Metagenomic Next-Generation Sequencing versus Traditional Pathogen Detection in the Diagnosis of Peripheral Pulmonary Infectious Lesions

Clinical applications of metagenomics next-generation sequencing in infectious diseases

Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.

Diagnostic value of DNA or RNA-based metagenomic next-generation sequencing in lower respiratory tract infections

Objectives

We aimed to evaluate and compare the diagnostic performance of RNA-mNGS and DNA-mNGS workflow in bacterial pneumonia, fungal pneumonia and tuberculosis.

Methods

A total of 134 cases suspected pneumonia undergoing both DNA and RNA based mNGS of bronchoalveolar lavage fluid (BALF) and also traditional etiological examination were evaluated retrospectively.Sensitivity, specificity, PPV, NPV and accuracy rate of DNA and RNA based mNGS were estimated.

Results

In the diagnosis performance of bacterial pathogens in LRTIs,the specificity of RNA-mNGS was higher than that of DNA-mNGS(82.3 % vs. 61.9 %, P < 0.01). There was no significant difference of sensitivity between the two process(71.4 % vs. 85.7 %, P = 0.375).In the diagnosis performance of fungal pathogens in LRTIs,the specificity of RNA-mNGS was higher than that of DNA-mNGS (72.3 % vs. 27.3 %,p < 0.001). There was no significant difference of sensitivity between the two process(96.5 % vs. 98.8 %,p = 0.125).In the diagnosis performance of tuberculosis in LRTIs,the sensitivity of DNA-mNGS was higher than that of RNA-mNGS (91.7 % vs. 33.3 %,p = 0.016),the specificity was similar in the two process (100 %).

Conclusions

RNA-mNGS may reduced the misdiagnosis rate of bacterial and fungal pathogens in LRTIs.Compared to RNA-mNGS, DNA-mNGS may could improve the diagnostic rate of tuberculosis.

A Rare Case Report of Disseminated Nocardia Farcinica Granulomatous Hepatitis and Clinical Management Experience

Background

Nocardiosis is primarily an opportunistic infection affecting immunocompromised individuals, with a predilection for the lungs, brain, or skin in those with compromised immune function. Granulomatous hepatitis caused by Nocardia is a rare clinical manifestation. This study aims to provide a systematic overview of the clinical features of Nocardiosis caused by Nocardia farcinica, enhancing our understanding of this disease.

Methods

We report a case of a 75-year-old male with no underlying diseases presenting with a history of "recurrent fever for more than 4 months", along with fatigue, poor appetite, and pleural and abdominal effusion. Despite treatment at multiple hospitals, the patient showed little improvement. Chest CT revealed chronic inflammation, small nodules, bilateral pleural effusion, and pleural thickening. Abdominal CT indicated multiple low-density lesions in the liver, multiple small calcifications, and abdominal effusion.

Results

Liver biopsy suggested inflammatory changes, with focal granuloma formation. Metagenomic next-generation sequencing (mNGS) of liver tissue indicated Nocardia farcinica, leading to the final diagnosis of disseminated Nocardia farcinica granulomatous hepatitis.

Conclusion

Nocardia infection is a rare disease primarily observed in immunocompromised patients but can also occur in those with normal immune function. The clinical and radiological features lack specificity; however, the utilization of mNGS technology enables rapid identification of the pathogenic microorganism. Nocardia farcinica is generally susceptible to sulfonamide drugs and amikacin, offering viable treatment options.

Assessment and clinical utility of metagenomic next-generation sequencing for suspected lower respiratory tract infections

OBJECTIVES

This study aims to compare the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) to traditional diagnostic methods in patients with lower respiratory tract infections (LRTIs), elucidate the etiological spectrum of these infections, and explore the impact of mNGS on guiding antimicrobial therapy.

METHODS

We retrospectively analyzed data from 128 patients admitted to the Respiratory Department of Anqing 116 Hospital between July 2022 and July 2023. All patients had undergone both mNGS and conventional microbiological techniques (CMT) for LRTI diagnosis. We assessed the diagnostic performance of these methods and examined the influence of mNGS on antimicrobial decision-making.

RESULTS

Overall, mNGS demonstrated superior sensitivity (96.8%) and accuracy (96.8%) compared to CMT. For Mycobacterium tuberculosis detection, the accuracy and sensitivity of mNGS was 88.8% and 77.6%, which was lower than the 94.7% sensitivity of the T-spot test and the 79.6% sensitivity of CMT. In fungal pathogen detection, mNGS showed excellent sensitivity (90.5%), specificity (86.7%), and accuracy (88.0%). Bacteria were the predominant pathogens detected (75.34%), with Mycobacterium tuberculosis (41.74%), Streptococcus pneumoniae (21.74%), and Haemophilus influenzae (16.52%) being most prevalent. Bacterial infections were most common (62.10%), followed by fungal and mixed infections (17.74%). Of the 118 patients whose treatment regimens were adjusted based on mNGS results, 102 (86.5%) improved, 7 (5.9%) did not respond favorably, and follow-up was lost for 9 patients (7.6%).

CONCLUSIONS

mNGS offers rapid and precise pathogen detection for patients with suspected LRTIs and shows considerable promise in diagnosing Mycobacterium tuberculosis and fungal infections. By broadening the pathogen spectrum and identifying polymicrobial infections, mNGS can significantly inform and refine antibiotic therapy.

COVID-19 in pulmonary critically ill patients: metagenomic identification of fungi and characterization of pathogenic microorganisms

Background

Fungal co-infection is prevalent in critically ill patients with COVID-19. The conventional approach applied to fungal identification has relatively low sensitivity and is time-consuming. The metagenomic next-generation sequencing (mNGS) technology can simultaneously detect a variety of microorganisms, and is increasingly being used for the rapid detection and diagnosis of pathogens.

Methods

In this single-center retrospective study, we described the clinical presentation and outcomes of COVID-19 and mNGS positive for fungi in pulmonary critically ill patients during the outbreak of Omicron infection from December 2022 to January 2023.

Results

Among 43 COVID-19 patients with acute respiratory distress syndrome (ARDS) on a single intensive care unit (ICU), 10 were reported to be fungal positive using the mNGS test. The number of pathogenic microorganisms detected by mNGS was significantly higher than that via traditional methods, especially in the detection of fungi and viruses. Aspergillus infection was dominant, and most of these patients also had concurrent bacterial or viral infections. Probable or possible COVID-19-associated pulmonary aspergillosis (CAPA) was diagnosed in all 10 patients, and the prognosis was poor.

Conclusion

Patients with COVID-19 may be at increased risk of developing fungal infections as well as concurrent bacterial or viral infections, and mNGS can be a powerful tool in identifying these infections. Clinicians should be aware of the increased risk of fungal infections in COVID-19 patients, particularly those who have underlying immunocompromising conditions, and should monitor for early signs of infection.

Application of plasma metagenomic next-generation sequencing improves prognosis in hematology patients with neutropenia or hematopoietic stem cell transplantation for infection

Introduction

Metagenomic next-generation sequencing (mNGS) is a novel technique for detecting pathogens. This retrospective study evaluated the diagnostic value of mNGS using plasma for infections in hematology patients and its impact on clinical treatment and prognosis in different subgroups of hematology patients.

Methods

A total of 153 hematology patients with suspected infection who underwent mNGS using plasma were enrolled in the study. Their clinical histories, conventional microbiological test (CMT) results, mNGS results, treatment and prognosis were retrospectively analyzed.

