Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples.
Chen Yuqian,Feng Wei,Ye Kai,Guo Li,Xia Han,Guan Yuanlin,Chai Limin,Shi Wenhua,Zhai Cui,Wang Jian,Yan Xin,Wang Qingting,Zhang Qianqian,Li Cong,Liu Pengtao,Li Manxiang
Frontiers in cellular and infection microbiology
Background:Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections. Methods:From February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis. Results:We employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases. Conclusions:The study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future.
10.3389/fcimb.2021.541092
Metagenomic next-generation sequencing technology for detection of pathogens in blood of critically ill patients.
Geng Shike,Mei Qing,Zhu Chunyan,Fang Xiaowei,Yang Tianjun,Zhang Lei,Fan Xiaoqin,Pan Aijun
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
OBJECTIVE:To explore the applicability of metagenomic next-generation sequencing (mNGS) technology for the detection of blood pathogens in intensive care unit patients. METHODS:The clinical data of 63 critically ill patients who could not be diagnosed with blood culture (BC) and who underwent mNGS blood sample testing were retrospectively analyzed. The diagnostic efficacy of mNGS was compared with that of traditional detection methods; the distribution of the pathogens identified by mNGS was analyzed; and the differences in laboratory tests, comorbidities, treatment, and prognosis between the mNGS-positive and mNGS-negative groups were compared. RESULTS:The positive rate of mNGS was 41.3% (26/63), and 16 patients were found to have mixed infections. However, the positive rate of BCs performed simultaneously with mNGS was only 7.9% (5/63). The results of univariate analysis showed that the average length of intensive care unit stay (β, -8.689 [95% CI, -16.176, -1.202]; P = 0.026) and the time from onset to sequencing (β, -5.816 [95% CI,-9.936, -1.696]; P = 0.007) of the mNGS-positive group were significantly shorter than those of the mNGS-negative group. More patients in the positive group were adjusted for anti-infective treatment after mNGS (OR, 3.789 [95% CI,1.176, 12.211]; P < 0.001). CONCLUSIONS:Detection of blood pathogens by mNGS has good applicability for critically ill patients who cannot be diagnosed by BC in the early stages of infection, and mNGS should be performed as early as possible to obtain higher pathogen detection rates.
10.1016/j.ijid.2020.11.166
Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections.
Open forum infectious diseases
BACKGROUND:Osteoarticular infections (OAIs) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children. METHODS:This was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children's hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon's discretion per standard care (fluid or tissue) and based on imaging and operative findings. We compared mNGS to culture and usual care testing (culture and polymerase chain reaction [PCR]) from the same site. RESULTS:We recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In 4 subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS. CONCLUSIONS:In this single-site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.
10.1093/ofid/ofab346
Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection.
Xie Guijuan,Zhao Bo,Wang Xun,Bao Liang,Xu Yiming,Ren Xian,Ji Jiali,He Ting,Zhao Hongqing
Infectious diseases and therapy
INTRODUCTION:We aimed to explore the real-world clinical application value and challenges of metagenomic next-generation sequencing (mNGS) for pulmonary infection diagnosis. METHODS:We retrospectively reviewed the results of mNGS and conventional tests from 140 hospitalized patients with suspected pulmonary infections from January 2019 to December 2020. The sample types included bronchoalveolar lavage fluid, lung tissue by transbronchial lung biopsy, pleural effusion, blood, and bronchial sputum. Apart from the mNGS reports that our patients received, an extra comprehensive and thorough literature search was conducted. RESULTS:Significant differences were noticed in the positive detection rates of pathogens between mNGS and conventional diagnostic testing (115/140, 82.14% vs 50/140, 35.71%, P < 0.05). The percentage of mNGS-positive patients was significantly higher than that of conventional testing-positive patients with regard to bacterial detection (P < 0.01), but no significant differences were found with regard to fungal detection (P = 0.67). Significant statistical differences were found between mixed infection cases (15, 22.70%) and single infection cases (4, 7.84%) in terms of diabetes (P = 0.03). The most frequent pattern of mixed infection was bacteria and fungi mixed infection (40, 40/89 = 44.94%), followed by bacteria mixed infection (29, 29/89 = 32.58%). The sensitivity of mNGS in pulmonary infection diagnosis was much higher than that of conventional test (89.17% vs 50.00%; P < 0.01), but the specificity was the opposite (75.00% vs 81.82%; P > 0.05). CONCLUSION:mNGS is a valuable tool for the detection of pulmonary infections, especially mixed pulmonary infections. The most common combinations we found were bacterial-fungal coinfection and bacterial-bacterial coinfection. Still, there are many challenges in the clinical application of mNGS in the diagnosis of pulmonary infections. There is still a lot of work to be done in interpreting the mNGS reports, because both clinical judgment and literature analysis strategy need to be refined.
10.1007/s40121-021-00476-w
Optimizing culture methods according to preoperative mNGS results can improve joint infection diagnosis.
Fang Xinyu,Cai Yuanqing,Mei Jian,Huang Zida,Zhang Chaofan,Yang Bin,Li Wenbo,Zhang Wenming
The bone & joint journal
AIMS:Metagenomic next-generation sequencing (mNGS) is useful in the diagnosis of infectious disease. However, while it is highly sensitive at identifying bacteria, it does not provide information on the sensitivity of the organisms to antibiotics. The purpose of this study was to determine whether the results of mNGS can be used to guide optimization of culture methods to improve the sensitivity of culture from intraoperative samples. METHODS:Between July 2014 and October 2019, patients with suspected joint infection (JI) from whom synovial fluid (SF) was obtained preoperatively were enrolled. Preoperative aspirated SF was analyzed by conventional microbial culture and mNGS. In addition to samples taken for conventional microbial culture, some samples were taken for intraoperative culture to optimize the culture method according to the preoperative mNGS results. The demographic characteristics, medical history, laboratory examination, mNGS, and culture results of the patients were recorded, and the possibility of the optimized culture methods improving diagnostic efficiency was evaluated. RESULTS:A total of 56 cases were included in this study. There were 35 cases of JI and 21 cases of non-joint infection (NJI). The sensitivity, specificity, and accuracy of intraoperative microbial culture after optimization of the culture method were 94.29%, 76.19%, and 87.5%, respectively, while those of the conventional microbial culture method were 60%, 80.95%, and 67.86%, respectively. CONCLUSION:Preoperative aspirated SF detected via mNGS can provide more aetiological information than preoperative culture, which can guide the optimization and improve the sensitivity of intraoperative culture. Cite this article: 2021;103-B(1):39-45.
10.1302/0301-620X.103B1.BJJ-2020-0771.R2
Variation, Indispensability, and Masking in the M protein.
Ghosh Partho
Trends in microbiology
The M protein is the major surface-associated virulence factor of group A Streptococcus (GAS) and an antigenically variable target of host immunity. How selection pressures to escape immune recognition, maintain indispensable functions, and mask vulnerabilities have shaped the sequences of the >220M protein types is unclear. Recent experiments have shed light on this question by showing that, hidden within the antigenic variability of many M protein types, are sequence patterns conserved for recruiting human C4b-binding protein (C4BP). Other host factors may be recruited in a similar manner by conserved but hidden sequence patterns in the M protein. The identification of such patterns may be applicable to the development of a GAS vaccine.
10.1016/j.tim.2017.08.002