The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis

The role of mNGS in the diagnosis of talaromycosis and case series

BACKGROUND

Talaromycosis is a rare fungal infection characterized by non-specific clinical features, often resulting in misdiagnosis. This study aimed to analyze four classic cases of Talaromyces marneffei infection diagnosed using metagenomic next-generation sequencing (mNGS) to improve understanding of its diagnosis and treatment.

METHODS

This study retrospectively analyzed cases of T. marneffei identified through mNGS at Peking Union Medical College Hospital. Four confirmed cases of talaromycosis were selected based on clinical diagnoses, supplemented by a review of relevant literature. We reviewed and compared the clinical features, laboratory indicators, treatment regimens, and outcomes of these cases, which exhibited varied characteristics.

RESULTS

Among the four patients, two were human immunodeficiency virus (HIV)-positive, and two were HIV-negative. All the participants presented with fever and varying respiratory symptoms, with distinct clinical characteristics aiding diagnosis. Three cases exhibited significant pulmonary infection lesions. Both HIV-positive patients showed T. marneffei bloodstream dissemination and suffered mixed infection with virus. Within them, one case was positive in blood culture, blood mNGS and sputum culture. Another case was positive in blood and bone marrow cultures, brain tissue culture and mNGS. They were both treated with voriconazole and improved. Both HIV-negative patients were T. marneffei positive for BALF mNGS, and only one of them was positive for BALF culture. One of them was mix infected by fungi, bacteria, Mycobacterium tuberculosis and virus, improved by voriconzole and followed by introconaole. The other case was cured by introconazole.

CONCLUSIONS

Traditional diagnostic methods are limited by factors such as the long time and low sensitivity of fungal culture, the effect of prior antibiotic treatment, the invasiveness and complexities of tissue biopsies, and so on. Emerging technologies, particularly mNGS, offer advantages such as rapid processing, high accuracy, and comprehensive pathogen coverage, significantly reducing the risk of missed diagnoses and facilitating timely intervention.

Effect of Metagenomic Next-Generation Sequencing on Clinical Outcomes of Patients With Severe Community-Acquired Pneumonia in the ICU: A Multicenter, Randomized Controlled Trial

BACKGROUND

Metagenomic next-generation sequencing (mNGS) was previously established as a method that can increase the pathogen identification rate in patients with severe community-acquired pneumonia (SCAP).

RESEARCH QUESTION

What is the impact on clinical outcomes of mNGS of BAL fluid (BALF) in patients with SCAP in the ICU?

STUDY DESIGN AND METHODS

A multicenter randomized controlled open-label clinical trial was conducted in 10 ICUs. Patients were randomized in a 1:1 ratio to undergo BALF assessment with conventional microbiological tests (CMTs) only (ie, the CMT group) or BALF assessment with both mNGS and CMTs (ie, the mNGS group). The primary outcome was the time to clinical improvement, defined as the time from randomization to either an improvement of two points on a six-category ordinal scale or discharge from the ICU, whichever occurred first.

RESULTS

A total of 349 patients were randomized to treatment between January 1, 2021, and November 18, 2022; 170 were assigned to the CMT group and 179 to the mNGS group. In the intention-to-treat analysis, the time to clinical improvement was better in the mNGS group than in the CMT group (10 days vs 13 days; difference, -2.0 days; 95% CI, -3.0 to 0.0 days). Similar results were obtained in the per-protocol analysis. The proportion of patients with clinical improvement within 14 days was significantly higher in the mNGS group (62.0%) than in the CMT group (46.5%). There was no significant difference in other secondary outcomes.

INTERPRETATION

We found that compared with the use of CMTs alone, mNGS combined with CMTs reduced the time to clinical improvement for patients with SCAP.

CLINICAL TRIAL REGISTRATION

Chinese Clinical Trial Registry, ChiCTR; www.chictr.org.cn/index.html; ChiCTR2000037894.

HIV-associated neurocognitive disorders (HAND): Optimal diagnosis, antiviral therapy, pharmacological treatment, management, and future scopes

In the context of HIV infection, HIV-associated neurocognitive disorders (HAND) have become a serious concern. An extensive summary of the diagnosis, care, and mental health consequences related to HAND is given in this article. The diagnosis of HAND entails a multimodal approach that includes neuroimaging, cognition tests, and clinical examinations. Numerous screening instruments and standardized evaluations have been created to support the early identification and tracking of HAND. Appropriate actions and individualized treatment plans are made possible by prompt diagnosis. A multidisciplinary approach is used in the treatment of HAND, aiming to address various elements of cognitive impairment. The main stream of treatment is still antiretroviral medication (ART), which successfully lowers viral loads and stops further neurocognitive deterioration. Adjunctive treatments are essential for treating cognitive symptoms and improving overall quality of life. These therapies include cognitive rehabilitation, pharmaceutical interventions, and psychological support. Our knowledge of the pathophysiology of HAND has improved with the identification of the inflammatory milieu and persistent viral persistence in the central nervous system (CNS), which has also aided in the creation of biomarkers for CNS illness. Although biomarkers show inflammation, neuronal damage, and monocyte activity, their clinical use is still restricted. Although new techniques to treating HAND have been developed as a result of a better knowledge of pathogenic processes, the best course of action is still unknown.

Advances and Challenges in the Diagnosis of Leishmaniasis

Leishmaniasis remains a significant public health challenge, particularly in endemic regions with limited resources. Traditional diagnostic methods, including microscopy, culture, and serology, though widely utilized, often suffer from limitations such as variable  sensitivity, time delays, and the need for specialized infrastructure. Some of these limitations have been addressed with the emergence of molecular diagnostic techniques. Quantitative PCR (q-PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA) assays have improved  the diagnostic sensitivity and specificity, enabling species identification and detection of asymptomatic infections. Further, nanodiagnostics and portable sequencing technologies such as the MinION™, along with lab-on-chip platforms, are revolutionizing the diagnostic landscape of leishmaniasis by offering point-of-care (POC) options for remote settings and field-based diagnosis. This review provides an in-depth analysis of these cutting-edge advances, discusses their application in resource-constrained settings, and evaluates their potential to reshape the future of leishmaniasis diagnosis and management.

Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing

According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses.

Mutational signature analysis predicts bacterial hypermutation and multidrug resistance

Bacteria of clinical importance, such as Pseudomonas aeruginosa, can become hypermutators upon loss of DNA mismatch repair (MMR) and are clinically correlated with high rates of multidrug resistance (MDR). Here, we demonstrate that hypermutated MMR-deficient P. aeruginosa has a unique mutational signature and rapidly acquires MDR upon repeated exposure to first-line or last-resort antibiotics. MDR acquisition was irrespective of drug class and instead arose through common resistance mechanisms shared between the initial and secondary drugs. Rational combinations of drugs having distinct resistance mechanisms prevented MDR acquisition in hypermutated MMR-deficient P. aeruginosa. Mutational signature analysis of P. aeruginosa across different human disease contexts identified appreciable quantities of MMR-deficient clinical isolates that were already MDR or prone to future MDR acquisition. Mutational signature analysis of patient samples is a promising diagnostic tool that may predict MDR and guide precision-based medical care.

Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing

Background

Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples.

Methods

A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data.

Results

Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P<0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the β-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions.

Conclusions

mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs.

Clinical application value of simultaneous plasma and bronchoalveolar lavage fluid metagenomic next generation sequencing in patients with pneumonia-derived sepsis

BACKGROUND

Despite the increasing use of metagenomic next-generation sequencing (mNGS) in sepsis, identifying clinically relevant pathogens remains challenging. This study was aimed to evaluate the clinical utility of simultaneous plasma and bronchoalveolar lavage fluid (BALF) detection using mNGS.

METHODS

This retrospective study enrolled 95 patients with pneumonia-derived sepsis (PDS) admitted to the intensive care unit (ICU) between October 2021 and January 2023. Patients were divided into two groups: mNGS group (n = 60) and the non-mNGS group (n = 35), based on whether simultaneous plasma and BALF mNGS were conducted. All patients underwent conventional microbiological tests (CMT), including bacterial/fungal culture of peripheral blood and BALF, as well as sputum culture, detection of 1, 3-beta-D- glucan in BALF and RT-PCR testing. The clinical data of the enrolled patients were collected, and the detection performance and prognosis of plasma mNGS, BALF mNGS and CMT were compared.

RESULTS

The mNGS group exhibited a lower mortality rate than the non-mNGS group (35.0% vs. 57.1%, P = 0.034). Simultaneous detection in dual-sample resulted in a higher proportion of microorganisms identified as definite causes of sepsis alert compared to detection in either plasma or BALF alone (55.6% vs. 20.8% vs. 18.8%, P<0.001). Acinetobacter baumannii, Stenotrophomonas maltophilia, Candida albicans, and human mastadenovirus B were the primary strains responsible for infections in PDS patients. Patients with lower white blood cells and neutrophil indices had a greater consistency in dual-sample mNGS. Patients in the mNGS group had more antibiotic adjustments compared to the non-mNGS group (85.71% vs. 33.33%, P<0.001). The percentage of neutrophils was a risk factor for mortality in PDS patients (P = 0.002).

CONCLUSION

Dual sample mNGS has the advantage of detecting and determining the pathogenicity of more pathogens and has the potential to improve the prognosis of patients with PDS.

Diagnostic performance of metagenomic next-generation sequencing based on alveolar lavage fluid in unexplained lung shadows

BACKGROUND

Unexplained lung shadows are challenging in respiratory medicine, with both infectious and non-infectious etiologies. Lung biopsy is definitive but invasive, prompting a need for non-invasive alternatives. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) is emerging as a promising diagnostic tool.

METHODS

We retrospectively analyzed 105 patients with unexplained lung shadows, collecting general information, mNGS results from BALF, and clinical diagnosis. We evaluated mNGS's diagnostic performance by comparing with final diagnosis.

RESULTS

mNGS showed good diagnostic performance in differentiating infectious from non-infectious causes. The specificity and accuracy for bacteria and fungi exceeded 90%, while the sensitivity and precision for fungi were lower than for bacteria. Atypical pathogens were frequently identified, especially in mixed infections.

CONCLUSIONS

mNGS of BALF is efficient in diagnosing infectious and non-infectious causes of unexplained lung shadows. While effective for bacteria and fungi detection, the sensitivity and precision for fungi are lower.

Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery

Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from upper respiratory swab and bronchoalveolar lavage samples in <24 h. The mNGS assay achieved mean limits of detection of 543 copies/mL, viral load quantification with 100% linearity, and 93.6% sensitivity, 93.8% specificity, and 93.7% accuracy compared to gold-standard clinical multiplex RT-PCR testing. Performance increased to 97.9% overall predictive agreement after discrepancy testing and clinical adjudication, which was superior to that of RT-PCR (95.0% agreement). To enable discovery of novel, sequence-divergent human viruses with pandemic potential, de novo assembly and translated nucleotide algorithms were incorporated into the automated SURPI+ computational pipeline used by the mNGS assay for pathogen detection. Using in silico analysis, we showed that after removal of all human viral sequences from the reference database, 70 (100%) of 70 representative human viral pathogens could still be identified based on homology to related animal or plant viruses. Our assay, which was granted breakthrough device designation from the US Food and Drug Administration (FDA) in August of 2023, demonstrates the feasibility of routine mNGS testing in clinical and public health laboratories, thus facilitating a robust and rapid response to the next viral pandemic.

Hypervirulent and carbapenem-resistant Klebsiella pneumoniae: A global public health threat

The evolution of hypervirulent and carbapenem-resistant Klebsiella pneumoniae can be categorized into three main patterns: the evolution of KL1/KL2-hvKp strains into CR-hvKp, the evolution of carbapenem-resistant K. pneumoniae (CRKp) strains into hv-CRKp, and the acquisition of hybrid plasmids carrying carbapenem resistance and virulence genes by classical K. pneumoniae (cKp). These strains are characterized by multi-drug resistance, high virulence, and high infectivity. Currently, there are no effective methods for treating and surveillance this pathogen. In addition, the continuous horizontal transfer and clonal spread of these bacteria under the pressure of hospital antibiotics have led to the emergence of more drug-resistant strains. This review discusses the evolution and distribution characteristics of hypervirulent and carbapenem-resistant K. pneumoniae, the mechanisms of carbapenem resistance and hypervirulence, risk factors for susceptibility, infection syndromes, treatment regimens, real-time surveillance and preventive control measures. It also outlines the resistance mechanisms of antimicrobial drugs used to treat this pathogen, providing insights for developing new drugs, combination therapies, and a "One Health" approach. Narrowing the scope of surveillance but intensifying implementation efforts is a viable solution. Monitoring of strains can be focused primarily on hospitals and urban wastewater treatment plants.

Study on the value of second-generation sequencing technology in the clinical diagnosis of osteoarticular brucellosis

To assess the value of next-generation sequencing (NGS) technology in the diagnosis of osteoarticular brucellosis pathogenesis. Fifty eight patients admitted to the Department of Orthopaedics, Hebei Provincial Chest Hospital from January 2021 to January 2023 were retrospectively analyzed, and the patients were classified into 48 cases in the osteoarticular brucellosis group and 10 cases in the nonosteoarticular brucellosis group according to the final clinical diagnosis. All patients underwent serum agglutination test (SAT), CT-guided puncture or surgical sampling of lesions for bacteriological culture and NGS after admission. The diagnostic efficacy of these three methods for osteoarticular brucellosis was compared using the final clinical diagnosis as the reference standard. Among the 58 patients with suspected osteoarticular brucellosis, 40 cases (68.97%) were positive by NGS, 33 cases (56.89%) by SAT and 10 cases (17.24%) by culture, and the differences were statistically significant (p < 0.05). Using the final clinical diagnosis as a criterion, the sensitivity of NGS, SAT, and culture for the detection of osteoarticular brucellosis was 83.33%, 62.50%, and 20.83%, respectively, the specificity was 100.00%, 70.00%, and 100.00%, the diagnostic accuracy was 86.20%, 63.79%, and 34.49%, and the κ values were 0.799, 0.590, and 0.504, respectively. NGS has a high pathogen detection rate and sensitivity in the pathogenetic diagnosis of patients with osteoarticular brucellosis and can provide clinical guidance for the diagnosis and management of patients with osteoarticular brucellosis.

Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions

Vibrio fischeri is a model mutualist for studying molecular processes affecting microbial colonization of animal hosts. We present a detailed protocol for a barcode sequencing (BarSeq) approach that combines targeted gene deletion with short-read sequencing technology to enable studies of mixed bacterial populations. This protocol includes wet lab steps to plan and produce the deletions, approaches to scale up mutant generation, protocols to prepare and conduct the strain competition, library preparation for sequencing on an Illumina iSeq 100 instrument, and data analysis with the barseq python package. Aspects of this protocol could be readily adapted for tagging wild-type V. fischeri strains with a neutral barcode for examination of population dynamics or BarSeq analyses in other species. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Production of the erm-bar DNA Basic Protocol 2: Generation of a targeted and barcoded deletion strain of V. fischeri Alternate Protocol: Parallel generation of multiple barcode-tagged V. fischeri deletion strains Basic Protocol 3: Setting up mixed populations of barcode-tagged strains Basic Protocol 4: Performing a competitive growth assay Basic Protocol 5: Amplicon library preparation and equimolar pooling Basic Protocol 6: Sequencing on Illumina iSeq 100 Basic Protocol 7: BarSeq data analysis.

Emerging research trends in artificial intelligence for cancer diagnostic systems: A comprehensive review

This review article offers a comprehensive analysis of current developments in the application of machine learning for cancer diagnostic systems. The effectiveness of machine learning approaches has become evident in improving the accuracy and speed of cancer detection, addressing the complexities of large and intricate medical datasets. This review aims to evaluate modern machine learning techniques employed in cancer diagnostics, covering various algorithms, including supervised and unsupervised learning, as well as deep learning and federated learning methodologies. Data acquisition and preprocessing methods for different types of data, such as imaging, genomics, and clinical records, are discussed. The paper also examines feature extraction and selection techniques specific to cancer diagnosis. Model training, evaluation metrics, and performance comparison methods are explored. Additionally, the review provides insights into the applications of machine learning in various cancer types and discusses challenges related to dataset limitations, model interpretability, multi-omics integration, and ethical considerations. The emerging field of explainable artificial intelligence (XAI) in cancer diagnosis is highlighted, emphasizing specific XAI techniques proposed to improve cancer diagnostics. These techniques include interactive visualization of model decisions and feature importance analysis tailored for enhanced clinical interpretation, aiming to enhance both diagnostic accuracy and transparency in medical decision-making. The paper concludes by outlining future directions, including personalized medicine, federated learning, deep learning advancements, and ethical considerations. This review aims to guide researchers, clinicians, and policymakers in the development of efficient and interpretable machine learning-based cancer diagnostic systems.

Tuberculosis Diagnosis: Current, Ongoing, and Future Approaches

Tuberculosis (TB) remains an impactful infectious disease, leading to millions of deaths every year. Mycobacterium tuberculosis causes the formation of granulomas, which will determine, through the host-pathogen relationship, if the infection will remain latent or evolve into active disease. Early TB diagnosis is life-saving, especially among immunocompromised individuals, and leads to proper treatment, preventing transmission. This review addresses different approaches to diagnosing TB, from traditional methods such as sputum smear microscopy to more advanced molecular techniques. Integrating these techniques, such as polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP), has significantly improved the sensitivity and specificity of M. tuberculosis identification. Additionally, exploring novel biomarkers and applying artificial intelligence in radiological imaging contribute to more accurate and rapid diagnosis. Furthermore, we discuss the challenges of existing diagnostic methods, including limitations in resource-limited settings and the emergence of drug-resistant strains. While the primary focus of this review is on TB diagnosis, we also briefly explore the challenges and strategies for diagnosing non-tuberculous mycobacteria (NTM). In conclusion, this review provides an overview of the current landscape of TB diagnostics, emphasizing the need for ongoing research and innovation. As the field evolves, it is crucial to ensure that these advancements are accessible and applicable in diverse healthcare settings to effectively combat tuberculosis worldwide.

Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges

Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.

Diagnosis of a Rare Rickettsia felis Infection Complicated with Unusual Pericardial Effusion and Cardiac Tamponade Using an mNGS Test

The occurrence of sporadic rickettsial infections has been consistently undervalued and overlooked, primarily owing to a limited emphasis on routine examinations for rickettsioses in clinical practice. At present, the immunofluorescence assay is the prevailing diagnostic method for suspected rickettsioses that enables the detection of specific antibodies against rickettsia in human serum. Herein, we present an exceptional instance of rickettsial infection that was characterized by a rare manifestation of extensive pericardial effusion leading to dyspnea and cardiac tamponade. A diagnosis of chronic fibrosing pericarditis was established based on pericardium tissue obtained through pericardiotomy, and a conclusive metagenomic next-generation sequencing test confirmed the presence of Rickettsia felis infection. The cat flea, scientifically known as Ctenocephalides felis, is the predominant carrier of R. felis. An escalating incidence of human R. felis infections has raised concerns, particularly in light of the burgeoning population of domesticated animals in many contemporary societies.

Optimizing treatment administration strategies using negative mNGS results in corticosteroid-sensitive diffuse parenchymal lung diseases

Timely adjustments of antibiotic and corticosteroid treatments are vital for patients with diffuse parenchymal lung diseases (DPLDs). In this study, 41 DPLD patients with negative metagenomic next-generation sequencing (mNGS) results who were responsive to corticosteroids were enrolled. Among these patients, about 26.8% suffered from drug-induced DPLD, while 9.8% presented autoimmune-related DPLD. Following the report of the negative mNGS results, in 34 patients with complete antibiotics administration profiles, 79.4% (27/34) patients discontinued antibiotics after receiving negative mNGS results. Moreover, 70.7% (29/41) patients began or increased the administration of corticosteroid upon receipt of negative mNGS results. In the microbiota analysis, Staphylococcus and Stenotrophomonas showed higher detection rates in patients with oxygenation index (OI) below 300, while Escherichia and Stenotrophomonas had higher abundance in patients with pleural effusion. In summary, our findings demonstrated the clinical significance of mNGS in assisting the antibiotic and corticosteroid treatment adjustments in corticosteroid-responsive DPLD. Lung microbiota may imply the severity of the disease.

The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples

Objectives

Metagenomic next-generation sequencing (mNGS) is a powerful tool for pathogen detection. The accuracy depends on both wet lab and dry lab procedures. The objective of our study was to assess the influence of read length and dataset size on pathogen detection.

