Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

The diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in pathogen identification of pediatric pneumonia using bronchoalveolar lavage fluid (BALF): A systematic review and meta-analysis

OBJECTIVE

This meta-analysis evaluates and compares the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) with conventional microbiological tests (CMTs) in diagnosing pediatric pneumonia using bronchoalveolar lavage fluid (BALF).

METHODS

Data were sourced from Embase, PubMed, Web of Science, and the Cochrane Library. The pooled positive detection rate (PDR) of pathogens was estimated using fixed-effects or random-effects models. Subgroup analyses explored factors influencing mNGS diagnostic performance. Data analysis was conducted using Review Manager (RevMan) 5.4 and Stata version 16.0.

RESULTS

The pooled PDR of mNGS was 85.83 %, which is higher than the pooled PDR of 49.97 % for CMTs. A random-effects model indicated that, compared to CMTs, mNGS has a significantly higher PDR in pediatric pneumonia (OR = 3.99, 95 %CI: 2.12-7.50, P < 0.0001, I2 = 81 %). Subgroup analysis indicated that mNGS exhibited greater advantages in the group using the QIAamp kit (OR = 5.55, 95 % CI: 3.03-10.16, P < 0.00001), the group using the Illumina Nextseq platform (OR = 4.87, 95 % CI: 2.97-7.99, P < 0.00001), the DNA-only mNGS group (OR = 4.54, 95 % CI: 2.73-7.54, P < 0.00001), and the non-severe pneumonia group (OR = 4.76, 95 % CI: 3.51-6.46, P < 0.00001). However, when the subgroups were categorized as mixed infections or single-pathogen infections, no statistically significant differences were observed (Mixed: OR = 1.77, 95 % CI: 0.30-10.56, P = 0.53; Single: OR = 3.97, 95 % CI: 0.42-37.87, P = 0.23) CONCLUSION: mNGS demonstrates high diagnostic efficacy in detecting pathogens in BALF from pediatric patients with pneumonia. The diagnostic stability of mNGS is influenced by sample extraction, sequencing platforms, positive interpretation criteria, and disease status. Standardized procedures and technologies can enhance mNGS diagnostic performance.

GenomicGapID: leveraging spatial distribution of conserved genomic sites for broad-spectrum microbial identification

Bacterial detection and identification methods can be broadly classified as either untargeted with expansive taxonomic coverage or targeted with narrow taxonomic focus. Untargeted approaches, such as culture and sequencing, are often time-consuming and/or costly, whereas targeted methods, such as PCR, can offer faster and more cost-effective results but require a priori knowledge of the likely pathogen to select the appropriate assay. GenomicGapID, a novel approach that leverages the spatial distribution of conserved genetic regions across microbial genomes, represents a significant advancement in the field of microbial identification. This technique has the potential to provide the taxonomic breadth of culture and sequencing while maintaining the speed, simplicity, and cost-effectiveness of PCR. By leveraging the conservation and relative positioning of highly conserved coding regions across different species, GenomicGapID enables the development of universal primer sets that amplify the non-conserved gaps between these regions. This creates a unique electrophoretic signature that facilitates rapid and accurate target-agnostic microbial identification. In this study, we apply the principles of GenomicGapID to the critical task of identifying clinical pathogens. We focus on expanding the coverage of a previously developed universal bacterial identification system, which initially targeted the 16s-23s internal transcribed spacer (ITS) region and was capable of discerning 45 pathogens. To enhance this system, we assembled a comprehensive database of 189 clinically relevant bacterial species. We then identified conserved primer binding sites that produce unique amplicon size signatures for each species. While we found that the use of amplicon size signatures alone would require an impractical number of universal primer sets, we demonstrate that this challenge can be effectively mitigated through concurrent melt analysis. Ultimately, we show that just three universal primer sets, guided by the GenomicGapID framework, are sufficient to cover 189 clinical bacterial pathogens, representing a majority of microbes identified in positive cultures in a clinical microbiology setting, with experimental validation of a subset of these pathogens. This study not only enhances the existing universal bacterial identification system but also establishes GenomicGapID as a versatile and powerful tool in microbial diagnostics and beyond, paving the way for new avenues of research in genomics with the potential to advance molecular biology, clinical practice, and public health.IMPORTANCERapid and accurate microbial identification is critical in both clinical and research settings. Traditional untargeted methods, such as culture and sequencing, are often time-consuming and expensive, while targeted techniques like PCR offer speed and cost-effectiveness but require pre-selection of pathogens. Our work introduces GenomicGapID, a novel bacterial identification system that provides the taxonomic breadth of untargeted methods, coupled with the speed, simplicity, and affordability of targeted PCR-based techniques. By leveraging the gap between conserved genetic regions and analyzing the associated unique electrophoretic and melt analysis signatures, GenomicGapID enables target-agnostic bacterial identification using a parsimonious set of universal primers.Our work has significant implications not only in clinical microbiology but also in genomics, environmental microbiology, and public health. We believe this manuscript aligns well with the mission of Microbiology Spectrum to publish innovative and impactful research that advances the field of microbial sciences.

Detection of bacterial pathogens directly from synovial fluids using digital PCR: A proof of concept study

Diagnosis of joint infections is often challenging due to low specimen volumes, low sensitivity of Gram stains and long incubation times of cultures. Digital PCR (dPCR) is a molecular tool that can detect nucleic acid targets with high sensitivity and resistance to inhibition. A 3 hour dPCR assay targeting the 16S gene was performed on archived synovial fluids. The assay detected the 16S gene directly from 4 µL of joint fluid without nucleic acid extraction. In 43 culture positive neat synovial fluids, the dPCR instrument detected 31 (72%) as positive, and 12 (28%) as indeterminate. In 49 culture negative specimens, dPCR was negative for 34 (69%), indeterminate for 14 (29%). The detection of bacteria was similar to real-time PCR performed on extracted specimens and demonstrated superior sensitivity to Gram stain. This technique shows potential as a rapid detection method for bacterial pathogens in synovial fluids, with optimization to improve specificity.

Infection in Childhood Arterial Ischemic Stroke: Metagenomic Next-Generation Sequencing Results of the VIPS II Study

BACKGROUND

Acute respiratory infection transiently increases risk for childhood arterial ischemic stroke (AIS). We hypothesize that this paradox of a common exposure linked to a rare outcome could be explained by either (1) the infection hypothesis: unusual or multiple pathogens or (2) the host response hypothesis: heterogeneity in the inflammatory response to infection. We leverage metagenomic next-generation sequencing (mNGS), a comprehensive microbial detection tool, to test the first hypothesis.

METHODS

The VIPS II study (Vascular Effects of Infection in Pediatric Stroke II) prospectively enrolled children with AIS at 22 international sites over 5 years (December 2016 to January 2022). Sites measured prestroke clinical infection via standardized parental interviews and chart abstraction. To assess more broadly the background spectrum of pathogens, a central research laboratory performed mNGS on plasma and oropharyngeal swabs collected within 72 hours of stroke. mNGS was also performed on biological samples from stroke-free children (June 2017 to January 2022), both without (well) and with (ill) documentation of clinical infection.

RESULTS

VIPS II enrolled 205 patients with AIS, 95 stroke-free well children, and 47 stroke-free ill children. Clinical infection, most commonly upper respiratory tract infection, was detected in 81 of 205 (40%) of patients. Both plasma and oropharyngeal swab mNGS data were available for 190 of 205 patients with AIS, 91 of 95 stroke-free well children, and 27 of 47 stroke-free ill children. mNGS detected viruses in 27 of 190 (14%) patients with AIS, 9 of 91 stroke-free well children (10%), and 9 of 27 (33%) stroke-free ill children. Most were common upper respiratory viruses. Coinfections were rare. Similar viruses were found in patients with AIS and stroke-free children.

CONCLUSIONS

mNGS detected a variety of common childhood viruses in both patients with AIS and stroke-free children, suggesting that the type of infection does not explain AIS susceptibility. Rather, the alternative hypothesis regarding an unusual host immune response to common infections in the pathogenicity of AIS should be further explored.

