Applying the pathogen-targeted next-generation sequencing method to pathogen identification in cerebrospinal fluid

Comparison of targeted next-generation sequencing and metagenomic next-generation sequencing in the identification of pathogens in pneumonia after congenital heart surgery: a comparative diagnostic accuracy study

BACKGROUND

This study aimed to compare targeted next-generation sequencing (tNGS) with metagenomic next-generation sequencing (mNGS) for pathogen detection in infants with severe postoperative pneumonia after congenital heart surgery.

METHODS

We conducted a retrospective observational study using data from the electronic medical record system of infants who developed severe pneumonia after surgery for congenital heart disease from August 2021 to August 2022. Infants were divided into tNGS and mNGS groups based on the pathogen detection methods. The primary outcome was the efficiency of pathogen detection, and the secondary outcomes were the timeliness and cost of each method.

RESULTS

In the study, 91 infants were included, with tNGS detecting pathogens in 84.6% (77/91) and mNGS in 81.3% (74/91) of cases (P = 0.55). No significant differences were found in sensitivity, specificity, PPA, and NPA between the two methods (P > 0.05). tNGS identified five strains with resistance genes, while mNGS detected one strain. Furthermore, tNGS had a faster detection time (12 vs. 24 h) and lower cost ($150 vs. $500) compared to mNGS.

CONCLUSION

tNGS offers similar sensitivity to mNGS but with greater efficiency and cost-effectiveness, making it a promising approach for respiratory pathogen detection.

Evaluation of metagenomic and pathogen-targeted next-generation sequencing for diagnosis of meningitis and encephalitis in adults: A multicenter prospective observational cohort study in China

BACKGROUND

Next-generation sequencing (NGS) might aid in the identification of causal pathogens. However, the optimal approaches applied to cerebrospinal fluid (CSF) for detection are unclear, and studies evaluating the application of different NGS workflows for the diagnosis of intracranial infections are limited.

METHODS

In this multicenter, prospective observational cohort study, we described the diagnostic efficacy of pathogen-targeted NGS (ptNGS) and metagenomic NGS (mNGS) compared to that of composite microbiologic assays, for infectious meningitis/encephalitis (M/E).

RESULTS

In total, 152 patients diagnosed with clinically suspected M/E at four tertiary hospitals were enrolled; ptNGS and mNGS were used in parallel for pathogen detection in CSF. Among the 89 patients who were diagnosed with definite infectious M/E, 57 and 39 patients had causal microbial detection via ptNGS and mNGS, respectively. The overall accuracy of ptNGS was 65.1%, with a positive percent agreement (PPA) of 64% and a negative percent agreement (NPA) of 66.7%; and the overall accuracy of mNGS was 47.4%, with a PPA of 43.8% and an NPA of 52.4% after discrepancy analysis. There was a significant difference in the detection efficiency between these two methods both for PPA (sensitivity) and overall accuracy for pathogen detection (P < 0.05).

CONCLUSIONS

NGS tests have provided new information in addition to conventional microbiologic tests. ptNGS seems to have superior performance over mNGS for common causative pathogen detection in CSF for infectious M/E.

Coxsackie B virus-induced myocarditis in a patient with a history of lymphoma: A case report and review of literature

INTRODUCTION

In rare occasions, coxsackievirus infections can cause serious illness, such as encephalitis and myocarditis. The immunotherapies of cancer could increase the risk of myocarditis, especially when applying immune checkpoint inhibitors. Herein, we report a rare case of Coxsackie B virus-induced myocarditis in a patient with a history of lymphoma.

CASE PRESENTATION

A 32-year-old woman was admitted to the hospital with recurrent fever for more than 20 days, and she had a history of lymphoma. Before admission, the positron emission tomography/computed tomography result indicated that the patient had no tumor progression, and she was not considered the cancer-related fever upon arriving at our hospital. Patient's red blood cell, platelet count, and blood pressure were decreased. In addition, she had sinus bradycardia and 3 branch blocks, which was consistent with acute high lateral and anterior wall myocardial infarction. During hospitalization, the patient had recurrent arrhythmia, repeated sweating, poor mentation, dyspnea, and Coxsackie B virus were detected in patient's blood samples by pathogen-targeted next-generation sequencing. The creatine kinase, creatine kinase MB, and N-terminal pro-brain natriuretic peptide were persistently elevated. Consequently, the patient was diagnosed with viral myocarditis induced by Coxsackie B virus, and treated with acyclovir, gamma globulin combined with methylprednisolone shock therapy, trimetazidine, levosimendan, sildenan, continuous pump pressors with m-hydroxylamine, entecavir, adefovir, glutathione, pantoprazole, and low-molecular-weight heparin. Her symptoms worsened and died.

