinical value of mNGS for infection in hematology patients.

METHODS

We searched for studies that assessed the clinical value of mNGS for infection in hematology patients published in Embase, PubMed, Cochrane Library, Web of Science, and CNKI from inception to August 30, 2023. We compared the detection positive rate of pathogen for mNGS and conventional microbiological tests (CMTs). The diagnostic metrics, antibiotic adjustment rate and treatment effective rate were combined.

RESULTS

Twenty-two studies with 2325 patients were included. The positive rate of mNGS was higher than that of CMT (blood: 71.64% vs. 24.82%, P < 0.001; BALF: 89.86% vs. 20.78%, P < 0.001; mixed specimens: 82.02% vs. 28.12%, P < 0.001). The pooled sensitivity and specificity were 87% (95%CI: 81-91%) and 59% (95%CI: 43-72%), respectively. The reference standard/neutropenia and research type/reference standard may be sources of heterogeneity in sensitivity and specificity, respectively. The pooled antibiotic adjustment rate according to mNGS was 49.6% (95% CI: 41.8-57.4%), and the pooled effective rate was 80.9% (95% CI: 62.4-99.3%).

CONCLUSION

mNGS has high positive detection rates in hematology patients. mNGS can guide clinical antibiotic adjustments and improve prognosis, especially in China.

A case report of diagnosis of cat-scratch disease using metagenomic next-generation sequencing

Cat-scratch disease (CSD) is an anthropozoonotic infection caused by Bartonella henselae, and it is one of the most common causes of lymph node infections in children and adolescents. B. henselae, belonging to the genus Bartonella, is a common human pathogen of human beings. CSD commonly develops as a result of cat scratches and bites or when injured skin comes into contact with cat saliva. The manifestation of CSD clinically differs for each patient based on their immune system. Individuals who have healthy immune systems generally manifest minimal clinical symptoms and do not necessitate any form of treatment. However, patients who have hypo-immunity require prompt medical attention due to the potential manifestation of severe symptoms that affect multiple systems of the body. Long latency and atypical clinical manifestations are characteristics of CSD. Bartonella isolation and identification are challenging procedures that require specialized equipment. There is no gold standard method for CSD diagnosis, and misdiagnosis and missed diagnosis rates are typically high. We present the case of a middle-aged male patient who developed fever, chills, anal distension, dizziness, and muscle pain for 10 days. The patient had a documented history of cat bites 1 month prior to the onset of symptoms. Following admission, he underwent an examination to determine superficial lymphadenopathy and hypoimmunity. Additionally, he had a fever during the disease. As the patient refused a needle biopsy of lymph nodes, metagenomic next-generation sequencing (mNGS) was employed and B. henselae was detected in the peripheral blood. The patient was diagnosed with CSD and treated with a combination of azithromycin and doxycycline. The fever symptoms were alleviated, and the patient was ultimately discharged. As a result of this case, we suggest that mNGS be used as a crucial supplementary diagnostic tool for individuals with compromised immune systems who may have CSD, especially when conventional diagnostic methods are inconclusive.

Joint application of metagenomic next-generation sequencing and histopathological examination for the diagnosis of pulmonary infectious disease

IMPORTANCE

The diagnosis of some pulmonary infectious diseases and their pathogens is very difficult. A more precise diagnosis of pulmonary infectious diseases can help clinicians use proper antibiotics as well as reduce the development of drug-resistant bacteria. In this study, we performed both mNGS and pathology on lung puncture biopsy tissue from patients and found that combined mNGS and histopathology testing was significantly more effective than histopathology testing alone in detecting infectious diseases and identifying infectious diseases. In addition, the combined approach improves the detection rate of pathogenic microorganisms in infectious diseases and can be used to guide precision clinical treatment.

Clinical application of amplification-based versus amplification-free metagenomic next-generation sequencing test in infectious diseases

Background

Recently, metagenomic next-generation sequencing (mNGS) has been used in the diagnosis of infectious diseases (IDs) as an emerging and powerful tool. However, whether the complicated methodological variation in mNGS detections makes a difference in their clinical performance is still unknown. Here we conducted a method study on the clinical application of mNGS tests in the DNA detection of IDs.

