High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

Identification of pathogen composition in a Chinese population with iatrogenic and native vertebral osteomyelitis by using mNGS

BACKGROUND

Early antimicrobial therapy is crucial regarding the prognosis of vertebral osteomyelitis, but early pathogen diagnosis remains challenging.

OBJECTIVE

In this study, we aimed to differentiate the types of pathogens in iatrogenic vertebral osteomyelitis (IVO) and native vertebral osteomyelitis (NVO) to guide early antibiotic treatment.

METHODS

A total of 145 patients, who had confirmed spinal infection and underwent metagenomic next-generation sequencing (mNGS) testing, were included, with 114 in the NVO group and 31 in the IVO group. Using mNGS, we detected and classified 53 pathogens in the 31 patients in the IVO group and 169 pathogens in the 114 patients in the NVO group. To further distinguish IVO from NVO, we employed machine learning algorithms to select serum biomarkers and developed a nomogram model.

RESULTS

The results revealed that the proportion of the Actinobacteria phylum in the NVO group was approximately 28.40%, which was significantly higher than the 15.09% in the IVO group. Conversely, the proportion of the Firmicutes phylum (39.62%) in the IVO group was markedly increased compared to the 21.30% in the NVO group. Further genus-level classification demonstrated that Staphylococcus was the most common pathogen in the IVO group, whereas Mycobacterium was predominant in the NVO group. Through LASSO regression and random forest algorithms, we identified 5 serum biomarkers including percentage of basophils (BASO%), percentage of monocytes (Mono%), platelet volume (PCT), globulin (G), activated partial thromboplastin time (APTT) for distinguishing IVO from NVO. Based on these biomarkers, we established a nomogram model capable of accurately discriminating between the two conditions.

CONCLUSION

The results of this study hold promise in providing valuable guidance to clinical practitioners for the differential diagnosis and early antimicrobial treatment of vertebral osteomyelitis.

Integrative analyses identify opportunistic pathogens of patients with lower respiratory tract infections based on metagenomic next-generation sequencing

Lower respiratory tract infections (LRTIs) represent some of the most globally prevalent and detrimental diseases. Metagenomic next-generation sequencing (mNGS) technology has effectively addressed the requirement for the diagnosis of clinical infectious diseases. This study aimed at identifying and classifying opportunistic pathogens from the respiratory tract-colonizing microflora in LRTI patients using data acquired from mNGS analyses. A retrospective study was performed employing the mNGS data pertaining to the respiratory samples derived from 394 LRTIs patients. Linear discriminant analysis effect size (LEfSe) analysis was conducted to discern the discriminant bacteria. Receiver operating characteristic curves (ROC) were established to demonstrate discriminant bacterial behavior to distinguish colonization from infection. A total of 443 discriminant bacteria were identified and segregated into three cohorts contingent upon their correlation profiles, detection frequency, and relative abundance in order to distinguish pathogens from colonizing microflora. Among them, 119 emerging opportunistic pathogens (cohort 2) occupied an average area under the curve (AUC) of 0.976 for exhibiting the most prominent predictability in distinguishing colonization from infection, 39 were colonizing bacteria (cohort 1, 0.961), and 285 were rare opportunistic pathogens (cohort 3, 0.887). The LTRIs patients appeared modular in the form of cohorts depicting complex microbial co-occurrence networks, reduced diversity, and a high degree of antagonistic interactions in the respiratory tract microbiome. The study findings indicate that therapeutic interventions should target interaction networks rather than individual microbes, providing an innovative perspective for comprehending and combating respiratory infections. Conclusively, this study reports a profile of LRTIs-associated bacterial colonization and opportunistic pathogens in a relatively large-scale cohort, which might serve as a reference panel for the interpretation of mNGS results in clinical practice.

Clinical applications of metagenomics next-generation sequencing in infectious diseases

Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.

Clinical applications of metagenomic next-generation sequencing in the identification of pathogens in periprosthetic joint infections: a retrospective study

BACKGROUND

This study aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) technology to identify pathogens in periprosthetic joint infection (PJI).

METHODS

A retrospective analysis was conducted on 65 patients suspected of having PJI between April 2020 and July 2023. The patients were categorized into PJI (46 patients) and non-PJI (19 patients) groups based on the 2018 International Consensus Meeting criteria. Clinical data were collected, and both conventional bacterial culture and mNGS were performed. The diagnostic performance of the two methods was compared and analyzed.

RESULTS

mNGS exhibited a sensitivity of 89.13%, a specificity of 94.74%, a positive predictive value of 97.62%, a negative predictive value of 78.26%, and an overall diagnostic accuracy of 90.77%. Compared to microbial culture, mNGS demonstrated superior diagnostic sensitivity while maintaining similar specificity. A total of 48 pathogens were successfully identified using mNGS, with Coagulase-negative staphylococci, Streptococci, Staphylococcus aureus, and Cutibacterium acnes being the most common infectious agents. Notably, mNGS was used to identify 17 potential pathogens in 14 culture-negative PJI samples, highlighting its ability to detect rare infectious agents, including Cutibacterium acnes (n = 5), Granulicatella adiacens (n = 1), Mycobacterium tuberculosis complex (n = 1), and Coxiella burnetii (n = 1), among others, which are not detectable by routine culture methods. However, mNGS failed to detect the pathogen in 4 culture-positive PJI patients, indicating its limitations. Among the 46 PJI patients, 27 had positive culture and mNGS results. The results of mNGS were concordant with those of culture at the genus level in 6 patients with PJI and at the species level in 18 patients. Furthermore, the present study revealed a significantly greater proportion of Staphylococcus aureus in the sinus tract group (45.45%) than in the non-sinus tract group (14.29%), indicating the association of this pathogen with sinus formation in PJI (P = 0.03). Additionally, there was no significant difference in the occurrence of polymicrobial infections between the sinus tract group (27.27%) and the non-sinus tract group (33.33%) (P = 0.37).

CONCLUSIONS

Metagenomic next-generation sequencing can serve as a valuable screening tool in addition to traditional culture methods to improve diagnostic accuracy through optimized culture strategies.

Diagnostic and Therapeutic Challenges in Lemierre Syndrome: A Case Report Using Metagenomic Next Generation Sequencing

Lemierre syndrome (LS) is a rare and life-threatening condition predominantly caused by Fusobacterium necrophorum. Currently, there are no standardized clinical guidelines for LS management. Here, we describe the case of a 40-year-old male with fever, productive cough, and dyspnea but no sore throat. Diagnostic radiological examinations revealed multiple pulmonary cavitary nodules and an internal jugular vein occlusion. Metagenomic Next-Generation Sequencing (mNGS) of the alveolar lavage fluid identified Fusobacterium necrophorum, thereby confirming the diagnosis of LS. Intriguingly, the patient exhibited a delayed clinical response despite receiving the appropriate antibiotic. After integrating tigecycline into the treatment to address potential co-infecting bacteria, we observed a marked improvement in his clinical symptoms. Subsequent follow-up over 12 weeks post-discharge revealed complete alleviation of symptoms, and a chest CT scan showed marked regression of the lung lesions.

Application of metagenomic next-generation sequencing technology in the etiological diagnosis of peritoneal dialysis-associated peritonitis

Pathogens detected by metagenomic next-generation sequencing (mNGS) and the laboratory blood culture flask method were compared to understand the advantages and clinical significance of mNGS assays in the etiological diagnosis of peritoneal dialysis-associated peritonitis (PDAP). The study involved a total of 37 patients from the hospital's peritoneal dialysis centre, six of whom were patients with non-peritoneal dialysis-associated peritonitis. Peritoneal dialysis samples were collected from the 37 patients, who were divided into two groups. One group's samples were cultured using conventional blood culture flasks, and the other samples underwent pathogen testing using mNGS. The results showed that the positive rate of mNGS was 96.77%, while that of the blood culture flask method was 70.97% (p < 0.05). A total of 29 pathogens were detected by mNGS, namely 24 bacteria, one fungus, and four viruses. A total of 10 pathogens were detected using the bacterial blood culture method, namely nine bacteria and one fungus. The final judgment of the PDAP's causative pathogenic microorganism was made by combining the clinical condition, response to therapy, and the whole-genome sequencing findings. For mNGS, the sensitivity was 96.77%, the specificity was 83.33%, the positive predictive value was 96.77%, and the negative predictive value was 83.33%. For the blood culture flask method, the sensitivity was 70.97%, the specificity was 100%, the positive predictive value was 100%, and the negative predictive value was 0%. In conclusion, mNGS had a shorter detection time for diagnosing peritoneal dialysis-related peritonitis pathogens, with a higher positive rate than traditional bacterial cultures, providing significant advantages in diagnosing rare pathogens.

