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Objectives: Metagenomic next-generation sequencing (mNGS) is emerging as a novel diagnostic technology for various infectious diseases; however, limited studies have investigated its application in etiological diagnosis of early onset pneumonia (EOP) among patients undergoing extracorporeal cardiopulmonary resuscitation (ECPR) following in-hospital cardiac arrest (IHCA), The clinical significance of early mNGS in predicting short-term prognosis of IHCA patients after ECPR remains unclear. Methods: This retrospective study included 76 patients with IHCA who underwent ECPR at the First Affiliated Hospital of Zhengzhou University from January 2018 to December 2022. Baseline characteristics and etiological data of all patients during their hospitalization were collected and statistically analyzed. The primary outcome of this study was the diagnosis of EOP, while the secondary outcomes included successful extracorporeal membrane oxygenation (ECMO) weaning and survival at discharge. Additionally, the characteristics of bronchoalveolar lavage fluid (BALF) flora in these patients were compared by analyzing both mNGS results and culture results. Results: Multivariate logistic regression were employed to analyze the predictors of ECMO weaning failure, mortality at discharge, and the incidence of EOP. Ultimately, patients with lower SOFA scores on admission [OR (95%CI): 1.447 (1.107-1.890), p=0.007] and those who underwent early mNGS testing within 48 hours after ECPR [OR (95%CI): 0.273 (0.086-0.865), p=0.027] demonstrated a higher probability of successful weaning from ECMO. Patients with higher SOFA scores on admission [OR (95%CI): 2.404 (1.422-4.064), p=0.001], and elevated lactate levels [OR (95%CI): 1.176 (1.017-1.361), p=0.029] exhibited an increased likelihood of mortality at discharge. Furthermore, early mNGS detection [OR (95%CI): 0.186 (0.035-0.979), p=0.047], and lower CRP levels (48h-7d after ECMO) [OR (95%CI):1.011 (1.003-1.019), p=0.006] were associated with a reduced incidence of EOP. In addition, the pathogens detected by mNGS within 48 hours after ECPR were mainly oral colonizing bacteria and viruses, and viruses were in the majority, while all BALF cultures were negative. In contrast, between 48 hours and 7 days after ECPR, BALF cultures were positive in all EOP patients. Conclusions: Early mNGS testing to identify microbial flora facilitates timely adjustment of antibiotic regimens, thereby reducing the incidence of EOP and improving short-term prognosis in patients undergoing ECPR following IHCA. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens. Methods: In this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. Individuals were classified into PC and non-PC groups according to the diagnostic criteria for PC, and conventional fungal cultures were performed. A serum/BALF cryptococcal antigen (CrAg) test was performed in some patients with PC. The diagnostic efficiencies of three methods for PC (mNGS, conventional culture, and CrAg) were compared. Additionally, two mNGS methods were used in this study: original mNGS (OmNGS, testing time from January 2021 to December 2022) and modified mNGS (MmNGS, testing time from January to December 2023). The diagnostic efficiency of the two mNGS methods on PC was simultaneously compared. Results: Among the 321 patients, 23 (7.2%) had PC and 298 (92.8%) did not. Compared with the composite reference standard for PC diagnosis, the sensitivity, specificity, and accuracy of mNGS for PC were 78.3% (95% confidence interval [CI], 55.8%–91.7%), 98.7% (95% CI, 96.4%–99.6%), and 97.2% (95% CI, 94.7%–98.7%), respectively. The sensitivity of mNGS was similar to that of CrAg (80.0%, 12/15) (P > 0.05). The diagnostic sensitivity of both mNGS and CrAg was higher than that of conventional culture (35.0%, 7/20) (P = 0.006, P = 0.016), and the combined detection of mNGS and CrAg further improved the diagnostic sensitivity of PC (93.3%, 14/15). The area under the receiver operating characteristic curve of mNGS was superior to that of conventional culture (0.885 vs. 0.675). In addition, the diagnostic sensitivity of PC was higher than that of OmNGS (P = 0.046). Conclusion: The sensitivity of mNGS is better than that of conventional culture. The combination of mNGS and CrAg improves the testing sensitivity of Cryptococcus. MmNGS could further improve the detection of Cryptococcus. Conventional PC detection methods are indispensable and mNGS can be used as a rapid and accurate auxiliary diagnostic method for PC. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to identify the risk factors and construct the diagnostic model associated with pneumocystis pneumonia (PCP) in pediatric patients. Methods: This retrospective observational study analyzed 34 cases of PCP and 51 cases of other types of pneumonia treated at Children's Hospital Affiliated to Shandong University between January 2021 and August 2023. Multivariate binary logistic regression was used to identify the risk factors associated with PCP. Receiver operating characteristic curves and calibration plots were constructed to evaluate the diagnostic model. Results: Twenty clinical variables significantly differed between the PCP and non-PCP groups. Multivariate binary logistic regression analysis revealed that dyspnea, body temperature>36.5°C, and age<1.46 years old were risk factors for PCP. The area under the curve of the diagnostic model was 0.958, the P -value of Hosmer‐Lemeshow calibration test was 0.346, the R2 of the calibration plot for the actual and predicted probability of PCP was 0.9555 (P <0.001), and the mean Brier score was 0.069. In addition, metagenomic next-generation sequencing revealed 79.41% (27/34) and 52.93% (28/53) mixed infections in the PCP and non-PCP groups, respectively. There was significantly more co-infection with cytomegalovirus and Streptococcus pneumoniae in the PCP group than that in the non-PCP group (p<0.05). Conclusions: Dyspnea, body temperature>36.5°C, and age<1.46 years old were found to be independent risk factors for PCP in pediatric patients. The probability of co-infection with cytomegalovirus and S. pneumoniae in the PCP group was significantly higher than that in the non-PCP group. [ABSTRACT FROM AUTHOR]

Background: The incidence of non-tuberculous mycobacterium infection has shown a gradual increasing trend in recent years, among which cutaneous manifestations as an important aspect. This study aimed to describe the clinical features and microbiological findings in 6 cases of primary cutaneous nontuberculous mycobacterium infection. Methods: In this retrospective study from June 2021 to June 2022, the clinical data and microbiological results of six cases diagnosed with primary cutaneous non-tuberculous mycobacterium infection in department of dermatology, Hangzhou Third People's Hospital were analyzed. Results: All six cases were primary cutaneous non-tuberculous mycobacterium infections, four of which had a history of trauma or exposure, and two had an underlying disease that could lead to compromised immunity. All patients presented with erythema nodular skin lesions, four on the upper or lower extremities, one on the face, and one on the right hip. The histopathological findings of five patients who underwent biopsy were granulomatous inflammatory changes with mixed infiltration. Laboratory cultures using tissue or tissue fluid were all successful, including four Mycobacterium marinum, one Mycobacterium abscessus, and one Mycobacterium avium. Metagenomics next-generation sequencing detected results consistent with culture colonies in only two cases. With the exception of case 4, all patients responded well to oral medication, with a course of treatment ranging from 4 months to 1 year, and the prognosis was good. Conclusions: The clinical features of primary cutaneous non-tuberculous mycobacterium infection are often lacking in specificity, and the identification of related strains is difficult for a variety of reasons. Although the results of metagenomics next-generation sequencing are useful for pathogen spectrum identification, its diagnostic value should be carefully reevaluated under certain circumstances. Patients with suspected triggers who do not respond well to conventional treatments should be suspected as atypical infection and potential immunosuppression. If diagnosed and treated promptly, the prognosis of primary cutaneous non-tuberculous mycobacterium infection is generally good. [ABSTRACT FROM AUTHOR]