Methods

In this study, 43 clinical BALF samples, which tested positive via clinical mNGS and were consistent with the diagnosis, were subjected to re-sequencing on the Illumina NovaSeq 6000 platform. The raw re-sequencing data, consisting of 100 million (M) paired-end 150 bp (PE150) reads, were divided into simulated datasets with eight different data sizes (5 M, 10 M, 15 M, 20 M, 30 M, 50 M, 75 M, 100 M) and five different read lengths (single-end 50 bp (SE50), SE75, SE100, PE100, and PE150). Both Kraken2 and IDseq bioinformatics pipelines were employed to analyze the previously diagnosed pathogens in the simulated data. Detection of pathogens was based on read counts ranging from 1 to 10 and RPM values ranging from 0.2 to 2.

Results

Our results revealed that increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection. However, a larger data sizes for mNGS require higher economic costs and longer turnaround time for data analysis. Our findings indicate 20 M reads being sufficient for SE75 mode to achieve high recall rates. Additionally, high nucleic acid loads in samples can lead to increased stability in pathogen detection efficiency, reducing the impact of sequencing strategies. The choice of bioinformatics pipelines had a significant impact on recall rates achieved in pathogen detection.

Conclusions

Increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection but increase the economic and time costs of sequencing and data analysis. Currently, the 20 M reads in SE75 mode may be the best sequencing option.

Spinal Infections? mNGS Combined with Microculture and Pathology for Answers

Introduction

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.

Application of next-generation sequencing in acute tonsillitis complicated with descending necrotizing mediastinitis: A case report

RATIONALE

Descending necrotizing mediastinitis (DNM) is a rare but serious complication of oral and cervical infections that is associated with high mortality because diagnosis can be difficult or delayed. Early diagnosis and accurate identification of the causative pathogen can significantly reduce mortality, and are critical for the management of these patients.

PATIENT CONCERNS

A 56-year-old female was admitted with a sore throat and fever. The initial diagnosis was acute tonsillitis, but she was transferred to the intensive care unit after developing dyspnea.

DIAGNOSES

Pleural effusion and mediastinal lesions were detected by computed tomography, and a diagnosis of DNM was confirmed by laboratory tests.

INTERVENTIONS

Initial treatment consisting of ceftriaxone and vancomycin with chest tube drainage were not effective. Thoracic surgery was performed to completely remove the "moss" tissue, blood clots, and pus. Next-generation sequencing was then performed, and the anti-infective treatment was changed to imipenem and linezolid based on these results.

OUTCOMES

Eventually, the patient's symptoms were controlled, all vital signs were stable, and she was successfully transferred out of the intensive care unit.

LESSONS

Next-generation sequencing is a rapid and accurate method for identification of pathogens that can provide a basis for early treatment of DNM, thereby improving patient prognosis and reducing mortality.

Advances in aptamer-based biosensors for monitoring foodborne pathogens

Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05889-8.

The Blood Virome: A new frontier in biomedical science

Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.

Use of Metagenomic Next-Generation Sequencing in the Identification of Pneumocystis Jiroveci Pneumonia in a Previously Healthy Infant Diagnosed With X-Linked Hyper-IgM Syndrome

This case describes a four-month-old male who was admitted to the pediatric intensive care unit for acute respiratory failure in the setting of a co-infection requiring increased ventilatory support. Immunodeficiency workup demonstrated poor vaccination response and low immunoglobulin titers. mNGS via Karius® test was positive for Pneumocystis jiroveci (PJP), Parvovirus, and Bocavirus. The patient was successfully treated with trimethoprim-sulfamethoxazole and prednisone. Genetic workup via Invitae panel confirmed that the patient had X-linked Hyper-IgM Syndrome. Use of mNGS can help with early identification of pathogens that conventional testing does not detect, even in patients not already identified as immunocompromised.

Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia

Fast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires approximately 15 hours to detect the presence of a pathogen. We, therefore, assessed the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 17 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 88% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1-mL sample input and sample-to-answer time of 6 hours. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection.

The clinical value of mNGS of bronchoalveolar lavage fluid versus traditional microbiological tests for pathogen identification and prognosis of severe pneumonia (NT-BALF):study protocol for a prospective multi-center randomized clinical trial

BACKGROUND

Early, rapid, and accurate pathogen diagnosis can help clinicians select targeted treatment options, thus improving prognosis and reducing mortality rates of severe pneumonia. Metagenomic next-generation sequencing (mNGS) has a higher sensitivity and broader pathogen spectrum than traditional microbiological tests. However, the effects of mNGS-based antimicrobial treatment procedures on clinical outcomes and cost-effectiveness in patients with severe pneumonia have not been evaluated.

METHODS

This is a regional, multi-center, open, prospective, randomized controlled trial to evaluate that whether the combination of mNGS and traditional testing methods could decrease 28-day call-cause mortality with moderate cost-effectiveness. A total of 192 patients with severe pneumonia will be recruited from four large tertiary hospitals in China. Bronchoalveolar lavage fluid will be obtained in all patients and randomly assigned to the study group (mNGS combined with traditional microbiological tests) or the control group (traditional microbiological tests only) in a 1:1 ratio. Individualized antimicrobial treatment and strategy will be selected according to the analysis results. The primary outcome is 28-day all-cause mortality. The secondary outcomes are ICU and hospital length of stay (LOS), ventilator-free days and ICU-free days, consistency between mNGS and traditional microbiological tests, detective rate of mNGS and traditional microbiological tests, turn-out time, time from group allocation to start of treatment, duration of vasopressor support, types and duration of anti-infective regimens, source of drug-resistant bacteria or fungi, and ICU cost.

DISCUSSION

The clinical benefits of mNGS are potentially significant, but its limitations should also be considered.

TRIAL REGISTRATION

ChineseClinicalTrialRegistry.org, ChiCTR2300076853. Registered on 22 October 2023.

A Rare Case Report of Disseminated Nocardia Farcinica Granulomatous Hepatitis and Clinical Management Experience

Background

Nocardiosis is primarily an opportunistic infection affecting immunocompromised individuals, with a predilection for the lungs, brain, or skin in those with compromised immune function. Granulomatous hepatitis caused by Nocardia is a rare clinical manifestation. This study aims to provide a systematic overview of the clinical features of Nocardiosis caused by Nocardia farcinica, enhancing our understanding of this disease.

Methods

We report a case of a 75-year-old male with no underlying diseases presenting with a history of "recurrent fever for more than 4 months", along with fatigue, poor appetite, and pleural and abdominal effusion. Despite treatment at multiple hospitals, the patient showed little improvement. Chest CT revealed chronic inflammation, small nodules, bilateral pleural effusion, and pleural thickening. Abdominal CT indicated multiple low-density lesions in the liver, multiple small calcifications, and abdominal effusion.

Results

Liver biopsy suggested inflammatory changes, with focal granuloma formation. Metagenomic next-generation sequencing (mNGS) of liver tissue indicated Nocardia farcinica, leading to the final diagnosis of disseminated Nocardia farcinica granulomatous hepatitis.