Methods

We analyzed the effect of several potential factors in the whole process of mNGS for DNA detection on microorganism identification in 98 samples of suspected ID patients by amplification-based mNGS. The amplification-based and amplification-free mNGS tests were successfully performed in 41 samples. Then we compared the clinical application of the two mNGS methods in the DNA detection of IDs.

Results

We found that a higher concentration of extracted nucleic acid was more conducive to detecting microorganisms. Other potential factors, such as read depth and proportion of human reads, might not be attributed to microorganism identification. The concordance rate of amplification-based and amplification-free mNGS results was 80.5% (33/41) in the patients with suspected IDs. Amplification-based mNGS showed approximately 16.7% higher sensitivity than amplification-free mNGS. However, 4 cases with causative pathogens only detected by amplification-based mNGS were finally proved false-positive. In addition, empirical antibiotic treatments were adjusted in 18 patients following mNGS testing with unexpected pathogens.

Conclusions

Amplification-based and amplification-free mNGS tests showed their specific advantages and disadvantages in the diagnosis of IDs. The clinical application of mNGS still needs more exploration from a methodological perspective. With advanced technology and standardized procedure, mNGS will play a promising role in the diagnosis of IDs and help guide the use of antibiotics.

Analysis of the utility of transbronchial lung biopsy culture under endobronchial ultrasonography with a guide-sheath

Transbronchial lung biopsy (TBLB) culture is not common in clinical practice, and TBLB culture for patients with mycobacterial disease provide limited value because the diagnostic accuracy of TBLB culture is very low. Recently, bronchoscopic devices have been further developed, such as endobronchial ultrasonography with a guide-sheath (EBUS-GS). Therefore, this study investigated the utility of TBLB culture obtained by using EBUS-GS compared to washing cultures. A total of 31 patients who underwent TBLB culture by using EBUS-GS (GS-TBLB) were collected retrospectively at Fukujuji Hospital from January 2018 to December 2022. The diagnostic accuracies of GS-TBLB culture and bronchial and device washing cultures (namely, washing culture) were compared. The patients comprised 13 individuals with nontuberculous mycobacteriosis, 7 with pulmonary aspergillosis, 6 with lung abscess, and 5 with pulmonary tuberculosis. The diagnostic accuracy of GS-TBLB culture was lower to that of TBLB culture than those of washing culture (n = 11 [35.5%] vs. n = 20 [64.5%], p = 0.016), and there was only one patient with positive GS-TBLB culture results and negative washing culture results. Comparing between patients with mycobacteria and non-mycobacteria, GS-TBLB culture positivity were no significant difference between patients with mycobacteria and non-mycobacteria (n = 6 [33.3%] vs. n = 5 [38.5%], p = 1.000), however, patients with mycobacteria diagnosed by washing culture more than those with non-mycobacteria (n = 15 [83.3%] vs. n = 5 [38.5%], p = 0.021). Our results demonstrate that the utility of TBLB culture for the diagnosis of pulmonary infections might provide limited value even if EBUS-GS is performed and lung tissue is successfully obtained.

High specificity of metagenomic next-generation sequencing using protected bronchial brushing sample in diagnosing pneumonia in children

BACKGROUND

Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. The low detection efficiency of conventional methods and low specificity using respiratory samples seriously hindered the accurate detection of pathogens.

METHODS

In this study, we retrospectively enrolled 1,032 children to evaluate the performance of metagenomics next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) sample and protected bronchial brushing (BB) sample in diagnosing pneumonia in children. In addition, conventional tests (CTs) were also performed.

RESULTS

The specificity of BB mNGS [67.3% (95% CI 58.6%-75.9%)] was significantly higher than that of BALF mNGS [38.5% (95% CI 12.0%-64.9%)]. The total coincidence rate of BB mNGS [77.6% (95% CI 74.8%-80.5%)] was slightly higher than that of BALF mNGS [76.5% (95% CI 68.8%-84.1%)] and CTs [38.5% (95% CI 35.2%-41.9%)]. During the epidemics of Mycoplasma pneumoniae, the detection rate of M. pneumoniae in the >6-year group (81.8%) was higher than that in the 3-6-year (78.9%) and <3-year groups (21.5%). The highest detection rates of bacteria, fungi, and viruses were found in the <3-year, >6-year, and 3-6-year groups, respectively. mNGS detection should be performed at the duration of 5-7 days after the start of continuous anti-microbial therapy or at the duration of 6-9 days from onset to mNGS test.

