Metagenomic Next-Generation Sequencing Can Clinch Diagnosis of Non-Tuberculous Mycobacterial Infections: A Case Report

Primary cutaneous Mycobacteria avium complex infection in a systemic lupus erythematosus patient: A case report and review

RATIONALE

Nontuberculous mycobacteria infection is becoming more and more common in clinical practice, while skin and soft tissue infection is an important part. The evaluation of the immune status of patients has certain reference value for diagnosis and treatment.

PATIENT CONCERNS

A 48-year-old woman developed an erythematosus nodule with purulent discharge on the right hip for 4 months. She had a history of systemic lupus erythematosus for more than 20 years, in stable control with prednisone 10 mg/d, azathioprine 50 mg/12 h, and hydroxychloroquine 200 mg/12 h. There was no trauma prior to the lesion.

DIAGNOSES

After excluding other sites involved, the patient was diagnosed as Mycobacterium avium primary cutaneous infection based on laboratory culture, biopsy, and sequencing techniques.

INTERVENTIONS

After surgical resection, a combination of oral azithromycin, rifampicin, and ethambutol hydrochloride was given.

OUTCOMES

The lesion healed after 4 months with no relapse.

LESSONS

Primary cutaneous nontuberculous mycobacteria infection should raise more attention in immunocompromised and even immunocompetent populations.

Case report: co-infection of Scedosporium and Mycobacterium in lungs

Background

There are hundreds of pathogens that cause lung infections. Compared to infections caused by a single pathogen, mixed infections account for a larger proportion of pulmonary infections and have a more severe clinical presentation, while treatment options differ between the two. We aimed to explore the advantages of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of mixed infections.

Case Description

To investigate the specific pathogens in a 79-year-old male pneumonia patient who had recurrent cough with poor empirical treatment, we collected bronchoalveolar lavage fluid (BALF) from the patient and performed mNGS technology, along with Sanger sequencing and polymerase chain reaction (PCR) was carried out to confirm the authenticity of the pathogens detected by mNGS. The findings showed that rare pathogen Scedosporium boydii (S. boydii, reads: 18) and Mycobacterium avium complex (MAC, reads: 19) were detected, and the patient was subsequently transferred to another hospital for the same mNGS with the same results as the first detection. Therefore, combined treatment with voriconazole, ethambutol, azithromycin, and levofloxacin were given to the S. boydii and MAC for 1 week, and then patient's condition improved and discharged.

Conclusions

mNGS, a non-targeted sequencing technology, could improve the efficiency of clinical diagnosis for mixed infection of rare or atypical pathogens, bring new ideas for clinical pathogen diagnosis, and improve patient prognosis.

Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification

Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.

Nanopore sequencing for smear-negative pulmonary tuberculosis-a multicentre prospective study in China

PURPOSE

In this prospective study, the diagnosis accuracy of nanopore sequencing-based Mycobacterium tuberculosis (MTB) detection was determined through examining bronchoalveolar lavage fluid (BALF) samples from pulmonary tuberculosis (PTB) -suspected patients. Compared the diagnostic performance of nanopore sequencing, mycobacterial growth indicator tube (MGIT) culture and Xpert MTB/rifampin resistance (MTB/RIF) assays.

METHODS

Specimens collected from suspected PTB cases across China from September 2021 to April 2022 were tested then assay diagnostic accuracy rates were compared.

RESULTS

Among the 111 suspected PTB cases that were ultimately diagnosed as PTB, the diagnostic rate of nanopore sequencing was statistically significant different from other assays (P < 0.05). Fleiss' kappa values of 0.219 and 0.303 indicated fair consistency levels between MTB detection results obtained using nanopore sequencing versus other assays, respectively. Respective PTB diagnostic sensitivity rates of MGIT culture, Xpert MTB/RIF and nanopore sequencing of 36.11%, 40.28% and 83.33% indicated superior sensitivity of nanopore sequencing. Analysis of area under the curve (AUC), Youden's index and accuracy values and the negative predictive value (NPV) indicated superior MTB detection performance for nanopore sequencing (with Xpert MTB/RIF ranking second), while the PTB diagnostic accuracy rate of nanopore sequencing exceeded corresponding rates of the other methods.