Objective: This study aims to evaluate the clinical management and effectiveness of metagenomic next-generation sequencing (mNGS) in patients with pyogenic spinal infections. Methods: We conducted a retrospective review of 17 patients diagnosed with pyogenic spinal infections and treated at our institution between October 2022 and February 2024. The cohort included 8 males and 9 females, with a mean age of 63.59 ± 10.18 years (range: 41–71 years). The infections comprised 9 epidural abscesses, 6 intervertebral space infections, and 2 deep abscesses. All patients underwent open surgical procedures and mNGS-based bacterial identification using intraoperative pus or tissue specimens, in addition to conventional blood bacterial cultures. Clinical outcomes were assessed using CRP, PCT, WBC inflammatory markers, and VAS scores postoperatively. Results: All 17 patients with pyogenic spinal infections underwent open surgery and mNGS bacterial detection at our institution. Among the 17 patients, mNGS yielded positive results in 14 cases (82.4%), significantly higher than the 5.9% positivity rate of conventional bacterial cultures (p < 0.001). The mNGS test time was notably shorter than conventional cultures (1.0 vs. 5.88 days, p < 0.001). Postoperative antibiotic therapy was adjusted based on mNGS findings. There were significant reductions in postoperative VAS, WBC, PCT, and CRP values compared to preoperative levels (p < 0.01). Conclusion: Metagenomic next-generation sequencing is effective in managing pyogenic spinal infections by facilitating rapid and sensitive detection of pathogens. This technique improves the timeliness and accuracy of diagnosis, highlighting its potential for broader clinical use. [ABSTRACT FROM AUTHOR]

Background: Information on the comparison of blood microbiota between human immunodeficiency virus (HIV)-infected and HIV-uninfected patients with suspected sepsis by metagenomic next-generation sequencing (mNGS) is limited. Methods: Retrospectively analysis was conducted in HIV-infected and HIV-uninfected patients with suspected sepsis at Changsha First Hospital (China) from March 2019 to August 2022. Patients who underwent blood mNGS testing were enrolled. The blood microbiota detected by mNGS were analyzed. Results: A total of 233 patients with suspected sepsis who performed blood mNGS were recruited in this study, including 79 HIV-infected and 154 HIV-uninfected patients. Compared with HIV-uninfected patients, the proportions of mycobacterium (p = 0.001), fungus (p < 0.001) and viruses (p < 0.001) were significantly higher, while the proportion of bacteria (p = 0.001) was significantly lower in HIV-infected patients. The higher positive rates of non-tuberculous mycobacteriosis (NTM, p = 0.022), Pneumocystis jirovecii (P. jirovecii) (p = 0.014), Talaromyces marneffei (T. marneffei) (p < 0.001) and cytomegalovirus (CMV) (p < 0.001) were observed in HIV-infected patients, compared with HIV-uninfected patients. In addition, compared with HIV-uninfected patients, the constituent ratio of T. marneffei (p < 0.001) in the fungus spectrum were significantly higher, while the constituent ratios of Candida (p < 0.001) and Aspergillus (p = 0.001) were significantly lower in HIV-infected patients. Conclusions: Significant differences in the blood microbiota profiles exist between HIV-infected and HIV-uninfected patients with suspected sepsis. [ABSTRACT FROM AUTHOR]

Background: Pantoea agglomerans (P. agglomerans) is a gram-negative bacterium that is commonly isolated from plant surfaces, seeds, and the environment. As an opportunistic pathogen, it can cause blood, urinary and soft tissue infections in immunocompromised patients. In central nervous system, P. agglomerans infection has been report in children and immune-compromised patients, however, infection by such bacterium in nontraumatized immune competent adults has not been reported. Here, we report a case of P. agglomerans cerebrospinal meningitis accompanied by positive anti-myeloperoxidase (MPO) antibody in a 49-year-old female who has a history of black fungus planting. Case presentation: The patient manifested with repeated fever, headache, generalized muscle pain, and neurological defects. Cerebrospinal fluid (CSF) tests revealed a moderately elevated number of polymorphonuclear leukocytes (50–193 × 106/L), low glucose levels (0.54–2.44 mmo1/L), and extremely high protein content (2.42–25.42 g/L). Blood tests showed positive anti-myeloperoxidase antibodies lasting for 1.5 year before turning negative. Spine MRI showed thickening and enhancement of the whole spinal meninges. CSF metagenomic next-generation sequencing (mNGS) revealed 75,189 specific DNA reads of P. agglomerans. The patient underwent spinal laminectomy due to meningeal adhesions. Pathological results revealed fibrous tissue proliferation, inflammatory infiltration with focal necrosis and calcification in the dura mater. The patient was successfully treated with sufficient antibiotics at 1-year follow-up. Conclusions: People should be alert to CNS infections caused by P. agglomerans which presented with relatively mild clinical symptoms at onset, especially for those who contucts relevant agricultural and forestry work. The CSF characterization of P. agglomerans meningitis is elevated multiple nuclei white blood cells, significantly reduced glucose content, and markedly increased protein level which may be related to the secondary spinal membrane adhesions. [ABSTRACT FROM AUTHOR]

Background: Early targeted antibiotic therapy is crucial for improving the prognosis of immunocompromised patients with severe respiratory infections (SRIs) in the intensive care unit (ICU). Metagenomic next-generation sequencing (mNGS) has shown significant value in pathogen detection, but research on lower respiratory tract microorganisms remains limited. Methods: This study enrolled 234 patients with SRIs in the ICU, and individuals were categorized into immunocompromised and immunocompetent groups. We compared the diagnostic performance of mNGS using bronchoalveolar lavage fluid (BALF) with conventional microbiological tests (CMTs) and analyzed the value of mNGS in immunocompromised patients with SRIs in the ICU. Results: Among all patients, the pathogenic microorganism detection rate of mNGS was higher than that of CMTs (94.02% vs 66.67%, P < 0.05), both in the immunocompromised group (95.0% vs 58.75%, P < 0.05) and the immunocompetent group (93.51% vs 71.43%, P < 0.05). mNGS detected more pathogens than CMTs did (167 vs 51), identifying 116 organisms that were missed by CMTs. The proportion of antibiotic regimen adjustments based on mNGS results was significantly higher compared to CMTs in both the immunocompromised (70.00% vs 17.50%, P < 0.05) and immunocompetent groups (48.70% vs 15.58%, P < 0.05). In the immunocompromised group, patients who had their antibiotic treatment adjusted on mNGS results had improved prognosis, with significantly lower ICU mortality (8.93% vs 50%, P < 0.05) and 28-day mortality rates (30.36% vs 68.75%, P < 0.05) than CMTs. In the immunocompetent group, no statistically significant differences were observed in ICU mortality or 28-day mortality (20.00% vs 33.33%, P > 0.05; 42.67% vs 45.83%, P > 0.05). Conclusion: mNGS shows significant value in detecting pathogens in immunocompromised patients with SRIs in ICU. For immunocompromised patients who respond poorly to empirical treatment, mNGS can provide an etiological basis, helping adjust antibiotic regimens more precisely and thereby improving patient prognosis. [ABSTRACT FROM AUTHOR]

Objective To analyze the clinical value of metagenomic next-generation sequencing (mNGS) in the pathogen detection of elderly patients with community-acquired pneumonia (CAP). Methods A total of 112 elderly CAP patients were included in the study. The detection efficiency of pathogens using mNGS was compared with conventional microbiological tests (CMTs). Statistical analyses were conducted using Fisher′s exact test and ROC curves to evaluate the diagnostic differences between mNGS and CMTs. Results The overall diagnostic rate of mNGS was significantly higher than that of CMTs (94.6% vs. 65.2%, P＜0.001). The detection time for mNGS was significantly shorter than that for CMTs [ (26.3±5.9)h vs. (85.5±6.4)h; t=21.034, P＜0.05]. mNGS detected a higher number of bacterial, viral, fungal, and atypical pathogens compared to CMTs. The detection rate for mixed infections with mNGS was 76.4%, significantly higher than CMTs′ 60.3% (χ²=6.851, P＜0.05). Of the detected pathogens, there were 64 cases of agreement, 35 cases of partial agreement, and 13 cases of complete disagreement between mNGS and CMTs. Conclusion mNGS demonstrates superior capability in detecting a broader spectrum of pathogens in elderly patients with community-acquired pneumonia, highlighting its significant clinical value. [ABSTRACT FROM AUTHOR]