Conclusion

Nocardia infection is a rare disease primarily observed in immunocompromised patients but can also occur in those with normal immune function. The clinical and radiological features lack specificity; however, the utilization of mNGS technology enables rapid identification of the pathogenic microorganism. Nocardia farcinica is generally susceptible to sulfonamide drugs and amikacin, offering viable treatment options.

The clinical importance of metagenomic next-generation sequencing in detecting disease-causing microorganisms in cases of sepsis acquired in the community or hospital setting

Objectives

Although metagenomic next-generation sequencing (mNGS) is commonly used for diagnosing infectious diseases, clinicians face limited options due to the high costs that are not covered by basic medical insurance. The goal of this research is to challenge this bias through a thorough examination and evaluation of the clinical importance of mNGS in precisely identifying pathogenic microorganisms in cases of sepsis acquired in the community or in hospitals.

Methods

A retrospective observational study took place at a tertiary teaching hospital in China from January to December 2021. Data on 308 sepsis patients were collected, and the performance of etiological examination was compared between mNGS and traditional culture method.

Results

Two hundred twenty-nine cases were observed in the community-acquired sepsis (CAS) group and 79 cases in the hospital-acquired sepsis (HAS) group. In comparison with conventional culture, mNGS showed a significantly higher rate of positivity in both the CAS group (88.21% vs. 25.76%, adj.P < 0.001) and the HAS group (87.34% vs. 44.30%, adj.P < 0.001), particularly across various infection sites and specimens, which were not influenced by factors like antibiotic exposure or the timing and frequency of mNGS technology. Sepsis pathogens detected by mNGS were broad, especially viruses, Mycobacterium tuberculosis, and atypical pathogens, with mixed pathogens being common, particularly bacterial-viral co-detection. Based on the optimization of antimicrobial therapy using mNGS, 58 patients underwent antibiotic de-escalation, two patients were switched to antiviral therapy, and 14 patients initiated treatment for tuberculosis, resulting in a reduction in antibiotic overuse but without significant impact on sepsis prognosis. The HAS group exhibited a critical condition, poor prognosis, high medical expenses, and variations in etiology, yet the mNGS results did not result in increased medical costs for either group.

Conclusions

mNGS demonstrates efficacy in identifying multiple pathogens responsible for sepsis, with mixed pathogens of bacteria and viruses being prevalent. Variability in microbiological profiles among different infection setting underscores the importance of clinical vigilance. Therefore, the adoption of mNGS for microbiological diagnosis of sepsis warrants acknowledgment and promotion.

Metagenomic Analysis for Diagnosis of Hemorrhagic Fever in Minas Gerais, Brazil

Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In this study, we applied viral metagenomic analysis to 43 serum samples collected by the Public Health Laboratory (Fundação Ezequiel Dias, FUNED) in Minas Gerais State, Brazil, from patients diagnosed with hemorrhagic fever who had tested negative for the standard local hemorrhagic disease testing panel. This panel includes tests for Dengue virus (DENV) IgM, Zika virus IgM, Chikungunya virus IgM, yellow fever IgM, Hantavirus IgM, Rickettsia rickettsii IgM/IgG, and Leptospira interrogans IgM, in addition to respective molecular tests for these infectious agents. The samples were grouped into 18 pools according to geographic origin and analyzed through next-generation sequencing on the NextSeq 2000 platform. Bioinformatic analysis revealed a prevalent occurrence of commensal viruses across all pools, but, notably, a significant number of reads corresponding to the DENV serotype 2 were identified in one specific pool. Further verification via real-time PCR confirmed the presence of DENV-2 RNA in an index case involving an oncology patient with hemorrhagic fever who had initially tested negative for anti-DENV IgM antibodies, thereby excluding this sample from initial molecular testing. The complete DENV-2 genome isolated from this patient was taxonomically classified within the cosmopolitan genotype that was recently introduced into Brazil. These findings highlight the critical role of considering the patient's clinical condition when deciding upon the most appropriate testing procedures. Additionally, this study showcases the potential of viral metagenomics in pinpointing the viral agents behind hemorrhagic diseases. Future research is needed to assess the practicality of incorporating metagenomics into standard viral diagnostic protocols.

Comparison of metagenomic next-generation sequencing and conventional culture for the diagnostic performance in febrile patients with suspected infections

BACKGROUND

Timely and accurate identification of pathogens is crucial for appropriate treatment and prognosis of infectious diseases. As an increasingly popular pathogen detection method, the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in febrile patients with suspected infection requires further exploration.

METHODS

This study included 368 febrile patients with suspected infections who were admitted to the Infectious Disease Department of Qilu Hospital, Shandong University between January 5, 2021 and April 14, 2023. Both mNGS testing and conventional culture were performed in all patients. Clinical data of enrolled patients were collected, and the diagnostic performances of mNGS and culture were compared.

RESULTS

Of the 368 enrolled patients, 231 were finally diagnosed with infection and 137 were with diseases other than infection. The sensitivity (58.01% vs. 21.65%, p < 0.001) and negative predictive value (54.67% vs. 42.9%) of mNGS were superior to those of culture. In contrast, the culture exhibited higher specificity (99.27% vs. 85.40%, p < 0.001) and positive predictive value (98.84% vs. 87.01%) than mNGS. Among infected patients with positive mNGS results, 64 received adjusted antibiotic therapy including treatment transitions, antibiotic downgrading, and combination therapy. Among them, 9 had additional antifungal drugs and 21 patients had a treatment turning point based on the mNGS results and these patients recovered and discharged due to timely antibiotic adjustment. Both positive rates of puncture fluid mNGS and tissue mNGS were higher than those of culture in the patients who had prior antibiotic use, and this difference was statistically significant (p = 0.000).

CONCLUSION

mNGS is more sensitive and accurate than traditional culture, making it ideal for identifying pathogens and screening infectious diseases, especially for those with uncultivated or difficult-to-cultivate species. Early diagnosis allows for prompt treatment with targeted antibiotics, and mNGS is recommended when samples are limited.

Tackling Infectious Diseases with Rapid Molecular Diagnosis and Innovative Prevention

Infectious diseases (IDs) are a leading cause of death. The diversity and adaptability of microbes represent a continuing risk to health. Combining vision with passion, our transdisciplinary medical research team has been focussing its work on the better management of infectious diseases for saving human lives over the past five decades through medical discoveries and innovations that helped change the practice of medicine. The team used a multiple-faceted and integrated approach to control infectious diseases through fundamental discoveries and by developing innovative prevention tools and rapid molecular diagnostic tests to fulfill the various unmet needs of patients and health professionals in the field of ID. In this article, as objectives, we put in context two main research areas of ID management: innovative infection prevention that is woman-controlled, and the rapid molecular diagnosis of infection and resistance. We also explain how our transdisciplinary approach encompassing specialists from diverse fields ranging from biology to engineering was instrumental in achieving success. Furthermore, we discuss our vision of the future for translational research to better tackle IDs.

Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health

To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.

Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing

Multi-drug-resistant Neisseria gonorrhoeae infection is a significant public health risk. Rapidly detecting N. gonorrhoeae and antimicrobial-resistant (AMR) determinants by metagenomic sequencing of urine is possible, although high levels of host DNA and overgrowth of contaminating species hamper sequencing and limit N. gonorrhoeae genome coverage. We performed Nanopore sequencing of nucleic acid amplification test-positive urine samples and culture-positive urethral swabs with and without probe-based target enrichment, using a custom SureSelect panel, to investigate whether selective enrichment of N. gonorrhoeae DNA improves detection of both species and AMR determinants. Probes were designed to cover the entire N. gonorrhoeae genome, with tenfold enrichment of probes covering selected AMR determinants. Multiplexing was tested in a subset of samples. The proportion of sequence bases classified as N. gonorrhoeae increased in all samples after enrichment, from a median (IQR) of 0.05 % (0.01-0.1 %) to 76 % (42-82 %), giving a corresponding median improvement in fold genome coverage of 365 times (112-720). Over 20-fold coverage, required for robust AMR determinant detection, was achieved in 13/15(87 %) samples, compared to 2/15(13 %) without enrichment. The four samples multiplexed together also achieved >20-fold genome coverage. Coverage of AMR determinants was sufficient to predict resistance conferred by changes in chromosomal genes, where present, and genome coverage also enabled phylogenetic relationships to be reconstructed. Probe-based target enrichment can improve N. gonorrhoeae genome coverage when sequencing DNA extracts directly from urine or urethral swabs, allowing for detection of AMR determinants. Additionally, multiplexing prior to enrichment provided enough genome coverage for AMR detection and reduces the costs associated with this method.

The Report Says What?: How the Medical Microbiologist can aid in the Interpretation of Next-Generation Sequencing Results

The applications of next-generation sequencing (NGS) in the clinical microbiology laboratory are expanding at a rapid pace. The medical microbiologist thus plays a key role in translating the results of these emerging technologies to the practicing clinician. Here we discuss the factors to consider to successfully develop standardized reporting for microbial targeted or metagenomic NGS testing in the clinical laboratory.

Study on the microbial diversity of ear canal secretions from patients with otomycosis

Otomycosis is caused by fungi, which usually cause discharge and additional discomfort. The highest incidence of otomycosis occurs in summer. To better treat this disease, it is necessary to study the microbial diversity of otomycosis secretions. In this regard, this study used high-throughput sequencing technology to determine the microbial diversity of the ear canal secretions of six typical patients with otomycosis in Wuhan via internal transcribed spacer (ITS) and 16S rRNA analyses and proposed a reasonable clinical treatment plan. Six patients with otomycosis in the Department of Otorhinolaryngology, Hubei Third People's Hospital Affiliated with Jianghan University, were selected from June 2022 to August 2022. The results showed that Staphylococcus spp. (average abundance 29.05%) was the dominant bacteria and Aspergillus spp. (average abundance 90.68%) was the dominant fungus involved in otomycosis secretion. Aspergillus spp. can cause inflammation of the external auditory canal combined with bacterial infections such as Staphylococcus spp., which can cause discharge in the ear canal. High-throughput sequencing provides comprehensive information on the microbial community involved in otomycosis discharge and will aid in evaluating the efficacy of clinical treatment and medication.

Spinal infection caused by Aspergillus flavus in a diabetic: a case report and literature review

Spinal infections, notably those induced by Aspergillus flavus (A. flavus), represent a complex and uncommon clinical challenge. In individuals with diabetes mellitus, the risk is exacerbated due to a compromised immune response and a heightened vulnerability to non-standard pathogens. This case report chronicles the intricate diagnostic and treatment journey of a 59-year-old diabetic patient grappling with a spinal infection attributed to A. flavus. The diagnosis was delayed due to non-specific symptoms and unclear radiological signs. The administration of voriconazole, a targeted antifungal treatment, resulted in a significant clinical and radiological improvement, underscoring its effectiveness in treating such unusual fungal spinal infections; meanwhile, we found that terbinafine hydrochloride also has a similar effect in treating fungal spinal infections. This case underscores the importance of considering fungal causes in spinal infections among diabetic patients and highlights prompt diagnosis and individualized targeted antifungal therapy.

Metagenomics next-generation sequencing (mNGS) reveals emerging infection induced by Klebsiella pneumoniaeniae

OBJECTIVES

The increasing emergence of hypervirulent Klebsiella pneumoniae (hv-Kp) and carbapenem-resistant K. pneumoniae (CR-Kp) is a serious and substantial public health problem. The use of the last resort antimicrobials, tigecycline and polymyxin to combat infections is complicated by the expanding repertoire of newly-identified CR-hvKp. The transmission and co-occurrence of the corresponding antimicrobial resistance and virulence determinants are largely unknown. The aim of this study was to investigate the dissemination and dynamics of CR-Kp and its antibiotic resistance in a hospitalised patient.

METHODS

Metagenomic next-generation sequencing (mNGS) was conducted for different specimens collected from an elderly male hospitalised patient. CR-Kp strains were examined using antibiotic susceptibility and string testing. Antimicrobial and virulence genes were annotated using whole-genome sequencing (WGS).

RESULTS

A clinical case of a patient infected with a variety of CR-Kp isolates was reported. The co-occurrence of KPC-2 and NDM-1 in the patient was revealed. The CR-Kp isolates, such as BALF2, and Sputum T1 and T3, were classified into ST11 and ST147, respectively. The genetic signature (iuc operon) of hypervirulence was identified in strain T1, although string testing indicated its intermediate virulence.

CONCLUSIONS

In this study, multiple infections of CR-Kp isolates were revealed by mNGS, and their dissemination was attributed to plasmid variations, mgrB inactivation and integrative conjugative elements (ICEs). Furthermore, the finding indicated one likely convergence to form CR-hvKp, different from acquisition of carbapenem-resistance determinants in hvKp. A combination of mNGS and WGS is beneficial for clinical diagnosis and anti-infection therapy, and facilitates a better understanding of genetic variants conferring antimicrobial and virulence properties.

The Clinical Value of Metagenomic Next-Generation Sequencing in Pneumocystis jirovecii Pneumonia

Background

The incidence of Pneumocystis jirovecii pneumonia (PJP) is increasing.

Methods

108 patients were analysed retrospectively at the Wuhan Union Hospital. The patients were classified into the PJP group or the P. jirovecii colonisation (PJC) group based on clinical diagnosis. Clinical data included demographics, laboratory examinations, treatment, and outcomes.

Results

A notable difference in the fungal load was seen between two groups, with median reads of 3215.79 vs. 5.61 in two groups, respectively (P<0.001). The optimal threshold value for discriminating P. jirovecii infection between colonisation for mNGS was six, and serum (1,3)-β-D-glucan (BDG) was 47.6 pg/mL. Besides, the positive detection rate of mNGS for co-pathogens in PJP patients was significantly higher than that of culture (88.16% vs. 22.37%, P<0.0001). Epstein-Barr virus and cytomegalovirus were the most common pathogens of co-infection in PJP patients. The antibiotic therapy in PJP patients was adjusted according to the mNGS results, of which seventeen (22.37%) were downgraded, 38 (50.0%) patients were upgraded, and 21 (27.63%) were unchanged. And almost all patients showed significant improvement in C-reactive protein.

