Use of Metagenomic Next-Generation Sequencing in the Clinical Microbiology Laboratory

Stratton, Charles W.; Schutzbank, Ted E.; Tang, Yi‐Wei

doi:10.1016/j.jmoldx.2021.09.003

Cited by 13 publications

(9 citation statements)

References 59 publications

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“…Though with higher sensitivity, the detection rate of false-positive pathogens (referred to causative or possibly causative pathogens reported by laboratory) by mNGS is also higher. Thus, it is important to distinguish between true-and false-positive pathogens when interpreting mNGS results for physicians [17]. This is often di cult because of limited con rmatory testing, extra cost and insu cient sample volumes.…”

Section: Discussionmentioning

confidence: 99%

Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice

Lai,

Chen,

Chen

et al. 2024

Preprint

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Background Pulmonary infection remains one of the leading infectious diseases of hospitalization. Metagenomic next-generation sequencing (mNGS) has been proven to be a promising diagnostic technology in etiological identification for pulmonary infection. But when applying mNGS to clinical practice, physicians still face many challenges. Methods We retrospectively analyzed the data of 97 patients admitted to our hospital with suspected pulmonary infection prescribed to mNGS during the past 3 years. The clinical application of mNGS in the diagnosis and management of pulmonary infection and also challenges were investigated. Results Causative or possibly causative pathogens were detected in 63.9% of patients by mNGS, performing consistently well for Mycobacterium tuberculosis, non-tuberculous mycobacteria, fungus and rare pathogens. In 43.3% of patients, 65 microbes reported as causative or possibly causative pathogens by laboratory were reclassified as colonization after fully interpretation by physicians. Antibiotics were adjusted for 34.0% of patients mainly based on positive mNGS results and not adjusted for 41.2% with pathogens identified already covered by empirical therapy or negative mNGS results. Conclusions mNGS is a promising tool in etiological diagnosis of pulmonary infection. However, physicians should go beyond the reported pathogens by laboratory and investigate fully in clinical practice. The effect on clincal treatment deserves further investigation from aspect of cost effectiveness and also application scenarios should be illustrated.

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Section: Discussionmentioning

confidence: 99%

Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice

Lai,

Chen,

Chen

et al. 2024

Preprint

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“…Moreover, mNGS is currently unable to provide reliable data on antimicrobial sensitivity and resistance, suggesting that the professional ability of the result interpretation team, especially infectious disease expertise, is directly related to the clinical utility of mNGS testing ( 21 ). Establishing a clinical microbial sequencing board or team composed of experienced clinical microbiologists, infectious disease specialists, and treating physicians has been strongly recommended to avoid misinterpretation of mNGS results ( 22 ). Our laboratory has established a stable reporting team for the mNGS assay (described in the Supplementary Methods) and carefully interprets each result through close communication with the treating team.…”

Section: Discussionmentioning

confidence: 99%

The Real-World Clinical Impact of Plasma mNGS Testing: an Observational Study

Han

Zhang

et al. 2023

Microbiol Spectr

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In this study, we show that although plasma mNGS testing significantly improved the detection rate of tested samples, nearly one in four (24.5%, 48/196) mNGS tests reported organisms were not clinically relevant, emphasizing the importance of cautious interpretation and infectious disease consultation. Moreover, based on clinical adjudication, plasma mNGS testing resulted in no or a negative impact in nearly half (43.5%, 64/147) of patients in the current study, indicating that how best to integrate this advanced method into current infectious disease diagnostic frameworks to maximize its clinical utility in real-world practice is an important question.

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“…Compared to the traditional fungal culture, which often takes 3–7 days, mNGS provides rapid pathogen detection in <24 h. However, the current cost of mNGS is higher, ¥3000 Renminbi (approximately US$ 500) per sample, compared to fungal culture, which costs 80 Renminbi (approximately US$ 12). Moreover, the lack of standardized criteria for interpreting mNGS results is a considerable challenge and requires collaborations among clinicians, infectious diseases specialists, and clinical microbiologists [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

The first suspected disseminated Hormographiella aspergillata infection in China, diagnosed using metagenomic next-generation sequencing: a case report and literature review

Wang

Song

Han

et al. 2023

Emerging Microbes & Infections

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Hormographiella aspergillata is a rare and emerging cause of invasive mould infections in patients with haematological malignancies, with a mortality rate of approximately 70%. Here, we present the first reported case of suspected disseminated H. aspergillata infection in China. The patient experienced a second relapse of acute myeloid leukaemia and developed neutropenia, fever, discrepant blood pressure between limbs, and cutaneous lesions limited to the left upper extremity. Since lung tissue biopsy was not feasible, metagenomic next-generation sequencing (mNGS) and panfungal polymerase chain reaction (PCR) analysis of bronchoalveolar lavage fluid and blood samples were performed, which indicated probable H. aspergillata pulmonary infection. Histopathology of cutaneous lesions revealed numerous fungal hyphae within dermal blood vessels. mNGS of a skin biopsy sample identified H. aspergillata sequences, and the fungi was subsequently recovered from fungal culture, proving cutaneous H. aspergillata infection. Despite combined antifungal therapy, the patient died owing to disease progression. Additionally, 22 previously reported cases of invasive H. aspergillata infection were reviewed in patients with haematological malignancies. Thus, mNGS is a powerful diagnostic tool for the early and effective detection of invasive H. aspergillata infections, with the advantage of sequencing all potential pathogens, and providing results within 24 h.

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Use of Metagenomic Next-Generation Sequencing in the Clinical Microbiology Laboratory

Cited by 13 publications

References 59 publications

Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice

Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice

The Real-World Clinical Impact of Plasma mNGS Testing: an Observational Study

The first suspected disseminated Hormographiella aspergillata infection in China, diagnosed using metagenomic next-generation sequencing: a case report and literature review

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