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At least 19 recordsLinked to original sources

PubMed2025

Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study.

BACKGROUND: Most clinical metagenomic studies do not provide rapid results, detect pathogens from all microbial kingdoms, or measure clinical impacts. We aimed to evaluate the feasibility, performance, and clinical impacts of a rapid pan-microbial respiratory metagenomic service for patients admitted to intensive care units (ICUs). METHODS: This was a single-centre observational study of a rapid metagenomics service that tests respiratory samples from ICU patients at Guy's and St Thomas' hospitals, London, UK, between Dec 5, 2023, and April 12, 2024. Testing used a previously published pan-microbial metagenomics workflow, which simultaneously detects bacteria, fungi, and DNA and RNA viruses; provides same-day preliminary results after 2 h; and provides final results after 24 h. Patients were included if they were aged 18 years or older, admitted to the ICU, had confirmed respiratory failure requiring supplemental oxygen or advanced airway support, and had at least one of the following: (1) clinical suspicion of lower respiratory tract infection based on clinical, biochemical, or radiological findings, (2) sepsis of unknown origin, and (3) concern from an intensive care physician regarding inflammatory pathology. Patients with a suspected or confirmed containment level three organism were excluded. The outcome was performance characteristics of the metagenomic test compared with routine diagnostic testing, detection of additional pathogens by metagenomics, change in antimicrobial prescribing within 24 h of testing, and initiation of immunomodulation. FINDINGS: We processed 114 samples (1-5 per day) from 74 patients (39 [53%] female and 35 [47%] male). 107 (94%) of 114 samples passed quality control, of which 101 (94%) provided same-day preliminary results. Bacteria were detected in 45 (43%) of 104 tested specimens, fungal organisms in 17 (16%) of 104 tested specimens, and viruses in 28 (34%) of 83 tested specimens. Sensitivity in lower respiratory tract samples after 24 h was 97% (95% CI 87-100) for bacteria, 89% (65-99) for fungi, and 89% (71-98) for viruses, with only one false positive for bacteria. Metagenomics identified 42 pathogens not detected by other tests in 32 (30%) of 107 samples. Antimicrobial therapy was changed after metagenomic results from 30 (28%) of 107 samples: 22 (21%) were de-escalated and eight (7%) were escalated. Metagenomics contributed to the initiation of immunomodulation in 15 (20%) of 74 patients for a range of inflammatory conditions. Pathogens with clinical significance to local infection control or national public health were found in ten (14%) of 74 patients, including three invasive Group A streptococci, two parvovirus B19, and one each of HIV-1, measles virus, Mycobacterium tuberculosis, Neisseria meningitidis, and Mycoplasma pneumoniae. INTERPRETATION: Respiratory metagenomics for ICU patients showed good performance and turnaround time, and diverse clinical and public health benefits. This ability to inform both personalised patient therapy and infectious disease surveillance needs evaluation in multicentre studies. FUNDING: None.

Humans↗

PubMedDate not supplied

Isoenzyme analysis of Entamoeba histolytica for evaluation of pathogenicity: detection of zymodeme XIX in South America.

Authors report the results of the isoenzyme analysis of strains of Entamoeba histolytica isolated from international travellers. This recently developed method allows the detection of pathogenic strains by evaluating the electrophoretic mobility of cytoplasmic enzymes and was proved to be more reliable and quickly feasible than previous ones. The experience reported refers to three strains isolated from travellers coming from Ecuador, Brazil and Indonesia, respectively; the zymodeme XIX (in accordance with the Sargeaunt's classification) was identified in all the three cases. This zymodeme has been first detected in 1981 and should currently be considered rare; moreover, it has never been previously reported from the Americas.

Amebiasis↗

PubMed2026

VisPan: real-time visualisation of multiplex amplicon-based sequencing panels for rapid syndromic surveillance and pathogen detection.