Application of Mono and Trinuclear Cyclometalated Iridium (III) Complexes in Differential Bacterial Imaging and Antimicrobial Photodynamic Therapy

The application of transition metal complexes for antimicrobial photodynamic therapy (PDT) has emerged as an attractive alternative in mitigating a broad range of bacterial pathogens, including multidrug-resistant pathogens. In view of their photostability, long excited-state lifetimes, and tunable emission properties, transition metal complexes also contribute as bioimaging agents. In the present work, we designed mono and trinuclear cyclometalated iridium (III) complexes to explore their imaging application and antibacterial potential. For this, we used Methicillin-resistant S. aureus (MRSA), the most prevalent of community-associated (CA) multidrug-resistant (MDR) bacteria (CA MDR) and Lactococcus lactis (L. lactis) as Gram-positive while Campylobacter jejuni (C. jejuni) and E. coli as Gram-negative bacteria. In addition to differential bioimaging of these bacteria, we assessed the antibacterial effects of both mono and trinuclear Ir(III) complexes under exposure to 427 nm LED light. The data presented herein strongly suggest better efficacy of trinuclear Ir(III) complex over the mononuclear complex in imparting photoinduced cell death of MRSA. Based on the safety profile of these complexes, we propose that trinuclear cyclometalated iridium(III) complex holds great promise for selective recognition and targeting MDR bacteria with minimal off-target effect.

Lessons from Multiple Infections Such as Lymphoma Complicated with Pneumocystis Infection: A Case Report

Background

Lymphoma is complicated by intricate infections, notably Pneumocystis jirovecii pneumonia (PJP), marked by rapid progression, respiratory failure, and high mortality. Rapid diagnosis of PJP and effective administration of the first-line treatment trimethoprim-sulfamethoxazole (TMP-SMX) are important. For patients intolerant to TMP-SMX, selecting appropriate alternatives is challenging, necessitating careful decisions to optimize diagnosis and treatment. We present a lymphoma case complicated by PJP, illustrating medication adjustment until a positive response was observed.

Case Description

A 41-year-old male patient with lymphoma presented with a week-long history of fever, fatigue, cough, sputum, chest tightness, and exertional dyspnea, unresponsive to treatment. Routine laboratory examinations revealed no pathogenic bacteria. PJ and Mycobacterium tuberculosis (MTB) were detected in bronchoalveolar lavage fluid (BALF) using metagenomic next-generation sequencing (mNGS). On Day 1 of admission, meropenem, TMP-SMX, and rifampicin+isoniazid+levofloxacin were administered. However, the patient developed drug-induced hepatotoxicity and gastrointestinal adverse reactions after six days of treatment. After a multidisciplinary team discussion, anti-tuberculosis therapy was stopped because of insufficient evidence of tuberculosis infection. A reduced dose of TMP-SMX with micafungin was used for PJP; however, symptoms persisted and repeated computed tomography showed extensive deterioration of bilateral pulmonary plaques. The PJP regimen was modified to include a combination of TMP-SMX and caspofungin. Due to the high fever and elevated infection indices, the patient was treated with teicoplanin to enhance the anti-infection effects. By Day 13, the patient's temperature had normalized, and infection control was achieved by Day 30. CT revealed that the infection in both lung lobes fully resolved. Subsequently, lymphoma treatment commenced.

Conclusion

BALF-NGS facilitates early and rapid diagnosis of PJP. mNGS reads of MTB bacillus <5 may indicate a bacterial carrier state, warranting other detection techniques to support it. There is insufficient evidence for using TMP-SMX with micafungin to treat PJP; however, TMP-SMX combined with caspofungin is suitable.

Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.

A novel method for simultaneous detection of hematological tumors and infectious pathogens by metagenomic next generation sequencing of plasma

BACKGROUND

Metagenomic next-generation sequencing (mNGS) is valuable for pathogen identification; however, distinguishing between infectious diseases and conditions with potentially similar clinical manifestations, including malignant tumors, is challenging. Therefore, we developed a method for simultaneous detection of infectious pathogens and cancer in blood samples.

METHODS

Plasma samples (n = 244) were collected from 150 and 94 patients with infections and hematological malignancies, respectively, and analyzed by mNGS for pathogen detection, alongside human tumor chromosomal copy number variation (CNV) analysis (≥5Mbp or 10Mbp CNV region). Further, an evaluation set, comprising 87 plasma samples, was analyzed by mNGS and human CNV analysis, to validate the feasibility of the method.

RESULTS

Among 94 patients with hematological malignancy, sensitivity values of CNV detection for tumor diagnosis were 69.15 % and 32.98 % for CNV region 5Mbp and 10Mbp, respectively, with corresponding specificities of 92.62 % and 100 % in the infection group. Area under the ROC curve (AUC) values for 5Mbp and 10Mbp region were 0.825 and 0.665, respectively, which was a significant difference of 0.160 (95 % CI: 0.110-0.210; p < 0.001), highlighting the superiority of 5Mbp output region data. Six patients with high-risk CNV results were identified in the validation study: three with history of tumor treatment, two eventually newly-diagnosed with hematological malignancies, and one with indeterminate final diagnosis.

CONCLUSIONS

Concurrent CNV analysis alongside mNGS for infection diagnosis is promising for detecting malignant tumors. We recommend adopting a CNV region of 10Mbp over 5Mbp for our model, because of the lower false-positive rate (FPR).

Clinical Manifestation, mNGS Based Diagnosis and Treatment of Pulmonary Mucormycosis with Rhizopus delemar in a Diabetic Patient

Pulmonary mucormycosis is a severe and often fatal disease that commonly affects patients with underlying conditions, such as diabetes. Early diagnosis and appropriate treatment are crucial for improving survival rates. However, clinical diagnosis remains challenging due to difficulty in obtaining etiological evidence. In this particular case, the patient presented with a cough-producing bloody sputum, and a chest CT revealed lesions in the right upper lobe of the lung. The patient was ultimately diagnosed with pulmonary mucormycosis caused by Rhizopus delemar through clinical bronchoscopy biopsy and metagenomic next-generation sequencing (mNGS) analysis of bronchoalveolar lavage fluid sample. Subsequently, antifungal therapy using the less toxic Amphotericin B cholesterol Organosulfate complex was initiated, improving the patient's condition. In conclusion, our findings underscore the potential of mNGS to provide an accurate and rapid etiological diagnosis of pulmonary mucormycosis, offering a foundation for treatment.

Illumina and Nanopore sequencing in culture-negative samples from suspected lower respiratory tract infection patients

Objective

To evaluate the diagnostic value of metagenomic sequencing technology based on Illumina and Nanopore sequencing platforms for patients with suspected lower respiratory tract infection whose pathogen could not be identified by conventional microbiological tests.

Methods

Patients admitted to the Respiratory and Critical Care Medicine in Shanghai Ruijin Hospital were retrospectively studied from August 2021 to March 2022. Alveolar lavage or sputum was retained in patients with clinically suspected lower respiratory tract infection who were negative in conventional tests. Bronchoalveolar lavage fluid (BALF) samples were obtained using bronchoscopy. Sputum samples were collected, while BALF samples were not available due to bronchoscopy contraindications. Samples collected from enrolled patients were simultaneously sent for metagenomic sequencing on both platforms.

Results

Thirty-eight patients with suspected LRTI were enrolled in this study, consisting of 36 parts of alveolar lavage and 2 parts of sputum. According to the infection diagnosis, 31 patients were confirmed to be infected with pathogens, while 7 patients were diagnosed with non-infectious disease. With regard to the diagnosis of infectious diseases, the sensitivity and specificity of Illumina and Nanopore to diagnose infection in patients were 80.6% vs. 93.5% and 42.9 vs. 28.6%, respectively. In patients diagnosed with bacterial, Mycobacterium, and fungal infections, the positive rates of Illumina and Nanopore sequencer were 71.4% vs. 78.6%, 36.4% vs. 90.9%, and 50% vs. 62.5%, respectively. In terms of pathogen diagnosis, the sensitivity and specificity of pathogens detected by Illumina and Nanopore were 55.6% vs. 77.8% and 42.9% vs. 28.6%, respectively. Among the patients treated with antibiotics in the last 2 weeks, 61.1% (11/18) and 77.8% (14/18) cases of pathogens were accurately detected by Illumina and Nanopore, respectively, among which 8 cases were detected jointly. The consistency between Illumina and diagnosis was 63.9% (23/36), while the consistency between Nanopore and diagnosis was 83.3% (30/36). Between Illumina and Nanopore sequencing methods, the consistency ratio was 55% (22/42) based on pathogen diagnosis.

Conclusion

Both platforms play a certain value in infection diagnosis and pathogen diagnosis of CMT-negative suspected LRTI patients, providing a theoretical basis for clinical accurate diagnosis and symptomatic treatment. The Nanopore platform demonstrated potential advantages in the identification of Mycobacterium and could further provide another powerful approach for patients with suspected Mycobacterium infection.

Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China

Background

Infection is the main cause of death for patients after allogeneic hematopoietic stem cell transplantation (HSCT). However, pathogen profiles still have not been reported in detail due to their heterogeneity caused by geographic region.

Objective

To evaluate the performance of metagenomic next-generation sequencing (mNGS) and summarize regional pathogen profiles of infected patients after HSCT.

Methods

From February 2021 to August 2022, 64 patients, admitted to the Department of Hematology of The First Hospital of Jilin University for HSCT and diagnosed as suspected infections, were retrospectively enrolled.

Results

A total of 38 patients were diagnosed as having infections, including bloodstream (n =17), pulmonary (n =16), central nervous system (CNS) (n =4), and chest (n =1) infections. Human betaherpesvirus 5 (CMV) was the most common pathogen in both bloodstream (n =10) and pulmonary (n =8) infections, while CNS (n =2) and chest (n =1) infections were mainly caused by Human gammaherpesvirus 4 (EBV). For bloodstream infection, Mycobacterium tuberculosis complex (n =3), Staphylococcus epidermidis (n =1), and Candida tropicalis (n =1) were also diagnosed as causative pathogens. Furthermore, mNGS combined with conventional tests can identify more causative pathogens with high sensitivity of 82.9% (95% CI 70.4-95.3%), and the total coincidence rate can reach up to 76.7% (95% CI 64.1-89.4%).

Conclusions

Our findings emphasized the importance of mNGS in diagnosing, managing, and ruling out infections, and an era of more rapid, independent, and impartial diagnosis of infections after HSCT can be expected.

OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier

Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in both clinical and environmental health, e.g., detection of bacterial outbreaks. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. For instance, metagenomics classifiers usually require a large amount of memory or specific operating systems/libraries. In this work, we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases (e.g., selection of bacteria of public health priority), making it ideal for running on smartphones or tablets. We indexed both OCTOPUS and Kraken2 on a bacterial database with ~4,000 reference genomes, then simulated a positive (bacterial genomes from the same species, but different genomes) and two negative (viral, mammalian) Nanopore test sets. On the bacterial test set OCTOPUS yielded sensitivity and precision comparable to Kraken2 (94.4% and 99.8% versus 94.5% and 99.1%, respectively). On non-bacterial sequences (mammals and viral), OCTOPUS dramatically decreased (4- to 16-fold) the false positive rate when compared to Kraken2 (2.1% and 0.7% versus 8.2% and 11.2%, respectively). We also developed customized databases including viruses, and the World Health Organization's set of bacteria of concern for drug resistance, tested with real Nanopore data on an Android smartphone. OCTOPUS is publicly available at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.

Sepsis and Hepatapostema Secondary to Chromobacterium Violaceum Infection on Lower Limb Skin: A Case Report

Background

Chromobacterium violaceum (C. violaceum) is a Gram-negative bacterium capable of causing severe infections in both humans and specific animals. Despite its infrequency, C. violaceum infections exhibit a notably high mortality rate. The timely and precise detection of this pathogen stands as a critical factor in achieving effective diagnosis and treatment. Traditional diagnostic approaches possess limitations, particularly in terms of their time-consuming nature and the range of pathogens they can identify. Metagenomic next-generation sequencing (mNGS) testing has emerged as a highly promising diagnostic tool for infectious diseases.

Methods

Within this case report, we present a patient who developed a C. violaceum infection subsequent to a lower limb infection, leading to the progression of sepsis, a liver abscess, septic shock, multi-organ dysfunction, and altered mental status. Samples of the patient's blood and tissue from the lower limb skin are collected, and the infection is swiftly diagnosed through mNGS, allowing for the immediate initiation of suitable treatment.

Results

The mNGS results revealed the patient's infection with C. violaceum. Subsequent conventional bacterial culture results were concordant with the mNGS findings. Following comprehensive management measures, including prompt and effective anti-infective treatment, the patient achieved cure and was successfully discharged.

Conclusion

This case underscores the significance of employing advanced diagnostic methodologies like mNGS for the early detection of uncommon pathogens such as C. violaceum. The expedited diagnosis and timely intervention hold the potential to substantially enhance patient outcomes in cases of severe infections instigated by this bacterium.

Nanopore targeted sequencing-based diagnosis of central nervous system infections in HIV-infected patients

BACKGROUND

Early and accurate etiological diagnosis is very important for improving the prognosis of central nervous system (CNS) infections in human immunodeficiency virus (HIV)-infected patients. The goal is not easily achieved by conventional microbiological tests. We developed a nanopore targeted sequencing (NTS) platform and evaluated the diagnostic performance for CNS infections in HIV-infected patients, with special focus on cryptococcal meningitis (CM). We compared the CM diagnostic performance of NTS with conventional methods and cryptococcal polymerase chain reaction (PCR).

METHODS

This study included 57 hospitalized HIV-infected patients with suspected CNS infections from September 2018 to March 2022. The diagnosis established during hospitalization includes 27 cases of CM, 13 CNS tuberculosis, 5 toxoplasma encephalitis, 2 cytomegalovirus (CMV) encephalitis and 1 Varicella-zoster virus (VZV) encephalitis. The 2 cases of CMV encephalitis also have co-existing CM. Target-specific PCR amplification was used to enrich pathogen sequences before nanopore sequencing. NTS was performed on stored cerebrospinal fluid (CSF) samples and the results were compared with the diagnosis during hospitalization.

RESULTS

53 (93.0%) of the patients were male. The median CD4 cell count was 25.0 (IQR: 14.0-63.0) cells/uL. The sensitivities of CSF culture, India ink staining, cryptococcal PCR and NTS for CM were 70.4% (95%CI: 51.5 - 84.1%), 76.0% (95%CI: 56.6 - 88.5%), 77.8% (59.2 - 89.4%) and 85.2% (95%CI: 67.5 - 94.1%), respectively. All those methods had 100% specificity for CM. Our NTS platform could identify Cryptococcus at species level. Moreover, NTS was also able to identify all the 5 cases of toxoplasma encephalitis, 2 cases of CMV encephalitis and 1 VZV encephalitis. However, only 1 of 13 CNS tuberculosis cases was diagnosed by NTS, and so did Xpert MTB/RIF assay.

CONCLUSIONS

NTS has a good diagnostic performance for CM in HIV-infected patients and may have the ability of simultaneously detecting other pathogens, including mixed infections. With continuing improving of the NTS platform, it may be a promising alterative microbiological test for assisting with the diagnosis of CNS infections.

Case report: Metagenomics next-generation sequencing in the diagnosis of septic shock due to Fusobacterium necrophorum in a 6-year-old child

Fusobacterium necrophorum (F. necrophorum) infection is rare in pediatrics. In addition, the detection time of F. necrophorum by blood culture is long, and the positive rate is low. Infection with F. necrophorum bacilli usually follows rapid disease progression, resulting in high mortality. In previous reports of F. necrophorum-related cases, the most dangerous moment of the disease occurred after the appearance of Lemierre's syndrome. We report an atypical case of a 6-year-old female patient who developed septic shock within 24 h of admission due to F. necrophorum infection in the absence of Lemierre's syndrome. F. necrophorum was identified in a blood sample by metagenomics next-generation sequencing (mNGS) but not by standard blood culture. The patient was finally cured and discharged after receiving timely and effective targeted anti-infection treatment. In the present case study, it was observed that the heightened virulence and invasiveness of F. necrophorum contribute significantly to its role as a primary pathogen in pediatric septic shock. This can precipitate hemodynamic instability and multiple organ failure, even in the absence of Lemierre's syndrome. The use of mNGS can deeply and rapidly identify infectious pathogens, guide the use of targeted antibiotics, and greatly improve the survival rate of patients.

Metagenomic Next-generation Sequencing May be a Tool for Timely Diagnosis of Seronegative and Primary Toxoplasma Infection After Allogeneic Hematopoietic Stem Cell Transplantation: A Case Report and Literature Review

We report a case of Toxoplasma gondii ( T. gondii ) antibody seronegativity in a 14-year-old boy with a primary infection of T. gondii after allogeneic hematopoietic stem cell transplantation for acute T-cell lymphoblastic leukemia who was rapidly diagnosed through metagenomic next-generation sequencing of peripheral blood as well as clinical manifestations. He was successfully cured with timely administration of trimethoprim-sulfamethoxazole due to early diagnosis.

Metagenomic next-generation sequencing in detecting pathogens in pediatric oncology patients with suspected bloodstream infections

BACKGROUND

Studies on mNGS application in pediatric oncology patients, who are at high risk of infection, are quite limited.

METHODS

From March 2020 to June 2022, a total of 224 blood samples from 195 pediatric oncology patients who were suspected as bloodstream infections were enrolled in this study. Their clinical and laboratory data were retrospectively reviewed, and the diagnostic performance of mNGS was assessed.