Background: Suppurative perichondritis of the auricle is a common disease that can easily cause malformations if it develops into an uncontrolled infection. In nearly half of the cases, otolaryngologists cannot identify the pathogens involved. Case presentation: In the present work, we described two cases of pyogenic perichondritis, with negative on conventional culture. However, using metagenomic next-generation sequencing (mNGS), we detected fungal infections in the patients and after the patients were given anti-fungal treatment, the patients achieved a good prognosis. Conclusions: These cases highlighted the possibility that fungi might be the involved pathogens in patients who have had multiple negative bacterial cultures, and mNGS should be applied in these cases. mNGS could be used as a supplement to traditional culture methods. [ABSTRACT FROM AUTHOR]

The role of the bronchoalveolar lavage fluid (BALF) microbiome in acute exacerbations of chronic obstructive pulmonary disease (AECOPD) remains unclear. The advent of the metagenomic next-generation sequencing (mNGS) has made it possible to reveal the complex microbiome composition of the respiratory tract. This study aimed to explore whether there are differences in the BALF microbiome of AECOPD patients with different lung functions. We enrolled 55 AECOPD patients and divided them into a mild group (n = 31) and a severe group (n = 24) according to their lung function. We collected BALF and submitted it to mNGS and bioinformatics analysis. At the species level, mNGS identified 264 bacteria, 13 fungi and 12 viruses in the mild group, and 174 bacteria, 6 fungi and 6 viruses in the severe group. Mixed bacterial and viral infection occurred in both groups. At the genus level, Rothia and Veillonella were more abundant in the mild group, while Pseudomonas and Staphylococcus were more abundant in the severe group. At the species level, compared with the mild group, the relative abundance of Haemophilus influenzae and Pseudomonas aeruginosa was increased in the severe group. Besides, the BALF microbiome composition was similar between the two groups, and there was no significant difference in α and β diversity. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) (%) showed no significant correlation with the Shannon or Simpson index. The microbiome abundance was different between the mild and severe groups; however, microbiome diversity was similar between the two groups. Based on our findings, Haemophilus influenzae and Pseudomonas aeruginosa may be the pathogenic bacteria that cause the difference in lung function in patients with AECOPD. [ABSTRACT FROM AUTHOR]

Sepsis patients have low survival rates, high mortality rates, and poor prognosis, making early identification of pathogens particularly crucial. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all microorganisms in clinical samples, providing greater sensitivity, accuracy, and efficiency in early detection of sepsis pathogenic microorganism compared to traditional culture techniques. With the continuous development of next-generation sequencing technology, the clinical application value of mNGS in sepsis diagnosis will further improve. This article reviews the advantages, clinical applications, progress, challenges, and prospects of mNGS in the early diagnosis of sepsis. [ABSTRACT FROM AUTHOR]

Background: Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited. Methods: To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis. Results: In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS. Conclusion: In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS. [ABSTRACT FROM AUTHOR]

Objective: Pulmonary infection is one of the leading causes of death in patients with ANCA-associated vasculitis (AAV). It is sometimes difficult to differentiate pulmonary infection from pulmonary involvement of vasculitis in AAV patients. Fiberoptic bronchoscopy and bronchoalveolar lavage fluid (BALF) assays are useful diagnostic methods. In addition to conventional microbiological tests (CMTs), metagenomic next-generation sequencing (mNGS) facilitates rapid and sensitive detection of various pathogens. The current study aimed to evaluate the advantages of additional BALF mNGS in the management of pulmonary infection in AAV patients. Methods: 27 patients with active AAV and suspected pulmonary infection whose BALF samples were tested by mNGS and CMTs and 17 active AAV patients whose BALF were tested by CMTs alone were retrospectively recruited. The results of microbiological tests, and adjustments of treatment following BALF mNGS, were described. The durations of antimicrobial treatment and in-hospital mortality in patients were compared. Results: Among the 27 patients whose BALF samples were tested by mNGS, 25.9% of patients did not have evidence of pathogenic microorganism in their BALF samples, 55.6% had polymicrobial infections, including bacteria, fungi and viruses. Of these 27 patients, 40.7% did not have evidence of pathogenic microorganism in their BALF or serum samples according to CMTs. Patients in the BALF mNGS/CMT group received a significantly shorter duration of antibacterial and total antimicrobial treatment than patients in the CMT alone group (17.3 ± 14.7 vs. 27.9 ± 19.0 days, P = 0.044; 18.9 ± 15.0 vs. 29.5 ± 17.7 days, P = 0.040, respectively). Fewer patients in the BALF mNGS/CMT group died than in the CMT alone group (4/27 vs. 7/17, P = 0.049). Conclusion: Compared with CMT alone, additional mNGS tests may shorten the duration of antimicrobial treatment and possibly decrease death from severe infection by providing precise and quick diagnosis of infection. [ABSTRACT FROM AUTHOR]

Background: A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs. Methods: A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity. Results: A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR) = 2.87, 95% confidence interval [CI]: 1.72–4.81, p < 0.001, I2 = 90%). The GRADE score presented a very low CoE. Then, the pooled sensitivity was 0.89 (95% CI: 0.86–0.91, I2 = 39.65%, p = 0.06), and the pooled specificity was 0.75 (95% CI: 0.51–0.90, I2 = 88.64%, p < 0.001). The AUROC of the studies analyzed was 0.89 (95% CI: 0.86–0.92). The GRADE score indicated a low CoE. Conclusion: The current evidence shows that mNGS has favorable diagnostic performance for UTIs. More high-quality prospective randomized controlled trials (RCTs) are expected to verify these findings and provide more information about mNGS in UTI treatment and prognosis. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

AbstractObjectiveMethodsResultsConclusionsAccurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a.We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology.The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%).Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected. [ABSTRACT FROM AUTHOR]

Background: Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished. Objective: The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity. Methods: We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS. Results: Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS. Conclusions: mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment. [ABSTRACT FROM AUTHOR]

Objective: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from joint infection (JI) synovial fluid (SF) samples with previous antibiotic exposure. Methods: From January 2019 to January 2022, 59 cases with suspected JI were enrolled. All cases had antibiotic exposure within 2 weeks before sample collection. mNGS and conventional culture were performed on SF samples. JI was diagnosed based on history and clinical symptoms in conjunction with MSIS criteria. The diagnostic values, including sensitivity, specificity, positive/negative predictive values (PPV/NPV), and accuracy, were in comparison with mNGS and culture. Results: There were 47 of the 59 cases diagnosed with JI, while the remaining 12 were diagnosed with non-infectious diseases. The sensitivity of mNGS was 68.1%, which was significantly higher than that of culture (25.5%, p<0.01). The accuracy of mNGS was significantly higher at 71.2% compared to the culture at 39.0% (p <0.01). Eleven pathogenic strains were detected by mNGS but not by microbiological culture, which included Staphylococcus lugdunensis, Staphylococcus cohnii, Finegoldia magna, Enterococcus faecalis, Staphylococcus saprophytics, Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Acinetobacter pittii, Brucella ovis, andCoxiella burnetii. Antibiotic therapy was adjusted based on the mNGS results in 32 (68.1%) patients, including 12 (25.5%) and 20 (42.6%) patients, in whom treatment was upgraded and changed, respectively. All JI patients underwent surgery and received subsequent antibiotic therapy. They were followed up for an average of 23months (20-27 months), and the success rate of treatment was 89.4%. Out of the 33 patients who had positive results for pathogens, reoperation was performed in 1 case (3.03%), while out of the 14 cases with negative results for both mNGS and cultures, reoperation was performed in 4 cases (28.6%). Conclusions: mNGS has advantages over conventional culture in detecting pathogens in SF samples from JI patients previously treated with antibiotics, potentially improving clinical outcomes. [ABSTRACT FROM AUTHOR]