MOTIVATION: Infectious diseases persist as a major global public health challenge. Diverse factors, including climate change, globalization, deforestation, human-animal interactions, lifestyle choices, and various biological factors, can contribute to their emergence and reemergence. Rapid detection and characterization of (re)emerging pathogens are therefore critical for effective outbreak management and for enhancing our understanding of epidemics by monitoring the transmission, spread, evolution, and genomics of pathogens. In this context, next-generation sequencing technologies (NGS), particularly long-read platforms such as Oxford Nanopore Technologies (ONT), have opened new avenues for real-time pathogen monitoring. However, the bioinformatics bottleneck remains a challenge, emphasizing the need for efficient, accessible, and user-friendly analysis tools. RESULTS: Here, we present a tool adapted from the RAMPART software that enables real-time data visualisation of multiplex PCR syndromic panels combined with Oxford Nanopore sequencing. This real-time analysis enables rapid pathogen detection, from raw data acquisition to taxonomic assignment, within minutes. The interface offers dynamic visual tracking of the sequencing run and amplicon coverage, facilitating immediate insights during diagnostic workflows. Validation experiments confirmed the system's reliability, accurately identifying all pathogens present in complex clinical or environmental samples. This tool provides an integrated, user-friendly solution for genomic pathogen surveillance in field or clinical settings.

Software↗

PubMed2026

Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.

UNLABELLED: Metagenomic next-generation sequencing (mNGS) in the infectious disease diagnostic space has been gaining traction and is popular for aiding in the diagnosis of central nervous system infections. However, many challenges and obstacles remain in making this technology a gold standard for infectious disease diagnostic testing. One major challenge is being able to distinguish between the clinically relevant organisms from background contamination. We performed a validation study for mNGS on cerebrospinal fluid (CSF) that utilized positive clinical samples and contrived samples that incorporated a bioinformatics pipeline that can better distinguish between background contamination and clinically relevant organisms and used a three-tiered reporting algorithm meant to decrease the inherent subjectivity that comes with interpreting and reporting data from clinical metagenomic sequencing. The validation of this assay and category-based reporting pipeline revealed an overall concordance of 91.8%, with a sensitivity of 100% and a specificity of 72.4%. In addition, we improved the detection of clinically relevant RNA viruses to almost 100% in the CSF by modifying the wet lab processing of the sample. This bioinformatics pipeline with a category-based reporting algorithm will provide more confidence in reporting microorganisms detected with this technology, mNGS, and improving patient care. IMPORTANCE: Metagenomic next-generation sequencing (mNGS) can offer a broad, unbiased approach for the detection of infectious pathogens and has shown promise in diagnosing central nervous system infections. Despite its potential, clinical implementation remains limited by challenges in distinguishing clinically relevant organisms from background contamination. This study validated an mNGS assay for cerebrospinal fluid that incorporates an optimized bioinformatics pipeline with a three-tiered reporting algorithm designed to reduce subjectivity and enhance diagnostic confidence. The assay also has improved detection of clinically relevant RNA viruses through modified wet-lab processing. These findings support the clinical utility of a structured, category-based reporting approach for mNGS, advancing its reliability as a diagnostic tool in infectious disease testing.

Metagenomics↗

PubMed2026

Microbial DNA analysis of paired blood-bronchoalveolar lavage fluid in post-HSCT patients with pneumonia implying application conditions of blood as a surrogate in pathogen detection.

BACKGROUND: Blood testing aids pneumonia diagnosis, but its effectiveness varies. Given the invasiveness of bronchoalveolar lavage fluid (BALF) sampling versus blood testing's simplicity, this study investigates when blood can reliably substitute for BALF in detecting microbial presence, especially for pathogens. RESULTS: Metagenomic sequencing was performed on paired BALF-blood samples from 21 post-HSCT immunocompromised (ICP) and 21 immunocompetent (ICT) patients. The ICP cohort was expanded to 62 for biomarker validation. Host responses were profiled via metatranscriptomics (30 BALF samples). Microbial alpha and beta diversity differed significantly between blood and BALF in ICP, but not ICT, patients. ICP patients' BALF contained a greater diversity and abundance of microbes. A higher proportion of microbial DNA sequences in ICP patients' blood was also present in their BALF, suggesting a potentially more permeable alveolar-capillary barrier. Related genes (e.g., NABA CORE MATRISOME, extracellular matrix organization, cell-cell adhesion) were downregulated. Upregulated pathways like VEGFA-VEGFR2 signaling and Rho GTPases suggested increased vascular permeability. In ICP patients, 419 microbial sequences in blood indicated their presence in the lower respiratory tract with > 70% certainty. CONCLUSION: Host immune status significantly influences blood-BALF microbial diversity differences. Shared blood-BALF microbial DNA sequences show potential for aiding pneumonia pathogen diagnosis, offering a novel biomarker identification approach.

Humans↗

PubMed2026

Portable metagenomics for preventive surveillance and outbreak control in livestock and poultry: Pathogen detection, resistome profiling, and antimicrobial stewardship.