Metaviromic and metagenomic study of the pathogens in unexplained pneumonia cases in goats

Goats are an economically important livestock species in China. However, the high mortality rate due to pneumonia represents a significant challenge to the development of intensive goat farms. 10 goat lung tissue samples were collected in this study, and all samples exhibited pneumonia of different severity as determined by lung lesion scoring and histopathological examination. Subsequently, this study employed qRT-PCR to measure the relative expression level of pro-inflammatory cytokines in lung tissue, and conducted metaviromic and metagenomic analyses to elucidate the structure and composition of the pulmonary microbiota, the correlation between the abundance of specific microbes and inflammatory factors, and between microbial abundance and the expression of virulence genes. Metaviromic results indicated that Ungulate tetraparvovirus 4 (83.3 %) had the highest relative abundance in the viral composition. Metagenomic data showed that Mycoplasma (28.2 %) and Streptococcus (24.8 %) are the primary dominant genus in goat pneumonia. Notably, a total of 8 pathogens associated with pneumonia in humans or animals were identified across all samples, including Mycoplasma ovipneumoniae, Streptococcus agalactiae, Streptococcus pneumoniae, Escherichia coli, Bordetella hinzii, Bibersteinia trehalosi, Bordetella pertussis, and Pasteurella multocida, with mixed infections with multiple pathogens are very common in this study. Correlation analysis indicates a significant association between the degree of pathogen co-infection and the severity of pulmonary lesions. Furthermore, Pasteurella multocida showed a significant positive correlation with the expression of IL-6 (P< 0.01). The pneumonia samples also revealed a multitude of virulence factors associated with bacterial pathogenicity including those related to biofilm formation, endotoxin production, bacterial invasion and evasion of host immunity. In conclusion, the present study can provide a reference for clinical pathogen diagnosis of unexplained pneumonia in goats.

Diagnosis of donor-derived Malassezia restricta &Aspergillus species invasive fungal infection in renal transplant recipient using next generation sequencing - A report of 2 cases and literature review

Diagnosing donor-derived fungal infection in solid organ transplant recipients can be particularly challenging and is associated with high mortality. Here, we report two cases of Malassezia restricta and Aspergillus spp donor-derived fungal infection in renal transplant recipients leading to graft loss. Fortunately, both patients achieved full recovery with the administration of antifungal therapy.

Enhancing the detection sensitivity of mNGS in Bronchoalveolar Lavage fluid through cell Counting: An empirical study

OBJECTIVES

Lower respiratory tract infections pose significant clinical challenges due to their high morbidity and mortality rates. While metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool, its sensitivity is often compromised by host DNA contamination that overwhelms microbial signals. Selective host DNA depletion through cell lysis effectively reduces host DNA; however, it has an impact on microorganisms with relatively thin cell walls, and samples with low host content may introduce more environment or reagent-derived microbial contamination, interfering the detection results. Methods for determining host DNA depletion based on sample type, sample characteristics or using Spike-in controls to monitor sensitivity do not fully consider the potential limitations of host depletion technology on microbial detection, nor do they evaluate the possible significant impact on detection efficiency. This study aimed to develop a pre-analytical method for accurate host DNA content assessment.

METHODS

We established a cell-counting-based method for precise cellular content measurement in clinical BALF samples. The protocol involved: (1) evaluating the linearity and robustness of cell-counting dyes in BALF samples with varying characteristics, (2) assessing the correlation between cell counts and extracted nucleic acid mass, (3) investigating cellular counting thresholds for host depletion in clinical BALF analysis, and (4) implementing the optimized cell-counting method in clinical mNGS testing to guide selective-lysis treatment.

RESULTS

Acridine orange/propidium iodide (AO/PI) staining demonstrated superior performance compared to trypan blue and DAPI, particularly in turbid and bloody BALF samples. Implementing a host depletion threshold at 1 × 10^6 cell counts significantly improves pathogen detection rates in high host background samples, while effectively preserving the detection sensitivity for pathogens in moderate and low host background samples.

CONCLUSIONS

Our findings demonstrate that cell counting serves as a reliable pre-analytical tool for determining optimal selective-lysis treatment in BALF mNGS testing, enhancing diagnostic accuracy while preserving pathogen integrity.

Clinical Bioinformatician Body of Knowledge-Molecular Diagnostics Core: A Report of the Association for Molecular Pathology

Clinical bioinformaticians play a critical role in clinical molecular diagnostics laboratories as developers of data analysis pipelines, tools, and databases. They also contribute to a variety of other tasks, such as genomic data interpretation, database administration, hardware engineering, informatics, information technology, infrastructure support, and software engineering. To effectively perform these functions, the clinical bioinformatician must possess a strong foundational knowledge of molecular biology, genetics, genomics, computational biology, and the relevant federal, state, and/or regional regulations, laboratory accreditation requirements, and other standards and best practices. This first article in the Association for Molecular Pathology's Clinical Bioinformatician Body of Knowledge series provides a comprehensive core knowledge base on molecular biology, genetics, genomics, clinical laboratory practices, sequencing technologies, databases, and clinical applications. This resource serves not only to equip clinical bioinformaticians for their professional roles but also as a valuable reference for laboratorians.

Diagnosis and surgical treatment of chronic destructive septic hip arthritis

Septic hip arthritis (SHA) is a relatively rare but hazardous disease. Much controversy exists regarding the definition, diagnosis and treatment of chronic destructive SHAs. This review aims to provide an overview of the diagnostic and therapeutic approaches for chronic, destructive SHA and suggest possible research directions for this disease's future diagnosis and treatment. There is no unified naming or classification standard for SHAs. Chronic destructive SHA still requires a comprehensive diagnosis combining history, signs, bacterial culture, histopathological examination, inflammation and other indicators, of which metagenomic next-generation sequencing is a promising diagnostic tool. Previous treatment options for this disease include debridement, debridement + Girdlestone femoral head and neck resection, and debridement + Girdlestone femoral head and neck resection + two-stage arthroplasty. Among them, one-stage spacer implantation + two-stage arthroplasty is the current standard surgical option with a high success rate and low reinfection rate, while one-stage arthroplasty is a new treatment option proposed in recent years with unique advantages but limitations in terms of surgical indications. In the future, more high-quality studies are needed to provide the latest evidence to support clinical decision-making.

18F-FDG PET/CT Imaging of Talaromyces marneffei Infection with Bone Destruction in an HIV-Negative Patient: Case Report and Review

Background

Talaromycosis is an opportunistic fungal infection caused by Talaromyces marneffei (T. marneffei), commonly occurs in HIV-positive individuals. While less common, it can also affect HIV-negative individuals. We reported a T. marneffei infection in an HIV-negative patient, whose imaging findings and diagnostic process offer valuable clinical insights.

Case Presentation

An HIV-negative male adult patient with an intermittent cough for more than two years and worsened for more than one month. Enhanced CT scan indicated lung cancer with rib and lymph nodes metastasis. The lower respiratory tract and bronchial lavage fluid culture of the patient were negative. He received two bronchoscopies, two biopsies and two metagenomic next-generation sequencing (mNGS) tests, which failed to find the malignant cell but sequentially identified the presence of Pasteurella multocida and the Epstein-Barr virus. His condition did not improve after anti-infective treatment for 2weeks. An 18-fluorodeoxy glucose (18F-FDG) PET/CT scan revealed increased radioactivity in right supraclavicular lymph node, left lung and the right tenth rib. Ultimately, a biopsy at the hypermetabolic lesion of left lung, and a third mNGS test confirmed the presence of Talaromyces marneffei. Subsequently, the patient started antifungal therapy with amphotericin B and itraconazole and showed a favorable response.

Conclusion

We reviewed all reported PET/CT findings of T. marneffei infection patients, suggesting that fungus T. marneffei should be considered in patients identified as infection and exhibited bone destruction and also highlight the role of PET/CT in guiding the biopsy site.

Microbiome succession on the pomegranate phylloplane during bacterial blight dysbiosis: Functional implications for blight suppression

Bacterial blight of pomegranate caused by Xanthomonas axonopodis pv. punicae poses significant challenges to sustainable cultivation, necessitating eco-friendly management strategies, and this study explores the role of the phylloplane microbiome in disease suppression through metabarcoding, traditional microbiology, and antibacterial screening of microbial candidates. Here, we mapped the phylloplane microbiome of pomegranate cultivar 'Bhagwa' during bacterial blight development using metabarcoding sequencing (2443,834 reads), traditional microbiological methods (nutrient-rich and minimal media), and scanning electron microscopy. We observed shifts in microbial diversity, with Xanthomonas typically released through stomata as the blight progressed from water-soaked early lesion to advanced necrotic lesion. The Shannon diversity index peaked at 2.6 in early necrotic stages but dropped to 2.1 in advanced blight. Proteobacteria and Firmicutes were the dominant phyla, with significant compositional changes between disease stages. Bacillus species were prevalent throughout, peaking in both early and severe lesions. Pantoea and Curtobacterium increased during severe blight, while Exiguobacterium thrived on the abaxial surface. A core microbiome, including Pantoea, Enterobacter, and Pseudomonas, remained consistent across stages. Antibacterial screening of 116 bacterial candidates, dominated by Pantoea (32), Bacillus (18), and Pseudomonas (11), revealed multipronged activities against X. axonopodis pv. punicae. Bacillus amyloliquefaciens P2-1 and Pantoea dispersa Pg-Slp-6 suppressed the pathogen through secreted metabolites, while Pantoea dispersa Pg-Slp-6, Pseudomonas oryzihabitans Pg-Slp-82, and Pantoea dispersa Pg-slp-117 exhibited volatile-mediated suppression. Among these, Bacillus amyloliquefaciens P2-1 and Pantoea dispersa Pg-slp-6 showed 55 % and 42 % blight suppression, respectively, highlighting their potential as biocontrol agents.