CONCLUSIONS

This is the first report to evaluate the performance of BB mNGS in diagnosing pulmonary infections in children on a large scale. Based on our findings, extensive application of BB mNGS could be expected.

Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome

BACKGROUND

Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation sequencing (mNGS) technology to identify and classify pathogens.

RESULTS

This study enrolled 75 patients with AIDS and suspected pulmonary infections who were admitted to Nanning Fourth People's Hospital. Specimens were collected for traditional microbiological testing and mNGS-based diagnosis. The diagnostic yields of the two methods were compared to evaluate the diagnostic value (detection rate and turn around time) of mNGS for infections with unknown causative agent. Accordingly, 22 cases (29.3%) had a positive culture and 70 (93.3%) had positive valve mNGS results (P value < 0.0001, Chi-square test). Meanwhile, 15 patients with AIDS showed concordant results between the culture and mNGS, whereas only one 1 patient showed concordant results between Giemsa-stained smear screening and mNGS. In addition, mNGS identified multiple microbial infections (at least three pathogens) in almost 60.0% of patients with AIDS. More importantly, mNGS was able to detect a large variety of pathogens from patient tissue displaying potential infection and colonization, while culture results remained negative. There were 18 members of pathogens which were consistently detected in patients with and without AIDS.

CONCLUSIONS

In conclusion, mNGS analysis provides fast and precise pathogen detection and identification, contributing substantially to the accurate diagnosis, real-time monitoring, and treatment appropriateness of pulmonary infection in patients with AIDS.

Validation of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for diagnosis of suspected pulmonary infections in patients with systemic autoimmune rheumatic diseases receiving immunosuppressant therapy

Background

The accuracy and sensitivity of conventional microbiological tests (CMTs) are insufficient to identify opportunistic pathogens in patients with systemic autoimmune rheumatic diseases (SARDs). The study aimed to assess the usefulness of metagenomic next-generation sequencing (mNGS) vs. CMTs for the diagnosis of pulmonary infections in patients with SARDs receiving immunosuppressant therapy.

Methods

The medical records of 40 patients with pulmonary infections and SARDs treated with immunosuppressants or corticosteroids were reviewed retrospectively. Bronchoalveolar lavage fluid (BALF) samples were collected from all patients and examined by mNGS and CMTs. Diagnostic values of the CMTs and mNGS were compared with the clinical composite diagnosis as the reference standard.

Results

Of the 40 patients included for analysis, 37 (92.5%) were diagnosed with pulmonary infections and 3 (7.5%) with non-infectious diseases, of which two were considered primary diseases and one an asthma attack. In total, 15 pathogens (7 bacteria, 5 fungi, and 3 viruses) were detected by CMTs as compared to 58 (36 bacteria, 12 fungi, and 10 viruses) by mNGS. Diagnostic accuracy of mNGS was superior to that of the CMTs for the detection of co-infections with bacteria and fungi (95 vs. 53%, respectively, p < 0.01), and for the detection of single infections with fungi (97.5 vs. 55%, respectively, p < 0.01). Of the 31 patients diagnosed with co-infections, 4 (12.9%) were positive for two pathogens and 27 (87.1%) for three or more. The detection rate of co-infection was significantly higher for mNGS than CMTs (95 vs. 16%, respectively, p < 0.01).

Conclusion

The accuracy of mNGS was superior to that of the CMTs for the diagnosis of pulmonary infections in patients with SARDs treated with immunosuppressants. The rapid diagnosis by mNGS can ensure timely adjustment of treatment regimens to improve diagnosis and outcomes.

Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia

BACKGROUND

Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking.

METHODS

In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT).

RESULTS

Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication.

CONCLUSION

mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.