Conclusion

mNGS is a promising and valuable technique with good performance for differentiating P. jirovecii infection and colonisation, the detection of pathogens, and antibiotic treatment.

Applicability of Bronchoalveolar Lavage Fluid and Plasma Metagenomic Next-Generation Sequencing Assays in the Diagnosis of Pneumonia

Background

Metagenomic next-generation sequencing (mNGS) provides innovative solutions for predicting complex infections. A comprehensive understanding of its strengths and limitations in real-world clinical settings is necessary to ensure that it is not overused or misinterpreted.

Methods

Two hundred nine cases with suspected pneumonia were recruited to compare the capabilities of 2 available mNGS assays (bronchoalveolar lavage fluid [BALF] mNGS and plasma mNGS) to identify pneumonia-associated DNA/RNA pathogens and predict antibiotic resistance.

Results

Compared to clinical diagnosis, BALF mNGS demonstrated a high positive percent agreement (95.3%) but a low negative percent agreement (63.1%). Plasma mNGS revealed a low proportion of true negatives (30%) in predicting pulmonary infection. BALF mNGS independently diagnosed 65.6% (61/93) of coinfections and had a remarkable advantage in detecting caustic, rare, or atypical pathogens. Pathogens susceptible to invasive infection or bloodstream transmission, such as Aspergillus spp, Rhizopus spp, Chlamydia psittaci, and human herpesviruses, are prone to be detected by plasma mNGS. BALF mNGS tests provided a positive impact on the diagnosis and treatment of 128 (61.2%) patients. Plasma mNGS, on the other hand, turned out to be more suitable for diagnosing patients who received mechanical ventilation, developed severe pneumonia, or developed sepsis (all P < .01). BALF mNGS was able to identify resistance genes that matched the phenotypic resistance of 69.4% (25/36) of multidrug-resistant pathogens.

Conclusions

Our data reveal new insights into the advantages and disadvantages of 2 different sequencing modalities in pathogen identification and antibiotic resistance prediction for patients with suspected pneumonia.

Interstitial pneumonia combined with nocardia cyriacigeorgica infection: A case report

BACKGROUND

Nocardia infection is a relatively uncommon disease, with no reports among patients with interstitial pneumonia. Due to its atypical clinical symptoms and chest computed tomography (CT) findings and the frequent yielding of negative results by conventional cultures, it poses challenges for timely diagnosis and treatment.

CASE SUMMARY

A 63-year-old female patient presented to our hospital in July 2022 with a 3-mo history of intermittent cough and poor appetite, accompanied by a 2-wk long duration of headaches. She had a previous medical history of interstitial pneumonia and was on oral prednisone and cyclosporine. Chest CT revealed the presence of newly developed round nodules. The diagnosis of Nocardia cyriacigeorgica infection was confirmed through metagenomic next-generation sequencing (mNGS) performed on bronchoalveolar lavage fluid. Targeted anti-infection therapy was initiated, resulting in symptom improvement and radiological resolution, further validating the mNGS results.

CONCLUSION

Nocardia cyriacigeorgica infection is a clinically rare condition that is primarily observed in immunocompromised patients. Its clinical and radiological manifestations lack specificity, but mNGS can aid in rapidly obtaining pathogenic information. Early initiation of targeted antimicrobial therapy based on mNGS results can improve patient prognosis.

Next-Generation sequencing transforming clinical practice and precision medicine

Next-generation sequencing (NGS) has revolutionized the field of genomics and is rapidly transforming clinical diagnosis and precision medicine. This advanced sequencing technology enables the rapid and cost-effective analysis of large-scale genomic data, allowing comprehensive exploration of the genetic landscape of diseases. In clinical diagnosis, NGS has proven to be a powerful tool for identifying disease-causing variants, enabling accurate and early detection of genetic disorders. Additionally, NGS facilitates the identification of novel disease-associated genes and variants, aiding in the development of targeted therapies and personalized treatment strategies. NGS greatly benefits precision medicine by enhancing our understanding of disease mechanisms and enabling the identification of specific molecular markers for disease subtypes, thus enabling tailored medical interventions based on individual characteristics. Furthermore, NGS contributes to the development of non-invasive diagnostic approaches, such as liquid biopsies, which can monitor disease progression and treatment response. The potential of NGS in clinical diagnosis and precision medicine is vast, yet challenges persist in data analysis, interpretation, and protocol standardization. This review highlights NGS applications in disease diagnosis, prognosis, and personalized treatment strategies, while also addressing challenges and future prospects in fully harnessing genomic potential within clinical practice.

Clinical application of metagenomic next-generation sequencing in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation

Objectives

This study aims to explore the pathogen-detected effect of mNGS technology and its clinical application in non-immunocompromised patients with severe pneumonia supported by vv-ECMO.

Methods

A retrospective analysis was conducted on a cohort of 50 non-immunocompromised patients who received vv-ECMO support for severe pneumonia between January 2016 and December 2022. These patients were divided into two groups based on their discharge outcomes: the deterioration group (Group D), which included 31 cases, and the improvement group (Group I), consisting of 19 cases. Baseline characteristics and clinical data were collected and analyzed.

Results

Among the 50 patients enrolled, Group D exhibited a higher prevalence of male patients (80.6% vs. 52.6%, p < 0.05), more smokers (54.8% vs. 21.1%, p < 0.05), and were older than those in Group I (55.16 ± 16.34 years vs. 42.32 ± 19.65 years, p < 0.05). Out of the 64 samples subjected to mNGS detection, 55 (85.9%) yielded positive results, with a positivity rate of 83.7% (36/43) in Group D and 90.5% (19/21) in Group I. By contrast, the positive rate through traditional culture stood at 64.9% (74/114). Among the 54 samples that underwent both culture and mNGS testing, 23 (42.6%) displayed consistent pathogen identification, 13 (24.1%) exhibited partial consistency, and 18 (33.3%) showed complete inconsistency. Among the last cases with complete inconsistency, 14 (77.8%) were culture-negative, while two (11.1%) were mNGS-negative, and the remaining two (11.1%) presented mismatches. Remarkably, mNGS surpassed traditional culture in pathogen identification (65 strains vs. 23 strains). Within these 65 strains, 56 were found in Group D, 26 in Group I, and 17 were overlapping strains. Interestingly, a diverse array of G+ bacteria, fungi, viruses, and special pathogens were exclusive to Group D. Furthermore, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae were more prevalent in Group D compared to Group I. Importantly, mNGS prompted antibiotic treatment adjustments in 26 patients (52.0%).

Conclusions

Compared with the conventional culture, mNGS demonstrated a higher positive rate, and emerges as a promising method for identifying mixed pathogens in non-immunodeficient patients with severe pneumonia supported by vv-ECMO. However, it is crucial to combine the interpretation of mNGS data with clinical information and traditional culture results for a comprehensive assessment.