Metagenomic Sequencing of Tomato Plants with Wilt Symptoms Allows for Strain-Level Pathogen Identification and Genome-Based Characterization

Diseases that affect the vascular system or the pith are of great economic impact because they can rapidly destroy the affected plants, leading to complete loss in production. Fast and precise identification is thus important to inform containment and management, but many identification methods are slow because they are culture-dependent and do not reach strain resolution. Here we used culture-independent long-read metagenomic sequencing of DNA extracted directly from the stems of two tomato samples that displayed wilt symptoms. We obtained enough sequencing reads to assemble high-quality metagenome-assembled genomes of Ralstonia solanacearum from one sample and of Pseudomonas corrugata from the other. The genome sequences allowed us to identify both pathogens to the strain level using the genomeRxiv platform, perform phylogenetic analyses, predict virulence genes, and infer antibiotic and copper resistance. In the case of R. solanacearum, it was straightforward to exclude the pathogen from being the Select Agent race 3 biovar 2. Using the Branchwater tool, it was also possible to determine the worldwide distribution of both pathogen strains based on public metagenomic sequences. The entire analysis could have been completed within 2 days, starting with sample acquisition. Steps necessary toward establishing metagenomic sequencing as a more routine approach in plant diseases clinics are discussed.

The diagnostic value of third-generation nanopore sequencing in non-tuberculous mycobacterial infections

Background

This study aimed to investigate the diagnostic value of nanopore sequencing technology in non-tuberculous mycobacterial pulmonary disease (NTMPD) and compare it with traditional culture methods.

Methods

A retrospective analysis was conducted on 225 suspected NTMPD patients admitted to the Fourth People's Hospital of Nanning City from January 2022 to July 2024. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), kappa coefficient, and area under the receiver operating characteristic curve (AUC) of nanopore sequencing, culture, and combined diagnostic methods were compared to evaluate their diagnostic performance. In addition, patients were divided into different groups to investigate the detection of NTMPD by nanopore sequencing technology under different pathogen concentrations, in cases of concurrent Mycobacterium tuberculosis (MTB) infection, and among the elderly (aged > 60 years).

Results

Among 139 NTMPD samples, nanopore sequencing detected positives in 113 cases, with a sensitivity of 81.3%, PPV of 99.1%, NPV of 76.6%, kappa coefficient of 0.759, and AUC of 0.901, demonstrating high specificity (98.8%) comparable to culture. The combined diagnostic approach significantly improved the sensitivity (90.6%), NPV (98.4%), kappa coefficient (0.862), and AUC (0.942) of NTMPD diagnosis. Nanopore sequencing showed superior diagnostic value in samples with various bacterial concentrations and in cases of concurrent MTB infection.

Conclusion

Third-generation nanopore sequencing technology serves as a rapid and effective diagnostic tool, which may profoundly impact the current diagnosis of NTMPD.

Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study

BACKGROUND

Accurate pathogen identification is critical for managing sepsis. However, traditional microbiological methods are time-consuming and exhibit limited sensitivity, particularly with blood samples. Metagenomic sequencing of plasma or whole blood was highly affected by the proportion of host nucleic acid.

METHODS

We developed a Probe-Capture Metagenomic assay and established a multicentre prospective cohort to assess its clinical utility. In this study, 184 blood samples from patients suspected of sepsis were sent for blood culture and Probe-Capture Metagenomic sequencing before using antibiotics. The pathogen-positive rate and auxiliary abilities in diagnosis were compared among Probe-Capture Metagenomics, blood culture and real-time PCR (RT-PCR). Antibiotic therapy adjustments were based on the identification of pathogens, and changes in the Sequential Organ Failure Assessment (SOFA) score were monitored on days 0, 3 and 7 of admission.

RESULTS

A total of 184 sepsis patients were enrolled, with a mean age of 66 years (range 56-74). The Probe-Capture Metagenomics method, confirmed by RT-PCR, demonstrated a significantly higher pathogen detection rate than blood culture alone (51.6% vs. 17.4%, p < .001). When combining the results of blood culture and RT-PCR, Probe-Capture Metagenomics achieved a concordance rate of 91.8% (169/184), with a sensitivity of 100% and specificity of 87.1%. In terms of clinical impact, antibiotic therapy was adjusted for 64 patients (34.8%) based on the results from Probe-Capture Metagenomics, and 41 patients (22.3%) showed a > 2-point decrease in SOFA score following antibiotic adjustments.

CONCLUSION

Probe-Capture Metagenomics significantly enhances the ability of pathogen detection compared with traditional metagenomics. Compared to blood culture and RT-PCR in sepsis patients, it leads to improved antibiotic treatment and better patient outcomes. This study, for the first time, evaluates the clinical impact of metagenomic sequencing by integrating antibiotic adjustments and SOFA score changes, indicating that approximately one-fifth of sepsis patients benefit from this advanced diagnostic approach.

TRIAL REGISTRATION

This study has been registered in clinical trials (clinicaltrials.gov) on 30 November 2018, and the registration number is NCT03760315.

KEY POINTS

Probe-Capture Metagenome had a significantly higher positive rate than blood culture (51.6% vs. 17.4%, p < .001). Combining blood culture and RT-PCR results, Probe-Capture Metagenome achieved a consistency rate of 91.8%. Antibiotics were adjusted in 34.8% of patients based on Probe-Capture Metagenome results, and 22.3% of patients experienced a more than 2-point decrease in SOFA score.

Clinical Value of Metagenomic Next-Generation Sequencing From Blood Samples to Identify Pneumocystis jirovecii Pneumonia in Patients With Human Immunodeficiency Virus

Background

The aim of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for identifying Pneumocystis jirovecii pneumonia (PJP) in patients with human immunodeficiency virus (HIV).

Methods

A total of 76 people with HIV (PWH) with suspected lung infections were enrolled in the study. The patients were divided into two groups: the PJP group and the non-PJP group.All patients underwent pulmonary computed tomography scans, and blood or respiratory tract specimens were subjected to mNGS and conventional microbiological tests. Patient characteristics were collected from their medical records.

Results

Thirty patients were diagnosed with PJP and 46 were confirmed to have non-P jirovecii (Pj) infectious pneumonia. mNGS was conducted on bronchoalveolar lavage fluid samples from 25 patients and on blood samples from 59 patients. Twenty-one of 22 (95.5%) blood samples from the PIP group contained sequences of Pi, with the number of specific reads for circulating Pj sequences ranging from 2 to 2035. In the non-PJP group, 4 blood samples exhibited low Pj sequences, ranging from 1 to 2 reads. The sensitivity and specificity for blood samples were 95.5% (95% confidence interval [CI], 91.2%-98.4%) and 90.0% (95% Cl, 89.5%-100%), respectively.

Conclusions

Our study indicates that mNGS of blood samples exhibits high sensitivity and specificity for diagnosing PJP in PWH. Caution should be exercised when interpreting low Pj mNGS read counts in blood samples; the definitive diagnosis of PJP relies on the synthesis of clinical data with Pj mNGS results. Further studies are necessary to validate this finding.

Metagenomic next-generation sequencing enhances the diagnosis of Q fever: A retrospective observational study

BACKGROUND

Q fever, a global zoonosis, poses a significant challenge for public health due to its varied and nonspecific clinical presentations, making diagnosis difficult. Metagenomic next-generation sequencing (mNGS) is a potential tool for diagnosing Q fever.

METHODS

This retrospective observational study was conducted on patients with Q fever admitted to Peking University People's Hospital, from May 2023 to November 2024. mNGS was performed using the patient's peripheral blood, and the qPCR of Coxiella burnetii was also adopted. Subsequently, the clinical data of patients diagnosed with Q fever were systematically evaluated.

RESULTS

Twelve peripheral blood samples of 12 patients were detected Coxiella burnetii positive by mNGS. Most patients were male (10, 83.33 %). Fever (12, 100 %), muscle soreness (8, 66.7 %), and headache (4, 33.3 %) were the most common clinical manifestations. Specific qPCR of Coxiella burnetii was detected positive in 8 patients. Chronic Q fever was diagnosed in two patients, who had aortic valve replacement, and their immunological markers, like anti-nuclear were elevated. Once the diagnosis was clear, proper antibiotics were used, and all patients were discharged in better health.

CONCLUSION

Metagenomic next-generation sequencing enhances the diagnosis of Q fever, especially for patients displaying atypical and various clinical symptoms and having unclear epidemiological data or histories of antibiotic use.