Metagenomic next-generation sequencing assists in the diagnosis of Cryptococcus pneumonia: Case series and literature review

Background

Pulmonary cryptococcosis (PC) was once thought to occur only in patients with immune deficiencies, such as tested positive for the Human Immunodeficiency Virus (HIV). However, in recent years, it has been discovered that more than half of the patients with PC in our nation are individuals with normal immune function. As more and more PC cases are recorded, our diagnosis and treatment approaches, as well as our understanding of PC, are gradually improving. In reality, most PC patients still have a high incidence of misdiagnosis on their initial visit. It is primarily linked to the diverse clinical manifestations, atypical imaging findings, and inaccurate diagnostic approaches.

Methods

The research was conducted from 2019 to 2020. We performed traditional microbiological testing and mNGS on sample from patients with fever of Pulmonary nodules or lung infections. Furthermore, we collected patients' baseline information, clinical features, laboratory and imaging examination results, diagnosis, treatment and outcome. In the end, we confirmed three cases of PC using biopsy and mNGS.

Conclusion

Our data demonstrates that mNGS can be utilized as an auxiliary method for PC diagnosis. Early mNGS aids in the identification of pathogens, enabling early diagnosis and treatment, as well as a reduction in the rate of misdiagnosis and illness progression.

Negative results of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients

Objective

Reports on negative results of metagenomic next-generation sequencing (mNGS) are scarce. We aimed to explore the diagnostic value of negative results in bronchoalveolar lavage fluid (BALF) mNGS and how to deal with the negative results in patients with severe respiratory disease.

Methods

A retrospective analysis was performed on patients suspected severe community-acquired pneumonia who were admitted to the respiratory intensive care unit of the First Affiliated Hospital of Zhengzhou University from January 2020 to December 2021. According to the final diagnosis as the reference standard, the negative results of mNGS were divided into a true negative group and a false negative group. For enrolled patients, we recorded their demographic data, imaging results, laboratory results, therapeutic processes, and prognoses.

Results

A total of 21 patients were enrolled in this study, including 16 true negative patients and 5 false negative patients. In the true negative group, interstitial lung diseases were the most and neoplastic diseases were following. In addition to mNGS, 9 patients underwent pathological examination, 7 patients were finally diagnosed by medical history, autoantibodies, and point-of-care (POC) ultrasound. 14 patients eventually discontinued antibiotics, 2 patients underwent antibiotic de-escalation, the average interval time of treatment adjustment was 3.56 ± 2.00 days. In the false negative group, the leading missed pathogen was fungi, followed by tuberculosis bacilli. In contrast to 2 patients underwent pathological examination, 3 patients were confirmed by routine microbiological tests.

Conclusions

Negative results of BALF mNGS can help to rule out infection, but missed diagnoses may also exist. It should be re-evaluated with other clinical informations. Pathological examination or repeated mNGS may be viable options when the diagnosis cannot be confirmed.

Metagenomic next-generation sequencing may assist diagnosis of cat-scratch disease

Bartonella henselae, the pathogen that causes cat-scratch disease (CSD), is relatively rare in the clinic. CSD usually causes mild clinical manifestations, which self-heal in a matter of weeks. However, in immunocompromised patients, CSD may cause systemic disorders that can lead to critical illness. Due to the diversity of symptom signs and the lack of a golden standard for diagnosis, identifying atypical CSD in a timely manner presents a challenge. Metagenomic next-generation sequencing (mNGS), is a promising technology that has been widely used in the detection of pathogens in clinical infectious diseases in recent years. mNGS can detect multiple pathogens quickly and accurately from any given source. Here, we present a case of atypical CSD, which was diagnosed using mNGS. The patient manifested a fever of unknown infectious origin, and routine antibiotic treatment was ineffective. mNGS was employed to test the patient’s peripheral blood, which led to the detection of B. henselae. This was rarely seen in previous CSD reports. We surmised that the patient presented with atypical CSD and thus a targeted therapy was recommended. Crucially, the patient recovered rapidly. Based on this case study findings, we recommend that CSD should be included in the differential diagnosis for fever of unknown origin and that mNGS may be helpful in the diagnosis of CSD.