Comparative performance of microbiological methods for the detection of tuberculous meningitis pathogens in cerebrospinal fluid

The aim of this study was to comprehensively evaluate metagenomic next-generation sequencing (mNGS), Acid-fast bacillus stain (AFB), MGIT960 culture, polymerase-chain-reaction (PCR), and Xpert MTB/RIF in the diagnosis of tuberculous meningitis (TBM). A cohort of 280 patients who presented with suspected TBM (ie, headache or altered mental status with clinical signs of meningism) were analyzed. The sensitivities of the 5 assays for the diagnosis of TBM ranged from 10.0% to 70.0%. The AFB had the lowest sensitivity of 10.0% (0.5-45.9), while mNGS and PCR had the highest sensitivity, both at 70.0% (35.4-91.9). mNGS demonstrated a distinct advantage in identifying a wider array of pathogens, including viruses, in CSF samples. PCR was a cost-effective option with excellent sensitivity and specificity. However, no single method was statistically significantly better than any other in the diagnosis of TBM. New diagnostic techniques are urgently needed for the independent, rapid and accurate detection of Mycobacterium tuberculosis to guide the diagnosis of TBM.

Universal digital high resolution melt analysis for the diagnosis of bacteremia

Fast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires ∼15 hours to detect the presence of a pathogen. Here, we assess the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 21 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 90.5% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1 mL sample input and sample-to-answer time of 6 hrs. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection.

Universal digital high resolution melt analysis for the diagnosis of bacteremia

April Aralar, Tyler Goshia, Nanda Ramchandar, Shelley M. Lawrence, Aparajita Karmakar, Ankit Sharma, Mridu Sinha, David Pride, Peiting Kuo, Khrissa Lecrone, Megan Chiu, Karen Mestan, Eniko Sajti, Michelle Vanderpool, Sarah Lazar, Melanie Crabtree, Yordanos Tesfai, Stephanie I. Fraley.

Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution

Next-generation sequencing technologies have enabled many advances across diverse areas of biology, with many benefiting from increased sample size. Although the cost of running next-generation sequencing instruments has dropped substantially over time, the cost of sample preparation methods has lagged behind. To counter this, researchers have adapted library miniaturization protocols and large sample pools to maximize the number of samples that can be prepared by a certain amount of reagents and sequenced in a single run. However, due to high variability of sample quality, over and underrepresentation of samples in a sequencing run has become a major issue in high-throughput sequencing. This leads to misinterpretation of results due to increased noise, and additional time and cost rerunning underrepresented samples. To overcome this problem, we present a normalization method that uses shallow iSeq sequencing to accurately inform pooling volumes based on read distribution. This method is superior to the widely used fluorometry methods, which cannot specifically target adapter-ligated molecules that contribute to sequencing output. Our normalization method not only quantifies adapter-ligated molecules but also allows normalization of feature space; for example, we can normalize to reads of interest such as non-ribosomal reads. As a result, this normalization method improves the efficiency of high-throughput next-generation sequencing by reducing noise and producing higher average reads per sample with more even sequencing depth. IMPORTANCE High-throughput next generation sequencing (NGS) has significantly contributed to the field of genomics; however, further improvements can maximize the potential of this important tool. Uneven sequencing of samples in a multiplexed run is a common issue that leads to unexpected extra costs or low-quality data. To mitigate this problem, we introduce a normalization method based on read counts rather than library concentration. This method allows for an even distribution of features of interest across samples, improving the statistical power of data sets and preventing the financial loss associated with resequencing libraries. This method optimizes NGS, which already has huge importance across many areas of biology.

Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort

Background

Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples.

Methods

A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data.

Results

Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%).

Conclusions

mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.

Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-free DNA Testing in the Management of Patients With Suspected Infectious Diseases

Metagenomic next-generation sequencing (mNGS) of cell-free DNA is an emerging modality for the diagnosis of infectious diseases, but studies on its clinical utility are limited. We conducted a retrospective single-center study including all patients who had plasma mNGS sent at the University of Michigan between 1 January 2021 and 25 July 2022. Test results were assessed for clinical impact. A total of 71 tests were sent on 69 patients; the mean ± SD age was 52 ± 19 years; and 35% of patients were immunocompromised. Forty-five (63%) mNGS test results were positive and 14 (31%) had clinical impact-from starting new antimicrobials (n = 7), discontinuing antimicrobials (n = 4), or changing antimicrobial duration (n = 2) or by affecting surgical decision making (n = 1). Twenty-six (37%) mNGS test results were negative and only 4 (15%) were impactful, leading to discontinuation of antimicrobials. Overall, just 25% of mNGS tests were clinically relevant. There was no significant difference in the proportion of tests that were clinically relevant between negative and positive results (P = .16) or if patients were immunocompromised (P = .57). Plasma mNGS was most frequently impactful (in 50% of patients) when included in the diagnostic workup of cardiovascular infection but less impactful in other clinical syndromes, including fever of unknown origin and pulmonary infection. Our findings underscore the need to further study this testing modality, particularly with prospective research including negative controls, before it is considered for widespread use.

[Value of metagenomic next-generation sequencing in children with hematological malignancies complicated with infections]

OBJECTIVES

To explore the value of metagenomic next-generation sequencing (mNGS) in the pathogen identification in children with hematological malignancies complicated with infections.

METHODS

A retrospective analysis was conducted on clinical data and pathogenic test results of 43 children with hematological malignancies who underwent microbial culture and mNGS due to infections in the Third Xiangya Hospital of Central South University between June 2020 and July 2022. Differences in detection rates and characteristics of pathogenic microorganisms detected by mNGS and microbial culture were compared.

RESULTS

A total of 54 specimens were examined, and the overall detection rate of pathogen by mNGS (80%, 43/54) was significantly higher than that by microbial culture (30%, 16/54) (P<0.001). The most commonly detected infection type by mNGS was viral infection, followed by fungal infection combined viral infection, while that by microbial culture was bacterial infection, followed by fungal infection. The detection rate of fungi by mNGS (33%, 18/54) was higher than that by microbial culture (6%, 3/54) (P<0.001). The detection rate of two or more pathogenic microorganisms by mNGS was higher at 48% compared to microbial culture at 9% (P<0.05). The detection rate of two or more types of pathogenic microorganisms by mNGS was also significantly higher at 33% compared to microbial culture at 2% (P<0.05). The most commonly detected bacteria and fungi by mNGS were Pseudomonas aeruginosa and Candida tropicalis, respectively, in peripheral blood, while Streptococcus pneumoniae and Pneumocystis jirovecii were most commonly detected in bronchoalveolar lavage fluid. Treatment adjustments based on mNGS results were beneficial for 35% (15/43) of the cases.

CONCLUSIONS

mNGS has a higher detection rate than microbial culture and has obvious advantages in diagnosing mixed and fungal infections, making it a useful supplementary diagnostic method to microbial culture.

Clinical metagenomics-challenges and future prospects

Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.