Conventional diagnostics for livestock and poultry outbreaks commonly rely on culture or targeted PCR panels, which may be too slow or too narrow to guide early control decisions. Portable metagenomics, particularly real-time nanopore sequencing, offers a route to broad pathogen detection, antimicrobial-resistance gene profiling, and outbreak investigation within an integrated workflow. This implementation-focused review evaluates how near-point-of-care metagenomics may support preventive veterinary medicine through earlier detection, surveillance, cohorting, biosecurity decisions, and antimicrobial stewardship. We synthesize sample-to-answer workflows for enteric and respiratory disease in food-producing animals, including sampling, nucleic-acid extraction, host depletion or target enrichment, library preparation, sequencing, bioinformatics, quality control, and interpretation. Applications in calf diarrhea, bovine respiratory disease, poultry outbreaks, mastitis, and resistome monitoring are considered alongside the central limitation that detection alone does not establish causation. Pathogen and resistance-gene signals must therefore be interpreted with clinical signs, lesions, epidemiology, controls, and confirmatory testing. We also propose a minimum reporting checklist, intended as a practical framework rather than a validated consensus standard. Portable metagenomics is not a replacement for conventional diagnostics, but appropriately validated workflows can reduce uncertainty during time-sensitive outbreaks and support more judicious antimicrobial use.

Animals↗

PubMed2026

TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score. RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest. AVAILABILITY AND IMPLEMENTATION: Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.

Software↗

PubMed2025

nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets.

SUMMARY: nf-UnO is a pipeline implemented in Nextflow to identify novel pathogens from metagenomic shotgun sequencing of epidemiologically related foodborne outbreak specimens. nf-UnO uses MIDAS2, metagenomic co-assembly, multiple binning programs, and read mapping to metagenomically assembled genomes to detect potential etiological agents found in common across outbreak specimens. AVAILABILITY AND IMPLEMENTATION: https://github.com/uel3/nf-UnO.

Metagenomics↗

PubMed1975

Vibrio parahaemolyticus -- a marine pathogen detected in South African coastal waters.

Vibrio parahaemolyticus has been detected in the Natal and Eastern Cape costal water of South Africa. As a proven cause of gastro-enteritis or a potential pathogen to humans, it is an organism of importance to public health. Outlines of the history, pathogenicity and identification are given, as well as the results of the local investigation of this organism.

Culture Media↗

PubMed1992

[Infections with Borrelia burgdorferi in Würzburg blood donors: antibody prevalence, clinical aspects and pathogen detection in antibody positive donors].

The prevalence of antibodies against Borrelia burgdorferi, the etiologic agent of Lyme borreliosis, was determined in a group of blood donors from the Würzburg area (Southern Germany). 26 of 472 donors (5.5%) tested positive in a hemagglutination test. When performing immunoblots only 13 donors (2.7%) gave rise to B. burgdorferi-specific antibodies. 9 of them were examined in more detail by anamnesis, physical examination, determination of inflammation parameters of the blood and polymerase chain reaction (PCR) analysis of urine. All persons were asymptomatic for Lyme borreliosis. One of 4, who remembered a tick bite, actually had suffered from an erythema migrans 5 years ago. Another one had been affected by fever, headaches and pains in the limbs, arthralgia and motoric disorder in both hands 6 months before examination. Analysis of the blood did not provide any evidence of an acute infection. In the urine of 2 donors we detected B. burgdorferi-specific DNA by PCR. No seroconversion due to blood transfusion could be observed, when 9 recipients of blood products provided by the 13 seropositive donors were serologically reexamined. PCR analysis of urine samples of 5 recipients was also negative.

Antibodies, Bacterial↗

PubMed1989

[Microscopy procedures for direct pathogen detection in Lyme borreliosis].

Dark-field microscopy, fuchsin stain and Fontana silver stain were used for a rapid detection of spirochaetes in fresh materials from patients with Lyme-borreliosis. The spirochaetes were shown to be present in 2 cerebrospinal fluids, 2 synovial fluids and in one brain cyst fluid. It is pointed out that these techniques require further improvement and optimization.

Bacteriological Techniques↗

PubMed1991

[Isolation of enteropathogenic microorganism from patients with infection of the digestive tract during 1976 to 1988 in Tenri Hospital].