RESULTS

Compared to the reference tests, mNGS showed significantly higher sensitivity (89.8% vs 32.5%, P < 0.001) and clinical agreement (76.3% vs 51.3%, P < 0.001) in detecting potential pathogens and distinguishing BSI from non-BSI. Especially, mNGS had an outstanding performance for virus detection, contributing to 100% clinical diagnosed virus. Samples from patients with neutropenia showed higher incidence of bacterial infections (P = 0.035). The most identified bacteria were Escherichia coli, and the overall infections by gram-negative bacteria were significantly more prevalent than those by gram-positive ones (90% vs 10%, P < 0.001). Overall, mNGS had an impact on the antimicrobial regimens' usage in 54.3% of the samples in this study.

CONCLUSIONS

mNGS has the advantage of rapid and effective pathogen diagnosis in pediatric oncology patients with suspected BSI, especially for virus.

IMPACT

Compared with reference tests, mNGS showed significantly higher sensitivity and clinical agreement in detecting potential pathogens and distinguishing bloodstream infections (BSI) from non-BSI. mNGS is particularly prominent in clinical diagnosed virus detection. The incidence of bacterial infection was higher in patients with neutropenia, and the overall infection rate of Gram-negative bacteria was significantly higher than that of Gram-positive bacteria. mNGS affects the antimicrobial regimens' usage in more than half of patients.

Clinical application of metagenomic next-generation sequencing in patients with different organ system infection: A retrospective observational study

Microbiological identification is essential for appropriate treatment, but conventional methods are time-consuming and have a low sensitivity. In contrast, metagenomic next-generation sequencing (mNGS) is a culture-free and hypothesis-free technique that can detect a wide array of potential pathogens. This study aimed to reveal the overall diagnostic value of mNGS for infectious diseases of different organ systems and compare the sensitivity and specificity of mNGS with conventional methods. In a retrospective cohort study, 94 patients with mNGS results were enrolled, and clinical data were recorded and analyzed to compare the positive rate of mNGS with traditional methods including as smears, serological tests, and traditional PCR, etc. In this study, mNGS and culture were both positive in 12.77% cases and were both negative in 23.4% cases. There were positive results in 56 cases (54.26%) only by mNGS and 4 cases (4.26%) were positive only by culture. There were significant differences in sensitivity of pathogen detection between of ID and NID group for mNGS (χ2 = 10.461, P = .001)and conventional methods(χ2 = 7.963, P = .005). The positive predictive values and negative predictive values of diagnosing infectious disease by mNGS were 94.12% and 30.77%, respectively. mNGS increased the sensitivity rate by approximately 53.66% compared with that of culture (78.05% vs24.39%; χ2 = 47.248, P < .001) and decreased the specificity rate by 12.5% compared with that of culture (66.67% vs 100.0%; χ2 = 4.8, P = .028). mNGS can identify emerging or rare pathogen and further guide treatment regimens. mNGS has advantages in identifying overall pathogens and bacteria, however, there was no obvious advantage in identifying fungi, virus and tuberculosis. mNGS has higher specificity than conventional methods in identifying pathogens and advantages in detecting emerging or rare pathogens.

Metagenomic next-generation sequencing testing from the perspective of clinical benefits

BACKGROUND AND AIMS

Metagenomic next-generation sequencing (mNGS) provided promising supports to rapid pathogen diagnosis. However, summary of scientific application strategy based on clinical practice study is still necessary for enhancing clinical benefits.

MATERIALS AND METHODS

We conducted a retrospective analysis of 775 samples from patients with suspected infectious diseases (IDs). Based on final diagnosis, diagnostic performance, clinical relevance and clinical impact of mNGS among various clinical settings were assessed, and influencing factors were deeply explored.

RESULTS

84.26 % tests were clinically relevant; sample, but not sequencing, was the influencing factor. 40.77 % tests contributed to positive clinical impact, while 0.13 % and 59.10 % to negative and no impact respectively. mNGS utility in patients with IDs, definite infection site, BALF and CSF contributed to higher positive impacts. Days of empirical treatment before sampling ≤ 5 in ICU and ≤ 2 or between 11 and 20 in non-ICU, and reporting in 2 days brought about higher clinical benefit rates. Characteristic pathogen spectrum between ICU and non-ICU cases were revealed.

CONCLUSIONS

Our findings highlighted clinical benefits from mNGS varied among different clinical settings, and elucidated choices on patients, samples, sampling and reporting time were four key factors. Rational strategy should be concerned to promote scientific application of mNGS and better improve clinical value.

Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance

OBJECTIVE

The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance.

METHODS

A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs).

RESULTS

The detection rate of mNGS was 96.15%, higher than CMTs (45.05%) with a significant difference (χ 2 = 114.46, P < .01). The pathogen spectrum identified by mNGS was significantly wider than CMTs. Interestingly, the detection rate of mNGS was substantially higher than that of CMTs (70.33% vs 23.08%, P < .01) in patients with but not without antibiotic exposure. There was a significant positive correlation between mapped reads and pro-inflammatory cytokines (interleukin-6 and interleukin-8). However, mNGS failed to predict antimicrobial resistance in 5 of 12 patients compared to phenotype antimicrobial susceptibility testing results.

CONCLUSIONS

Metagenomic next-generation sequencing has a higher detection rate, a wider pathogen spectrum, and is less affected by prior antibiotic exposure than CMTs in identifying Gram-negative pathogens. The mapped reads may reflect a pro-inflammatory state in GNB-infected patients. Inferring actual resistance phenotypes from metagenomic data remains a great challenge.

Metagenomic next-generation sequencing for detecting Aspergillosis pneumonia in immunocompromised patients: a retrospective study

Purpose

The identification of Aspergillus by metagenomic next-generation sequencing (mNGS) remains a challenging task due to the difficulty of nucleic acid extraction. The objective of this study was to determine whether mNGS could provide an accurate and efficient method for detecting invasive pulmonary aspergillosis (IPA) in immunocompromised patients (ICP).

Methods

A total of 133 ICP admitted to the ICU between January 2020 and September 2022 were enrolled in the study, of which 46 were diagnosed with IPA and 87 were non-IPA cases. The bronchoalveolar lavage fluid (BALF) was analyzed for the presence of Aspergillosis and other co-pathogens using mNGS, and its diagnostic performance was compared to conventional microbial tests (CMTs) that included smear, cultures, serum and BALF galactomannan (GM) test. Clinical composite diagnosis was used as the reference standard.

Results

mNGS had a sensitivity, specificity, and accuracy of 82.6%, 97.7%, and 92.5%, respectively, in diagnosing IPA. These findings were comparable to those of the combination of multiple CMTs. Interestingly, the sensitivity of mNGS was superior to that of any single CMT method, as demonstrated by comparisons with smears (8.7%, P < 0.001), culture (39.1%, P < 0.001), serum GM (23.9%, P < 0.001) and BALF GM (69.6%, P = 0.031). mNGS was capable of accurately distinguish strains of Aspergillus genus, with a consistency of 77.8% with culture. Furthermore, mNGS also identified A. fumigatus, A. flavus, A. terrestris, A. oryzae and Mucor spp. in culture-negative cases. The sequencing reads of Aspergillus by mNGS exhibited extensive variation, ranging from 11 to1702. A positive correlation was observed between the optical density index of BALF GM and unique reads by mNGS (r = 0.607, P = 0.001) in BALF-GM positive patients. Notably, mNGS was able to diagnose 35 out of 37 cases with mixed infection, with P. jirovecii and cytomegalovirus being the most common co-pathogens.

Conclusions

mNGS presents a feasible and remarkably sensitive approach for detecting Aspergillus in ICP, thereby serving as a valuable adjunctive tool to CMT. Furthermore, mNGS's ability to accurately identify fungal species and co-pathogens can assist in guiding appropriate antimicrobial therapy.

Blood metagenomics next-generation sequencing has advantages in detecting difficult-to-cultivate pathogens, and mixed infections: results from a real-world cohort

Background

Blood is a common sample source for metagenomics next-generation sequencing (mNGS) in clinical practice. In this study, we aimed to detect the diagnostic value of blood mNGS in a large real-world cohorts.

Methods

Blood mNGS results of 1,046 cases were collected and analyzed along with other laboratory tests. The capabilities and accuracy of blood mNGS were compared with other conventional approaches.

Results

Both the surgical department and the intensive care unit had a positive rate of over 80% in blood mNGS. The positive rate of mNGS was consistent with clinical manifestations. Among the 739 positive samples, 532 were detected as mixed infections. Compared to pathogen cultures, the negative predictive value of blood mNGS for bacteria and fungi detection was 98.9% [95%CI, 96.9%-100%], with an accuracy rate of 89.39%. When compared with polymer chain reaction, the consistency rates of blood mNGS for virus identification were remarkably high.