Invasive Candidiasis in the Intensive Care Unit: Where Are We Now?

Invasive fungal infections in the intensive care unit (ICU) are not uncommon and most cases are caused by Candida species, specifically Candida albicans. However, recently, there has been an increase in non-albicans Candida spp. (C. glabrata; C. parapsilosis) causing invasive fungal infections. This has led to an increasing awareness of this infection due to the increase in documented antifungal resistance in many of these Candida species. In addition, manifestations of invasive candidiasis are often non-specific, and the diagnosis remains extremely challenging. Unfortunately, delays in antifungal therapy continue to hamper the morbidity; length of stay; and the mortality of these infections. Although the echinocandins are the drugs of choice in these infections, antifungal resistance among the non-albicans species (C. glabrata; C. krusei; C. auris; C. parapsilosis) is being observed more frequently. This has led to an increase in morbidity and mortality, specifically in critically ill patients. Overall, the diagnosis and management of invasive candidiasis in the ICU remain challenging. It is imperative that the critical care physician keeps this infection at the forefront of their differential diagnosis in order to decrease the mortality rate of these individuals. In this review, we discuss the current epidemiologic trends, diagnosis, and management of invasive candidiasis in the intensive care unit setting.

Application of metagenomic next-generation sequencing in treatment guidance for deep neck space abscess

BACKGROUND

Infectious etiologies of deep neck space abscess (DNSA) by conventional culture tests can be challenging, which also leads to frequent irrational antibiotic usage. Metagenomic next-generation sequencing (mNGS), as a novel method for analyzing the complex microbial ecosystem from clinical samples, has been utilized in clinical research and practice of various infectious diseases but deep neck space abscess. We here aimed to explore the clinical value of mNGS for pathogen detection and treatment guidance in DNSA patients compared with conventional culture tests.

METHODS

One hundred six patients diagnosed with DNSA were retrospectively enrolled and allocated into mNGS group and culture group according to whether mNGS was conducted. The pathogen detection effectiveness was of mNGS was compared with conventional culture. Effectiveness of mNGS-modified antimicrobial therapy was evaluated by comparing the treatment outcomes between two groups.

RESULTS

mNGS showed a significantly higher detection rate than conventional culture (p < 0.05) with faster result acquisition. Treatment success rate of patients in the mNGS group was significantly higher than in the culture group (RR: 1.22, 95%CI: 1.07-1.82, p = 0.033). Besides, patients in the mNGS group had shorter duration of irrational antimicrobial therapy, shorter hospital stay and less medical costs (p < 0.05).

CONCLUSIONS

mNGS is an effective technology for facilitating pathogen detection and improving treatment outcomes of DNSA patients.

Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples

OBJECTIVES

This study aims to evaluate and compare the effectiveness of metagenomic next-generation sequencing (mNGS) in identifying pathogens from clinical body fluid samples, with a specific focus on the application of microbial cell-free DNA (cfDNA) mNGS.

METHODS

A total of 125 clinical body fluid samples were collected. All samples underwent mNGS targeting whole-cell DNA (wcDNA), with 30 samples also analyzed for cfDNA mNGS and 41 subjected to 16S rRNA NGS for comparative analysis. Patient clinical data, including culture results, were obtained from electronic medical records.

RESULTS

In comparison to cfDNA mNGS, the mean proportion of host DNA in wcDNA mNGS was 84%, significantly lower than the 95% observed in cfDNA mNGS (p < 0.05). Using culture results as a reference, concordance rates were 63.33% (19/30) for wcDNA mNGS and 46.67% (14/30) for cfDNA mNGS. Additionally, wcDNA mNGS showed greater consistency in bacterial detection with culture results, achieving a rate of 70.7% (29/41) compared to 58.54% (24/41) for 16S rRNA NGS. The sensitivity and specificity of wcDNA mNGS for pathogen detection in body fluid samples were 74.07% and 56.34%, respectively, when compared to culture results.

CONCLUSION

Whole-cell DNA mNGS demonstrates significantly higher sensitivity for pathogen detection and identification compared to both cfDNA mNGS and 16S rRNA NGS in clinical body fluid samples, particularly those associated with abdominal infections. However, the compromised specificity of wcDNA mNGS highlights the necessity for careful interpretation in clinical practice.

Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples

Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens.

Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection

BACKGROUND

Acute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections (URIs) is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential to overcome several limitations of other methods. In addition, RNA-seq may reveal novel host-response biomarkers for development of future diagnostic assays that distinguish bacterial from viral infections. There are however no available RNA-seq datasets of pediatric AS that provide a comprehensive view of both pathogen etiology and host immune response.

METHODS

Here, we performed untargeted RNA-seq (metatranscriptomics) of nasopharyngeal samples from 221 children with AS and performed a comprehensive analysis of pathogen etiology and the impact of bacterial and viral infections on host immune responses. Accuracy of RNA-seq-based pathogen detection was evaluated by comparison with culture tests for three common bacterial pathogens and qRT-PCR tests for 12 respiratory viruses. Host gene expression patterns were explored to identify potential host responses that distinguish bacterial from viral infections.

RESULTS

RNA-seq-based pathogen detection showed high concordance with culture or qRT-PCR, showing 87%/81% sensitivity (sens) / specificity (spec) for detecting three AS-associated bacterial pathogens, and 86%/92% (sens/spec) for detecting 12 URI-associated viruses, respectively. RNA-seq also detected an additional 22 pathogens not tested for clinically and identified plausible pathogens in 11/19 (58%) of cases where no organism was detected by culture or qRT-PCR. We reconstructed genomes of 196 viruses across the samples including novel strains of coronaviruses, respiratory syncytial virus, and enterovirus D68, which provide useful genomic data for ongoing pathogen surveillance programs. By analyzing host gene expression, we identified host-response signatures that differentiate bacterial and viral infections, revealing hundreds of candidate gene biomarkers for future diagnostic assays.

CONCLUSIONS

Our study provides a one-of-kind dataset that profiles the interplay between pathogen infection and host responses in pediatric AS and URI. It reveals bacterial and viral-specific host responses that could enable new diagnostic approaches and demonstrates the potential of untargeted RNA-seq in diagnostic analysis of AS and URI.

DNA metabarcoding and its potential in microbial risk assessment in waste sorting plants

Exposure to hazardous microorganisms during waste handling is a potential health concern. Molecular biological techniques provide means of profiling the microbial community at high taxonomic resolution, allow the identification of critical human pathogens on the species level and thereby aid the risk assessment of work tasks. The present study used high-throughput sequencing to characterise the microbiome in personal full-shift air samples collected at contemporary waste sorting plants (WSPs) and identified large variations in community composition within (alpha diversity) and between (beta diversity) WSPs. Seasonality did not contribute to differences in the community composition. Cladosporium sp. was dominant among fungi, whereas Aerococcus sp. was dominant among bacteria. The personal air-samples contained potential human pathogens, such as Aspergillus sp., Fusarium sp. and Enterobacteriaceae, that encompass strains with the potential to develop drug-resistance. This study provided characterization of the microbial community composition of personal bioaerosol samples and provided evidence for the occurrence of potential human pathogens in contemporary waste sorting plants. Furthermore, this study highlighted the potential of microbial metabarcoding to detect critical human pathogens that may be encountered in working environments.

Clinical Analyses of 4 Cases of Microsporidial Keratoconjunctivitis

OBJECTIVE

To report four cases of microsporidial keratoconjunctivitis (MKC) from The Affiliated Eye Hospital of Nanjing Medical University (from May 2023 to October 2024) and to aid ophthalmologists in diagnosing and treating MKC, as MKC has been increasingly reported in Asian healthy individuals but not much in Mainland China.

METHODS

Four patients with MKC were studied. Demographic information, symptoms, and clinical data were collected. Diagnosis involved ophthalmic examinations, corneal scraping microscopy (including Giemsa staining, modified Ziehl-Neelsen staining, Calcofour white staining), bacterial and fungal cultures, and metagenomic next-generation sequencing (mNGS). Treatment included various topical medications like polyhexamethylene biguanide (PHMB), fluconazole, tacrolimus, sodium hyaluronate, and systemic medication such as albendazole.

RESULTS

Three cases were caused by Encephalitozoon hellem proved by mNGS. Patients had symptoms like eye redness, swelling, pain, foreign body sensation, and vision loss. Risk factors included improper contact lens - wearing habits, contact with birds, or exposure to potentially contaminated environments. All patients showed improvements after treatment, with 3 cases cured and 1 case improved.