Background: Sepsis remains a leading cause of mortality in intensive care units, and rapid and accurate pathogen detection is crucial for effective treatment. This study evaluated the clinical application of multi-site metagenomic next-generation sequencing (mNGS) for the diagnosis of sepsis, comparing its performance against conventional methods. Methods: A retrospective analysis was conducted on 69 patients with sepsis consecutively admitted to the Department of Intensive Care Medicine, Meizhou People's Hospital. Samples of peripheral blood and infection sites were collected for mNGS and conventional method tests to compare the positive rate of mNGS and traditional pathogen detection methods and the distribution of pathogens. The methods used in this study included a comprehensive analysis of pathogen consistency between peripheral blood and infection site samples. Additionally, the correlation between the pathogens detected and clinical outcomes was investigated. Results: Of the patients with sepsis, 57.97% experienced dyspnea, and 65.2% had underlying diseases, with hypertension being the most common. mNGS demonstrated a significantly higher pathogen detection rate (88%) compared to the conventional method tests (26%). The pathogen consistency rate was 60% between plasma and bronchoalveolar lavage fluid samples, and that of plasma and local body fluid samples was 63%. The most frequently detected pathogens were gram-negative bacteria, and Klebsiella pneumonia. There were no significant differences in the clinical features between the pathogens. Conclusion: mNGS is significantly superior to conventional methods in pathogen detection. There was a notable high pathogen consistency detection between blood and local body fluid samples, supporting the clinical relevance of mNGS. This study highlights the superiority of mNGS in detecting a broad spectrum of pathogens quickly and accurately. Trial registration: Not applicable. [ABSTRACT FROM AUTHOR]

This article aims to bring clinicians' awareness to the widespread impact of urinary tract infection (UTI) on the lives of women and to the advances that offer hope for future improvements in the diagnosis and management of UTI. Thanks to physiological, anatomical, and lifestyle factor differences, women face heightened vulnerability to UTIs compared to men. In fact, women are four times more likely than men to develop a UTI and around half of these women encounter UTI recurrence, which is a significant source of both physical and psychosocial burdens. Despite the current shortcomings in diagnosis and management, emerging diagnostic technologies promise to identify UTIs more accurately and rapidly, offering women hope for a revolution in UTI management. Meanwhile, clinicians have the opportunity to reduce the psychosocial burden by recognizing the value of patients' lived experiences and ensuring their care plan is in alignment with their patients' goals and expectations for medical care. [ABSTRACT FROM AUTHOR]

Objective To explore the role of metagenomic next-generation sequencing (mNGS) in pathogen detection of patients with skin infections of unknown origin. Methods A 68-year-old female patient presented with red, swollen nodules and pain in the left knee for 4 months, and ulceration for 20 days. mNGS was performed on the patient's skin lesion samples, and the microbial nucleic acid sequences in the samples were analyzed and compared with the pathogen database to identify pathogenic microorganisms. Results mNGS detected Mycobacterium chelonae (28 specific sequences), which was verified by PCR detection and Sanger sequencing, indicating that the pathogenic microorganism causing the skin tissue infection was Mycobacterium chelonae. Based on the patient's clinical symptoms, the final diagnosis was Mycobacterium chelonae skin infection. Conclusion mNGS can assist in the diagnosis of rare pathogenic microorganism infections and provide directions for clinical treatment. [ABSTRACT FROM AUTHOR]

Aim: Cryptococcus neoformans osteomyelitis coupled with tuberculosis and tuberculous lymphadenitis, is a rare occurrence in clinical. Diagnostic challenges arise due to the clinical radiological similarity of this condition to other lung infections and the limited and sensitive nature of traditional approaches. Here, we present a case of co-infection diagnosed using Metagenomic Next-Generation Sequencing, highlighting the effectiveness of advanced genomic techniques in such complex scenarios. Case Presentation: We present a case of a 67-year-old female infected with cryptococcal osteomyelitis and presented with swelling and pain in the right ankle. Following a biopsy of the right ankle joint, Metagenomic Next-Generation Sequencing (mNGS) of the biopsy tissue revealed Cryptococcus neoformans infection. Positive results for Cryptococcus capsular antigen and pathological findings confirmed the presence of Cryptococcus neoformans. The patient underwent surgical debridement, coupled with oral fluconazole treatment (300mg/day), leading to the resolution of symptoms. Conclusion: Cryptococcus neoformans is an uncommon cause of ankle infection. Metagenomic Next-Generation Sequencing (mNGS) serves as a valuable diagnostic tool, aiding clinicians in differentiating cryptococcal osteomyelitis from other atypical infections. [ABSTRACT FROM AUTHOR]

Streptococcus pyogenes, also known as Group A Streptococcus (GAS), can cause severe invasive diseases with high fatality rates. We report a case of necrotizing fasciitis and myositis complicated by Streptococcal Toxic Shock-Like Syndrome (STSS) caused by the invasive emm 22/ST46 strain of Streptococcus pyogenes in China. A previously healthy 57-year-old Chinese Canadian man presented with right calf pain and ulceration following a hike in the Gobi Desert, which progressed to unconsciousness and severe infection. Despite initial treatment, his condition deteriorated, leading to his transfer to our intensive care unit. Metagenomic Next-Generation Sequencing identified Streptococcus pyogenes, and antimicrobial susceptibility testing revealed resistance to erythromycin, tetracycline, and clindamycin. Despite broad-spectrum antimicrobial therapy, debridement, and supportive measures, the patient's condition necessitated amputation of the right lower limb. He recovered and was discharged from the hospital on Day 43. Whole-genome sequencing of the isolate identified 15 multiple virulence factors. Phylogenetic analysis revealed that the closest relative of the isolate was a strain identified in China. This case underscores the importance of early recognition and treatment of invasive GAS infections to prevent severe outcomes, and we should pay attention to invasive emm 22/ST46 GAS infections in China. [ABSTRACT FROM AUTHOR]

Abstract Reports on the application of metagenomic next-generation sequencing (mNGS) in adult patients with severe pneumonia after cardiac surgery remain limited. This study aimed to evaluate the clinical outcomes of mNGS analysis of bronchoalveolar lavage fluid (BALF) in such patients.A retrospective cohort study was conducted on adult patients with severe pneumonia after cardiac surgery. Samples were collected from patients in the surgical intensive care unit (SICU) of Sichuan Provincial People’s Hospital between January 2019 and March 2024. Upon diagnosis of severe pneumonia, bronchoalveolar lavage fluid was obtained via bronchoscopy within 24 h. The mNGS group was composed of patients tested using mNGS and conventional microbiological tests. BALF was detected only by the conventional microbiological test (CMT) method in the CMT group, which involved examining bacterial and fungal smears and cultures at least. We reviewed a total of 4,064 cardiac surgeries, and based on the inclusion criteria, a total of 113 adult patients with severe pneumonia after cardiac surgery were included in this study. The overall positive rate detected by mNGS was significantly higher than that of the culture method (98% vs. 58%, P

Abstract Background Identifying the responsible pathogen is crucial for precision medicine in intracranial infections, and Cerebrospinal Fluid (CSF) Metagenomic Next-Generation Sequencing (mNGS) is a reliable method for this detection. However, the indiscriminate utilization of this approach may impose a financial burden on both patients and society. The study aims to investigate the optimal conditions for applying CSF mNGS in patients with suspected intracranial infections, offering valuable references for precision medicine of intracranial infections. Methods A total of 175 hospitalized patients presenting with suspected intracranial infections were selected for retrospective analysis. Base on the detection of responsible pathogens using CSF mNGS, the patients were categorized into two groups, responsible pathogens in Group A were detected but not in Group B. The types of responsible pathogens in group A and the final diagnosis of patients in group B were analyzed. Demographic data, clinical presentation, CSF analysis, imaging results, and electroencephalography (EEG) findings were analyzed for both groups. Finally, a scoring system was established to promptly assess the appropriateness of CSF mNGS for patients with suspected intracranial infections. Each independent predictor was assigned a score of 1, and the patients were subsequently scored. We advocate sending patients’ CSF for mNGS when the cumulative score is ≥ 2. Results In Group A, the predominant responsible pathogen was the varicella-zoster virus (VZV), while Group B exhibited the highest proportion of final diagnoses related to epilepsy. The logistic regression model indicates that headache [OR = 2.982, 95% CI (1.204–7.383), p = 0.018], increased cerebrospinal fluid white cell count [OR = 4.022, 95% CI (1.331–12.156), p = 0.014], and decreased cerebrospinal fluid glucose levels [OR = 9.006, 95% CI (2.778–29.194), P