Results

In 153 plasma samples, mNGS yielded a higher positivity rate than CMT (total: 88.24% vs. 40.52%, P<0.001; bacteria: 35.95% vs. 21.57%, P < 0.01; virus: 69.93% vs. 21.57%, P<0.001; fungi: 20.26% vs. 7.84%, P<0.01). mNGS had a higher positivity rate for bacteria and fungi in the neutropenia group than in the non-neutropenia group (bacteria: 48.61% vs. 24.69%, P<0.01; fungi: 27.78% vs. 13.58%, P<0.05). mNGS demonstrated a greater advantage in the group of patients with hematopoietic stem cell transplantation (HSCT). Both the 3-day and 7-day efficacy rates in the HSCT group were higher than those in the non-HSCT group (3-day: 82.22% vs. 58.65%, P < 0.01; 7-day: 88.89% vs. 67.31%, P < 0.01), and the 28-day mortality rate was lower in the HSCT group than in the non-HSCT group (6.67% vs. 38.89%, P < 0.000). The neutropenia group achieved similar efficacy and mortality rates to the non-neutropenia group (7-day efficiency rate: 76.39% vs. 71.43%, P > 0.05; mortality rate: 29.17% vs. 29.63%, P > 0.05) with more aggressive antibiotic adjustments (45.83% vs. 22.22%, P < 0.01).

Conclusion

mNGS can detect more microorganisms with higher positive rates, especially in patients with neutropenia. mNGS had better clinical value in patients with hematopoietic stem cell transplantation (HSCT) or neutropenia, which had a positive effect on treatment and prognosis.

Clinical application of metagenomic next-generation sequencing in patients with different organ system infection: A retrospective observational study

Microbiological identification is essential for appropriate treatment, but conventional methods are time-consuming and have a low sensitivity. In contrast, metagenomic next-generation sequencing (mNGS) is a culture-free and hypothesis-free technique that can detect a wide array of potential pathogens. This study aimed to reveal the overall diagnostic value of mNGS for infectious diseases of different organ systems and compare the sensitivity and specificity of mNGS with conventional methods. In a retrospective cohort study, 94 patients with mNGS results were enrolled, and clinical data were recorded and analyzed to compare the positive rate of mNGS with traditional methods including as smears, serological tests, and traditional PCR, etc. In this study, mNGS and culture were both positive in 12.77% cases and were both negative in 23.4% cases. There were positive results in 56 cases (54.26%) only by mNGS and 4 cases (4.26%) were positive only by culture. There were significant differences in sensitivity of pathogen detection between of ID and NID group for mNGS (χ2 = 10.461, P = .001)and conventional methods(χ2 = 7.963, P = .005). The positive predictive values and negative predictive values of diagnosing infectious disease by mNGS were 94.12% and 30.77%, respectively. mNGS increased the sensitivity rate by approximately 53.66% compared with that of culture (78.05% vs24.39%; χ2 = 47.248, P < .001) and decreased the specificity rate by 12.5% compared with that of culture (66.67% vs 100.0%; χ2 = 4.8, P = .028). mNGS can identify emerging or rare pathogen and further guide treatment regimens. mNGS has advantages in identifying overall pathogens and bacteria, however, there was no obvious advantage in identifying fungi, virus and tuberculosis. mNGS has higher specificity than conventional methods in identifying pathogens and advantages in detecting emerging or rare pathogens.

Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid on Antimicrobial Stewardship in Patients With Lower Respiratory Tract Infections: A Retrospective Cohort Study

BACKGROUND

The impact of metagenomic next-generation sequencing (mNGS) on antimicrobial stewardship in patients with lower respiratory tract infections (LRTIs) is still unknown.

METHODS

This retrospective cohort study included patients who had LRTIs diagnosed and underwent bronchoalveolar lavage between September 2019 and December 2020. Patients who underwent both mNGS and conventional microbiologic tests were classified as the mNGS group, while those with conventional tests only were included as a control group. A 1:1 propensity score match for baseline variables was conducted, after which changes in antimicrobial stewardship between the 2 groups were assessed.

RESULTS

A total of 681 patients who had an initial diagnosis of LRTIs and underwent bronchoalveolar lavage were evaluated; 306 patients were finally included, with 153 in each group. mNGS was associated with lower rates of antibiotic escalation than in the control group (adjusted odds ratio, 0.466 [95% confidence interval, .237-.919]; P = .02), but there was no association with antibiotic de-escalation. Compared with the control group, more patients discontinued the use of antivirals in the mNGS group.

CONCLUSIONS

The use of mNGS was associated with lower rates of antibiotic escalation and may facilitate the cessation of antivirals, but not contribute to antibiotic de-escalation in patients with LRTIs.

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.

Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study

Introduction

Pneumonia are the leading cause of death worldwide, and antibiotic treatment remains fundamental. However, conventional sputum smears or cultures are still inefficient for obtaining pathogenic microorganisms.Metagenomic next-generation sequencing (mNGS) has shown great value in nucleic acid detection, however, the NGS results for lower respiratory tract microorganisms are still poorly studied.

Methods

This study dealt with investigating the efficacy of mNGS in detecting pathogens in the lower respiratory tract of patients with pulmonary infections. A total of 112 patients admitted at the First Affiliated Hospital of Zhengzhou University between April 30, 2018, and June 30, 2020, were enrolled in this retrospective study. The bronchoalveolar lavage fluid (BALF) was obtained from lower respiratory tract from each patient. Routine methods (bacterial smear and culture) and mNGS were employed for the identification of pathogenic microorganisms in BALF.

Results

The average patient age was 53.0 years, with 94.6% (106/112) obtaining pathogenic microorganism results. The total mNGS detection rate of pathogenic microorganisms significantly surpassed conventional methods (93.7% vs. 32.1%, P < 0.05). Notably, 75% of patients (84/112) were found to have bacteria by mNGS, but only 28.6% (32/112) were found to have bacteria by conventional approaches. The most commonly detected bacteria included Acinetobacter baumannii (19.6%), Klebsiella pneumoniae (17.9%), Pseudomonas aeruginosa (14.3%), Staphylococcus faecium (12.5%), Enterococcus faecium (12.5%), and Haemophilus parainfluenzae (11.6%). In 29.5% (33/112) of patients, fungi were identified using mNGS, including 23 cases of Candida albicans (20.5%), 18 of Pneumocystis carinii (16.1%), and 10 of Aspergillus (8.9%). However, only 7.1 % (8/112) of individuals were found to have fungi when conventional procedures were used. The mNGS detection rate of viruses was significantly higher than the conventional method rate (43.8% vs. 0.9%, P < 0.05). The most commonly detected viruses included Epstein-Barr virus (15.2%), cytomegalovirus (13.4%), circovirus (8.9%), human coronavirus (4.5%), and rhinovirus (4.5%). Only 29.4% (33/112) of patients were positive, whereas 5.4% (6/112) of patients were negative for both detection methods as shown by Kappa analysis, indicating poor consistency between the two methods (P = 0.340; Kappa analysis).

Conclusion

Significant benefits of mNGS have been shown in the detection of pathogenic microorganisms in patients with pulmonary infection. For those with suboptimal therapeutic responses, mNGS can provide an etiological basis, aiding in precise anti-infective treatment.

[Application of metagenomic next-generation sequencing of bronchoalveolar lavage fluid in the diagnosis and treatment of refractory pneumonia in children]

OBJECTIVES

To investigate the clinical application of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the etiological diagnosis and treatment of refractory pneumonia (RTP) in children.

METHODS

A retrospective analysis was performed on 160 children with RTP who were admitted to the Department of Pediatric Internal Medicine, Maternal and Child Health Hospital of Inner Mongolia Autonomous Region, from January 2020 to March 2023. According to whether mNGS was performed, they were divided into two groups: mNGS (n=80) and traditional testing (n=80). All children received the tests of inflammatory markers and pathogen tests after admission. Traditional pathogenicity tests included microbial culture (sputum specimen collected by suction tube), nucleic acid detection of respiratory pathogens, and serological test (mycoplasma, tuberculosis, and fungi). For the mNGS group, BALF specimens were collected after bronchoscopy and were sent to the laboratory for mNGS and microbial culture. The two groups were analyzed and compared in terms of the detection of pathogens and treatment.