CONCLUSIONS

In comparison with MGIT culture and Xpert MTB/RIF assays, BALF's nanopore sequencing provided superior MTB detection sensitivity and thus is suitable for testing of sputum-scarce suspected PTB cases. However, negative results obtained using these assays should be confirmed based on additional evidence before ruling out a PTB diagnosis.

Diagnosis of mycobacterium avium complex infection utilizing metagenomics next-generation sequencing: a case report

Mycobacterium avium-intracellulare complex (MAC) is a type of nontuberculous mycobacteria (NTM) and is associated with underlying pulmonary diseases, such as chronic obstructive pulmonary disease, bronchiectasis, chronic aspiration or recurrent pneumonia, inactive or active tuberculosis, pneumoconiosis, and bronchogenic carcinoma. The risk factors for NTM-PD include host, drug, and environmental factors. In this report, we present the case of a 61-year-old man who developed bilateral lung nodules and was experiencing severe hemoptysis. The repeat acid-fast bacilli test performed on both sputum and bronchoalveolar lavage fluid (BALF) samples showed a negative result, as did the GeneXpert test. We employed metagenomic next-generation sequencing (mNGS) to analyze the lung nodule and BALF samples collected from the patient. Both samples tested positive for MAC within 3 days. In addition, traditional MAC culture, conducted for 2 months, confirmed the growth of MAC in the patient's BALF. Then, the patient was treated accordingly. Following treatment, a high-resolution chest computed tomography scan revealed a significant reduction in lung nodules of the patient after 2 months. These results indicate that MAC-associated lung nodules were responsible for the patient's symptoms, emphasizing the need for vigilance in diagnosing MAC infection in the patient without predisposing conditions. Furthermore, these results highlight the potential utility of mNGS as a promising rapid diagnostic tool for MAC infection and its potential role in the diagnosis of NTM disease.

Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis

BACKGROUND

To determine the diagnostic accuracy of a nanopore sequencing assay of PCR products from a M. tuberculosis complex-specific region for testing of bronchoalveolar lavage fluid (BALF) samples or sputum samples from suspected pulmonary tuberculosis (PTB) patients and compare the results to results obtained for MGIT and Xpert assays.

METHODS

Cases with suspected PTB (n = 55) were diagnosed from January 2019 to December 2021 based on results of nanopore sequencing, MGIT culture, and Xpert MTB/RIF testing of BALF and sputum samples collected during hospitalization. Diagnostic accuracies of assays were compared.

RESULTS

Ultimately, data from 29 PTB patients and 26 non-PTB cases were analyzed. PTB diagnostic sensitivities of MGIT, Xpert MTB/RIF, and nanopore sequencing assays were 48.28%, 41.38%, and 75.86%, respectively, thus demonstrating that nanopore sequencing provided greater sensitivity than was provided by MGIT culture and Xpert assays (P < 0.05). PTB diagnostic specificities of the respective assays were 65.38%, 100%, and 80.77%, which corresponded with kappa coefficient (κ) values of 0.14, 0.40, and 0.56, respectively. These results indicate that nanopore sequencing provided superior overall performance as compared to Xpert and MGIT culture assays and provided significantly greater PTB diagnostic accuracy than Xpert and sensitivity comparable to that of the MGIT culture assay.

CONCLUSION

Our findings suggest that improved detection of PTB in suspected cases was achieved using nanopore sequencing-based testing of BALF or sputum samples than was achieved using Xpert and MGIT culture-based assays, and nanopore sequencing results alone cannot be used to rule out PTB.

Biofilm infection of a central venous port-catheter caused by Mycobacterium avium complex in an immunocompetent child with cystic fibrosis

BACKGROUND

Mycobacterium (M.) chimaera is a non-tuberculous mycobacterium (NTM) that belongs to M. avium complex (MAC). In patients with cystic fibrosis (CF), MAC can cause bronchopulmonary infections that can be prolonged and difficult to treat. MAC infections of sites other than the lungs or central catheters are rare and almost exclusively associated with immunodeficiency.