Conclusions

Blood mNGS have significant advantages in detecting difficult-to-cultivate bacteria or fungi, viruses, and mixed infections, which benefits patients of surgery department the most. Samples other than blood are recommended for mNGS test if a specific infection is suspected. The reporting threshold and reporting criteria of blood mNGS need to be optimized.

Metagenomic identification of pathogens and antimicrobial-resistant genes in bacterial positive blood cultures by nanopore sequencing

Nanopore sequencing workflows have attracted increasing attention owing to their fast, real-time, and convenient portability. Positive blood culture samples were collected from patients with bacterial bloodstream infection and tested by nanopore sequencing. This study compared the sequencing results for pathogen taxonomic profiling and antimicrobial resistance genes to those of species identification and phenotypic drug susceptibility using traditional microbiology testing. A total of 37 bacterial positive blood culture results of strain genotyping by nanopore sequencing were consistent with those of mass spectrometry. Among them, one mixed infection of bacteria and fungi was identified using nanopore sequencing and confirmatory quantitative polymerase chain reaction. The amount of sequencing data was 21.89 ± 8.46 MB for species identification, and 1.0 MB microbial strain data enabled accurate determination. Data volumes greater than or equal to 94.6 MB nearly covered all the antimicrobial resistance genes of the bacteria in our study. In addition, the results of the antimicrobial resistance genes were compared with those of phenotypic drug susceptibility testing for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Therefore, the nanopore sequencing platform for rapid identification of causing pathogens and relevant antimicrobial resistance genes complementary to conventional blood culture outcomes may optimize antimicrobial stewardship management for patients with bacterial bloodstream infection.

Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies

The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.

Chlamydia psittaci Pneumonia-Induced Pulmonary Thrombosis: A Case Report

Chlamydia psittaci pneumonia frequently leads to various extrapulmonary complications; however, reports of C. psittaci-pneumonia complicated by pulmonary thrombosis are uncommon. We report a case of severe C. psittaci pneumonia in a patient with a history of poultry contact and clinical manifestations including hyperpyrexia, dyspnea, and respiratory failure, which necessitated tracheal intubation for assisted ventilation. C. psittaci in bronchoalveolar lavage fluid was detected with metagenomic next-generation sequencing. Following targeted antibiotic therapy, the fever subsided, although dyspnea persisted without significant improvement, and chest pain developed. Compared to previous measurements, the D-dimer level increased, and CT pulmonary angiography revealed thromboses in the pulmonary artery trunk and left pulmonary artery. The symptoms improved after anticoagulant treatment, and the patient was discharged subsequently. This study suggests that C. psittaci infection may be associated with the formation of pulmonary thrombosis. Additional clinical data are required to support this inference. Following targeted antibiotic therapy, if persistent dyspnea, chest pain, and increased D-dimer level are present, pulmonary thrombosis should be considered, and pulmonary artery angiography can confirm the diagnosis.

Clinical treatment of patients with scrub typhus-induced liver injury and intracranial infection

Scrub typhus is an infectious disease caused by Orientia tsutsugamushi, a bacterium within the family Rickettsiaceae. The clinical symptoms are usually acute and are characterized by fever, eschar formation or ulceration, local or generalized lymphadenopathy, and rash. Because of the extensive damage to small blood vessels throughout the body, scrub typhus can involve multiple systems and organs, causing damage to the respiratory, digestive, and nervous systems and inducing kidney and liver dysfunction. Death can occur in severe cases. We herein report two cases of scrub typhus with liver damage and intracranial infection. Among patients with scrub typhus, the risk of death is significantly higher in those who develop liver injury and intracranial infection. However, there are few reports on the treatment of patients with liver injury and intracranial infection caused by scrub typhus, and relevant treatment experience is thus lacking. Our clinical case report helps to fill the knowledge gap in this area.

Composition of pathogenic microorganism in chronic osteomyelitis based on metagenomic sequencing and its application value in etiological diagnosis

BACKGROUND

Traditionally, conventional microbiological culture methods have been used to detect pathogenic microorganisms in chronic osteomyelitis. However, these methods have been found to have a low detection rate, complicating the precise guidance of infection treatment. This study employed metagenomic next-generation sequencing (mNGS) to detect these microorganisms in chronic osteomyelitis with three main objectives: 1). Gain a deeper understanding of the composition of pathogenic microorganisms in chronic osteomyelitis. 2). Compare the microbial detection rates between mNGS and the standard culture methods used in laboratories to enhance the effectiveness of the traditional culture methods. 3). Explore the potential of mNGS in etiological diagnosis.

METHODS

Fifty clinically confirmed intraoperative bone tissue samples of chronic osteomyelitis from January 2021 to December 2021 were collected and subjected to mNGS and microbiological testing, respectively. The orthopaedic surgeon combined clinical manifestations and related examinations to determine the causative pathogens.

RESULTS

The culture method obtained 29 aerobic and parthenogenic anaerobic bacteria, 3 specific anaerobic bacteria, and 1 yeast-like fungus. Thirty-six aerobic and parthenogenic anaerobic bacteria, 11 specific anaerobic bacteria, and 1 yeast-like fungus were obtained by mNGS, and 2 Mycobacterium tuberculosis(MTB) strains were detected. However, there was no significant difference in the overall positive detection rate between mNGS and the culture method (P = 0.07), and the two were not statistically significant in detecting aerobic and partly anaerobic bacteria (P = 0.625). But, mNGS was significantly superior to culture in detecting anaerobic bacteria and Mycobacterium tuberculosis (P<0.05).

CONCLUSIONS

The mNGS method has enhanced our understanding of the distribution of pathogenic microorganisms in chronic osteomyelitis. Traditional culture methods help isolate and cultivate aerobic and facultative anaerobic bacteria, and fungi, and are also utilized for antibacterial drug sensitivity tests. However, mNGS has shown superior capabilities in detecting anaerobic bacteria, MTB, and mixed infection bacteria. This finding offers invaluable guidance for improving laboratory microbial culture and detection conditions. Hence, mNGS should be judiciously used for chronic osteomyelitis, and PCR can be implemented for certain difficult-to-culture microorganisms, such as MTB.

Acute abdominal pain as the first symptom of Chlamydia psittaci pneumonia complicated by acute pancreatitis: a case report

Background

Chlamydia psittaci infections primarily cause damage to the lungs but may also affect the cardiovascular system, gastrointestinal tract, liver, kidney, and brain, resulting in a variety of extrapulmonary complications. However, reports regarding C. psittaci infection-associated pancreatitis are rare. In this report, a patient with C. psittaci pneumonia complicated by acute pancreatitis is presented.

Case description

The patient presented with acute upper abdominal pain and developed severe pyrexia and dyspnoea one day later. A chest computed tomography image revealed patchy consolidation in the left lung. The disease progressed rapidly, and the patient exhibited liver and kidney damage and type 1 respiratory failure within a short period of time. Metagenomic next-generation sequencing of alveolar lavage fluid revealed the presence of C. psittaci. The patient was administered doxycycline and moxifloxacin, after which the patient's abdominal pain and lung infection significantly resolved.

Conclusion

This case report demonstrates that extrapulmonary C. psittaci infections due to secondary acute pancreatitis can manifest as abdominal pain, although the exact mechanisms of C. psittaci caused by acute pancreatitis remain unclear. Timely diagnoses and treatments of such infections are necessary to achieve favorable clinical outcomes.

Case Report: Omadacycline in the treatment of macrolide-unresponsive Mycoplasma pneumoniae pneumonia in an adolescent patient

Omadacycline is a novel tetracycline antibiotic that exhibits good in vitro antibacterial activity against atypical pathogens such as Mycoplasma pneumoniae. It is approved for the treatment of adults with community-acquired bacterial pneumonia. However, the safety and efficacy of omadacycline in pediatric patients under 18 years of age have not yet been established. In the present paper, we report a case of pediatric community-acquired pneumonia in which initial empirical anti-infective therapy had failed. The patient received empirical anti-infective therapy with azithromycin and other antimicrobial agents upon admission but showed a poor clinical response and developed secondary tinnitus and liver dysfunction. After the confirmation of M. pneumoniae infection through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, an antibiotic switch to omadacycline was made. Thereafter, the patient's condition improved, and no adverse reactions were observed. These findings demonstrate that mNGS enables the identification of infection-causing pathogens in patients with unresponsive pneumonia. Omadacycline can be considered as an alternative option for anti-infective therapy in pediatric M. pneumoniae pneumonia, especially when the presence of bacterial resistance, adverse drug reactions, or organ failure are taken into consideration.