CONCLUSION

MKC is a unilateral, acute, non-purulent ocular surface infectious disease. Clinicians should be more aware of it. Diagnosis depends on recognizing clinical signs, exploring risk factors, and laboratory tests. There is no consensus on treatment, but combined topical and systemic anti-protozoal drugs showed good results. Further large-scale validation is needed. Relevant departments should strengthen water source management, and patients should pay attention to personal hygiene.

Systemic and localized infections in humans caused by Paenibacillus: a case report and literature review

BACKGROUND

As opportunistic pathogens, Paenibacillus organisms rarely induce human infections. This research paper details the clinical manifestations, treatment, and prognosis of an intraocular infection caused by Paenibacillus in a 43-year-old male patient.

CASE PRESENTATION

In this case, the patient initially presented with persistent ocular redness and a sensation of foreign bodies following trauma surgery. Upon admission, we performed intraocular fluid metagenomic next generation sequencing (mNGS) testing and systemic blood sampling for infection-related assessments. The results revealed a localized ocular infection with Paenibacillus organisms. Consequently, the patient received daily levofloxacin injections (500 mg) and clindamycin (300 mg) for systemic anti-infective therapy, along with subconjunctival injections of gentamicin (2 WIU) and dexamethasone (5 mg) for topical application. The infection was effectively managed, and their ocular symptoms showed improvement during the treatment course.

CONCLUSIONS

We conducted a comprehensive review of previously reported cases involving Bacillus-like organisms causing human infections, exploring mechanisms, diagnostic approaches, and treatment strategies.

Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol

Introduction

Infections with protozoan parasites associated with the consumption of fresh produce is an on-going issue in developed countries but mitigating the risk is hampered by the lack of adequate methods for their detection and identification.

Materials and methods

We developed a metagenomic next-generation sequencing (mNGS) assay using a MinION sequencer for the identification of parasites in intentionally contaminated lettuce to achieve a more accurate and rapid method than the traditional molecular and microscopy methods commonly used for regulatory purposes. Lettuce (25 g) was spiked with varying numbers of Cryptosporidium parvum oocysts, and microbes washed from the surface of the lettuce were lysed using the OmniLyse device. DNA was then extracted by acetate precipitation, followed by whole genome amplification. The amplified DNA was sequenced by nanopore technology and validated with the Ion Gene Studio S5, and the generated fastq files raw reads were uploaded to the CosmosID webserver for the bioinformatic identification of microbes in the metagenome. To demonstrate the ability of the procedure to distinguish other common food and waterborne protozoan parasites, lettuce was also spiked with C. hominis, C. muris, Giardia duodenalis and Toxoplasma gondii individually or together.

Results

The efficient lysis of oocysts and cysts was a prerequisite for the sensitive detection of parasite DNA and was rapidly achieved within 3 min. Amplification of extracted DNA led to the generation of 0.16-8.25 μg of DNA (median = 4.10 μg), sufficient to perform mNGS. Nanopore sequencing followed by bioinformatic analysis led to the consistent identification of as few as 100 oocysts of C. parvum in 25 g of fresh lettuce. Similar results were obtained using the Ion S5 sequencing platform. The assay proved useful for the simultaneous detection of C. parvum, C. hominis, C. muris, G. duodenalis and T. gondii.

Discussion

Our metagenomic procedure led to the identification of C. parvum present on lettuce at low numbers and successfully identified and differentiated other protozoa either of the same genus or of different genera. This novel mNGS assay has the potential for application as a single universal test for the detection of foodborne parasites, and the subtyping of parasites for foodborne outbreak investigations and surveillance studies.

Antimicrobial strategies of lower respiratory tract infections in immunocompromised patients based on metagenomic next-generation sequencing: a retrospective study

BACKGROUND

Immunocompromised patients with Lower Respiratory Tract Infections (LRTI) frequently encounter a diverse range of pathogenic infections, characterized by rapid disease progression and significant mortality rates due to reckless or excessive utilization of antibiotics. Therefore, it is crucial to promptly and accurately identify the causative microorganisms for pathogen diagnosis and clinical decision-making. The objective of this study is to evaluate the clinical applicability of metagenomic next-generation sequencing (mNGS) in the diagnosis and management of LRTI, as well as its impact on empirical antibacterial therapy for patients with varying immune statuses.

METHODS

We conducted a comparative analysis of positivity rate, detection accuracy, pathogen spectrum, duration of treatment (DOT), and antibiotic management in a cohort of 283 patients diagnosed with lower respiratory tract infections.

RESULTS

The positive detection rate was higher in mNGS compared to conventional culture in both immunocompetent group (89.92% vs. 28.57%, P < 0.001) and immunocompromised group (84.44% vs. 33.33%, P < 0.001). The antibiotic escalation in the immunocompromised group was more frequent than that in the immunocompetent group (49.00% vs. 31.00%, P = 0.018), but no difference was observed for antibiotic de-escalation (20.00% vs. 15.00%, P = 0.458).

CONCLUSIONS

The application of mNGS can significantly enhance the pathogen detection rate and optimize antimicrobial drug management in immunocompromised patients with LRTI.

Exploring the role of gut microbiota in colorectal liver metastasis through the gut-liver axis

Colorectal liver metastasis (CRLM) represents a major therapeutic challenge in colorectal cancer (CRC), with complex interactions between the gut microbiota and the liver tumor microenvironment (TME) playing a crucial role in disease progression via the gut-liver axis. The gut barrier serves as a gatekeeper, regulating microbial translocation, which influences liver colonization and metastasis. Through the gut-liver axis, the microbiota actively shapes the TME, where specific microbial species and their metabolites exert dual roles in immune modulation. The immunologically "cold" nature of the liver, combined with the influence of the gut microbiota on liver immunity, complicates effective immunotherapy. However, microbiota-targeted interventions present promising strategies to enhance immunotherapy outcomes by modulating the gut-liver axis. Overall, this review highlights the emerging evidence on the role of the gut microbiota in CRLM and provides insights into the molecular mechanisms driving the dynamic interactions within the gut-liver axis.

Hybrid Capture-Based Sequencing Enables Highly Sensitive Zoonotic Virus Detection Within the One Health Framework

Hybrid capture-based target enrichment prior to sequencing has been shown to significantly improve the sensitivity of detection for genetic regions of interest. In the context of One Health relevant pathogen detection, we present a hybrid capture-based sequencing method that employs an optimized probe set consisting of 149,990 probes, targeting 663 viruses associated with humans and animals. The detection performance was initially assessed using viral reference materials in a background of human nucleic acids. Compared to standard metagenomic next-generation sequencing (mNGS), our method achieved substantial read enrichment, with increases ranging from 143- to 1126-fold, and enhanced detection sensitivity by lowering the limit of detection (LoD) from 103-104 copies to as few as 10 copies based on whole genomes. This method was further validated using infectious samples from both animals and humans, including bovine rectal swabs and throat swabs from SARS-CoV-2 patients across various concentration gradients. In both sample types, our hybrid capture-based sequencing method exhibited heightened sensitivity, increased viral genome coverage, and more comprehensive viral identification and characterization. Our method bridges a critical divide between diagnostic detection and genomic surveillance. These findings illustrate that our hybrid capture-based sequencing method can effectively enhance sensitivity to as few as 10 viral copies and genome coverage to >99% in medium-to-high viral loads. This dual capability is particularly impactful for emerging pathogens like SARS-CoV-2, where early detection and genomic characterization are equally vital, thereby addressing the limitations of metagenomics in the surveillance of emerging infectious diseases in complex samples.

Metagenomic next-generation sequencing identifies native valve Aspergillus fumigatus endocarditis with cerebral involvement: a case report

Aspergillus endocarditis is a rare but highly fatal condition, particularly in immunocompromised patients. This case report describes a 74-year-old male with native valve Aspergillus fumigatus endocarditis and intracranial infection. Diagnosis was complicated by atypical presentation and negative blood cultures, but metagenomic next-generation sequencing (mNGS) enabled rapid identification of the pathogen. This case is notable for being the first to document Aspergillus fumigatus endocarditis with cerebral involvement confirmed by mNGS, highlighting the importance of early diagnosis and advanced diagnostic tools in improving outcomes.

A review of neural networks for metagenomic binning

One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.

Clinical application of acute Q fever -induced systemic capillary leak syndrome in a patient by using metagenomic next-generation sequencing: a case report and literature review

INTRODUCTION

Query fever (Q fever), a zoonotic disease, caused by Coxiella burnetii, is an infectious disease that has long been considered a rare and regionally restricted disease. It can be responsible for endocarditis and endovascular infections. Systemic capillary leak syndrome (SCLS), a rare disease of unknown etiology that most commonly develops in adults 50-70 years of age, is diagnosed clinically based on a characteristic symptomatic triad of hypotension, hemoconcentration (elevated hemoglobin or hematocrit), and serum hypoalbuminemia resulting from fluid extravasation. Although Q fever has increasingly been recognized and reported in recent years, the treatment of Q fever complicated by SCLS, with an etiological diagnosis aided by metagenomic next-generation sequencing (mNGS), remains uncommon.