CONCLUSION

We reported a case with a history of lymphoma presented with fever, myocardial injury, who was ultimately diagnosed with Coxsackie B virus-induced myocarditis. Moreover, pathogen-targeted next-generation sequencing indeed exhibited higher sensitivity compared to mNGS in detecting Coxsackie B virus.

Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario

Introduction

Infectious diseases are major causes of morbidity and mortality worldwide, necessitating the rapid identification and accurate diagnosis of pathogens. While unbiased metagenomic next-generation sequencing (mNGS) has been extensively utilized in clinical pathogen identification and scientific microbiome detection, there is limited research about the application of nanopore platform-based mNGS in the diagnostic performance of various infectious fluid samples.

Methods

In this study, we collected 297 suspected infectious fluids from 10 clinical centers and detected them with conventional microbiology culture and nanopore platform-based mNGS. The objective was to assess detective and diagnostic performance of nanopore-sequencing technology (NST) in real-world scenarios.

Results

Combined with gold-standard culture and clinical adjudication, nanopore sequencing demonstrated nearly 100% positive predictive agreements in microbial-colonized sites, such as the respiratory and urinary tracts. For samples collected from initially sterile body sites, the detected microorganisms were highly suspected pathogens, and the negative predictive agreements were relatively higher than those in the microbial-colonized sites, particularly with 100% in abscess and 95.7% in cerebrospinal fluid. Furthermore, consistent performance was also observed in the identification of antimicrobial resistance genes and drug susceptibility testing of pathogenic strains of Escherichia coli, Staphylococcus aureus, and Acinetobacter baumannii.

Discussion

Rapid NST is a promising clinical tool to supplement gold-standard culture, and it has the potential improve patient prognosis and facilitate clinical treatment of infectious diseases.

Next-Generation Sequencing-Based Identification of Enterobacter hormaechei as Causative Agent of High Mortality Disease in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) Mice

NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice, lacking many components of a mature immune system, are at increased risk of disease. General understanding of potential pathogens of these mice is limited. We describe a high mortality disease outbreak caused by an opportunistic bacterial infection in NSG mice. Affected animals exhibited perianal fecal staining, dehydration, and wasting. Histopathologic lesions included a primary necrotizing enterocolitis, with inflammatory and necrotizing lesions also occurring in the liver, kidneys, heart, and brain of some mice. All affected individuals tested negative for known opportunistic pathogens of immunodeficient mice. We initially identified a member of Enterobacter cloacae complex (ECC) in association with the outbreak by traditional diagnostics. ECC was cultured from extraintestinal organs, both with and without histopathologic lesions, suggesting bacteremia. Infrared spectroscopy and MALDI-TOF mass spectrometry demonstrated that isolates from the outbreak shared molecular features and likely a common origin. We subsequently hypothesized that advanced sequencing methods would identify a single species of ECC associated with clinical disease. Using a novel targeted amplicon-based next-generation sequencing assay, we identified Enterobacter hormaechei in association with this outbreak. Knowledge of this organism as a potential opportunistic pathogen in NSG mice is critical for preclinical studies to prevent loss of animals and confounding of research.

A case report of diagnosis and dynamic monitoring of Listeria monocytogenes meningitis with NGS

Listeria monocytogenes (LM) infections of the central nervous system are deadly and have vague symptoms. Traditional cerebro spinal fluid culture has a low positive rate, and because antibiotic use is common following therapy, it is more challenging to assess the response from pathogen content. In this case, a 66-year-old man who had a fever, a headache, and vomit was admitted to the hospital. He had diabetes, decline in thyroid function, and a history of pituitary tumor removal surgery. His initial treatment with ribavirin, ceftriaxone antibiotic, and moxifloxacin did not go well. Using two etiological tests (culture and metagenomic next-generation sequencing [mNGS]), his cerebrospinal fluid tested positively for LM. Ampicillin-sulbactam and meropenem were used as treatments once LM meningitis was identified. After treatment, his cerebrospinal fluid was assessed once more. Culture: negative; targeted next-generation sequencing (tNGS): positive and shows changes in the copy number of the LM. After 44 days of treatment, the patient finally stopped taking antibiotics, and the prognosis was good. Our study showed that mNGS and tNGS, as novel approaches for pathogen detection, are capable of identifying pathogens quickly, sensitively, and accurately, especially when there are few infections present (such as after antibiotic treatment). The two methods can be a powerful assistance for helping clinicians to choose the best course of action.