Enteropathogenic microorganisms isolated from feces of 9,393 patients with diarrhea or enteritis in our hospital between 1976 and 1988 were analyzed. As the result of the examination of 5,443 outpatients, 1,811 strains of pathogens were isolated from 1,686 cases (31.0%). Several species including Salmonella spp., Escherichia coli serotype, Vibrio parahaemolyticus, were isolated before 1978, and the incidence of pathogens was low (14.8%). For the 10-year period since 1979, the incidence markedly increased to 34.4%, and the number of pathogens isolated also increased to about twice that before 1978. The main cause of the increase was Campylobacter species. The major pathogens detected since 1979 were Campylobacter spp., E. coli serotype, Salmonella spp., V. parahaemolyticus, etc., but Rota virus, Clostridium difficile, Aeromonas spp., Vibrio fluvialis, etc. have also been detected, showing an increase in the number and diversity of the detected pathogens. As the result of the examination of 3,950 inpatients, 835 strains of pathogens were isolated from 800 cases (20.3%). The incidence of C. difficile was the highest, 423 of 800, followed by E. coli serotype, Salmonella spp., Campylobacter spp., V. parahaemolyticus and Aeromonas spp., in that order. All the inpatients from whom C. difficile was isolated manifested diarrhea or enteritis after administration of antimicrobial agents. The pathogens causing communicable disease were Salmonella spp. serovar Typhi, Salmonella spp. serovar Paratyphi A, Shigella flexneri, Shigella sonnei and Entamoeba histolytica, which were isolated from 5, 1, 3, 2 and inpatients, respectively.

Adolescent↗

PubMed1990

[Pneumonia in AIDS: pathogen spectrum and diagnostic value of various fiberoptic bronchoscopy methods for the detection of pathogens].

39 fibre-bronchoscopic examinations were performed prospectively in 29 AIDS-patients with pneumonia. Specimens were obtained from the central bronchial system with a protected brush and by suction, from the infiltrated peripheral area by catheter suction, protected brush, bronchoalveolar lavage (BAL) and transbronchial biopsy in randomized order. In patients with non-bacterial pneumonia, pneumocystis carinii (n = 20) was the most frequent pathogen. In this group BAL had a significantly higher rate of pathogen detection than other techniques. In patients with bacterial pneumonia (n = 10) the pathogens were found in all cases by suction from the central bronchial system. Fibre-bronchoscopy in patients with AIDS and pneumonia should include specimens from the central bronchial system and a bronchoalveolar lavage.

Acquired Immunodeficiency Syndrome↗

PubMed1989

Development and testing of a synthetic oligonucleotide probe for the detection of pathogenic Yersinia strains.

A 24-base oligonucleotide probe specific for a region of the Yersinia enterocolitica virulence plasmid (pYV) associated with HEp-2 cell cytotoxicity and the Sereny reaction was constructed by using sequences flanking critical TnphoA insertions in a subcloned fragment of pYV. This probe, highly specific and sensitive for virulent yersiniae, detected pathogenic Y. enterocolitica isolates in artificially inoculated foods.

Base Sequence↗

PubMed1989

Cryptosporidiosis in white patients in South Africa.

From January to December 1987, faecal specimens received from 3186 white children and adults with diarrhoea were examined for the presence of cryptosporidial oocysts. They were found in 129 patients, an incidence of 4.1%. Most of the infections were in children less than 5 years of age, giving an incidence of 6.2% in this age group. Cryptosporidium was usually the only pathogen detected, additional pathogens being identified in only 19 cases. A marked seasonal increase in incidence was seen in 107 cases (82.9%) between January and May, that is in late summer and early autumn in South Africa.

Adolescent↗

PubMed1992

Detection of pathogenic Yersinia enterocolitica by polymerase chain reaction and digoxigenin-labeled polynucleotide probes.