RESULTS

Compared with the traditional testing group, the mNGS group had a significantly higher detection rate of pathogens (92% vs 58%, P<0.05), with more types of pathogens and a higher diagnostic rate of mixed infections. Compared with the traditional testing group, the mNGS group had a significantly higher treatment response rate and a significantly lower incidence rate of complications during hospitalization (P<0.05). Treatment was adjusted for 68 children in the mNGS group according to the results of mNGS, with a treatment response rate of 96% (65/68) after adjustment.

CONCLUSIONS

Compared with traditional pathogen tests, BALF mNGS can significantly improve the detection rate of pathogens and find some rare pathogens. In clinical practice, when encountering bottlenecks during the diagnosis and treatment of children with RTP, it is advisable to promptly perform the mNGS to identify the pathogens.

Acute Pulmonary Actinomycosis Induced by Immunotherapy and Chemotherapy Used for SCLC Treatment: A Case Report and Literature Review

A 66-year-old male patient diagnosed with small-cell lung cancer received chemotherapy and immunotherapy, resulting in successful tumor control. However, the patient subsequently experienced a fever and rapid progression of the pulmonary cavity. Despite sampling bronchoscopic bronchoalveolar lavage fluid for targeted next-generation sequencing (tNGS), the cause remained unidentified. Adding bronchoalveolar lavage fluid to sense metagenomic next-generation sequencing (mNGS) confirmed the infection caused by actinomycetes. The patient's condition improved after active anti-infection treatment. This case was further analyzed and discussed through a comprehensive literature review, focusing on molecular microbiological diagnosis and treatment processes. The points outlined were as follows: the advancement of molecular microbiology has gradually reduced the challenges associated with diagnosing rare infectious diseases such as pulmonary actinomycosis. Additionally, in immunodeficient individuals, certain infectious diseases with a chronic course may exhibit acute and aggressive characteristics, which is of concern to all colleagues. Currently, tNGS and mNGS are widely employed in clinical settings as practical tools for diagnosing infectious diseases. Notably, these two methods are not substitutes for each other but complement each other.

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.

Interstitial pneumonia combined with nocardia cyriacigeorgica infection: A case report

BACKGROUND

Nocardia infection is a relatively uncommon disease, with no reports among patients with interstitial pneumonia. Due to its atypical clinical symptoms and chest computed tomography (CT) findings and the frequent yielding of negative results by conventional cultures, it poses challenges for timely diagnosis and treatment.

CASE SUMMARY

A 63-year-old female patient presented to our hospital in July 2022 with a 3-mo history of intermittent cough and poor appetite, accompanied by a 2-wk long duration of headaches. She had a previous medical history of interstitial pneumonia and was on oral prednisone and cyclosporine. Chest CT revealed the presence of newly developed round nodules. The diagnosis of Nocardia cyriacigeorgica infection was confirmed through metagenomic next-generation sequencing (mNGS) performed on bronchoalveolar lavage fluid. Targeted anti-infection therapy was initiated, resulting in symptom improvement and radiological resolution, further validating the mNGS results.

CONCLUSION

Nocardia cyriacigeorgica infection is a clinically rare condition that is primarily observed in immunocompromised patients. Its clinical and radiological manifestations lack specificity, but mNGS can aid in rapidly obtaining pathogenic information. Early initiation of targeted antimicrobial therapy based on mNGS results can improve patient prognosis.

Performance of mNGS in bronchoalveolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in non-neutropenic patients

The diagnosis of invasive pulmonary aspergillosis (IPA) diseases in non-neutropenic patients remains challenging. It is essential to develop optimal non-invasive or minimally invasive detection methods for the rapid and reliable diagnosis of IPA. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) can be a valuable tool for identifying the microorganism. Our study aims to evaluate the performance of mNGS in BALF in suspected IPA patients and compare it with other detection tests, including serum/BALF galactomannan antigen (GM) and traditional microbiological tests (BALF fungal culture and smear and lung biopsy histopathology). Ninety-four patients with suspicion of IPA were finally enrolled in our study. Thirty-nine patients were diagnosed with IPA, and 55 patients were non-IPA. There was significance between the IPA and non-IPA groups, such as BALF GM (P < 0.001), history of glucocorticoid use (P = 0.004), and pulmonary comorbidities (P = 0.002), as well as no significance of the other demographic data including age, sex, BMI, history of cigarette, blood GM assay, T-SPOT.TB, and NEUT#/LYMPH#. The sensitivity of the BALF mNGS was 92.31%, which was higher than that of the traditional tests or the GM assays. The specificity of BALF mNGS was 92.73%, which was relatively similar to that of the traditional tests. The AUC of BALF mNGS was 0.925, which presented an excellent performance compared with other traditional tests or GM assays. Our study demonstrated the important role of BALF detection by the mNGS platform for pathogen identification in IPA patients with non-neutropenic states, which may provide an optimal way to diagnose suspected IPA disease.

Weil's Disease in an HIV-Infected Patient: A Case Report and Literature Review

Weil's disease, an icterohemorrhagic infection, is the most severe and fatal form of leptospirosis and is characterized by jaundice, renal dysfunction, and hemorrhagic predisposition. Weil's disease with HIV infection has rarely been reported. A 68-year-old male with HIV infection presented to our hospital with fever and dyspnea that progressed to severe hemoptysis and systemic multiple organ failure, necessitating a tracheal intubation ventilator. A diagnosis of Weil's disease was made after Leptospira interrogans was identified via metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF). After immediately receiving supportive therapy and targeted antimicrobial agents, the patient achieved complete recovery upon discharge. The co-infection of HIV infection and leptospirosis resulting in systemic multi-organ failure is rare, but awareness should be raised of the differential diagnosis. mNGS can help identify pathogens and facilitate the use of targeted and efficacious antimicrobial therapy in unusual clinical environments.

Clinical application of metagenomic next-generation sequencing in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation

Objectives

This study aims to explore the pathogen-detected effect of mNGS technology and its clinical application in non-immunocompromised patients with severe pneumonia supported by vv-ECMO.

Methods

A retrospective analysis was conducted on a cohort of 50 non-immunocompromised patients who received vv-ECMO support for severe pneumonia between January 2016 and December 2022. These patients were divided into two groups based on their discharge outcomes: the deterioration group (Group D), which included 31 cases, and the improvement group (Group I), consisting of 19 cases. Baseline characteristics and clinical data were collected and analyzed.

Results

Among the 50 patients enrolled, Group D exhibited a higher prevalence of male patients (80.6% vs. 52.6%, p < 0.05), more smokers (54.8% vs. 21.1%, p < 0.05), and were older than those in Group I (55.16 ± 16.34 years vs. 42.32 ± 19.65 years, p < 0.05). Out of the 64 samples subjected to mNGS detection, 55 (85.9%) yielded positive results, with a positivity rate of 83.7% (36/43) in Group D and 90.5% (19/21) in Group I. By contrast, the positive rate through traditional culture stood at 64.9% (74/114). Among the 54 samples that underwent both culture and mNGS testing, 23 (42.6%) displayed consistent pathogen identification, 13 (24.1%) exhibited partial consistency, and 18 (33.3%) showed complete inconsistency. Among the last cases with complete inconsistency, 14 (77.8%) were culture-negative, while two (11.1%) were mNGS-negative, and the remaining two (11.1%) presented mismatches. Remarkably, mNGS surpassed traditional culture in pathogen identification (65 strains vs. 23 strains). Within these 65 strains, 56 were found in Group D, 26 in Group I, and 17 were overlapping strains. Interestingly, a diverse array of G+ bacteria, fungi, viruses, and special pathogens were exclusive to Group D. Furthermore, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae were more prevalent in Group D compared to Group I. Importantly, mNGS prompted antibiotic treatment adjustments in 26 patients (52.0%).

Conclusions

Compared with the conventional culture, mNGS demonstrated a higher positive rate, and emerges as a promising method for identifying mixed pathogens in non-immunodeficient patients with severe pneumonia supported by vv-ECMO. However, it is crucial to combine the interpretation of mNGS data with clinical information and traditional culture results for a comprehensive assessment.