Disseminated Mycobacterium thermoresistibile Infection presented with Lymphadenectasis in an AIDS patient: case report and review of literature

BACKGROUND

Nontuberculous mycobacteria disease is a common invasive infectious disease in patients with HIV. However, Mycobacterium thermoresistibile association with lymphadenectasis is unusual in AIDS patients.

CASE PRESENTATION

This report covers the case of a 25-year-old male AIDS patient infected with Mycobacterium thermoresistibile. The case was identified via pathogen-targeted next-generation sequencing (ptNGS).

CONCLUSION

This is the first report of disseminated M. thermoresistibile infection presented with lymphadenectasis in an AIDS patient. Prompt diagnosis and antimicrobial treatment are crucial.

Meningitis caused by oral anaerobes detected using mNGS tool: a case report and review of literature

BACKGROUND

Bacterial meningitis is a central nervous system (CNS) infection disease of the meninges and brain parenchyma caused by the bacteria. Few cases of meningitis related to oral anaerobes have been reported in the literature. Here, we report a case of meningitis in a middle-aged woman, caused by oral anaerobes.

CASE PRESENTATION

A 58-year-old woman was admitted to hospital with fever, headache for 21 days and left limb weakness for 2 days. The blood cell counts (11.73 × 109/L), neutrophil counts (9.22 × 109/L) and high-sensitivity C-reactive protein levels (> 5.00 mg/L) were elevated. The brain computerized tomography (CT) scanning indicated the new right thalamus infarct. The brain cranial-enhanced magnetic resonance imaging (MRI) showed the right lateral paraventricular and right thalamic infarct, and abnormal signal in occipital horns of bilateral lateral ventricles were increased. In addition, the brain enhanced nuclear magnetic resonance (NMR) scanning suggested that meninges were thickened and enhanced at the base of the brain, with meningitis changes. The neck CT angiography (CTA) revealed arteriosclerotic changes. The metagenomic next-generation sequencing (mNGS) revealed Eubacterium brachy, Porphyromonas gingivalis, Fusobacterium nucleatum and Torque teno virus in her cerebrospinal fluid (CSF). The patient was diagnosed with purulent meningitis caused by infection of oral anaerobes, and treated with mannitol, ceftriaxone and vancomycin. Her symptoms alleviated. Subsequently, she was transferred to the infectious department and treated with ceftriaxone plus metronidazole (anti-anaerobes) and mannitol (reduce intracranial pressure). Her symptoms improved and currently received rehabilitation treatment.

CONCLUSION

We herein report a rare case involving meningitis caused by infection of oral anaerobes. The mNGS can accurately detect the pathogens of infectious diseases.

Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis

Objectives

Periprosthetic joint infection (PJI) diagnosis remains challenging, and the identification of the causative microorganism is, by far, the most important aspect. Here, we use multiple PCR-based targeted next-generation sequencing (tNGS) to detect pathogens in PJI. To explore 1. the ability of targeted next-generation sequencing (tNGS) to detect pathogens in PJI; 2. the consistency of tNGS, metagenomic NGS (mNGS), and culture results; and 3. the ability of tNGS to detect drug resistance genes in PJI.

Methods

PJI was diagnosed according to the Musculoskeletal Infection Society (MSIS) criteria. The microorganisms were detected by culture, mNGS and tNGS to compare the diagnostic effectiveness of the three methods for PJI and to compare their consistency in detecting microorganisms. Drug resistance genes were detected using tNGS. The costs and turnaround times of mNGS and tNGS were compared.