Abstract Background The incidence of non-tuberculous mycobacterium infection has shown a gradual increasing trend in recent years, among which cutaneous manifestations as an important aspect. This study aimed to describe the clinical features and microbiological findings in 6 cases of primary cutaneous nontuberculous mycobacterium infection. Methods In this retrospective study from June 2021 to June 2022, the clinical data and microbiological results of six cases diagnosed with primary cutaneous non-tuberculous mycobacterium infection in department of dermatology, Hangzhou Third People’s Hospital were analyzed. Results All six cases were primary cutaneous non-tuberculous mycobacterium infections, four of which had a history of trauma or exposure, and two had an underlying disease that could lead to compromised immunity. All patients presented with erythema nodular skin lesions, four on the upper or lower extremities, one on the face, and one on the right hip. The histopathological findings of five patients who underwent biopsy were granulomatous inflammatory changes with mixed infiltration. Laboratory cultures using tissue or tissue fluid were all successful, including four Mycobacterium marinum, one Mycobacterium abscessus, and one Mycobacterium avium. Metagenomics next-generation sequencing detected results consistent with culture colonies in only two cases. With the exception of case 4, all patients responded well to oral medication, with a course of treatment ranging from 4 months to 1 year, and the prognosis was good. Conclusions The clinical features of primary cutaneous non-tuberculous mycobacterium infection are often lacking in specificity, and the identification of related strains is difficult for a variety of reasons. Although the results of metagenomics next-generation sequencing are useful for pathogen spectrum identification, its diagnostic value should be carefully reevaluated under certain circumstances. Patients with suspected triggers who do not respond well to conventional treatments should be suspected as atypical infection and potential immunosuppression. If diagnosed and treated promptly, the prognosis of primary cutaneous non-tuberculous mycobacterium infection is generally good.

Abstract Objective This study aims to evaluate the clinical management and effectiveness of metagenomic next-generation sequencing (mNGS) in patients with pyogenic spinal infections. Methods We conducted a retrospective review of 17 patients diagnosed with pyogenic spinal infections and treated at our institution between October 2022 and February 2024. The cohort included 8 males and 9 females, with a mean age of 63.59 ± 10.18 years (range: 41–71 years). The infections comprised 9 epidural abscesses, 6 intervertebral space infections, and 2 deep abscesses. All patients underwent open surgical procedures and mNGS-based bacterial identification using intraoperative pus or tissue specimens, in addition to conventional blood bacterial cultures. Clinical outcomes were assessed using CRP, PCT, WBC inflammatory markers, and VAS scores postoperatively. Results All 17 patients with pyogenic spinal infections underwent open surgery and mNGS bacterial detection at our institution. Among the 17 patients, mNGS yielded positive results in 14 cases (82.4%), significantly higher than the 5.9% positivity rate of conventional bacterial cultures (p

Abstract Background Information on the comparison of blood microbiota between human immunodeficiency virus (HIV)-infected and HIV-uninfected patients with suspected sepsis by metagenomic next-generation sequencing (mNGS) is limited. Methods Retrospectively analysis was conducted in HIV-infected and HIV-uninfected patients with suspected sepsis at Changsha First Hospital (China) from March 2019 to August 2022. Patients who underwent blood mNGS testing were enrolled. The blood microbiota detected by mNGS were analyzed. Results A total of 233 patients with suspected sepsis who performed blood mNGS were recruited in this study, including 79 HIV-infected and 154 HIV-uninfected patients. Compared with HIV-uninfected patients, the proportions of mycobacterium (p = 0.001), fungus (p

Yongru Chen,1 Chongyue Chen,1 Wei Chen,2,3 Wei Gai,4 Yafeng Zheng,4 Yuxin Guo,4 Zhaoning Wang,1 Yongsong Chen,1 Zhiming Cai1,5,6 1The First Affiliated Hospital of Shantou University, Shantou, Guangdong, People’s Republic of China; 2Department of Urology, Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, People’s Republic of China; 3Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, People’s Republic of China; 4WillingMed Technology (Beijing) Co., Ltd, Beijing, People’s Republic of China; 5BGI Genomics, BGI Shenzhen, Shenzhen, People’s Republic of China; 6Carson International Cancer Center, Shenzhen University, Shenzhen, People’s Republic of ChinaCorrespondence: Zhiming Cai, Carson International Cancer Center of Shenzhen University, No. 1066, Xueyuan Road, Shenzhen, Guangdong Province, People’s Republic of China, Tel +86 136 0253 0322, Email caizhiming2000@163.com Yongsong Chen, The First Affiliated Hospital of Shantou University, No. 57, Changping Road, Shantou, Guangdong Province, People’s Republic of China, Tel +86 0754-88905000, Email yongsongchen@126.comPurpose: This study aimed to evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) in sepsis patients who received early empirical antibiotic treatment.Patients and Methods: A retrospective analysis was conducted on clinical data from sepsis patients diagnosed in the Emergency Intensive Care Unit (EICU) between April 2019 and May 2023. All patients underwent standard conventional microbiological testing. Patients were categorized into either the mNGS group or the control group based on whether they underwent mNGS tests. Baseline variables were matched using propensity scores.Results: Out of 461 sepsis patients screened, 130 were included after propensity matching, with 65 patients in each group. Despite prior antibiotic treatment, 57 cases (87.69%) in the mNGS group had positive mNGS results, exceeding the culture detection rate (52.31%). Besides, a higher proportion of patients in the mNGS group experienced antibiotic adjustments compared to the control group (72.31% vs 53.85%). Mortality rates were also compared based on the duration of antibiotic exposure before mNGS sampling. Patients exposed to antibiotics for less than 24 hours had a lower mortality rate compared to those exposed for over 8 days (22.22% vs 42.86%). COX multivariate analysis identified mNGS testing, underlying diseases, lymphocyte percentage, infection site (respiratory and bloodstream) as independent risk factors for mortality in sepsis patients.Conclusion: With increased antibiotic exposure time, the positive rate of culture testing significantly decreased (44.44% vs 59.52% vs 35.71%, P = 0.031), whereas the positive rate of mNGS remained stable (77.78% vs 88.10% vs 92.86%, P = 0.557). mNGS demonstrated less susceptibility to antibiotic exposure. Early mNGS detection positively impacted the prognosis of sepsis patients.Keywords: metagenomic next-generation sequencing, sepsis, antibiotic management, clinical value, prognosis

Wei Wang,&ast; Yujuan Wang,&ast; Xiaowei Xin, Yi Yin, Chun Zhao, Youpeng Jin Department of Pediatric Intensive Care Unit, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, 250021, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Youpeng Jin, Department of Pediatric Intensive Care Unit, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Road, Huaiyin District, Jinan, 250021, Shandong Province, People’s Republic of China, Tel +86 15168863809, Email jinyp79@sina.cnBackground: Bacterial meningitis is a major cause of mortality and morbidity in children worldwide. Meanwhile, mixed bacterial meningitis is a rare entity. However, it is difficult to identify anaerobic pathogens using traditional culture methods. Disorders such as neurosurgical interventions are considered risk factors for the development of such cerebral infection. Early diagnosis and appropriate therapy may contribute to patient survival.Case Presentation: We report the use of metagenomic next-generation sequencing (mNGS) to facilitate the diagnosis and treatment of polymicrobial meningitis in a 35-month-old male child with a history of detethering procedure for tethered cord syndrome (TCS). The mNGS tests identified six bacterial species from CSF specimens, including four ones of anaerobic bacteria. The subsequent examination of magnetic resonance imaging (MRI) revealed abnormal imaging findings of the lumbosacral area. The patient eventually recovered from severe infections due to long-term antibiotic treatment and radical surgery.Conclusion: This case demonstrates the advantages of mNGS for the rapid and accurate diagnosis of mixed bacterial meningitis, highlighting its application of identifying uncommon pathogens in severe infections. For patients who suffered from exacerbated brain infection with history of detethering surgery, anaerobic cultivation is needed and empiric antibiotic therapy should consider mixed infection in these situations.Keywords: meningitis, metagenomic next-generation sequencing, children, case report