Metagenomic next-generation sequencing of bronchoalveolar lavage fluid assists in the diagnosis of pathogens associated with lower respiratory tract infections in children

Worldwide, lower respiratory tract infections (LRTI) are an important cause of hospitalization in children. Due to the relative limitations of traditional pathogen detection methods, new detection methods are needed. The purpose of this study was to evaluate the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) samples for diagnosing children with LRTI based on the interpretation of sequencing results. A total of 211 children with LRTI admitted to the First Affiliated Hospital of Guangzhou Medical University from May 2019 to December 2020 were enrolled. The diagnostic performance of mNGS versus traditional methods for detecting pathogens was compared. The positive rate for the BALF mNGS analysis reached 95.48% (95% confidence interval [CI] 92.39% to 98.57%), which was superior to the culture method (44.07%, 95% CI 36.68% to 51.45%). For the detection of specific pathogens, mNGS showed similar diagnostic performance to PCR and antigen detection, except for Streptococcus pneumoniae, for which mNGS performed better than antigen detection. S. pneumoniae, cytomegalovirus and Candida albicans were the most common bacterial, viral and fungal pathogens. Common infections in children with LRTI were bacterial, viral and mixed bacterial-viral infections. Immunocompromised children with LRTI were highly susceptible to mixed and fungal infections. The initial diagnosis was modified based on mNGS in 29.6% (37/125) of patients. Receiver operating characteristic (ROC) curve analysis was performed to predict the relationship between inflammation indicators and the type of pathogen infection. BALF mNGS improves the sensitivity of pathogen detection and provides guidance in clinical practice for diagnosing LRTI in children.

Etiologic characteristics revealed by mNGS-mediated ultra-early and early microbiological identification in airway secretions from lung transplant recipients

Background

Post-operative etiological studies are critical for infection prevention in lung transplant recipients within the first year. In this study, mNGS combined with microbial culture was applied to reveal the etiological characteristics within one week (ultra-early) and one month (early) in lung transplant recipients, and the epidemiology of infection occurred within one month.

Methods

In 38 lung transplant recipients, deep airway secretions were collected through bronchofiberscope within two hours after the operation and were subjected to microbial identification by mNGS and microbial culture. The etiologic characteristics of lung transplant recipients were explored. Within one month, the infection status of recipients was monitored. The microbial species detected by mNGS were compared with the etiological agents causing infection within one month.

Results

The detection rate of mNGS in the 38 airway secretions specimens was significantly higher than that of the microbial culture (P<0.0001). MNGS identified 143 kinds of pathogenic microorganisms; bacterial pathogens account for more than half (72.73%), with gram-positive and -negative bacteria occupying large proportions. Fungi such as Candida are also frequently detected. 5 (50%) microbial species identified by microbial culture had multiple drug resistance (MDR). Within one month, 26 (68.42%) recipients got infected (with a median time of 9 days), among which 10 (38.46%) cases were infected within one week. In the infected recipients, causative agents were detected in advance by mNGS in 9 (34.62%) cases, and most of them (6, 66.67%) were infected within one week (ultra-early). In the infection that occurred after one week, the consistency between mNGS results and the etiological agents was decreased.

Conclusion

Based on the mNGS-reported pathogens in airway secretions samples collected within two hours, the initial empirical anti-infection regimes covering the bacteria and fungi are reasonable. The existence of bacteria with MDR forecasts the high risk of infection within 48 hours after transplant, reminding us of the necessity to adjust the antimicrobial strategy. The predictive role of mNGS performed within two hours in etiological agents is time-limited, suggesting continuous pathogenic identification is needed after lung transplant.

Diagnostic efficiency of metagenomic next-generation sequencing for suspected infection in allogeneic hematopoietic stem cell transplantation recipients

Introduction

Immunosuppression predisposes allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients to infection. Prompt and accurate identification of pathogens is crucial to optimize treatment strategies. This multi-center retrospective study aimed to assess the ability of metagenomic next-generation sequencing (mNGS) to detect causative pathogens in febrile allo-HSCT recipients and examined its concordance with conventional microbiological tests (CMT).

Methods

We performed mNGS and CMT on samples obtained from 153 patients with suspected infection during allo-HSCT. Patients were grouped based on their neutropenic status at the time of sampling.

Results

The mNGS test was more sensitive than CMT (81.1% vs. 53.6%, P<0.001) for diagnosing clinically suspected infection, especially in the non-neutropenia cohort. mNGS could detect fungi and viruses better than bacteria, with a higher sensitivity than CMT. Immune events were diagnosed in 57.4% (35/61) of the febrile events with negative mNGS results, and 33.5% (48/143) with negative CMT results (P=0.002). The treatment success rate of the targeted anti-infection strategy was significantly higher when based on mNGS than on empirical antibiotics (85% vs. 56.5%, P=0.004).

Conclusion

The mNGS test is superior to CMT for identifying clinically relevant pathogens, and provides valuable information for anti-infection strategies in allo-HSCT recipients. Additionally, attention should be paid to immune events in patients with negative mNGS results.

Epidemiological and clinical characteristics of psittacosis among cases with complicated or atypical pulmonary infection using metagenomic next-generation sequencing: a multi-center observational study in China

BACKGROUND

Chlamydia psittaci (C. psittaci) causes parrot fever in humans. Development of metagenomic next-generation sequencing (mNGS) enables the identification of C. psittaci.

METHODS

This study aimed to determine the epidemiological and clinical characteristics of parrot fever cases in China. A multi-center observational study was conducted in 44 tertiary and secondary hospitals across 14 provinces and municipalities between April 2019 and October 2021.

RESULTS

A total of 4545 patients with complicated or atypical pulmonary infection were included in the study, among which the prevalence of C. psittaci was determined to be 2.1% using mNGS. The prevalence of C. psittaci was further determined across demographic groups and types of specimens. It was significantly higher in patients with senior age (2.6% in those > 50 years), winter-spring (3.6%; particularly in December, January, and February), and southwestern (3.4%) and central and southern China (2.7%) (each P < 0.001). Moreover, the prevalence was the highest in bronchoalveolar lavage fluid (BALF) (2.9%), compared with sputum (1.1%) and peripheral blood specimens (0.9%). Additionally, co-infection of principal microorganisms was compared. Certain microorganisms were more likely to co-infect in parrot fever cases, such as Candida albicans in BALF (26.7%) and peripheral blood (6.3%), compared with non-parrot fever cases (19.7% and 1.3%); however, they did not significantly differ (each P > 0.05).

CONCLUSION

Parrot fever remains low in patients with complicated or atypical pulmonary infection. It is likely to occur in winter-spring and southwestern region in China. BALF may be the optimal specimen in the application of mNGS. Co-infection of multiple microorganisms should be further considered.

Comparison of quality/quantity mNGS and usual mNGS for pathogen detection in suspected pulmonary infections

Improved metagenomic next-generation sequencing (mNGS), for example, quality/quantity mNGS (QmNGS), is being used in the diagnosis of pulmonary pathogens. There are differences between QmNGS and the usual mNGS (UmNGS), but reports that compare their detection performances are rare. In this prospective study of patients enrolled between December 2021 and March 2022, the bronchoalveolar lavage fluid of thirty-six patients with suspected pulmonary infection was assessed using UmNGS and QmNGS. The sensitivity of QmNGS was similar to that of UmNGS. The specificity of QmNGS was higher than that of UmNGS; however, the difference was not statistically significant. The positive likelihood ratios (+LR) of QmNGS and UmNGS were 3.956 and 1.394, respectively, and the negative likelihood ratios (-LR) were 0.342 and 0.527, respectively. For the co-detection of pathogens, the depth and coverage of the QmNGS sequencing were lower than those of UmNGS, while for the detection of pathogens isolated from patients with pulmonary infection, the concordance rate was 77.2%. In the eleven patients with nonpulmonary infection, only viruses were detected using QmNGS, while UmNGS detected not only viruses but also bacteria and fungi. This study provides a basis for the selection of mNGS for the diagnosis of suspected pulmonary infection.