A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia

Purpose

Plasma metagenomic next-generation sequencing (mNGS) has emerged as an attractive and minimally invasive technique for pathogen detection. However, few studies have demonstrated the need for simultaneous plasma and bronchoalveolar lavage fluid (BALF) mNGS in patients with severe pneumonia.

Patients and Methods

This study retrospectively performed a paired comparison of BALF and plasma mNGS in critically ill patients with suspected severe pneumonia from April 2019 to December 2020. The diagnostic performance of BALF and plasma mNGS was compared using the clinical composite diagnosis as the reference standard.

Results

In total, 57 patients were included in this study. Patients with positive plasma mNGS had shorter hospital stay days at the time of specimen acquisition (4.5 vs 11, P = 0.028) and a higher positivity rate of BALF culture (50% vs 22.9%, P = 0.033) than patients with negative plasma mNGS. Fifty-three patients (93%) were finally diagnosed with severe pneumonia. Significant differences were observed in the sensitivity of BALF and plasma mNGS (100% vs 42%, P < 0.001), and the diagnostic accuracy was 96% and 46%, respectively. The proportion of virus in positive plasma mNGS results was higher than that in BALF mNGS (23% vs 11%, P = 0.173) without significant difference. Although plasma mNGS detected additional microorganisms in 11/53 patients, the beneficial effect was observed in only 5/53 (9%) patients.

Conclusion

In this study, the clinical effect of simultaneously conducting mNGS of BALF and plasma samples was found to be limited. For patients with the suspected virus infection, plasma mNGS may be a supplementary test. Further studies are needed to identify the optimal indications for plasma mNGS.

Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis

BACKGROUND

The identification of pathogens in patients with pulmonary infection has always been a major challenge in medicine. Compared with sputum and throat swabs, bronchoalveolar lavage fluid (BALF) can better reflect the actual state in the lungs. However, there has not been a meta-analysis of the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in detecting pathogens in BALF from patients with pulmonary infections.

METHODS

Data sources were PubMed, Web of Science, Embase, and the China National Knowledge Infrastructure. The pooled sensitivity and specificity were estimated by using random-effects or fixed-effect models. Subgroup analysis was performed to reveal the effect of potential explanatory factors on the diagnostic performance measures.

RESULTS

The pooled sensitivity was 78% (95% confidence interval: 67-87%; I² = 92%) and the pooled specificity was 77% (95% confidence interval: 64-94%; I² = 74%) for mNGS. Subgroup analyses for the sensitivity of mNGS revealed that patients with pulmonary infections who were severely ill or immunocompromised significantly affected heterogeneity (P < 0.001). The positive detection rate of mNGS for pathogens in BALF of severely or immunocompromised pulmonary-infected patients was 92% (95% confidence interval: 78-100%).

CONCLUSION

mNGS has high diagnostic performance for BALF pathogens in patients with pulmonary infections, especially in critically ill or immunocompromised patients.

Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens

Next-generation sequencing (NGS) workflows applied to bronchoalveolar lavage (BAL) fluid specimens could enhance the detection of respiratory pathogens, although optimal approaches are not defined. This study evaluated the performance of the Respiratory Pathogen ID/AMR (RPIP) kit (Illumina, Inc.) with automated Explify bioinformatic analysis (IDbyDNA, Inc.), a targeted NGS workflow enriching specific pathogen sequences and antimicrobial resistance (AMR) markers, and a complementary untargeted metagenomic workflow with in-house bioinformatic analysis. Compared to a composite clinical standard consisting of provider-ordered microbiology testing, chart review, and orthogonal testing, both workflows demonstrated similar performances. The overall agreement for the RPIP targeted workflow was 65.6% (95% confidence interval, 59.2 to 71.5%), with a positive percent agreement (PPA) of 45.9% (36.8 to 55.2%) and a negative percent agreement (NPA) of 85.7% (78.1 to 91.5%). The overall accuracy for the metagenomic workflow was 67.1% (60.9 to 72.9%), with a PPA of 56.6% (47.3 to 65.5%) and an NPA of 77.2% (68.9 to 84.1%). The approaches revealed pathogens undetected by provider-ordered testing (Ureaplasma parvum, Tropheryma whipplei, severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], rhinovirus, and cytomegalovirus [CMV]), although not all pathogens detected by provider-ordered testing were identified by the NGS workflows. The RPIP targeted workflow required more time and reagents for library preparation but streamlined bioinformatic analysis, whereas the metagenomic assay was less demanding technically but required complex bioinformatic analysis. The results from both workflows were interpreted utilizing standardized criteria, which is necessary to avoid reporting nonpathogenic organisms. The RPIP targeted workflow identified AMR markers associated with phenotypic resistance in some bacteria but incorrectly identified bla_OXA genes in Pseudomonas aeruginosa as being associated with carbapenem resistance. These workflows could serve as adjunctive testing with, but not as a replacement for, standard microbiology techniques.