Abstract Background Pantoea agglomerans (P. agglomerans) is a gram-negative bacterium that is commonly isolated from plant surfaces, seeds, and the environment. As an opportunistic pathogen, it can cause blood, urinary and soft tissue infections in immunocompromised patients. In central nervous system, P. agglomerans infection has been report in children and immune-compromised patients, however, infection by such bacterium in nontraumatized immune competent adults has not been reported. Here, we report a case of P. agglomerans cerebrospinal meningitis accompanied by positive anti-myeloperoxidase (MPO) antibody in a 49-year-old female who has a history of black fungus planting. Case presentation The patient manifested with repeated fever, headache, generalized muscle pain, and neurological defects. Cerebrospinal fluid (CSF) tests revealed a moderately elevated number of polymorphonuclear leukocytes (50–193 × 106/L), low glucose levels (0.54–2.44 mmo1/L), and extremely high protein content (2.42–25.42 g/L). Blood tests showed positive anti-myeloperoxidase antibodies lasting for 1.5 year before turning negative. Spine MRI showed thickening and enhancement of the whole spinal meninges. CSF metagenomic next-generation sequencing (mNGS) revealed 75,189 specific DNA reads of P. agglomerans. The patient underwent spinal laminectomy due to meningeal adhesions. Pathological results revealed fibrous tissue proliferation, inflammatory infiltration with focal necrosis and calcification in the dura mater. The patient was successfully treated with sufficient antibiotics at 1-year follow-up. Conclusions People should be alert to CNS infections caused by P. agglomerans which presented with relatively mild clinical symptoms at onset, especially for those who contucts relevant agricultural and forestry work. The CSF characterization of P. agglomerans meningitis is elevated multiple nuclei white blood cells, significantly reduced glucose content, and markedly increased protein level which may be related to the secondary spinal membrane adhesions.

Abstract Background Early targeted antibiotic therapy is crucial for improving the prognosis of immunocompromised patients with severe respiratory infections (SRIs) in the intensive care unit (ICU). Metagenomic next-generation sequencing (mNGS) has shown significant value in pathogen detection, but research on lower respiratory tract microorganisms remains limited. Methods This study enrolled 234 patients with SRIs in the ICU, and individuals were categorized into immunocompromised and immunocompetent groups. We compared the diagnostic performance of mNGS using bronchoalveolar lavage fluid (BALF) with conventional microbiological tests (CMTs) and analyzed the value of mNGS in immunocompromised patients with SRIs in the ICU. Results Among all patients, the pathogenic microorganism detection rate of mNGS was higher than that of CMTs (94.02% vs 66.67%, P 0.05; 42.67% vs 45.83%, P > 0.05). Conclusion mNGS shows significant value in detecting pathogens in immunocompromised patients with SRIs in ICU. For immunocompromised patients who respond poorly to empirical treatment, mNGS can provide an etiological basis, helping adjust antibiotic regimens more precisely and thereby improving patient prognosis.

Abstract Background A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs. Methods A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity. Results A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR) = 2.87, 95% confidence interval [CI]: 1.72–4.81, p

Abstract Background Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited. Methods To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis. Results In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS. Conclusion In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.

Abstract Objective Pulmonary infection is one of the leading causes of death in patients with ANCA-associated vasculitis (AAV). It is sometimes difficult to differentiate pulmonary infection from pulmonary involvement of vasculitis in AAV patients. Fiberoptic bronchoscopy and bronchoalveolar lavage fluid (BALF) assays are useful diagnostic methods. In addition to conventional microbiological tests (CMTs), metagenomic next-generation sequencing (mNGS) facilitates rapid and sensitive detection of various pathogens. The current study aimed to evaluate the advantages of additional BALF mNGS in the management of pulmonary infection in AAV patients. Methods 27 patients with active AAV and suspected pulmonary infection whose BALF samples were tested by mNGS and CMTs and 17 active AAV patients whose BALF were tested by CMTs alone were retrospectively recruited. The results of microbiological tests, and adjustments of treatment following BALF mNGS, were described. The durations of antimicrobial treatment and in-hospital mortality in patients were compared. Results Among the 27 patients whose BALF samples were tested by mNGS, 25.9% of patients did not have evidence of pathogenic microorganism in their BALF samples, 55.6% had polymicrobial infections, including bacteria, fungi and viruses. Of these 27 patients, 40.7% did not have evidence of pathogenic microorganism in their BALF or serum samples according to CMTs. Patients in the BALF mNGS/CMT group received a significantly shorter duration of antibacterial and total antimicrobial treatment than patients in the CMT alone group (17.3 ± 14.7 vs. 27.9 ± 19.0 days, P = 0.044; 18.9 ± 15.0 vs. 29.5 ± 17.7 days, P = 0.040, respectively). Fewer patients in the BALF mNGS/CMT group died than in the CMT alone group (4/27 vs. 7/17, P = 0.049). Conclusion Compared with CMT alone, additional mNGS tests may shorten the duration of antimicrobial treatment and possibly decrease death from severe infection by providing precise and quick diagnosis of infection.

Abstract Background Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished. Objective The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity. Methods We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS. Results Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS. Conclusions mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.

Abstract 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.

Abstract Background Sepsis remains a leading cause of mortality in intensive care units, and rapid and accurate pathogen detection is crucial for effective treatment. This study evaluated the clinical application of multi-site metagenomic next-generation sequencing (mNGS) for the diagnosis of sepsis, comparing its performance against conventional methods. Methods A retrospective analysis was conducted on 69 patients with sepsis consecutively admitted to the Department of Intensive Care Medicine, Meizhou People’s Hospital. Samples of peripheral blood and infection sites were collected for mNGS and conventional method tests to compare the positive rate of mNGS and traditional pathogen detection methods and the distribution of pathogens. The methods used in this study included a comprehensive analysis of pathogen consistency between peripheral blood and infection site samples. Additionally, the correlation between the pathogens detected and clinical outcomes was investigated. Results Of the patients with sepsis, 57.97% experienced dyspnea, and 65.2% had underlying diseases, with hypertension being the most common. mNGS demonstrated a significantly higher pathogen detection rate (88%) compared to the conventional method tests (26%). The pathogen consistency rate was 60% between plasma and bronchoalveolar lavage fluid samples, and that of plasma and local body fluid samples was 63%. The most frequently detected pathogens were gram-negative bacteria, and Klebsiella pneumonia. There were no significant differences in the clinical features between the pathogens. Conclusion mNGS is significantly superior to conventional methods in pathogen detection. There was a notable high pathogen consistency detection between blood and local body fluid samples, supporting the clinical relevance of mNGS. This study highlights the superiority of mNGS in detecting a broad spectrum of pathogens quickly and accurately. Trial registration Not applicable.

Aims: This aim of this study was to analyze the detection rate of rare pathogens in bone and joint infections (BJIs) using metagenomic next-generation sequencing (mNGS), and the impact of mNGS on clinical diagnosis and treatment. Methods: A retrospective analysis was conducted on 235 patients with BJIs who were treated at our hospital between January 2015 and December 2021. Patients were divided into the no-mNGS group (microbial culture only) and the mNGS group (mNGS testing and microbial culture) based on whether mNGS testing was used or not. Results: A total of 147 patients were included in the no-mNGS group and 88 in the mNGS group. The mNGS group had a higher detection rate of rare pathogens than the no-mNGS group (21.6% vs 10.2%, p = 0.016). However, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and higher infection control rates compared with the no-mNGS group (p = 0.017, p = 0.003, and p = 0.028, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.957). In culture-negative cases, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and a higher infection control rate than the no-mNGS group (p = 0.036, p = 0.033, p = 0.022, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.748). Conclusion: mNGS improves detection of rare pathogens in BJIs. mNGS testing reduces antibiotic-related complications, shortens hospital stay and antibiotic use duration, and improves treatment success rate, benefits which are particularly evident in culture-negative cases. Cite this article: Bone Joint Res 2024;13(8):401–410.