Case report: A toxoplasmic encephalitis in an immunocompromised child detected through metagenomic next-generation sequencing

There exist numerous pathogens that are capable of causing infections within the central nervous system (CNS); however, conventional detection and analysis methods prove to be challenging. Clinical diagnosis of CNS infections often depends on clinical characteristics, cerebrospinal fluid (CSF) analysis, imaging, and molecular detection assays. Unfortunately, these methods can be both insensitive and time consuming, which can lead to missed diagnoses and catastrophic outcomes, especially in the case of infrequent diseases. Despite the application of appropriate prophylactic regimens and evidence-based antimicrobial agents, CNS infections continue to result in significant morbidity and mortality in hospital settings. Metagenomic next-generation sequencing (mNGS) is a novel tool that enables the identification of thousands of pathogens in a target-independent manner in a single run. The role of this innovative detection method in clinical pathogen diagnostics has matured over time. In this particular research, clinicians employed mNGS to investigate a suspected CNS infection in a child with leukemia, and unexpectedly detected Toxoplasma gondii.

Case

A 3-year-old child diagnosed with T-cell lymphoblastic lymphoma was admitted to our hospital due to a 2-day history of fever and headache, along with 1 day of altered consciousness. Upon admission, the patient's Glasgow Coma Scale score was 14. Brain magnetic resonance imaging revealed multiple abnormal signals. Due to the patient's atypical clinical symptoms and laboratory test results, determining the etiology and treatment plan was difficulty.Subsequently, the patient underwent next-generation sequencing examination of cerebrospinal fluid. The following day, the results indicated the presence of Toxoplasma gondii. The patient received treatment with a combination of sulfamethoxazole (SMZ) and azithromycin. After approximately 7 days, the patient's symptoms significantly improved, and they were discharged from the hospital with oral medication to continue at home. A follow-up polymerase chain reaction (PCR) testing after about 6 weeks revealed the absence of Toxoplasma.

Conclusion

This case highlights the potential of mNGS as an effective method for detecting toxoplasmic encephalitis (TE). Since mNGS can identify thousands of pathogens in a single run, it may be a promising detection method for investigating the causative pathogens of central nervous system infections with atypical features.

Metagenomics as New Tool for Diagnosis of Scrub Typhus: Two Case Reports

Scrub typhus is a vector-borne infectious disease caused by Orientia tsutsugamushi. Accurate and timely diagnosis at the early infection stage could save the patients' lives. Traditional technologies were limited to rapidly and successfully detecting Orientia tsutsugamushi due to poor specificity, especially in the condition of atypical symptoms. The technology of Metagenomic next-generation sequencing (mNGS) is amenable to finding the real pathogen because it holds potential as a diagnostic platform for unbiased pathogen identification and precision medicine. Herein, we reported two clinical case reports relative to the Orientia tsutsugamushi infection diagnosed by mNGS. We hope these two cases will improve clinical diagnosis.

Microbiota of long-term indwelling hemodialysis catheters during renal transplantation perioperative period: a cross-sectional metagenomic microbial community analysis

Background: Catheter-related infection (CRI) is a major complication in patients undergoing hemodialysis. The lack of high-throughput research on catheter-related microbiota makes it difficult to predict the occurrence of CRI. Thus, this study aimed to delineate the microbial structure and diversity landscape of hemodialysis catheter tips among patients during the perioperative period of kidney transplantation (KTx) and provide insights into predicting the occurrence of CRI.Methods: Forty patients at the Department of Transplantation undergoing hemodialysis catheter removal were prospectively included. Samples, including catheter tip, catheter outlet skin swab, catheter blood, peripheral blood, oropharynx swab, and midstream urine, from the separate pre- and post-KTx groups were collected and analyzed using metagenomic next-generation sequencing (mNGS). All the catheter tips and blood samples were cultured conventionally.Results: The positive detection rates for bacteria using mNGS and traditional culture were 97.09% (200/206) and 2.65% (3/113), respectively. Low antibiotic-sensitivity biofilms with colonized bacteria were detected at the catheter tip. In asymptomatic patients, no statistically significant difference was observed in the catheter tip microbial composition and diversity between the pre- and post-KTx group. The catheter tip microbial composition and diversity were associated with fasting blood glucose levels. Microorganisms at the catheter tip most likely originated from catheter outlet skin and peripheral blood.Conclusions: The long-term colonization microbiota at the catheter tip is in a relatively stable state and is not readily influenced by KTx. It does not act as the source of infection in all CRIs, but could reflect hematogenous infection to some extent.

Fatal BK polyomavirus-associated pneumonia: report of two cases with literature review

BACKGROUND

In immunocompromised populations, such as patients with AIDS and recipients of solid organ and hematopoietic stem cell transplants, BK polyomavirus (BKPyV) can reactivate and cause several diseases, which can lead to death in their severe forms. Unlike hemorrhagic cystitis and BKPyV-associated nephropathy, BKPyV-associated pneumonia is rare, with only seven known cases worldwide. However, the disease can rapidly progress with extremely high mortality.

CASE PRESENTATION

Herein, we report two cases of BKPyV-associated pneumonia following hematopoietic stem cell transplantation. Both patients had consistent infectious pneumonia and graft-versus-host disease after stem cell transplantation. The diagnosis of BKPyV-associated pneumonia was confirmed by metagenomic next-generation sequencing and polymerase chain reaction after the sudden worsening of the pulmonary infection signs and symptoms concomitant with renal dysfunction and systemic immune weakening. Both patients eventually died of systemic multi-organ failure caused by severe pneumonia.

CONCLUSIONS

Currently, BKPyV reactivation cannot be effectively prevented. Immunocompromised patients must actively manage their primary lung infections, pay close attention to pulmonary signs and imaging changes. Especially during and after steroid pulse therapy or immunosuppressive therapy for graft versus host diseases, BKPyV load in blood/urine needs to be regularly measured, and the immunosuppressive intensity should be adjusted properly after the BKPyV reactivation diagnosis. Clinical trials of new antiviral drugs and therapies for BKPyV are urgently needed.

Case Report: Metagenomic next-generation sequencing assists in dynamic pathogen monitoring: powerful tool for progressing severe pneumonia

Background

Severe community-acquired pneumonia (sCAP) is life-threatening and characterized by intensive care unit (ICU) admission and high mortality. And they are vulnerable to hospital-acquired infection. In such a severe condition, metagenomic next-generation sequencing (mNGS) outperforms for short turnaround time and broad detection spectrum.

Case presentation

A 15-year-old male with severe influenza and methicillin-resistant Staphylococcus aureus (MRSA) pneumonia progressed rapidly, initially misdiagnosed as influenza co-infected with Aspergillus for misleading bronchoscopy manifestations. The turnaround time of mNGS is 13 h, which has the potential to expedite the clinical medication process. With the powerful support of mNGS and extracorporeal membrane oxygenation (ECMO), anti-infective therapy was adjusted accordingly, and vital signs gradually stabilized. After tortuous treatment and unremitting efforts, the patient recovered well.

Conclusions

Rapid mNGS applications, timely medication adjustments, strong ECMO support and active family compliance contribute to this miracle of life. False-negative or false-positive results are alarming, anti-infective medications should be adjusted after a comprehensive review of physical status and other indicators.

Metagenomic next-generation sequencing assistance in identifying non-tuberculous mycobacterial infections

Introduction

The advent of metagenomics next-generation sequencing (mNGS) has garnered attention as a novel method for detecting pathogenic infections, including Non-Tuberculous Mycobacterial (NTM) and tuberculosis (TB).However, the robustness and specificity of mNGS in NTM diagnostics have not been fully explored.

Methods

In this retrospective study, we enrolled 27 patients with NTM genomic sequences via mNGS and conducted a comprehensive clinical evaluation.

Results

Pulmonary NTM disease was the most commonly observed presentation, with a subset of patients also presenting with extrapulmonary NTM infections.mNGS analysis identified six distinct NTM species, primarily Mycobacteriumavium complex (MAC), followed by Mycobacterium intracellulare andMycobacterium abscessus. Conventional routine culture methods encountered challenges, resulting in negative results for all available 22 samples. Among the 10 patients who underwent quantitative polymerase chain reaction (qPCR) testing, five tested positive for NTM.

Discussion

It is important to note that further species typing is necessary to determine the specific NTM type, as traditional pathogen detection methods serve as an initial step. In contrast, when supplemented with pathogen data, enables the identification of specific species, facilitating precise treatment decisions. In conclusion, mNGS demonstrates significant potential in aidingthe diagnosis of NTMdisease by rapidly detecting NTM pathogens and guiding treatment strategies. Its enhanced performance, faster turnaround time (TAT), and species identification capabilities make mNGS a promising tool for managing NTM infections.