Analysis of Negative Results of Metagenomics Next-Generation Sequencing in Clinical Practice

Background

Metagenomics next-generation sequencing (mNGS) has been increasingly used in the clinic, which provides a powerful tool for the etiological diagnosis of infectious diseases. Precise treatment can be carried out according to the positive mNGS results. However, the role of negative results of mNGS remains poorly defined in clinical practice.

Methods

The results of 1,021 samples from patients who received the mNGS test at Zhongshan Hospital, Fudan University, between January 2019 and December 2019 were analyzed.

Results

There were 308 samples (30.17%) of negative results included in the current study. The top 2 types of negative samples were blood (130/308) and tissue (63/308), which also accounted for the highest negative proportion in diseases. Sputum and bronchoalveolar lavage fluid (BALF) were more likely to have positive results. In false-negative results (defined as negative in mNGS test but reported positive in other sample types or assays), 118 samples were found when compared to regular microbiological assays. The negative predictive value (NPV) of mNGS was 95.79% [95%CI, 93.8%–97.8%] as compared to culture and smear. Mycobacterium, Aspergillus, and Mycoplasma ranked as the top 3 microorganisms on the undetected pathogen list.

Conclusions

The present data indicate that when the mNGS test is negative, the negative prediction accuracy rate of the original specimen is significant. However, other laboratory assays results and clinical presentations should always be carefully considered prior to drawing a diagnosis.

Metagenomic Next-Generation Sequencing vs. Traditional Pathogen Detection in the Diagnosis of Infection After Allogeneic Hematopoietic Stem Cell Transplantation in Children

Infection is a severe complication of allo-HSCT in children, however, the accurate detection of the infection is hard. In this study, we traced the records of 101 pediatric recipients with allo-HSCT to investigate the pathogens of infection, and collected 54 bronchoalveolar lavage fluid, 32 blood, and 15 cerebrospinal fluid samples. In these samples, 87 was with post-transplant infection and 14 without infection. Using the metagenomic next-generation sequencing (mNGS) and traditional pathogen detection, we compared their sensitivity and specificity to detect pathogens of infection. Our results showed that mNGS was more sensitive (89.7%) than conventional pathogen detection (21.8%), with a difference of 67.9% (P < 0.001), However, mNGS was less specific (78.5%) than traditional methods (92.9%), with a difference of 14.4% (P = 0.596). The sensitivity of mNGS for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 91.7, 85.7, and 90.9%, respectively. In contrast, the sensitivity of conventional testing for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 22.9, 21.4, and 18.2%, respectively. There were significant differences in the sensitivity of mNGS and conventional testing in BALF, blood, and CSF samples, with P values of 0.000, 0.000, and 0.002 respectively. Among the patients with pulmonary infection, 11 pathogens were both identified by mNGS and conventional testing, and 33 by mNGS only. The percentage with the mNGS-positive result was 44/48 (91.7%), including viruses (n = 12), bacteria (n = 17), fungi (n = 9) and mixed infections (n = 6). Among the patients diagnosed with fungal pneumonia (n = 9), the most prevalent pathogenic fungi were Pneumocystis jiroveci (n = 6), which were also detected in 4 patients with mixed infectious pneumonia. In the 28 blood specimens of patients with bloodstream infections or viremia, five patients were positive by both mNGS and conventional testing, 19 were positive by mNGS, and 1 was positive by traditional testing only. The percentage with the mNGS-positive results was 24/28 (85.7%), including viruses (n = 12), bacteria (n = 4), fungi (n = 3), and mixed infections (n = 5). Of the 15 CSF specimens enrolled, 11 patients were eventually diagnosed with CNS infections. Ten pathogens were identified by mNGS in the 11 patients, including viruses (n = 8), bacteria (n = 1), and fungi (n = 1). These results suggest that mNGS is more sensitive than conventional pathogen detection for diagnosing infections post HSCT in children which may help the clinic diagnosis. Pneumocystis jiroveci was the most frequent pathogen of pulmonary infections post-transplant, while viruses were the most common pathogens of CNS infections in allo-HSCT recipients.