Abstract Background In this study, we aimed to evaluate the clinical utility of Metagenomic Next-Generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) in diagnosis of Lower Respiratory Tract Infections (LRTIs). Methods In this study, we retrospectively analyzed 186 hospitalized patients who were suspected with LRTIs and performed mNGS (DNA) test of BALF simultaneously at The Fifth Affiliated Hospital of Sun Yat-Sen University from March 2023 to August 2023. Suspected LRTI was based on LRTI related clinical manifestations or imaging examination. Among them, 155 patients had undergone conventional culture and mNGS (DNA) testing simultaneously. Finally, 138 cases (89.03%,138/155) were diagnosed as LRTI and 17 cases (10.97%,17/155) were diagnosed as non-LRTI. Both detecting rate and diagnostic efficacy of mNGS and conventional culture were compared. Results The positive detection rates of pathogens between mNGS and conventional culture were significant different (81.29% VS 39.35%, P 0.05). Furthermore, 77.54% and 35.51% of LRTI cases were being etiologically diagnosed by mNGS and culture respectively. Importantly, mNGS directly led to a change of treatment regimen in 58 (37.42%) cases, including antibiotic adjustment (29.68%) and ruling out active infection (7.74%). Moreover, treatment regimen remained unchanged in 97 (62.58%) cases, considering the current antibiotic therapy already covered the detected pathogens (36.13%) or empirical treatment was effective (11.61%). Conclusions mNGS can identify a wide range of pathogens in LRTIs, with improved sensitivity and being more superior at diagnosing LRTIs etiologically. mNGS has the potential to enhance clinical outcomes by optimizing the treatment regimens.

Xiyue Zhang,1,&ast; Jian Ye,2,&ast; Limin Wang,1 Liuhai Zhang,1 Liusheng Wang,1 Hualiang Jin1 1Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China; 2Department of Respiratory Medicine, Zhejiang Hospital, Hangzhou, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Hualiang Jin, Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Huansha Road 261, Hangzhou, 310006, People’s Republic of China, Tel +86 571-5600-6818, Fax +86 571-8791-4773, Email jinhualiang2008@126.comPurpose: Next-generation sequencing of the metagenome (mNGS) is gaining traction as a valuable tool for diagnosing infectious diseases. Compared to mNGS, pathogen detection based on Oxford Nanopore Technology further shortens the detection time. This study seeks to assess the efficacy of Nanopore sequencing in identifying pathogens associated with community-acquired pneumonia (CAP) among elderly individuals in China.Patients and Methods: From January 2023 to June 2023, elderly patients with CAP were prospectively recruited from Hangzhou First People’s Hospital. A comprehensive set of clinical data was gathered, and bronchoalveolar lavage (BAL) fluid samples were collected. Concurrently, pathogen identification was performed using conventional microbiological diagnostic methods, Illumina sequencing, and Nanopore sequencing, and the diagnostic efficacy of pathogen detection was compared.Results: The study included a total of 29 patients. The diagnostic positivity rates of traditional microbiological detection, Illumina sequencing, and Nanopore sequencing were 24.1%, 51.7%, and 48.3%, respectively. Their diagnostic specificities were 91.7%, 50%, and 75%, respectively. Compared to traditional microbiological detection, both Nanopore and Illumina sequencing showed significantly increased sensitivity. However, Nanopore sequencing exhibited relatively better consistency with the final clinical comprehensive diagnosis, with a Kappa value of 0.574. This outperformed traditional microbiological detection and Illumina sequencing, which had a Kappa value of 0.296 and 0.402, respectively. In addition, Nanopore sequencing required the shortest turnaround time.Conclusion: Nanopore sequencing technology demonstrates as a reliable and rapid method for detecting pathogens in elderly patients with CAP.Keywords: Nanopore sequencing technology, metagenomic next-generation sequencing, Elderly Community-Acquired Pneumonia, pathogen diagnosis

Abstract Background Acute exacerbation of fibrosing interstitial lung diseases (AE-ILD) is a serious life-threatening event per year. Methylprednisolone and/or immunosuppressive agents (ISA) are a mainstay in any regimen, under the premise that pulmonary infection has been promptly identified and controlled. We investigated the value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) on the treatment adjustment of AE-ILD. Methods We conducted a cross-sectional observational study. All data were collected prospectively and retrospectively analyzed. We included fifty-six patients with AE-ILD and nineteen stable ILD who underwent BALF mNGS at the beginning of admission. Results Patients with a variety of ILD classification were included. Connective–tissue disease related ILD (CTD-ILD) occupy the most common underlying non-idiopathic pulmonary fibrosis (non-IPF). The infection-triggered AE accounted for 39.29%, with the majority of cases being mixed infections. The microorganisms load in the AE-ILD group was significantly higher. After adjusted by mNGS, the therapy coverage number of pathogens was significantly higher compared to the initial treatment (p

Liying Zhan,1,&ast; Zhihua Lv,2,&ast; Yunjing Zhang,3,&ast; Jingdi Chen,4 Lu Wang,1 Raojuan Huang,5 Yaqi Sun,5 Wei Wu1 1Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China; 2Department of Clinical Laboratory, Institute of Translational medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China; 3Department of Ultrasound, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China; 4Department of Orthopedics, the Airborne Military Hospital, Wuhan, Hubei, People’s Republic of China; 5First Clinical College of Wuhan University, Wuhan, Hubei, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Wei Wu, Email weiwu2012@whu.edu.cnPurpose: Application of metagenomic next-generation sequencing (mNGS) in identifying nosocomial central nervous system (CNS) infections in critical care units remains understudied.Methods: We conducted a retrospective analysis of microbiological results through both mNGS and routine examination of cerebrospinal fluid (CSF) samples from patients with nosocomial CNS infections. The aim of this study was to assess the clinical diagnostic effect of nosocomial mNGS in this population.Results: The study included 26 cases of nosocomial CNS infections in total. A total of 69.2% (18/26) of the samples tested positive for mNGS, which is substantially greater than the 7.7% (2/26; p< 0.05) detected through conventional techniques. Administration of antibiotics before culture is most likely the cause of the low CSF culture rate. Twenty-five pathogenic strains that were missed by standard testing. Three pathogens that were consistent with the mNGS results were positive by routine tests. Eight cases were negative by mNGS due to low pathogen CSF titres. Compared to traditional testing, mNGS demonstrated 100% sensitivity and 33.3% specificity in diagnosing CNS infections. The thirty-day mortality rate was 26.9% (7/26).Conclusion: Routine microbiologic testing frequently falls short of detecting all neuroinvasive pathogens. Our research suggests that mNGS offers an alternative means of detecting nosocomial CNS infections. By applying mNGS to CSF samples from patients with meningitis or encephalitis, we were able to improve the ability to diagnose nosocomial neurologic infections.Keywords: metagenomic next-generation sequencing, cerebrospinal fluid, central nervous system infections, diagnosis

Abstract Background Angiostrongyliasis cantonensis is a severe yet rare parasitic infection caused by the larvae of Angiostrongylus cantonensis. The primary characteristic feature of this foodborne illness in humans is eosinophilic meningitis. Recently, there has been a gradual increase in reported cases globally. Due to the lack of typical clinical symptoms, signs, and specific laboratory tests, early diagnosis of this disease poses significant challenges. Failure to diagnose and treat this condition promptly can result in fatalities. Methods We present the case of a 13-year-old male patient who initially presented with fever and headache. The patient was preliminarily diagnosed with bacterial meningitis and received treatment with antibacterial drugs. However, the patient’s condition worsened, and he developed progressive consciousness disturbances. Eventually, metagenomic next-generation sequencing (mNGS) testing of cerebrospinal fluid samples indicated Angiostrongylus cantonensis infection. Following treatment with albendazole and prednisone, the patient made a full recovery. We include this case report as part of a literature review to emphasize the potential applications of mNGS in the early diagnosis of Angiostrongyliasis cantonensis. Conclusion mNGS technology plays a crucial role in the diagnosis of angiostrongyliasis cantonensis. As this technology continues to evolve and be applied, we believe it will play an increasingly important role in diagnosing, treating, and monitoring angiostrongyliasis cantonensis.