A complicated infection by cutaneous Nocardia wallacei and pulmonary Mycobacterium abscessus in a Chinese immunocompetent patient: a case report

Nocardiosis is an infectious disease caused by Nocardia that primarily affects immunocompromised hosts. Mycobacterium abscessus is a common opportunistic pathogen that causes disease in humans, including pulmonary and extrapulmonary infection. Nocardia spp. infection is uncommon, and infection with Nocardia wallacei and Mycobacterium abscessus is even rarer. A 59-year-old immunocompetent woman with risk factors for environmental exposure developed nocardiosis and presented to the hospital with a cough, shortness of breath, hemoptysis, and a back abscess. An enhanced computed tomography (CT) of the chest revealed partial destruction of the right lung, as well as consolidation of the right upper lobe. Rare pathogens N. wallacei and Mycobacterium abscessus were detected by metagenomic next-generation sequencing (mNGS) from abscess on the back and lung puncture tissue, respectively. She was treated with a combination of antibiotics and was finally discharged with a good prognosis. In this case, we present a patient who was successfully diagnosed with N. wallacei and Mycobacterium abscessus infection using mNGS. This importance of using mNGS in pathogen detection and the effective use of antibiotics in treating patients with long-term rare infections is highlighted in this report.

Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria

BACKGROUND

Oxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which improves the reconstruction of genomes and helps to resolve complex genomic contexts, especially in the case of metagenome analysis. To take the best advantage of long-read sequencing, DNA extraction methods must be able to isolate pure high molecular weight (HMW) DNA from complex metagenomics samples, without introducing any bias. New methods released on the market, and protocols developed at the research level, were specifically designed for this application and need to be assessed.

RESULTS

In this study, with different bacterial cocktail mixes, analyzed as pure or spiked in a synthetic fecal matrix, we evaluated the performances of 6 DNA extraction methods using various cells lysis and purification techniques, from quick and easy, to more time-consuming and gentle protocols, including a portable method for on-site application. In addition to the comparison of the quality, quantity and purity of the extracted DNA, the performance obtained when doing Nanopore sequencing on a MinION flow cell was also tested. From the obtained results, the Quick-DNA HMW MagBead Kit (Zymo Research) was selected as producing the best yield of pure HMW DNA. Furthermore, this kit allowed an accurate detection, by Nanopore sequencing, of almost all the bacterial species present in a complex mock community.

CONCLUSION

Amongst the 6 tested methods, the Quick-DNA HMW MagBead Kit (Zymo Research) was considered as the most suitable for Nanopore sequencing and would be recommended for bacterial metagenomics studies using this technology.

The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science

Background

Infectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis.

Methods

The literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3).

Results

In total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections.

Conclusion

This study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.

Comparison of quality/quantity mNGS and usual mNGS for pathogen detection in suspected pulmonary infections

Improved metagenomic next-generation sequencing (mNGS), for example, quality/quantity mNGS (QmNGS), is being used in the diagnosis of pulmonary pathogens. There are differences between QmNGS and the usual mNGS (UmNGS), but reports that compare their detection performances are rare. In this prospective study of patients enrolled between December 2021 and March 2022, the bronchoalveolar lavage fluid of thirty-six patients with suspected pulmonary infection was assessed using UmNGS and QmNGS. The sensitivity of QmNGS was similar to that of UmNGS. The specificity of QmNGS was higher than that of UmNGS; however, the difference was not statistically significant. The positive likelihood ratios (+LR) of QmNGS and UmNGS were 3.956 and 1.394, respectively, and the negative likelihood ratios (-LR) were 0.342 and 0.527, respectively. For the co-detection of pathogens, the depth and coverage of the QmNGS sequencing were lower than those of UmNGS, while for the detection of pathogens isolated from patients with pulmonary infection, the concordance rate was 77.2%. In the eleven patients with nonpulmonary infection, only viruses were detected using QmNGS, while UmNGS detected not only viruses but also bacteria and fungi. This study provides a basis for the selection of mNGS for the diagnosis of suspected pulmonary infection.

Clinical identification and microbiota analysis of Chlamydia psittaci- and Chlamydia abortus- pneumonia by metagenomic next-generation sequencing

Introduction

Recently, the incidence of chlamydial pneumonia caused by rare pathogens such as C. psittaci or C. abortus has shown a significant upward trend. The non-specific clinical manifestations and the limitations of traditional pathogen identification methods determine that chlamydial pneumonia is likely to be poorly diagnosed or even misdiagnosed, and may further result in delayed treatment or unnecessary antibiotic use. mNGS's non-preference and high sensitivity give us the opportunity to obtain more sensitive detection results than traditional methods for rare pathogens such as C. psittaci or C. abortus.

Methods

In the present study, we investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of pneumonia patients with different chlamydial infection patterns using mNGS.

Results

More co-infecting pathogens were found to be detectable in clinical samples from patients infected with C. psittaci compared to C. abortus, suggesting that patients infected with C. psittaci may have a higher risk of mixed infection, which in turn leads to more severe clinical symptoms and a longer disease course cycle. Further, we also used mNGS data to analyze for the first time the characteristic differences in the lower respiratory tract microbiota of patients with and without chlamydial pneumonia, the impact of the pattern of Chlamydia infection on the lower respiratory tract microbiota, and the clinical relevance of these characteristics. Significantly different profiles of lower respiratory tract microbiota and microecological diversity were found among different clinical subgroups, and in particular, mixed infections with C. psittaci and C. abortus resulted in lower lung microbiota diversity, suggesting that chlamydial infections shape the unique lung microbiota pathology, while mixed infections with different Chlamydia may have important effects on the composition and diversity of the lung microbiota.

Discussion

The present study provides possible evidences supporting the close correlation between chlamydial infection, altered microbial diversity in patients' lungs and clinical parameters associated with infection or inflammation in patients, which also provides a new research direction to better understand the pathogenic mechanisms of pulmonary infections caused by Chlamydia.

Clinical application value of metagenomic second-generation sequencing technology in hematologic diseases with and without transplantation

Introduction

Hematological patients are at risk of infections. It is unknown whether the pathogenic microbial spectrum differs between HSCT and non-HSCT patients, and whether metagenomic next-generation sequencing (mNGS) of peripheral blood can be used as a substitute test specimen such as alveolar lavage.

Methods

A retrospective study was conducted to evaluate the clinical application value of mNGS in hematological patients with and without HSCT.

Results

Viruses were prevalent pathogens in both non-HSCT (44%) and HSCT (45%) patients, chiefly human cytomegalovirus and Epstein-Barr virus. In non-HSCT patients, Gram-negative bacilli accounted for 33% (predominantly Klebsiella pneumonia), and Gram-positive cocci accounted for 7% (predominantly Enterococcus faecium) of pathogens. However, in HSCT patients, Gram-negative bacilli accounted for 13% (predominantly Stenotrophomonas maltophilia), and Gram-positive cocci accounted for 24% (predominantly Streptococcus pneumonia) of pathogens. Mucor was the most common fungu s in two groups. The positive rate of pathogens by mNGS was 85.82%, higher than conventional detection (20.47%, P < 0.05). Mixed infection accounted for 67.00%, among which the mixed infection of bacteria and virus (25.99%) was the most common. 78 cases had pulmonary infection, the positive rate of traditional laboratory tests was 42.31% (33/78), and of mNGS in peripheral blood was 73.08% (57/78), showing a statistical difference (P = 0.000). The non-HSCT patients had a higher frequency of Klebsiella pneumonia (OR=0.777, 95% CI, 0.697-0.866, P = 0.01) and Torque teno virus (OR=0.883, 95% CI, 0.820-0.950, P = 0.031) infections than HSCT patients, while the rates of Streptococcus pneumonia (OR=12.828, 95% CI, 1.378-119.367, P = 0.016), Candida pseudosmooth (OR=1.100, 95% CI, 0.987-1.225, P = 0.016), human betaherpesvirus 6B (OR=6.345, 95% CI, 1.105-36.437, P = 0.039) and human polyomavirus 1 (OR=1.100, 95% CI, 0.987-1.225, P = 0.016) infections were lower. Leishmania could be detected by mNGS.

Conclusion

mNGS of peripheral blood can be used as a substitute test method for hematological patients with pulmonary infection, the detection rate of mixed infections by mNGS was high, and mNGS has high clinical recognition rate and sensitivity in pathogen detection, and provides a basis for guiding the anti-infective treatment in hematological diseases with symptoms such as fever.

Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit

Background

Pneumonia is a significant cause of morbidity and mortality in children. Metagenomic next-generation sequencing (mNGS) has the potential to assess the landscape of pathogens responsible for severe pulmonary infection.

Methods

Bronchoalveolar lavage fluid (BALF) samples of 262 children with suspected pulmonary infections were collected from April 2019 to October 2021 in the Pediatric Intensive Care Unit (PICU) of Guangdong Women and Children Hospital. Both mNGS and conventional tests were utilized for pathogen detection.