Results

Forty-three patients with PJI, 21 patients without PJI and 10 negative control cases were included. The culture, tNGS, and mNGS sensitivities for PJI diagnosis were 74.41%, 88.37%, and 93.02%, respectively, with no significant differences. The specificities were 90.48%, 95.24%, and 95.24%, respectively, with no significant differences. tNGS detected drug resistance genes in 37.5% of culture-positive PJIs. tNGS was superior to mNGS for turnaround time (14.5 h vs. 28 h) and cost ($150 vs. $260).

Conclusions

tNGS can effectively identify PJI pathogens and may provide drug resistance information, while tNGS is superior to mNGS regarding cost and turnaround time. A multidisciplinary, multi-technology based algorithm to diagnose PJI is appropriate.

Highlights

298 microorganisms and 86 drug resistance genes were included in the tNGS panel.Diagnostic efficacy of tNGS is not inferior to that of commonly used indicators.tNGS is superior to mNGS in cost and turnaround time.

Diagnosis of Coxiella burnetii Prosthetic Joint Infection Using mNGS and ptNGS: A Case Report and Literature Review

BACKGROUND

Coxiella burnetii (C. burnetii) is the causative agent of Q fever and is found worldwide; however, prosthetic joint infections caused by C. burnetii are rarely seen. Because of advances in molecular diagnostic techniques, prosthetic joint infection (PJI) caused by C. burnetii can now be diagnosed.

CASE PRESENTATION

A 77-year-old male who had undergone total knee arthroplasty had a displaced prosthesis and periprosthetic osteolysis; he had no obvious signs of infection, and microbiological culture was negative. However, C. burnetii was detected by metagenomic next-generation sequencing (mNGS) and pathogen-targeted next-generation sequencing (ptNGS). Finally, polymerase chain reaction (PCR) confirmed the diagnosis of C. burnetii prosthetic joint infection (PJI). After revision surgery (one-stage revision) and oral antibiotics (doxycycline and moxifloxacin hydrochloride), the patient's symptoms disappeared, and he regained the ability to walk. During the 6-month follow-up, the patient's knee showed no signs of swelling, pain or the recurrence of infection, and he experienced no significant complications. We also present a review of the literature for other cases of C. burnetii PJI.

CONCLUSIONS

The symptoms of C. burnetii PJI may be different from those of Q fever, which may lead to misdiagnosis. mNGS and ptNGS may be helpful for the identification of C. burnetii. Once the diagnosis of C. burnetii PJI is confirmed, doxycycline in combination with a fluoroquinolone can be effectively administered after revision surgery.

Central nervous system aspergillosis misdiagnosed as Toxoplasma gondii encephalitis in a patient with AIDS: a case report

Background

Patients with acquired immunodeficiency syndrome (AIDS) tend to suffer from several central nervous system (CNS) infections due to hypoimmunity. However, CNS aspergillosis (CNSAG) is extremely rare and difficult to diagnose. Thus, it is easily misdiagnosed.

Case presentation

We reported a 47-year-old male AIDS patient with ghosting vision and anhidrosis on the left head and face. He was accordingly diagnosed with Toxoplasma gondii encephalitis (TE) at other hospitals, for which he received regular anti-Toxoplasma gondii and anti-human immunodeficiency virus (anti-HIV) treatment. Then, the patient was transferred to our hospital due to a lack of any improvement with the prescribed treatment. The patient's neurological examination revealed no abnormalities at admission, only a slight change in the cerebrospinal fluid. His cranial magnetic resonance imaging (MRI) revealed multiple abnormal signals in the brain parenchyma, and his blood was positive for Toxoplasma gondii IgG antibody. The initial diagnosis at our hospital was also TE. Considering the poor efficacy of anti-TE treatment, cerebrospinal fluid metagenomics next-generation sequencing (mNGS) was performed, but no pathogenic bacteria were detected. However, Aspergillus fumigatus was detected in the cerebrospinal fluid via targeted next-generation sequencing (tNGS) and bronchoalveolar alveolar lavage fluid via mNGS. The diagnosis was accordingly revised to CNSAG combined with his other clinical manifestations. After administering voriconazole antifungal therapy, the patient’s symptoms were relieved, with improved absorption of the intracranial lesions.

Conclusions

The present case experience indicates the need for clinicians to strengthen their understanding of CNSAG. Moreover, for patients with diagnostic difficulties, early mNGS and tNGS (using biological samples with only a few pathogens) are helpful for early diagnosis and treatment, potentially allowing patients to achieve favorable outcomes.

Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art

Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.