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.

Chlamydia Psittaci Pneumonia-Induced Myocarditis: A Case Report

The incidence of Chlamydia psittaci infection has been reported to increase in recent years. The presentation of psittacosis infection varied widely, from none to severe symptoms. Mainly, psittacosis infection presents with pulmonary manifestations. Here, we report the case of a 60-year-old female patient with Chlamydia psittaci pneumonia complicated by myocarditis. After administering antibiotics, the patient recovered from severe atypical pneumonia and myocarditis. In general, Chlamydia psittaci rarely induces myocarditis. Moreover, the optimal therapeutic strategies remain unclear for such cases, especially with a high troponin T level. Metagenomic Next-Generation Sequencing (mNGS) can provide a quick and effective diagnosis of Chlamydia psittaci pneumonia; early intervention (antibiotic therapy and nutritional supplements for myocarditis) favors a good outcome, although complications may worsen the condition. Therefore, more studies are required to help improve understanding of the disease.

A Case of Critical Japanese Spotted Fever in Zhejiang, China

Background

Japanese spotted fever (JSF) is a rare disease, caused by Rickettsia japonica; no case has been reported in Zhejiang Province, China.

Case Presentation

An elderly woman presented to the hospital with abdominal pain and fever. Her condition rapidly worsened with severe complications, such as multiple organ failure and central nervous system damage. The presence of R. japonica was quickly detected by metagenomic next-generation sequencing. On the basis of combined clinical manifestations and laboratory results, critical JSF was diagnosed and treated with doxycycline. The patient showed good prognosis. Typical symptoms (eschar and rash) were not observed in the early stage, consequently increasing the difficulty of clinical diagnosis.

Conclusion

The delay of treatment caused by non-specific symptoms is an important factor affecting the progression of JSF. As an emerging pathogen detection method, mNGS has been successfully applied for disease diagnosis and treatment, and can be an important complement for the diagnosis of this disease.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Metagenomic next-generation sequencing for pulmonary infections diagnosis in patients with diabetes

BACKGROUND

Diabetes mellitus is a major cause of high mortality and poor prognosis in patients with pulmonary infections. However, limited data on the application of metagenomic next-generation sequencing (mNGS) are available for diabetic patients. This study aimed to evaluate the diagnostic performance of mNGS in diabetic patients with pulmonary infections.

METHODS

We retrospectively reviewed 184 hospitalized patients with pulmonary infections at Guizhou Provincial People's Hospital between January 2020 to October 2021. All patients were subjected to both mNGS analysis of bronchoalveolar lavage fluid (BALF) and conventional testing. Positive rate by mNGS and the consistency between mNGS and conventional testing results were evaluated for diabetic and non-diabetic patients.

RESULTS

A total of 184 patients with pulmonary infections were enrolled, including 43 diabetic patients and 141 non-diabetic patients. For diabetic patients, the microbial positive rate by mNGS was significantly higher than that detected by conventional testing methods, primarily driven by bacterial detection (microbes: 95.3% vs. 67.4%, P = 0.001; bacteria: 72.1% vs. 37.2%, P = 0.001). mNGS and traditional tests had similar positive rates with regard to fungal and viral detection in diabetic patients. Klebsiella pneumoniae was the most common pathogen identified by mNGS in patients with diabetes. Moreover, mNGS identified pathogens in 92.9% (13/14) of diabetic patients who were reported negative by conventional testing. No significant difference was found in the consistency of the two tests between diabetic and non-diabetic groups.

CONCLUSIONS

mNGS is superior to conventional microbiological tests for bacterial detection in diabetic patients with pulmonary infections. mNGS is a valuable tool for etiological diagnosis of pulmonary infections in diabetic patients.

Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019

Objectives

This study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS).

Methods

In total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes.

Results

We assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness.

Conclusion

The sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.

Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital

Purpose

Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice.

Patients and Methods

In this single-center retrospective cohort study, 518 patients with suspected infectious diseases were assessed for inclusion. Among them, each patient had undergone mNGS testing; 407 patients had undergone both microbial culture and mNGS testing. The result of mNGS testing was compared to microbial culture performed concurrently. The diagnostic performance of mNGS was evaluated using the comprehensive clinical diagnosis as the reference standard.

Results

There was a significant difference in the positive detection rates of pathogens between mNGS and culture (331/407, 81.3% vs 79/407, 19.4%, P < 0.001). The sensitivity of mNGS was much higher than the culture method (79.5% vs 21.3%, P < 0.001), especially in sample types of sputum and bronchoalveolar lavage fluid (BALF). Notably, the sensitivity of blood mNGS was relatively lower than other sample types (67.4% vs 88.9-93.8%). Pathogen cfDNA load based on standardized stringently mapped read number at the species level of microorganisms (SDSMRN) was significantly lower in blood than in other sample types from the same patient (P = 0.0003). Importantly, mNGS directly led to a change of treatment regimen in 142 (27.4%) cases, including antibiotic escalation (15.3%), antibiotic de-escalation (9.1%), and early definitive diagnosis to initiate appropriate treatment (3.1%).

Conclusion

Our in-house mNGS platform significantly improved the sensitivity for the diagnosis of infectious diseases. mNGS has the potential to improve clinical outcomes by optimizing antimicrobial therapy.

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.

Metagenomics next-generation sequencing provides insights into the causative pathogens from critically ill patients with pneumonia and improves treatment strategies

Background

The metagenomics next-generation sequencing (mNGS) is a promising technique for pathogens diagnosis. However, whether the application of mNGS in critically ill patients with pneumonia could cause anti-infection treatment adjustment and thereby affect the prognosis of these patients has not been explored.

Methods

We retrospectively collected the clinical data of patients diagnosed with pulmonary infection in the ICU of the Affiliated Hospital of Qingdao University from January 2018 to January 2021. These patients with pneumonia were divided into mNGS group and no-mNGS group by whether being performed NGS or not. The clinical data, including demographics, illness history, APACHE II score, length of mechanical ventilation, length of stay in the hospital, length of stay in ICU and outcome, were collected. In addition, the data of pathogens and anti-infection treatment before and after NGS were also collected. Propensity score matching was performed to evaluate the mortality and deterioration rate between NGS group and non-NGS group.

Results

A total of 641 patients diagnosed with pneumonia were screened, and 94 patients were excluded based on exclusion criteria. Finally, 547 patients were enrolled, including 160 patients being performed NGS. Among these 160 patients, 142 cases had NGS-positive results. In addition, new pathogens were detected in 132 specimens by NGS, which included 82 cases with virus, 18 cases with fungus, 17 cases with bacteria, 14 cases with mycoplasma, and 1 case with mycobacterium tuberculosis. Anti-infection treatments were adjusted in some patients who performed NGS, including 48 anti-bacterial treatments, 20 antifungal treatments and 20 antiviral treatments. There were no significant differences in the mortality and deterioration rate between NGS and non-NGS group, but it exhibited a trend that the mortality and deterioration rate of NGS group was lower than non-NGS group after the propensity score matching analysis (15.8% vs 24.3%, P=0.173; 25.6% vs 37.8%, P=0.093).

Conclusion

NGS could affect the anti-infection treatments and had a trend of reducing the mortality and deterioration rate of critically ill patients with pneumonia.

Clinical values of metagenomic next-generation sequencing in patients with severe pneumonia: a systematic review and meta-analysis

Background

Clinical values of metagenomic next-generation sequencing (mNGS) in patients with severe pneumonia remain controversial. Therefore, we conduct this meta-analysis to evaluate the diagnostic performance of mNGS for pathogen detection and its role in the prognosis of severe pneumonia.

