[PDF] When Bacterial Culture Fails, Metagenomics Can Help: A Case of Chronic Hepatic Brucelloma Assessed by Next-Generation Sequencing | Semantic Scholar (2025)

The DNA extracted from the surgically-removed frozen valve tissue from a patient with suspected infective endocarditis with negative blood and valve cultures suggested an infection caused by Cardiobacterium hominis.

The data show that WMGS may be used as a diagnostic procedure to strengthen the diagnosis of IE and to obtain draft genomic sequence of the pathogen and typing information, and Neisseria meningitidis is commonly associated with meningitis and/or septicemia.

Several reports and case-series confirm that CMg is an innovative tool with which one can identify more microorganisms than with conventional methods in a single test, obtain results within hours, and tailor the antimicrobial regimen of patients, however, the cost-efficiency of CMg and its real impact on patient management are still to be determined.

An overview of current host DNA depletion approaches is presented along with explanations of their underlying principles, advantages and disadvantages and the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA is envisaged.

The removal of ‘host’ DNA by the modified enrichment protocol substantially improved bacterial detection in comparison to the other two extraction procedures and generated less distorted taxonomic profiles as compared to the original enrichment protocol.

The data show that metataxonomic analysis of frozen stool suspensions subjected to specific pre-treatments prior to DNA extractions might provide an interesting indication of bacterial resistance to stress conditions and thus of chances of survival in FMT recipients.

The shortest incubation times on the WASPLab for reliable MALDI-TOF/MS-based species identification and for the preparation of a 0.5 McFarland suspension for antimicrobial disk diffusion susceptibility testing are defined.

An overview of metagenomics methods with a discussion of computational challenges and limitations is presented and applications for strain identification of Mycobacterium tuberculosis, identification of infectious agents in cases of encephalitis, biomarkers for Inflammatory Bowel Disease, and explores the challenges of sampling the microbiome in various tissues are presented.

An etiologic bacterial diagnosis before starting antibiotic therapy is paramount; nevertheless, culture-independent methods may provide a microbiological diagnosis in those cases where antimicrobials are empirically used and when cultures remain negative.

The serum level of PIVKA-II was significantly higher in children with hepatic tumors, especially those with malignant tumors, and the combination of PIVKA-II with AFP further increased the diagnostic performance.

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This work presents 17 complete and 7 scaffolded genome assemblies of Brucella strains, which are intracellular zoonotic pathogens which cause, among other pathologies, increased rates of abortion in ruminants.

Clinical metagenomics, based on whole genome sequencing of clinical samples, could improve the diagnosis of HAP, however, many obstacles remain to be overcome, namely the turn-around time, the quantification of pathogens, the choice of antibiotic resistance determinants (ARDs), the inference of the AST from metagenomic data and the linkage between ARDs and their host.

The bacterial community diversity of the microbiota from oral and respiratory samples of intubated patients hospitalized in the intensive care unit is explored and the technical challenges that may arise while using culture-independent approaches to study these types of samples are discussed.

This study demonstrates the great potential of applying metagenomics within the clinical laboratory setting and that this can be achieved using infrastructure available to nondedicated sequencing centres.

It is demonstrated that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass.

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