CASE PRESENTATION

We present a case of an 8-year-old CF patient (delF508 homozygous) with recurrent pulmonary exacerbations, gradual clinical deterioration, B-symptoms (fever, fatigue, weight loss, night sweat), elevated transaminases and intermittent detection of M. chimaera in the sputum without radiological signs of NTM-associated lung disease with a central venous port-catheter. Next-generation sequencing (NGS) revealed M. chimaera port infection that was also confirmed by mycobacterial culture. The patient recovered within 4 weeks after removal of the catheter and initiation of MAC targeted antimicrobial therapy. Electron microscopy of the catheter illustrated the presence of mycobacteria in a biofilm.

CONCLUSIONS

MAC central venous catheter infection needs to be considered in immunocompetent people. NGS is a valuable tool for rapid identification of rare infections. MAC capability of biofilm formation renders catheter removal the central therapeutic intervention for the clearance of the infection.

Diagnostic performance of metagenomic next-generation sequencing in non-tuberculous mycobacterial pulmonary disease when applied to clinical practice

OBJECTIVE

To compare non-tuberculous mycobacterial pulmonary disease (NTMPD) diagnosis by metagenomic next-generation sequencing (mNGS) with Bactec mycobacterial growth indicator tube (MGIT) 960.

METHODS

A total of 422 patients with suspected NTMPD in Shanghai Pulmonary Hospital between January 2020 and May 2021 were retrospectively analyzed; 194 were diagnosed with NTMPD. The diagnostic performance of mNGS and MGIT 960 for NTMPD was assessed. Receiver operating characteristic (ROC) curves and areas under curve (AUCs) were compared.

RESULTS

The sensitivity of mNGS in NTMPD diagnosis was 81.4% and higher than that of MGIT 960 (53.6%). The specificity of mNGS in NTMPD diagnosis was 97.8%, similar to that of MGIT 960 (100%). The sensitivity of combined mNGS and MGIT 960 in NTMPD diagnosis was 91.8%. The sensitivity of mNGS for bronchoalveolar lavage fluid (BALF), pulmonary puncture tissue fluid, and sputum was 84.8%, 80.6%, and 77.5%, respectively; all were higher than that of MGIT 960 (P < 0.05). The AUC of mNGS and MGIT 960 was 0.897 and 0.768, respectively. The AUC of mNGS were BALF (0.916), pulmonary puncture tissue fluid (0.903), and sputum (0.870).

CONCLUSION

The sensitivity of mNGS was superior to that of Bactec MGIT 960; the specificity in NTMPD diagnosis was similar. mNGS shows effective performance in NTMPD diagnosis.

Use of Quantitative Metagenomics Next-Generation Sequencing to Confirm Fever of Unknown Origin and Infectious Disease

A body temperature >38.3°C that lasts ≥3 weeks and lacks a clear diagnosis after 1 week of standard hospital examination and treatment is called "fever of unknown origin" (FUO). The main causes of FUO are infections, hematological diseases, autoimmune diseases, and other non-infectious inflammatory diseases. In recent years, quantitative metagenomics next-generation sequencing (Q-mNGS) has been used widely to detect pathogenic microorganisms, especially in the contribution of rare or new (e.g., severe acute respiratory syndrome-coronavirus-2) pathogens. This review addresses the undetermined cause of fever and its evaluation by Q-mNGS.

Rapid Diagnosis of Mycobacterium marinum Infection by Next-Generation Sequencing: A Case Report

We present the first report of histology- and culture-proven Mycobacterium marinum infection diagnosed by next-generation sequencing (NGS). It took &lt;2 days to make a microbiological diagnosis using the Oxford Nanopore Technologies' MinION device, compared to 20 days for the mycobacterium to be isolated from the tissue biopsy. NGS is particularly useful for culture-negative and slow-growing microorganism infections, such as mycobacterial, fungal and partially treated pyogenic bacterial infections. Due to its low equipment cost, short turn-around-time and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.