Methods

We systematically searched the literature published in PubMed, Embase, Cochrane Library, Web of Science, Clinical Trials.gov, CNKI, Wanfang Data, and CBM from the inception to the 28th September 2022. Relevant trials comparing mNGS with conventional methods applied to patients with severe pneumonia were included. The primary outcomes of this study were the pathogen-positive rate, the 28-day mortality, and the 90-day mortality; secondary outcomes included the duration of mechanical ventilation, the length of hospital stay, and the length of stay in the ICU.

Results

Totally, 24 publications with 3220 patients met the inclusion criteria and were enrolled in this study. Compared with conventional methods (45.78%, 705/1540), mNGS (80.48%, 1233/1532) significantly increased the positive rate of pathogen detection [OR = 6.81, 95% CI (4.59, 10.11, P < 0.001]. The pooled 28-day and 90-day mortality in mNGS group were 15.08% (38/252) and 22.36% (36/161), respectively, which were significantly lower than those in conventional methods group 33.05% (117/354) [OR = 0.35, 95% CI (0.23, 0.55), P < 0.001, I² = 0%] and 43.43%(109/251) [OR = 0.34, 95% CI (0.21, 0.54), P < 0.001]. Meanwhile, adjusted treatment based on the results of mNGS shortened the length of hospital stay [MD = -2.76, 95% CI (- 3.56, - 1.96), P < 0.001] and the length of stay in ICU [MD = -4.11, 95% CI (- 5.35, - 2.87), P < 0.001].

Conclusion

The pathogen detection positive rate of mNGS was much higher than that of conventional methods. Adjusted treatment based on mNGS results can reduce the 28-day and 90-day mortality of patients with severe pneumonia, and shorten the length of hospital and ICU stay. Therefore, mNGS advised to be applied to severe pneumonia patients as early as possible in addition to conventional methods to improve the prognosis and reduce the length of hospital stay.

The performance of metagenomic next-generation sequencing in diagnosing pulmonary infectious diseases using authentic clinical specimens: The Illumina platform versus the Beijing Genomics Institute platform

Introduction: Metagenomic next-generation sequencing (mNGS) has been increasingly used to detect infectious organisms and is rapidly moving from research to clinical laboratories. Presently, mNGS platforms mainly include those from Illumina and the Beijing Genomics Institute (BGI). Previous studies have reported that various sequencing platforms have similar sensitivity in detecting the reference panel that mimics clinical specimens. However, whether the Illumina and BGI platforms provide the same diagnostic performance using authentic clinical samples remains unclear. Methods: In this prospective study, we compared the performance of the Illumina and BGI platforms in detecting pulmonary pathogens. Forty-six patients with suspected pulmonary infection were enrolled in the final analysis. All patients received bronchoscopy, and the specimens collected were sent for mNGS on the two different sequencing platforms. Results: The diagnostic sensitivity of the Illumina and BGI platforms was notably higher than that of conventional examination (76.9% vs. 38.5%, p < 0.001; 82.1% vs. 38.5%, p < 0.001; respectively). The sensitivity and specificity for pulmonary infection diagnosis were not significantly different between the Illumina and BGI platforms. Furthermore, the pathogenic detection rate of the two platforms were not significantly different. Conclusion: The Illumina and BGI platforms exhibited similar diagnostic performance for pulmonary infectious diseases using clinical specimens, and both are superior to conventional examinations.

The value of next-generation metagenomic sequencing in pathogen detection of pleural effusions and ascites from children with sepsis

Objective

To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) using pleural effusion and ascites from children with sepsis.

Methods

In this study, children with sepsis or severe sepsis and appeared pleural or peritoneal effusions were enrolled, of whom the pleural effusions or ascites and blood samples were conducted pathogen detection using both conventional and mNGS methods. The samples were divided into pathogen-consistent and pathogen-inconsistent groups based on the consistency of mNGS results from different sample types, and into exudate and transudate groups based on their pleural effusion and ascites properties. The pathogen positive rates, pathogen spectrum, consistency between different sample types, and clinical diagnosis consistency were compared between mNGS and conventional pathogen tests.

Results

A total of 42 pleural effusions or ascites and 50 other type samples were collected from 32 children. The pathogen positive rate of the mNGS test was significantly higher than that of traditional methods (78.57% vs. 14.29%, P < 0.001) in pleural effusion and ascites samples, with a consistent rate of 66.67% between the two methods. Nearly 78.79% (26/33) of mNGS positive results of the pleural effusions and ascites samples were consistent with clinical evaluation, and 81.82% (27/33) of these positive samples reported 1-3 pathogens. The pathogen-consistent group outperformed the pathogen-inconsistent group in terms of consistency with respect to clinical evaluation (88.46% vs. 57.14%, P = 0.093), while there was no significant difference between the exudate and transudate groups (66.67% vs. 50.00%, P = 0.483).

Conclusion

Compared to conventional methods, mNGS has great advantages in pathogen detection of pleural effusion and ascites samples. Moreover, consistent results of mNGS tests with different sample types provide more reference values in clinical diagnosis.

The clinical application of metagenomic next-generation sequencing in infectious diseases at a tertiary hospital in China

Background

Compared with traditional diagnostic methods (TDMs), rapid diagnostic methods for infectious diseases (IDs) are urgently needed. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic technology for clinical infections.

Methods

This retrospective observational study was performed at a tertiary hospital in China between May 2019 and August 2022. The chi-square test was used to compare the sensitivity and specificity of mNGS and TDMs. We also performed a subgroup analysis of the different pathogens and samples.

Results

A total of 435 patients with clinical suspicion of infection were enrolled and 372 (85.5%) patients were finally categorized as the ID group. The overall sensitivity of mNGS was significantly higher than that of the TDMs (59.7% vs. 30.1%, P < 0.05). However, there was no significant difference in the overall specificity between the two methods (83.3% vs. 89.6%, P = 0.37). In patients with identified pathogens, the positive rates of mNGS for detecting bacteria (88.7%), fungi (87.9%), viruses (96.9%), and Nontuberculous mycobacteria (NTM; 100%) were significantly higher than those of TDMs (P < 0.05). The positive rate of mNGS for detecting Mycobacterium tuberculosis was not superior to that of TDMs (77.3% vs. 54.5%, P = 0.11). The sensitivity rates of mNGS for pathogen identification in bronchoalveolar lavage fluid, blood, cerebrospinal fluid, pleural fluid, and tissue were 72.6%, 39.3%, 37.5%, 35.0% and 80.0%, respectively.

Conclusion

With the potential for screening multiple clinical samples, mNGS has an overall advantage over TDMs. It can effectively identify pathogens, especially those that are difficult to identify using TDMs, such as NTM, chlamydia, and parasites.

Clinical Characteristics and the Effect of Timing for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Sepsis

Background

Metagenomic next-generation sequencing (mNGS) has a good performance for the identification of pathogens in infectious diseases, but few studies on the clinical characteristics of mNGS and the effect of timing for mNGS in critically ill patients with sepsis.

Methods

We retrospectively included all patients diagnosed with sepsis after admission to the intensive care unit (ICU) of a university-affiliated hospital between Aug 1, 2019 and Apr 1, 2021. During the study period, pathogens for all enrolled subjects were obtained by mNGS. We analyzed the composition and positive rate of different samples type for mNGS. And then we used the univariable and multivariable logistic regression to explore the risk factors associated with all-cause mortality at 28 days.

Results

A total of 87 patients were included and 87 samples were analyzed among these patients. The most common sample for mNGS was bronchoalveolar lavage fluid (BALF), about 84% (73/87). The positive rate of pathogens identification by mNGS was higher than conventional culture (92% vs 36%, p < 0.001). In addition to the pathogens detected by conventional culture, mNGS can detect more viruses and fungi. Based on the mNGS report, clinicians made adjustments to the antibiotic regimen for 72% patients. The multivariate binary logistic regression analysis suggested that age (OR, 1.036; 95% CI, 1.005-1.067; p = 0.021) and the sequential organ failure assessment (SOFA) score on the day of mNGS sampling were independent risk factors of death at 28 days (OR, 1.204; 95% CI, 1.038-1.397; p = 0.014).