Value of metagenomic next-generation sequencing in children with severe infectious diseases

OBJECTIVES

To study the application value of metagenomic next-generation sequencing (mNGS) in children with severe infectious diseases.

METHODS

An analysis was performed on the clinical data and laboratory test results of 29 children with severe infection who were admitted to the Second Affiliated Hospital of Wenzhou Medical University from June 2018 to December 2020. Conventional pathogen culture was performed for the 29 specimens (27 peripheral blood specimens and 2 pleural effusion specimens) from the 29 children, and mNGS pathogen detection was performed at the same time.

RESULTS

Among the 29 children, 2 tested positive by conventional pathogen culture with 2 strains of pathogen, and the detection rate was 7% (2/29); however, 20 children tested positive by mNGS with 38 strains of pathogen, and the detection rate was 69% (20/29). The pathogen detection rate of mNGS was significantly higher than that of conventional pathogen culture (P<0.05), and mNGS could detect the viruses, fungi, and other special pathogens that conventional pathogen culture failed to detect, such as Orientia tsutsugamushi. The univariate analysis showed that gender, routine blood test results, C-reactive protein, procalcitonin, D-dimer, radiological findings, and whether antibiotics were used before admission did not affect the results of mNGS (P>0.05).

CONCLUSIONS

Compared with conventional pathogen culture, mNGS is more sensitive for pathogen detection, with fewer interference factors. Therefore, it is a better pathogenic diagnosis method for severe infectious diseases in children.

Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS

Background

Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS).

Methods

A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis.

Results

A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSL_B and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSL_B and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples.

Conclusion

High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSL_B and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.

Diagnosis of infectious diseases in immunocompromised hosts using metagenomic next generation sequencing-based diagnostics

The diagnosis of infectious diseases in immunocompromised hosts presents unique challenges for the clinician. Metagenomic next generation sequencing (mNGS) based diagnostics that identify microbial nucleic acids in clinical samples (mNGS for pathogen identification or mNGSpi) may be a useful tool in addressing some of these challenges. Studies of mNGSpi in immunocompromised hosts have demonstrated that these diagnostics are capable of identifying causative organisms in a subset of patients for whom conventional testing has been negative. While these studies provide proof of concept for mNGSpi utility, they have a number of limitations, which make it difficult to confidently assess test performance and clinical impact based on current data. Future studies will likely feature larger cohort sizes and controlled interventional study designs that assess the impact of mNGSpi on clinical endpoints. They will also likely include assessments of the clinical value of data generated by mNGS beyond pathogen identification.

The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection

Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.

Case Report: A Severe and Multi-Site Nocardia farcinica Infection Rapidly and Precisely Identified by Metagenomic Next-Generation Sequencing

Nocardia genus is an aerobic, gram-positive, and opportunistic pathogen, which mainly affects cell-mediated immunosuppressed patients. Early diagnosis and treatment greatly improve prognosis. However, the limitation of golden standard-bacterial culture exists. Here, we report a 61-year-old male with pneumonia, sepsis and intermuscular abscesses induced by Nocardia farcinica. Venous blood culture reported negative results. Former improper diagnosis and treatment did not improve his condition. With the assistant of metagenomic next-generation sequencing, the pathogen was identified as Nocardia farcinica. He was then applied with accurate treatment and had a remarkable clinical and radiological improvement.