Abstract Central nervous system Infections (CNSIs) is a disease characterized by complex pathogens, rapid disease progression, high mortality rate and high disability rate. Here, we evaluated the clinical value of metagenomic next generation sequencing (mNGS) in the diagnosis of central nervous system infections and explored the factors affecting the results of mNGS. We conducted a retrospective study to compare mNGS with conventional methods including culture, smear and etc. 111 suspected CNS infectious patients were enrolled in this study, and clinical data were recorded. Chi-square test were used to evaluate independent binomial variables, taking p 300*106/L), the positive rate of CSF mNGS is higher. To sum up, conventional microbiologic testing is insufficient to detect all neuroinvasive pathogens, and mNGS exhibited satisfactory diagnostic performance in CNSIs and with an overall detection rate higher than culture (p

Abstract Invasive pulmonary aspergillosis (IPA) in patients with diabetes mellitus has high incidence, especially in Type 2 diabetes mellitus (T2DM). The aim of this study was to evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) for IPA in patients with T2DM. A total of 66 patients with T2DM were included, including 21 IPA and 45 non-IPA patients, from January 2022 to December 2022. The demographic characteristics, comorbidities, laboratory test results, antibiotic treatment response, and 30-day mortality rate of patients were analyzed. The diagnostic accuracy of mNGS and conventional methods was compared, including sensitivity, specificity, positive predictive value and negative predictive value. The sensitivity and specificity of mNGS were 66.7% and 100.0%, respectively, which were significantly higher than those of fluorescence staining (42.1% and 100%), serum 1,3-β-D-glucan detection (38.1% and 90.9%), serum galactomannan detection (14.3% and 94.9%) and BALF galactomannan detection (47.3% and 70.7%). Although the sensitivity of BALF culture (75.0%) was higher than that of mNGS (66.7%), the turnover time of mNGS was significantly shorter than that of traditional culture (1.6 days vs. 5.0 days). The sensitivity of mNGS combined with BALF culture reached 100.0%. In addition, mNGS has a stronger ability to detect co-pathogens with IPA. 47.6% of T2DM patients with IPA were adjusted the initial antimicrobial therapy according to the mNGS results. This is the first study to focus on the diagnostic performance of mNGS in IPA infection in T2DM patients. MNGS can be used as a supplement to conventional methods for the diagnosis of IPA in patients with T2DM.

Abstract Background Microbial infection and colonization are frequently associated with disease progression and poor clinical outcomes in bronchiectasis. Identification of pathogen spectrum is crucial for precision treatment at exacerbation of bronchiectasis. Methods We conducted a prospective cohort study in patients with bronchiectasis exacerbation onset and stable state. Bronchoalveolar lavage fluid (BALF) was collected for conventional microbiological tests (CMTs) and metagenomic Next-Generation Sequencing (mNGS). Bronchiectasis patients were monitored for documenting the time to the next exacerbation during longitudinal follow-up. Results We recruited 168 eligible participants in the exacerbation cohorts, and 38 bronchiectasis patients at stable state at longitudinal follow-up. 141 bronchiectasis patients at exacerbation onset had definite or probable pathogens via combining CMTs with mNGS reports. We identified that Pseudomonas aeruginosa, non-tuberculous mycobacteria, Haemophilus influenzae, Nocardia spp, and Staphylococcus aureus were the top 5 pathogens with a higher detection rate in our cohorts via combination of CMTs and mNGS analysis. We also observed strong correlations of Pseudomonas aeruginosa, Haemophilus influenzae, non-tuberculous mycobacteria with disease severity, including the disease duration, Bronchiectasis Severity Index, and lung function. Moreover, the adjusted pathogenic index of potential pathogenic microorganism negatively correlated (r = -0.7280, p

Jiayi Chen,1,&ast; Yonghong Liu,2,&ast; Shengsheng Huang,1 Zixiang Pang,1 Qian Wei,1 Yuzhen Liu,1 Hongyuan Qin,1 Yuanming Chen1 1Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China; 2Department of Preventive Health Care, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Yuanming Chen, Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China, Email rkyygk@163.comIntroduction: This study evaluates the efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing spinal infections and developing therapeutic regimens that combine mNGS, microbiological cultures, and pathological investigations.Methods: Data were collected from 108 patients with suspected spinal infections between January 2022 and December 2023. Lesion tissues were obtained via C-arm assisted puncture or open surgery for mNGS, conventional microbiological culture, and pathological analysis. Personalized antimicrobial therapies were tailored based on these findings, with follow-up evaluations 7 days postoperatively. The sensitivity and specificity of mNGS were assessed, along with its impact on treatment and prognosis.Results: mNGS showed a significantly higher positive detection rate (61.20%) compared to conventional microbiological culture (30.80%) and PCT (28%). mNGS demonstrated greater sensitivity (79.41%) and negative predictive value (63.16%) than cultures (25% and 22.58%, respectively), with no significant difference in specificity and positive predictive value. Seven days post-surgery, a significant reduction in neutrophil percentage (NEUT%) was observed, though decreases in white blood cell count (WBC), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were not statistically significant. At the last follow-up, significant improved in Visual Analogue Scale (VAS) scores, Oswestry Disability Index (ODI), and Japanese Orthopaedic Association (JOA) scores were noted.Conclusion: mNGS outperforms traditional microbiological culture in pathogen detection, especially for rare and critical pathogens. Treatment protocols combining mNGS, microbiological cultures, and pathological examinations are effective and provide valuable clinical insights for treating spinal infections.Keywords: spinal infection, metagenomic next-generation sequencing, sensitivity, specificity treatment

Abstract Introduction Alveolar echinococcosis (AE), caused by the larval forms of Echinococcus multilocularis, is a zoonotic disease affecting the liver, lungs, lymph nodes, kidneys, brain, bones, thyroid, and other organs. Diagnosing AE in a non-endemic area is usually challenging. With the rapid development and increasing application of sequencing techniques in recent years, metagenomic next-generation sequencing (mNGS) has become a powerful tool for diagnosing rare infectious diseases. Case Presentation A 45-year-old woman was admitted to the hospital for the presence of pulmonary shadows for more than 3 months. The lung computed tomography (CT) at a local hospital revealed scattered solid and quasi-circular nodules in the left upper lobe, left lower lobe, right middle lobe, and right lower lobe. The largest nodule was located in the dorsal part of the right lung, measuring 2.0 × 1.7 × 1.5 cm. Moreover, abdominal CT revealed one space-occupying lesion each in the left and right lobes. The pathological analysis of the lung biopsy specimen revealed infiltration of lymphocytes, plasma cells, and eosinophils in the alveolar wall and interstitial area. No pathogenic bacteria were observed in the sputum smear and culture tests. There were no parasite eggs in the stool. The mNGS of the lung puncture tissue revealed 6156 sequence reads matching E. multilocularis; thus, the condition was diagnosed as AE. Albendazole 400 mg was administered twice daily, and the patient was stable during follow-up. Conclusion This case emphasizes the role of mNGS in diagnosing AE. As a novel, sensitive, and accurate diagnostic method, mNGS could be an attractive approach for facilitating early diagnosis and prompt treatment of infectious diseases, especially when the infection was caused by rare pathogens.