Conclusion

In critically ill patients with sepsis, the most common sample type for mNGS was BALF, and the positive rate of mNGS is higher than conventional cultures, especially in viruses and fungi. Meanwhile, mNGS can guide clinicians in adjusting antibiotic regimens. Age and the SOFA score on the day of mNGS sampling were independent risk factors for death.

Novel approaches to the prediction and diagnosis of pulmonary complications in the paediatric haematopoietic stem cell transplant patient

PURPOSE OF REVIEW

Haematopoietic stem cell transplant (HSCT) remains the only curative treatment option for many children with relapsed leukaemia, primary immunodeficiencies and haemoglobinopathies. Unfortunately, infectious and noninfectious pulmonary complications following HSCT continue to cause significant morbidity and mortality. This review will focus on recent advances in the field that enhance clinically available diagnostic tools and the role of novel diagnostic techniques.

RECENT FINDINGS

Research continues to highlight the role of standard diagnostic modalities, including imaging using computed topography chest and Fluorodeoxyglucose-positron emission tomography (FDG-PET) in the diagnosis of posttransplant pulmonary infections. Similarly, bronchoalveolar lavage using bronchoscopy to obtain samples for microbiological analysis remains an important tool in the clinical and diagnostic algorithm for these children. The application of more novel diagnostic techniques such as metagenomic next-generation sequencing and the use of specific biomarkers remain potential future tools in children in whom the aetiology of posttransplant lung disease is unknown. The impact of the pulmonary microbiome on infectious and noninfectious pulmonary disease post HSCT is a future research direction.

SUMMARY

Pulmonary infectious complications post HSCT remain a devastating complication for children and their families. Despite improvements in standard and novel diagnostic modalities, the aetiology of pulmonary disease remains unknown for many patients. There is an urgent need for ongoing collaborative research to bridge this critical knowledge gap and lead to better patient outcomes.

Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review

The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.

Rapid diagnosis of a complex oral mucosal infection using metagenomic next-generation sequencing: a case report

The most commonly used methods for pathogen detection and identification in oral mucosal infectious diseases are DNA or RNA quantitative polymerase chain reaction detection, bacterial or fungal cultures, and immunohistochemical analysis. These traditional methods are time-consuming and can only detect one specific targeted pathogen at a time. An efficient and sensitive method with higher species richness is urgently needed. Metagenomic next-generation sequencing (mNGS) is a new method of pathogen detection with high efficiency and sensitivity. In this case report, mNGS was used to identify the pathogens in oral mucosal tissues of a patient with complex oral mucosal infections and oral leukoplakia. Candida albicans, human gamma herpesvirus 4, and many other pathogens were identified using this method. For complex oral mucosal infections, mNGS is a more efficient and sensitive approach that can replace conventional detection methods.

Successful treatment of disseminated nocardiosis diagnosed by metagenomic next-generation sequencing: A case report and review of literature

BACKGROUND

Nocardia paucivorans is an infrequently found bacterium with the potential to cause severe infection, with a predilection for the central nervous system, both in immunocompromised and immunocompetent individuals. Rapid etiological diagnosis of nocardiosis can facilitate timely and rational antimicrobial treatment. Metagenomic next-generation sequencing (mNGS) can improve the rate and reduce the turnaround time for the detection of Nocardia.

CASE SUMMARY

A 49-year-old man was admitted to hospital with cough and hemoptysis. Imaging revealed pulmonary consolidation as well as multiple brain lesions. Nocardia asiatica and Nocardia beijingensis were rapidly detected by mNGS of bronchoalveolar lavage fluid (BALF) while bacterial culture of BALF and pathological biopsy of lung tissue were negative. In early stages, he was treated with trimethoprim-sulfamethoxazole (TMP-SMZ) and linezolid by individual dose adjustment based on serum concentrations and the adverse effects of thrombocytopenia and leukopenia. The treatment was then replaced by TMP-SMZ and ceftriaxone or minocycline. He was treated with 8 mo of parenteral and/or oral antibiotics, and obvious clinical improvement was achieved with resolution of pulmonary and brain lesions on repeat imaging.

CONCLUSION

mNGS provided fast and precise pathogen detection of Nocardia. In disseminated nocardiosis, linezolid is an important alternative that can give a better outcome with the monitoring of linezolid serum concentrations and platelet count.

Comparing the application of mNGS after combined pneumonia in hematologic patients receiving hematopoietic stem cell transplantation and chemotherapy: A retrospective analysis

Rapid and accurate pathogen identification is essential for timely and effective treatment of pneumonia. Here, we describe the use of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BALF) fluid to identify pathogens in patients with hematologic comorbid respiratory symptoms in a retrospective study with 84 patients. In the transplantation group, 8 cases (19.5%) and 47 cases (97.9%) were positive for BALF by conventional method detection and mNGS detection, respectively, and 6 cases (14.0%) and 41 cases (91.1%) in chemotherapy group, respectively. The detection rate of mNGS in both groups was significantly higher than that of conventional detection methods (all P&lt;0.05). Pseudomonas aeruginosa and Streptococcus pneumoniae were the most common bacterial infections in the transplantation and chemotherapy groups, respectively. Aspergillus was the most common fungal infection in both groups. Human betaherpesvirus 5 (HHV-5), torque teno virus and human betaherpesvirus 7 (HHV-7) were the most common pathogen species in both groups. The most common type of infection in patients in the transplantation and chemotherapy groups was the mixed infection of bacteria-virus. Most patients in the transplantation group had mixed infections based on multiple viruses, with 42 cases of viral infections in the transplantation group and 30 cases of viral infections in the chemotherapy group, which were significantly higher in the transplantation group than in the chemotherapy group (χ2 = 5.766, P=0.016). and the mixed infection of virus-virus in the transplantation group was significantly higher than that in the chemotherapy group (27.1% vs 4.4%, P=0.003). The proportion of death due to pulmonary infection was significantly higher in the transplantation group than in the chemotherapy group (76.9% vs 16.7%, χ2 = 9.077, P=0.003). This study demonstrated the value of mNGS of BALF in improving the diagnosis and prognosis of hematologic comorbid pneumonia, helping patients to obtain timely and effective treatment, and giving guidance on the overall treatment plan for patients, with particular benefit for patients with hematologic chemotherapy comorbid pneumonia.

Metabolomic profiling of exhaled breath condensate for the diagnosis of pulmonary aspergillosis

Objective

This study aims to ascertain the unique metabolic profile of exhaled breath condensate (EBC) samples in pulmonary aspergillosis (PA) patients, and explore their usefulness for the diagnosis of PA.

Methods

A total of 133 patients were included in the study, including 66 PA patients (invasive pulmonary aspergillosis, n=3; chronic pulmonary aspergillosis, n=60; allergic bronchopulmonary aspergillosis, n=3) and controls (n=67). Ultra high-performance liquid chromatography coupled with high-resolution mass spectrometry(UHPLC-HRMS) was used to analyze EBC samples. Metabolic profiling of EBC samples that were collected from 22 CPA patients at various times during treatment (before treatment, &lt;1 month, 1–2 months, 2–3 months, 3–6 months, and ≥6 months after treatment initiation) were performed using UHPLC-HRMS. Potential biomarkers were evaluated using cluster analysis, Venn diagram and receiver operating characteristic analysis (ROC).

Results

A total of 47 metabolites of potential interest were detected in the EBC samples. Further investigation showed that Asperpyrone C, Kotanin, Terphenyllin, Terrelumamide B, and Cyclotryprostatin D could be used as a diagnostic biomarker for PA. The classification between metabolic profiling of EBC samples from PA patients and controls was good with a sensitivity of 100%, specificity 89.6% for patients with PA, respectively. Venn diagram analysis of these biomarker candidates displayed three main types of compounds, which could be used for the further discrimination of aspergilloma and chronic cavitary PA. In addition, antifungal treatment had a limited influence on the value of the EBC results.