CASE PRESENTATION

This report describes a case of acute Q fever with concurrent SCLS in a 54-year-old male who worked in a slaughterhouse. The patient presented with fever, chest tightness, and shortness of breath, accompanied by severe headache. His condition rapidly deteriorated, leading to acute fever, generalized weakness, and hypotension. Due to respiratory failure and shock, he was admitted to the intensive care unit (ICU) for treatment. Despite empirical antibiotic therapy along with fluid resuscitation, his blood pressure continued to decline, and metabolic acidosis and respiratory distress worsened. As his condition failed to improve, tracheal intubation was performed. mNGS detected both Coxiella burnetii in his BALF and blood samples. Based on the mNGS results, he was started on doxycycline, alongside penicillin antibiotics, vasopressors, and continuous renal replacement therapy (CRRT). The patient's condition gradually improved, and he was discharged home after 12 days of treatment. At his 90-day follow-up, he had nearly fully recovered to his pre-illness status.

CONCLUSIONS

mNGS plays a crucial role in assisting the diagnosis of Q fever, which enables the timely treatment of the underlying disease triggering SCLS. This, combined with restrictive fluid resuscitation strategies, is essential for improving patient outcomes.

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.

Role of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis, a prospective cohort study in sepsis patients

PURPOSES

Sepsis caused great clinical burden all over the world. This study clarified the value of plasma metagenomic next-generation sequencing (p-mNGS) and blood cell mNGS (bc-mNGS) in sepsis diagnosis and evaluation.

METHODS

One hundred and fourty-seven blood samples were collected from sepsis patients who met sepsis 3.0 criteria. Blood culture (BC), qPCR, p-mNGS, bc-mNGS and necessary routine assays were conducted. Taking BC and qPCR as reference, diagnosis performance of p-mNGS and bc-mNGS was analyzed. Blood transcriptome was conducted to evaluate the immunological response of patients in groups with different p/bc-mNGS results. Impact of antibiotic use on different methods was also analyzed.

RESULTS

The p-mNGS demonstrated a sensitivity of 100% for bacteria/fungi and 97% for viruses, which was higher than bc-mNGS (88% for bacteria and fungi, 71% for viruses). However, bc-mNGS showed higher concordance with BC results, which indicated that co-mNGS (p-mNGS plus bc-mNGS) protocol increased sensitivity and was helpful to justify viable blood pathogens in sepsis patients. This study showed that p-mNGS(+) & bc-mNGS(+) samples represented more activated immunity response (low expression of interferon-induced genes and high expression of JAK-STAT pathway genes), poorer clinical laboratory indicators (higher Sequential Organ Failure Assessment, higher procalcitonin and higher C-reactive protein) and lower survival rate. This study also proved that the use of broad-spectrum antibiotics affected much less on p/bc-mNGS diagnostic ability than on BC.

CONCLUSIONS

This research highlighted the potential value of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis patients, which will benefit the management of sepsis patients.

Metagenomic next-generation sequencing on treatment strategies and prognosis of patients with lower respiratory tract infections: A systematic review and meta-analysis

OBJECTIVES

Controversy exists regarding the benefits of metagenomic next-generation sequencing (mNGS) in lower respiratory tract infections (LRTIs). We assessed the impact of mNGS on the treatment and prognosis of LRTI patients through a systematic review and meta-analysis.

METHODS

A literature search was conducted in PubMed, Embase, and CENTRAL databases up to 19 February 2024. Studies investigating the clinical value of mNGS in patients with LRTIs were included. The Risk-of-Bias Tool for randomized controlled trials and the Newcastle-Ottawa scale for observational studies were used to assess risk of bias. Antibiotic change rates and prognostic outcomes were evaluated using random-effects analyses with 95% confidence intervals (CIs). This study is registered with PROSPERO, CRD42024509738.

RESULTS

Twelve studies were included in the meta-analysis. The use of mNGS was associated with a higher rate of antibiotic change (odds ratio, 2.47; 95% CI, 1.42-4.28; P < 0.01). Consistent findings were observed in adults, patients with severe LRTIs, and in those who underwent mNGS testing exclusively on bronchoalveolar lavage fluid. We also observed a reduction in in-hospital mortality (odds ratio, 0.49; 95% CI, 0.36-0.67; P < 0.01), though no significant impact on length of hospital stay was observed (mean difference, -1.79; 95% CI, -5.20 -1.63; P = 0.31).

CONCLUSIONS

This meta-analysis indicates that the application of mNGS may lead to changes in antibiotic prescriptions for patients with LRTIs, and might reduce the risk of mortality. However, large-scale randomized controlled clinical trials are urgently needed to validate the findings of this study.

Human Metapneumovirus: Emergence, Impact, and Public Health Significance

Human metapneumovirus (hMPV) has re-emerged as a significant respiratory pathogen in recent times and has attracted significant attention worldwide. Initially, identified in children with respiratory infections with significant impact, hMPV has been implicated for its contribution to global respiratory illness. The unique features of this virus, its origin, evolution, and epidemiological importance has been explored in this narrative review. Additionally, it discusses factors contributing to its recent recognition, including advancements in diagnostic methods, its clinical impact, and public health implications.

Presepsin, procalcitonin, interleukin-6, and high-sensitivity C-reactive protein for predicting bacterial DNAaemia among patients with sepsis

Background

Anti-infective therapy against pathogens is the key to treatment of sepsis. Metagenomic next-generation sequencing (mNGS) has higher sensitivity than blood culture. The aim of this study was to use mNGS to identify DNAaemia of pathogens and to assess the diagnostic accuracy of presepsin (PSEP), procalcitonin (PCT), interleukin-6 (IL-6), and high-sensitivity C-reactive protein (hsCRP) in differentiating between bacterial and nonbacterial infections in patients with sepsis.

Methods

This retrospective study included patients with sepsis from November 2020 to September 2022 in the Shenzhen Second People's Hospital. Blood samples were sent for blood culture and mNGS when the patients were diagnosed with sepsis. Plasma PSEP, PCT, and IL-6 levels were measured using whole blood specimens that were collected and analyzed after a diagnosis of sepsis. Area under the receiver operating characteristic curve (AUC) was used to evaluate the accuracy of PSEP, PCT, IL-6, and hsCRP for prediction of bacterial DNAaemia detected by mNGS in patients with sepsis.

Results

This study included 230 patients with sepsis. The bacterial DNAaemia rate was 53.0% [Gram-positive DNAaemia (GPD), Gram-negative DNAaemia (GND), and fungi DNAaemia rate was 18.2%, 37.8%, and 10.9%, respectively]. Among GND, Klebsiella was the most common, followed by Escherichia coli; meanwhile, the GPD were mainly Enterococcus, and Aspergillus was identified in 5 patients with sepsis. The PSEP median values were significantly higher in GND than in non-GND [GND: 1,291 pg/mL, interquartile range (IQR) 456-3,502 pg/mL; non-GND: 707 pg/mL, IQR 332-2,417 pg/mL; P=0.035]. There was no significant difference in PSEP values between GPD and non-GPD groups, or between fungi DNAaemia and non-fungi DNAaemia groups. Receiver operating characteristics analysis indicated that the best cutoff values for PSEP, PCT, IL-6, and hsCRP were 869 pg/mL, 1.14 ng/mL, 85.5 pg/mL, and hsCRP 96.2 mg/L, respectively. Logistic regression indicated that PSEP, PCT, IL-6, and hsCRP had significant predictive value for GND in patients with sepsis. The levels of PCT and IL-6 were different between patients with GPD and those with non-GPD. Only PCT levels differed significantly between fungal DNAaemia and nonfungal DNAaemia.

Conclusions

Bacterial-DNAaemia was detected in half of the patients with sepsis. PSEP, PCT, IL-6, and hsCRP demonstrated significant predictive value for GND, PCT and IL-6 levels demonstrated significant predictive value for GPD. Meanwhile, only PCT demonstrated significant predictive value for fungal DNAaemia.

The application of endoscopic debridement combined with metagenomic next-generation sequencing technology in primary spinal infections: a retrospective study

PURPOSE

Spinal endoscopy is a novel minimally invasive spinal surgery technique used in recent years to treat various degenerative spinal diseases. Metagenomic next-generation sequencing (mNGS) is a new method for identifying infectious microorganisms in infectious diseases. We aim to evaluate the application effect of combining spinal endoscopy with mNGS in diagnosing and treating spinal infections.