Yersinia enterocolitica is widespread in nature, but only a few bioserotypes are involved in human infections. Pigs are considered to be the major reservoirs of pathogenic strains. It is essential to have an accurate and rapid method for the detection of pathogenic yersiniae. To achieve this objective, 19-base synthetic oligonucleotide primers were used in a polymerase chain reaction (PCR) to detect the ail gene (which is conserved only in pathogenic strains) in strains of Y. enterocolitica and related species originating from pigs or pork products. Digoxigenin-labeled probes derived from the ail, inv, and yst genes were also evaluated on these strains. The PCR amplified a 273-bp fragment of the ail gene involved in eukaryotic cell invasion and serum resistance. The PCR detected template DNA only in strains of Y. enterocolitica traditionally classified as human pathogens but not in biotype 1A strains and related species. Other members of the family Enterobacteriaceae were also negative for the target gene. The digoxigenin-labeled ail probe gave identical results to the PCR. By use of this nonisotopic method, inv-homologous DNA was detected only among yersiniae, except for Y. ruckeri. Although all pathogenic serotypes of Y. enterocolitica were positive for the heat-stable enterotoxin yst gene, two strains of biotype 1A, one Y. intermedia strain, and six other species of the Enterobacteriaceae were also positive. Our results support the notion that pigs constitute an important reservoir of pathogenic Y. enterocolitica and that the inv-homologous sequence is Yersinia specific.

Bacteria↗

PubMed2025

Inferring the sensitivity of wastewater metagenomic sequencing for early detection of viruses: a statistical modelling study.

BACKGROUND: Metagenomic sequencing of wastewater (W-MGS) can in principle detect any known or novel pathogen in a population. We aimed to quantify the sensitivity and cost of W-MGS for viral pathogen detection by jointly analysing W-MGS and epidemiological data for a range of human-infecting viruses. METHODS: In this statistical modelling study, we analysed sequencing data from four studies of untargeted W-MGS to estimate the relative abundance of 11 human-infecting viruses. Corresponding prevalence and incidence estimates were obtained or calculated from academic and public health reports. We combined these estimates using a hierarchical Bayesian model to predict relative abundance at set prevalence or incidence values, allowing comparison across studies and viruses. These predictions were then used to estimate the sequencing depth and concomitant cost required for pathogen detection using W-MGS with or without use of a hybridisation capture enrichment panel. FINDINGS: After controlling for variation in local infection rates, relative abundance varied by orders of magnitude across studies for a given virus. For instance, a local SARS-CoV-2 weekly incidence of 1% corresponded to a predicted SARS-CoV-2 relative abundance ranging from 3·8 × 10-10 to 2·4 × 10-7 across studies, translating to orders-of-magnitude variation in the cost of operating a system able to detect a SARS-CoV-2-like pathogen at a given sensitivity. Use of a respiratory virus enrichment panel in two studies greatly increased predicted relative abundance of SARS-CoV-2, lowering yearly costs by 27-fold (from US$7·87 million to $287 000) and 29-fold (from $1·98 million to $69 100) for a system able to detect a SARS-CoV-2-like pathogen before reaching 0·01% cumulative incidence. INTERPRETATION: The large variation in viral relative abundance after controlling for epidemiological factors indicates that other sources of inter-study variation, such as differences in sewershed hydrology and laboratory protocols, have a substantial impact on the sensitivity and cost of W-MGS. Well chosen hybridisation capture panels can greatly increase sensitivity and reduce cost for viruses in the panel, but might reduce sensitivity to unknown or unexpected pathogens. FUNDING: The Wellcome Trust, Open Philanthropy, and Musk Foundation.

Humans↗

PubMed2025

Using CRISPR for viral nucleic acid detection.

Pathogenic microorganisms, such as viruses, have threatened human health and will continue to contribute to future epidemics and pandemics, highlighting the importance of developing effective diagnostics. To contain viral outbreaks within populations, fast and early diagnosis of infected individuals is essential. Although current standard methods are highly sensitive and specific, like RT-qPCR, some can have slow turnaround times, which can hinder the prevention of viral transmission. The discovery of CRISPR-Cas systems in bacteria and archaea initially revolutionized the world of genome editing. Intriguingly, CRISPR-Cas enzymes also have the ability to detect nucleic acids with high sensitivity and specificity, which sparked the interest of researchers to also explore their potential in diagnosis of viral pathogens. In particular, the CRISPR-Cas13 system has been used as a tool for detecting viral nucleic acids. Cas13's capability to detect both target RNA and non-specific RNAs has led to the development of detection methods that leverage these characteristics through designing specific detection read-outs. Optimization of viral sample collection, amplification steps and the detection process within the Cas13 detection workflow has resulted in assays with high sensitivity, rapid turnaround times and the capacity for large-scale implementation. This review focuses on the significant innovations of various CRISPR-Cas13-based viral nucleic acid detection methods, comparing their strengths and weaknesses while highlighting Cas13's great potential as a tool for viral diagnostics.

CRISPR-Cas Systems↗