Results

A total of 80 underlying pathogens were identified using both mNGS and conventional tests. Respiratory syncytial virus (RSV), Staphylococcus aureus and rhinovirus were the most frequently detected pathogens in this cohort. The incidence rate of co-infection was high (58.96%, 148/251), with bacterial-viral agents most co-detected. RSV was the main pathogen in children younger than 6 months of age, and was also commonly found in older pediatric patients. Rhinovirus was prevalent in children older than 6 months. Adenovirus and Mycoplasma pneumoniae were more prevalent in children older than 3 years than in other age groups. Pneumocystis jirovecii was detected in nearly 15% of children younger than 6 months. Besides, influenza virus and adenovirus were rarely found in 2020 and 2021.

Conclusions

Our study highlights the importance of using advanced diagnostic techniques like mNGS to improve our understanding of the microbial epidemiology of severe pneumonia in pediatric patients.

Potential of metagenomic next-generation sequencing in detecting infections of ICU patients

BACKGROUND

Due to the limitations of traditional microbiological detection techniques in evaluating complicated infections in ICU patients, it is necessary to explore novel and effective methods to improve the clinical detection of ICU patients' infections.

OBJECTIVE

This study aimed to evaluate the efficiency and specificity of mNGS in screening pathogens in the blood, deep phlegm, urine, and other sample types of ICU patients exploring an effective method for infection detection.

METHODS

A total of 56 ICU patients with 131 samples were included in this study. The sample types included blood, deep phlegm, urine, drainage, anal swabs, and other types. Samples were analyzed by both conventional detection method and mNGS tests. The diagnosis efficiency and consistency of the two methods were compared. The distribution of the identified pathogens was analyzed. Moreover, the clinical features of patients with mNGS-positive or mNGS-negative results were compared.

RESULTS

The positive rate of mNGS was 81.7% (107/131) including 3.1% (4/131) weakly positive, while the positive rate of traditional detection was only 30.5%, including 29 strong positive results and 11 weak positive results. Additionally, there were 41 patients chose to adjust anti-infection strategies according to the results of mNGS, which significantly saved treatment costs. The mNGS-positive patients showed a shorter ICU hospitalization and higher intention to adjust anti-infection strategies than the mNGS-negative patients.

CONCLUSION

mNGS is of great potential for the pathogen detection of ICU patients, and has a higher detection rate than traditional detection methods. Further clinical application investigations can be carried out to expand the application of mNGS.

Nifuroxazide inhibits the growth of glioblastoma and promotes the infiltration of CD8 T cells to enhance antitumour immunity

INTRODUCTION

Glioblastoma is a primary intracranial tumour with extremely high disability and fatality rates among adults. Existing diagnosis and treatment methods have not significantly improved the overall poor prognosis of patients. Nifuroxazide, an oral antibiotic, has been reported to act as a tumour suppressor in a variety of tumours and to participate in the process of antitumour immunity. However, whether it can inhibit the growth of glioma is still unclear.

METHODS

We explored the potential mechanism of nifuroxazide inhibiting the growth of glioblastoma cells through in vitro and in vivo experiments.

RESULTS

nifuroxazide can inhibit the proliferation of glioblastoma cells, promote G2 phase arrest, induce apoptosis, and inhibit epithelial-mesenchymal transition through the MAP3K1/JAK2/STAT3 pathway. Similarly, clinical sample analysis confirmed that MAP3K1 combined with STAT3 can affect the prognostic characteristics of patients with glioma. In addition, nifuroxazide can drive the M1 polarization of microglioma cells, inhibit the expression of CTLA4 and PD-L1 in tumour cells, and promote the infiltration of CD8 T cells to exert antitumour effects. Combination treatment with PD-L1 inhibitors can significantly prolong the survival time of mice.

CONCLUSION

we found that nifuroxazide can inhibit the growth of glioblastoma and enhance antitumour immunity. Thus, nifuroxazide is an effective drug for the treatment of glioblastoma and has great potential for clinical application.

[Metagenomic next-generation sequencing of plasma for the identification of bloodstream infectious pathogens in severe aplastic anemia]

Objective: To analyze the diagnostic value of cell-free plasma metagenomic next-generation sequencing (mNGS) pathogen identification for severe aplastic anemia (SAA) bloodstream infection. Methods: From February 2021 to February 2022, mNGS and conventional detection methods (blood culture, etc.) were used to detect 33 samples from 29 consecutive AA patients admitted to the Anemia Diagnosis and Treatment Center of the Hematology Hospital of the Chinese Academy of Medical Sciences to assess the diagnostic consistency of mNGS and conventional detection, as well as the impact on clinical treatment benefits and clinical accuracy. Results: ①Among the 33 samples evaluated by mNGS and conventional detection methods, 25 cases (75.76%) carried potential pathogenic microorganisms. A total of 72 pathogenic microorganisms were identified from all cases, of which 65 (90.28%) were detected only by mNGS. ②All 33 cases were evaluated for diagnostic consistency, of which 2 cases (6.06%) were Composite, 18 cases (54.55%) were mNGS only, 2 cases (6.06%) were Conventional method only, 1 case (3.03%) was both common compliances (mNGS/Conventional testing) , and 10 cases (30.3%) were completely non-conforming (None) . ③All 33 cases were evaluated for clinical treatment benefit. Among them, 8 cases (24.24%) received Initiation of targeted treatment, 1 case (3.03%) received Treatment de-escalation, 13 cases (39.39%) received Confirmation, and the remaining 11 cases (33.33%) received No clinical benefit. ④ The sensitivity of 80.77%, specificity of 70.00%, positive predictive value of 63.64%, negative predictive value of 84.85%, positive likelihood ratio of 2.692, and negative likelihood ratio of 0.275 distinguished mNGS from conventional detection methods (21/12 vs 5/28, P<0.001) . Conclusion: mNGS can not only contribute to accurately diagnosing bloodstream infection in patients with aplastic anemia, but can also help to guide accurate anti-infection treatment, and the clinical accuracy is high.

Metagenomic Next-Generation Sequencing Assists in the Diagnosis of Mediastinal Aspergillus fumigatus Abscess in an Immunocompetent Patient: A Case Report and Literature Review

Background

Aspergillus fumigatus is an opportunistic fungal pathogen, which is commonly found in lungs and rarely causes infections in mediastinum. Mediastinal Aspergillus abscess is a serious infectious condition, and is characterized by difficult diagnosis due to its clinical manifestations being nonspecific.

Case Presentation

Here, we report a case of a mediastinal Aspergillus fumigatus abscess in an immunocompetent patient. The patient was a 45-year-old woman who presented with a 20-day history of sore throat without any underlying diseases. Chest computed tomography (CT) showed a mass in the anterior superior mediastinum. Metagenomic next-generation sequencing (mNGS) identified Aspergillus fumigatus sequences in endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) tissue, indicating the mediastinal Aspergillus fumigatus infection of this patient. The following mediastinal biopsy histological analysis and tissue fungi culture also suggested Aspergillus fumigatus infection, confirming the mNGS detection. The patient was diagnosed with mediastinal aspergillosis caused by Aspergillus fumigatus. After timely voriconazole treatment, the patient was discharged with good condition.

Conclusion

Our study presented a rare case with mediastinal Aspergillus fumigatus abscess in an immunocompetent patient. As a new clinical diagnostic method, mNGS could assist timely diagnosis and precise treatment of Aspergillus infection.

Diagnosis of Acute Q Fever in a Patient by Using Metagenomic Next-Generation Sequencing: A Case Report

Background

Q fever is a zoonotic disease caused by Coxiella burnetii infection, with domestic ruminants as the main source of infection and tick bites as one of the transmission vectors. The clinical manifestations of Q fever are varied and atypical. For the reason that C. burnetii is a strictly intracellular pathogen, it is difficult to be diagnosed by traditional culture methods. Additionally, serological and molecular diagnostic methods to assist in the diagnosis of Q fever are not routinely performed in most clinical laboratories. Therefore, early and rapid diagnosis of Q fever is a challenge.

Case Presentation

In the present study, a 34-year-old male patient presented with an acute onset and symptoms such as high fever, lethargy, pulmonary infection, and liver damage. In addition, he had a history of tick bites. Despite conducting relevant laboratory and radiological examinations, the etiology remained unknown. Subsequently, we detected the sequence reads of C. burnetii in a venous blood sample using metagenomic next-generation sequencing (mNGS), and the symptoms of patients were significantly improved after timely treatment with the special drug tetracycline. To our knowledge, this is the first report of Q fever associated with C. burnetii detected directly from venous blood sample in Wuhan, China.

Conclusion

Metagenomic next-generation sequencing is a new diagnostic technology that provides rapid and accurate detection of unexplained infections, including Q fever. Its application plays a crucial role in clinical diagnosis for identifying elusive pathogens.