Conclusions

This metabolomic approach using UHPLC-HRMS could be used as a noninvasive method for the diagnosis of PA.

Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission?

Aedes aegypti and Aedes albopictus are the main vectors of highly pathogenic viruses for humans, such as dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which cause febrile, hemorrhagic, and neurological diseases and remain a major threat to global public health. The high ecological plasticity, opportunistic feeding patterns, and versatility in the use of urban and natural breeding sites of these vectors have favored their dispersal and adaptation in tropical, subtropical, and even temperate zones. Due to the lack of available treatments and vaccines, mosquito population control is the most effective way to prevent arboviral diseases. Resident microorganisms play a crucial role in host fitness by preventing or enhancing its vectorial ability to transmit viral pathogens. High-throughput sequencing and metagenomic analyses have advanced our understanding of the composition and functionality of the microbiota of Aedes spp. Interestingly, shotgun metagenomics studies have established that mosquito vectors harbor a highly conserved virome composed of insect-specific viruses (ISV). Although ISVs are not infectious to vertebrates, they can alter different phases of the arboviral cycle, interfering with transmission to the human host. Therefore, this review focuses on the description of Ae. aegypti and Ae. albopictus as vectors susceptible to infection by viral pathogens, highlighting the role of the microbiota-virome in vectorial competence and its potential in control strategies for new emerging and re-emerging arboviruses.

Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections

OBJECTIVES

This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections (LRTIs).

METHODS

This retrospective study reviewed patients with suspected LRTIs in Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; and outcomes were recorded and analyzed.

RESULTS

mNGS identified pathogenic microbes in 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before the mNGS tests. Single bacterial infection (35/100, 35%) was the most common type of infection in patients with positive mNGS results, followed by single fungal infection (14/100, 14%), bacterial-viral co-infection (14/100, 14%), single viral infection (12/100, 12%), bacterial-fungal co-infection (9/100, 9%), fungal-viral co-infection (9/100, 9%), and bacterial-fungal-viral co-infection (7/100, 7%). Moreover, compared with culture test, mNGS showed higher sensitivity (63/85, 74.1% vs. 22/85, 25.9% P=0.001) and lower processing time (24 h vs 48 h). Antibiotic treatment was adjusted or confirmed based on the mNGS results in 123 (87.9%) patients, including 5 (3.6%), 33 (23.6%) and 85 (60.7%) patients in whom treatment was downgraded, upgraded and unchanged, respectively, and almost all patients, regardless of escalation, de-escalation, or no change in treatment, showed significant improvement in clinical symptoms and inflammatory indicators. Additionally, 17 (12.1%) patients were referred to Wuhan Pulmonary Hospital for further treatment because of confirmed or suspected tuberculosis.

CONCLUSIONS

mNGS could be a promising technique for microbiological diagnosis and antibiotic management, potentially improving outcomes of patients.

Early detection of gram‑negative bacteria using metagenomic next‑generation sequencing in acute respiratory distress syndrome: A case report

Metagenomic next-generation sequencing (mNGS) is an effective method that can be used for the identification of early pathogens in patients with suspected severe pneumonia. However, the potential of mNGS for evaluating the prognosis of acute respiratory distress syndrome (ARDS) in patients with severe pneumonia remains unclear. In the present report, hospital-acquired gram-negative bacteria infections were detected in a case using metagenomic next-generation sequencing (mNGS) in a sample of bronchoalveolar fluid. This was obtained from a 58-year-old male patient with traumatic wet lung after a neurosurgery. According to the results, of which the profiles of the resistance genes were detected by mNGS, drugs designed to control infection were adjusted, namely to polymyxin B (500,000 U/12 h), azithromycin (0.5 g/24 h) and ganciclovir (0.25 g/12 h). Following adjusting treatment for 8 days, the symptoms of lung infection and hypoxemia were markedly improved, resulting in the patient being transferred out of the intensive care unit 15 days after treatment. To conclude, observations from the present report suggest that mNGS is a useful method for the early identification of pathogens in patients with pneumonia caused by ARDS. However, further studies are required to identify the complementary role of mNGS in supporting conventional microbiological methods in routine clinical practice.

Metagenomic Next-Generation Sequencing Versus Traditional Laboratory Methods for the Diagnosis and Treatment of Infection in Liver Transplantation

Background

Metagenomic next-generation sequencing (mNGS) has emerged as an effective method for the noninvasive and precise detection of infectious pathogens. However, data are lacking on whether mNGS analyses could be used for the diagnosis and treatment of infection during the perioperative period in patients undergoing liver transplantation (LT).

Methods

From February 2018 to October 2018, we conducted an exploratory study using mNGS and traditional laboratory methods (TMs), including culture, serologic assays, and nucleic acid testing, for pathogen detection in 42 pairs of cadaveric liver donors and their corresponding recipients. Method performance in determining the presence of perioperative infection and guiding subsequent clinical decisions was compared between mNGS and TMs.

Results

The percentage of liver donors with mNGS-positive pathogen results (64.3%, 27/42) was significantly higher than that using TMs (28.6%, 12/42; P&lt;0.05). The percentage of co-infection detected by mNGS in liver donors was 23.8% (10/42) significantly higher than 0.0% (0/42) by TMs (P&lt;0.01). Forty-three pathogens were detected using mNGS, while only 12 pathogens were identified using TMs. The results of the mNGS analyses were consistent with results of the TM analyses in 91.7% (11/12) of donor samples at the species level, while mNGS could be used to detect pathogens in 66.7% (20/30) of donors deemed pathogen-negative using TMs. Identical pathogens were detected in 6 cases of donors and recipients by mNGS, among which 4 cases were finally confirmed as donor-derived infections (DDIs). For TMs, identical pathogens were detected in only 2 cases. Furthermore, 8 recipients developed early symptoms of infection (&lt;7 days) after LT; we adjusted the type of antibiotics and/or discontinued immunosuppressants according to the mNGS results. Of the 8 patients with infections, 7 recipients recovered, and 1 patient died of severe sepsis.

Conclusions

Our preliminary results show that mNGS analyses can provide rapid and precise pathogen detection compared with TMs in a variety of clinical samples from patients undergoing LT. Combined with symptoms of clinical infection, mNGS showed superior advantages over TMs for the early identification and assistance in clinical decision-making for DDIs. mNGS results were critical for the management of perioperative infection in patients undergoing LT.

Application of Next-Generation Sequencing in Infections After Allogeneic Haematopoietic Stem Cell Transplantation: A Retrospective Study

This retrospective study aimed to determine the characteristics of infection and diagnostic efficacy of next-generation sequencing (NGS) in patients with fever after allogeneic hematopoietic stem cell transplantation (allo-HSCT). A total of 71 patients with fever after HSCT were enrolled in this study. Compared with conventional microbiological test (CMT), we found that the sensitivity of NGS versus CMT in peripheral blood samples was 91.2% vs. 41.2%, and that NGS required significantly less time to identify the pathogens in both monomicrobial infections (P=0.0185) and polymicrobial infections (P= 0.0027). The diagnostic performance of NGS was not affected by immunosuppressant use. Viruses are the most common pathogens associated with infections. These results indicated that the sensitivity, timeliness, and clinical significance of NGS are superior for the detection of infections. Although NGS has the advantage of identifying a wide range of potential pathogens, the positive rate is related closely to the sample type. Therefore, we recommend that, in the clinical application of NGS to detect pathogens in patients after allo-HSCT, an appropriate sample type and time should be selected and submitted to improve the positive rate and accuracy of NGS. NGS holds promise as a powerful technology for the diagnosis of fever after HSCT.

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.