METHODS

The clinical data of 62 patients with suspected spinal infectious diseases admitted from January 2020 to December 2023 were retrospectively analyzed. All patients underwent spinal endoscopy to obtain tissue specimens, histopathological examination, routine bacterial culture, and mNGS sequencing. Describe the pathogenic microbial spectrum of spinal infection, and compare the differences in sensitivity (true positive rate) and specificity (true negative rate) between the two detection methods. White blood cell (WBC) erythrocyte deposition rate (ESR), C-reactive protein (CRP), visual analog scale (VAS), Japanese Orthopaedic Association (JOA) score, Oswestry Disability Index (ODI), and other clinical results were analyzed.

RESULTS

In 62 cases, mNGS, microbiological culture, serologic testing, and pathologic examination results were obtained. 49 cases of spinal infections and 13 cases of non-spinal infections were finally diagnosed clinically. Among the 49 patients with spinal infections, there were 31 cases of purulent bacterial infections, 8 cases of tuberculosis infections, and 10 cases of infections with unspecified etiological microorganisms. Among the 13 cases of non-spinal infections, there were 3 cases of spinal tumors, 6 cases of Modic changes of the endplates, and 4 cases of endplate fracture. The positive rate of microbial culture was 36.73% (18/49), and the positive rate of the mNGS test was 71.43% (35/49), which was statistically different from each other (P < 0.01). The sensitivity of the mNGS test was 71.43%, and the specificity of the mNGS test was 84.62%. At the 3-month follow-up, WBC, ESR, and CRP levels were normalized. The VAS, JOA score, and ODI of the lower back and legs at each follow-up point after surgery were significantly improved compared with those before surgery, and the difference was statistically significant (P < 0.01).

CONCLUSION

Metagenomic sequencing technology is fast, efficient, and accurate in detecting pathogenic microorganisms, and has high diagnostic value in the diagnosis and treatment of spinal infections. Spinal endoscopic debridement combined with mNGS can achieve good clinical results.

Uncovering the unseen: Metagenomic next-generation sequencing improves liver abscess diagnostics

BACKGROUND

This study retrospectively analyzed the metagenomic next-generation sequencing (mNGS) results and clinical data from patients with liver abscess (LA) to investigate the clinical value of mNGS in the diagnosis of LA.

METHODS

This retrospective observational study included patients with LA who were admitted to Peking Union Medical College Hospital (PUMCH) between April 2022 and July 2024. We comprehensively analyzed the final clinical etiological diagnosis, traditional pathogen detection through conventional microbiological testing (CMT), and mNGS results in terms of pathogen type and specimen turnaround time.

RESULTS

Among 60 patients with LA, 19 types of pathogens were identified. Using clinical etiological diagnosis as the standard, mNGS identified all pathogens, whereas CMT identified only 42.11 % of pathogens. The true-positivity rate of mNGS (86.67 %) was significantly higher than that of CMT (58.33 %; P < 0.001). The average specimen turnaround time for mNGS (57.66 h) was shorter than that for CMT (86.54 hours, P < 0.001).

CONCLUSIONS

Compared with existing CMT, mNGS offers higher true-positive rates, broader pathogen coverage, and shorter specimen turnaround time. These advantages contribute to more accurate clinical diagnosis and treatment.

Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis

Metagenomic next-generation sequencing (mNGS) has greatly improved our understanding of pathogens in infectious diseases such as pulmonary tuberculosis (PTB). However, high human DNA background (> 95%) impedes the detection sensitivity of mNGS in identifying intracellular Mycobacterium tuberculosis (MTB), posing a pressing challenge for MTB diagnosis. Therefore, there is an urgent need to improve MTB diagnosis performance in PTB patients. In this study, we optimized mNGS method for diagnosis of PTB. This led to the development of the host DNA depletion assisted mNGS (HDA-mNGS) technique, which we compared with conventional mNGS and the host DNA depletion-assisted Nanopore sequencing (HDA-Nanopore) in diagnostic performance. We collected 105 bronchoalveolar lavage fluid (BALF) samples from suspected PTB patients across three medical centers to assess the clinical performance of these methods. The results of our study showed that HDA-mNGS had the highest sensitivity (72.0%) and accuracy (74.5%) in PTB detection. This was significantly higher compared to mNGS (51.2%, 58.2%) and HDA-Nanopore (58.5%, 62.2%). Furthermore, HDA-mNGS provided an increased coverage of the MTB genome by up to 16-fold. Antibiotic resistance gene analysis indicated that HDA-mNGS could provide increased depth to the detection of Antimicrobial resistance (AMR) locus more effectively. These findings indicate that HDA-mNGS can significantly improve the clinical performance of PTB diagnosis for BALF samples, offering great potential in managing antibiotic resistance in PTB patients.

Pyogenic liver abscess and sepsis caused by mixed anaerobic bacteria in an immunocompetent adult: a case report

Background

Anaerobic bacterial communities in the digestive tract play an important role in digestive tract infections and aspiration pneumonia. However, ectopic infections originating from these communities are uncommon.

Case report

We present a rare case of a 64-year-old immunocompetent female was admitted with no significant medical history who developed a pyogenic liver abscess and sepsis caused by multiple anaerobic bacteria of digestive tract origin. Metagenomic next-generation sequencing (mNGS) detected four types of anaerobic bacteria in both peripheral blood and abscess puncture fluid. Culture confirmed the presence of three of these microorganisms. Treatment with a combination of meropenem and metronidazole resulted in the patient's subsequent recovery and discharge.

Conclusion

This report highlights the occurrence of ectopic infections caused by multiple anaerobic bacteria leading to pyogenic liver abscess and sepsis, underscoring the importance of considering anaerobic bacteria and conducting rapid comprehensive pathogen detection in clinical practice.

Clinical diagnosis of Q fever by targeted next-generation sequencing for identification of Coxiella burnetii

PURPOSE

Q fever is a zoonotic bacterial disease caused by Coxiella burnetii. Due to its variable and non-specific clinical symptoms, the disease is often overlooked and underreported. To date, the identification of C. burnetii as the causative pathogen of Q fever using targeted next-generation sequencing (tNGS) has not been previously documented.

METHODS

tNGS was performed on patients with acute fever of unknown etiology, and qPCR was confirmed for C. burnetii infection.

RESULTS

tNGS was performed on 112 patients with acute fever of unknown etiology at Peking University Third Hospital between March 27 and September 20, 2024. C. burnetii was identified in blood samples from five patients, leading to a clinical diagnosis of Q fever. These diagnoses were subsequently confirmed by qPCR at the Beijing CDC. The mean age of the patients was 39.6 years (range: 32-59 years). Although blood cultures were negative, elevated infection markers (CRP, PCT, and ferritin) and liver enzymes (ALT, AST, GGT, ALP, and LDH) were observed. No epidemiological links to Q fever were identified in these cases. All five patients were treated promptly with oral doxycycline (0.1 g twice daily for 2 weeks) and discharged in improved health.

CONCLUSIONS

tNGS is a promising and significant tool for rapidly detecting C. burnetii infection.

One-step diagnosis of infection and lung cancer using metagenomic sequencing

BACKGROUND

Traditional detection methods face challenges in meeting the diverse clinical needs for diagnosing both lung cancer and infections within a single test. Onco-mNGS has emerged as a promising solution capable of accurately identifying infectious pathogens and tumors simultaneously. However, critical evidence is still lacking regarding its diagnostic performance in distinguishing between pulmonary infections, tumors, and non-infectious, non-tumor conditions in real clinical settings.

METHODS

In this study, data were gathered from 223 participants presenting symptoms of lung infection or tumor who underwent Onco-mNGS testing. Patients were categorized into four groups based on clinical diagnoses: infection, tumor, tumor with infection, and non-infection-non-tumor. Comparisons were made across different groups, subtypes, and stages of lung cancer regarding copy number variation (CNV) patterns, microbiome compositions, and clinical detection indices.

RESULTS

Compared to conventional infection testing methods, Onco-mNGS demonstrates superior infection detection performance, boasting a sensitivity of 81.82%, specificity of 72.55%, and an overall accuracy of 77.58%. In lung cancer diagnosis, Onco-mNGS showcases excellent diagnostic capabilities with sensitivity, specificity, accuracy, positive predictive value, and negative predictive value reaching 88.46%, 100%, 91.41%, 100%, and 90.98%, respectively. In bronchoalveolar lavage fluid (BALF) samples, these values stand at 87.5%, 100%, 94.74%, 100%, and 91.67%, respectively. Notably, more abundant CNV mutation types and higher mutation rates were observed in adenocarcinoma (ADC) compared to squamous cell carcinoma (SCC). Concurrently, onco-mNGS data revealed specific enrichment of Capnocytophaga sputigeria in the ADC group and Candida parapsilosis in the SCC group. These species exhibited significant correlations with C reaction protein (CRP) and CA153 values. Furthermore, Haemophilus influenzae was enriched in the early-stage SCC group and significantly associated with CRP values.

CONCLUSIONS

Onco-mNGS has exhibited exceptional efficiencies in the detection and differentiation of infection and lung cancer. This study provides a novel technological option for achieving single-step precise and swift detection of lung cancer.

Effect of Interpretation of Positive Metagenomic Next-Generation Sequencing Reports on the Infection Diagnosis in Patients With Hematological Disorders

Background

Metagenomic next-generation sequencing (mNGS) has become a crucial diagnostic tool for infectious diseases in patients with hematological disorders. However, despite the abundant microbial information provided by positive mNGS reports, interpreting these results remains challenging due to the lack of standardized criteria.

Methods

We surveyed 92 clinicians to identify common challenges in understanding mNGS reports. Microbiologists then provided additional "report interpretation cards" (RICs) for positive mNGS results alongside original reports. The aim of using RICs was to determine whether each detected microorganism was likely cause of infection. After a 3-month period, a panel of clinical experts retrospectively reviewed 281 cases, involving 728 detected microorganisms, to assess RIC accuracy.

Results

In total, 82.6% of clinicians (76 of 92) experienced difficulties in interpreting mNGS reports. After receiving RICs, 97.8% of clinicians (90 of 92) reported satisfaction. The overall concordance rates between interpretation and adjudication in the 281 cases was 79.0% (222 of 281). In 203 cases in which multiple microorganisms were detected, 37.9% (77 of 203) and 37.4% (76 of 203) were interpreted and adjudicated as mixed infections. Among the 728 microorganisms, interpretation and adjudication revealed concordance rates of 93.9% (154 of 164), 95.7% (88 of 92), and 72.3% (339 of 469) for bacterial, fungal, and viral infections, respectively. In 68.7% of the cases (193 of 281), mNGS positively influenced pathogen diagnosis.

Conclusions

Not all microorganisms detected by mNGS are responsible for infection, and appropriate interpretation is essential. The provision of interpretations by microbiologists aids clinicians in accurately using mNGS for infection diagnosis.

Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: a prospective cohort study

OBJECTIVE

Accurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a.

METHODS

We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology.

RESULTS

The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%).

CONCLUSIONS

Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected.

The diagnosis and treatment progress of infectious endophthalmitis

Endophthalmitis is a blinding disease that may lead to permanent vision loss. The diagnosis of endophthalmitis relies on clinical findings. It is crucial to identify causative microorganisms in time for subsequent treatment and saving vision. For a long time, cultures of vitreous and/or aqueous humours have been the gold standard for the diagnosis of endophthalmitis. The development of modern molecular diagnostic techniques has brought new opportunities for identifying pathogens rapidly and improving sensitivity. Intravitreal antibiotic injection has the become standard treatment option for infectious endophthalmitis in clinical practice, however, the role and timing of pars plana vitrectomy remains controversial. Moreover, the development of new drugs for intravitreal injection and posterior segment drug delivery systems is expected to achieve the transition from invasive to non-invasive management. Thus, endophthalmitis is an ophthalmic emergency and timely diagnosis and treatment are crucial for preserving vision.

Clinical metagenomics: ethical issues

Metagenomics is increasingly used for diagnosis in hospital settings. It is useful particularly in cases of unknown aetiology, where novel or difficult-to-diagnose pathogens are suspected, and/or following unexplained disease outbreaks. In this paper, we present three use cases that draw on existing reports: one involving a patient in intensive care with encephalitis of unknown aetiology; a second case with likely infection with drug-resistant Klebsiella pneumoniae and an incidental finding of unknown relevance; and a third case situated in an unexplained outbreak of acute hepatitis in children, with severe outcomes due to co-infection. We examine each case in turn, highlighting ethical questions arising in relation to clinical issues including: disclosure to patients of untreatable disease, cost-effectiveness, the value of resistance testing, sensitivity and specificity, uncertain or unexpected findings, patient consent and data sharing. We conclude by proposing recommendations for further research and developing particular pieces of guidance to improve clinical uses of metagenomics for diagnosis.

Comparison of commercial next-generation sequencing assays to conventional culture methods for bacterial identification and antimicrobial susceptibility of samples obtained from clinical cases of canine superficial bacterial folliculitis

BACKGROUND

Bacterial identification and antimicrobial susceptibility testing is an important step in timely therapeutic decisions for canine superficial bacterial folliculitis (SBF), commonly caused by Staphylococcus pseudintermedius. Next-generation sequencing (NGS) offers the appeal of potentially expedited results with complete detection of bacterial organisms and associated resistance genes compared to culture. Limited studies exist comparing the two methodologies for clinical samples.

HYPOTHESIS/OBJECTIVES

To compare and contrast genotypic and phenotypic methods for bacterial identification and antimicrobial susceptibility from cases of canine SBF.

ANIMALS

Twenty-four client-owned dogs with lesions consistent with SBF were enrolled.

MATERIALS AND METHODS

A sterile culturette swab was used to sample dogs with SBF lesions. The swab was rinsed in 0.9 mL of sterile phosphate-buffered saline and vortexed to create a homogenous solution. Two swabs for NGS laboratories (Labs) and one swab for culture (Culture Lab) were randomly sampled from this solution and submitted for bacterial identification and antimicrobial susceptibility.

RESULTS

No statistical difference regarding turnaround time for NGS Labs compared to Culture Lab was found. NGS Lab 1 identified more organisms than NGS Lab 2 and Culture Lab, which were both statistically significant. There was no statistical difference in detection frequency for Staphylococcus spp. among all laboratories. There was poor agreement for the presence of meticillin resistance and most antimicrobials among all laboratories.

CONCLUSIONS AND CLINICAL RELEVANCE

Utilisation of NGS as a replacement for traditional culture when sampling canine SBF lesions is not supported at this time.

Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid

Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non-LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non-LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non-LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.

Retrospective analysis of 300 microbial cell-free DNA sequencing results in routine blood stream infection diagnostics

Introduction

Bloodstream infections are a critical challenge worldwide due to the slow turnaround time of conventional microbiological tests for detecting bacteremia in septic patients. Noscendo GmbH (Duisburg, Germany) has developed the CE/IVD pipeline DISQVER for clinical metagenomics testing based on cell-free DNA (cfDNA) from blood samples to address this issue.

Methods

We conducted a retrospective study to evaluate the diagnostic utility of this methodological setup in improving treatment decisions since it was introduced into our clinical setting. Between January 2021 and June 2022, the first 300 cases in which DISQVER was applied at our university hospital were collected and analyzed. The results were compared with routine microbiology test results, clinical picture, associated treatment decisions, and clinical course.

Results

Our findings demonstrate that DISQVER results where no pathogen was reported effectively ruled out bacterial bloodstream infections, whereas positive results varied in their usefulness. While the metagenomic approach proved highly valuable for detecting non-culturable and rare pathogens, its utility was limited in cases where detected microorganisms were commonly associated with the microbiota.

Discussion

Performing on-site analysis might mitigate delays resulting from logistical challenges and might help optimizing antibiotic stewardship. Once prompt results can be obtained, the relevance of incorporating molecular resistograms will become more pronounced. Further, the specific patient subgroups that most benefit from this analysis must be worked out. Guiding clinicians in identifying the infection focus based on the detected bacteria would significantly improve patient care. Lastly, evidence of filamentous fungi must be diligently followed up.

Transforming Microbiological Diagnostics in Nosocomial Lower Respiratory Tract Infections: Innovations Shaping the Future

Introduction: Nosocomial lower respiratory tract infections (nLRTIs), including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), remain significant challenges due to high mortality, morbidity, and healthcare costs. Implementing accurate and timely diagnostic strategies is pivotal for guiding optimized antimicrobial therapy and addressing the growing threat of antimicrobial resistance. Areas Covered: This review examines emerging microbiological diagnostic methods for nLRTIs. Although widely utilized, traditional culture-based techniques are hindered by prolonged processing times, limiting their clinical utility in timely decision-making. Advanced molecular tools, such as real-time PCR and multiplex PCR, allow rapid pathogen identification but are constrained by predefined panels. Metagenomic next-generation sequencing (mNGS) provides comprehensive pathogen detection and resistance profiling yet faces cost, complexity, and interpretation challenges. Non-invasive methods, including exhaled breath analysis using electronic nose (e-nose) technology, gene expression profiling, and biomarker detection, hold promise for rapid and bedside diagnostics but require further validation to establish clinical applicability. Expert Opinion: Integrating molecular, metagenomic, biomarker-associated, and traditional diagnostics is essential for overcoming limitations. Continued technological refinements and cost reductions will enable broader clinical implementation. These innovations promise to enhance diagnostic accuracy, facilitate targeted therapy, and improve patient outcomes while contributing to global efforts to mitigate antimicrobial resistance.