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2025
The Global Challenge of Antimicrobial Resistance: Mechanisms, Case Studies, and Mitigation Approaches
Health Science Reports
2025
Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification
Veterinary Sciences
2025
mlstverse-web: advancing real-time identification of mycobacteria from sputum using targeted sequencing NALC-Seq
Functional & Integrative Genomics
2025
Clinical Value of Metagenomic Next-Generation Sequencing From Blood Samples to Identify Pneumocystis jirovecii Pneumonia in Patients With Human Immunodeficiency Virus
Open Forum Infectious Diseases
2024
Clinical application of metagenomic next-generation sequencing for the diagnosis of suspected infection in adults: A cross-sectional study
Medicine
2024
Pili in Mycobacterium Tuberculosis
2024
Antimicrobial Resistance: Factors to Findings
2024
Exploring the Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Unexplained Pulmonary Infection
International Journal of General Medicine
2024
Culture-Free Whole Genome Sequencing of Mycobacterium tuberculosis Using Ligand-Mediated Bead Enrichment Method
Open Forum Infectious Diseases
2024
The value of metagenomic next-generation sequencing for the diagnosis of pulmonary tuberculosis using bronchoalveolar lavage fluid
Laboratory Medicine
2024
The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study
Infectious Diseases
2024
Metagenomic next generation sequencing of bronchoalveolar lavage fluids for the identification of pathogens in patients with pulmonary infection: A retrospective study
Diagnostic Microbiology and Infectious Disease
2023
A hybridization target enrichment approach for pathogen genomics
mBio
2023
Evaluation of genetic mutations associated with phenotypic resistance to fluoroquinolones, bedaquiline, and linezolid in clinical Mycobacterium tuberculosis: A systematic review and meta-analysis
Journal of Global Antimicrobial Resistance
2022
Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures
Journal of Medical Microbiology
2022
Biomedical Translational Research
2022
Risk Factors and Outcome of Sepsis in Traumatic Patients and Pathogen Detection Using Metagenomic Next-Generation Sequencing
Canadian Journal of Infectious Diseases and Medical Microbiology
2022
mNGS for identifying pathogens in febrile neutropenic children with hematological diseases
International Journal of Infectious Diseases
2022
Metagenomic Next-Generation Sequencing Is Highly Efficient in Diagnosing Pneumocystis Jirovecii Pneumonia in the Immunocompromised Patients
Frontiers in Microbiology
2022
Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum
Frontiers in Microbiology
2022
The performance of detecting Mycobacterium tuberculosis complex in lung biopsy tissue by metagenomic next-generation sequencing
BMC Pulmonary Medicine
2022
The clinical application of metagenomic next-generation sequencing in infectious diseases at a tertiary hospital in China
Frontiers in Cellular and Infection Microbiology
2022
Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field
Frontiers in Microbiology
2022
The application of metagenomic next-generation sequencing for detection of pathogens from dialysis effluent in peritoneal dialysis–associated peritonitis 
Peritoneal Dialysis International: Journal of the International Society for Peritoneal Dialysis
2022
Optimizing liquefaction and decontamination of sputum for DNA extraction from Mycobacterium tuberculosis
Tuberculosis
2021
The Diagnostic Value of Metagenomic Next–Generation Sequencing in Lower Respiratory Tract Infection
Frontiers in Cellular and Infection Microbiology
2021
Tuberculosis Diagnosis by Metagenomic Next-generation Sequencing on Bronchoalveolar Lavage Fluid: a cross-sectional analysis
International Journal of Infectious Diseases
2020
Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis
Tuberculosis
2020
Whole genome enrichment approach for rapid detection of Mycobacterium tuberculosis and drug resistance-associated mutations from direct sputum sequencing
Tuberculosis
2020
DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples
Journal of Clinical Microbiology
2020
Analytical Performance Validation of Next-Generation Sequencing Based Clinical Microbiology Assays Using a K-mer Analysis Workflow
Frontiers in Microbiology
2020
Advances in diagnosis of Tuberculosis: an update into molecular diagnosis of Mycobacterium tuberculosis
Molecular Biology Reports
2020
Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment
Journal of Clinical Microbiology
2020
Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study
The Lancet Microbe
2020
Tuberculosis, HIV, and viral hepatitis diagnostics in eastern Europe and central Asia: high time for integrated and people-centred services
The Lancet Infectious Diseases
2020
Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis
Journal of Infection
2020
Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China
International Journal of Infectious Diseases
2020
Bead-captured Mycobacterium tuberculosis for next-generation sequencing diagnosis of uncultured tuberculosis
European Journal of Clinical Microbiology & Infectious Diseases
2020
Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes!
Clinical Chemistry
2020
Diagnosis of complication in lung transplantation by TBLB + ROSE + mNGS
Open Medicine
2019
Metagenomic Next-Generation Sequencing in Clinical Microbiology
Indian Journal of Medical Microbiology
2019
Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
BMC Genomics
2019
Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis
Infection, Genetics and Evolution
2019
Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance
Current Opinion in Microbiology
2019
HIV and Tuberculosis
2019
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes
Nucleic Acids Research
2019
Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges
Genome Medicine
2019
The Lung Microbiome
2019
Whole-Genome Sequencing of Mycobacterium tilburgii Strain MEPHI
Microbiology Resource Announcements
2019
Whole-Genome Sequencing in Relation to Resistance of Mycobacterium Tuberculosis
Acta Medica Martiniana
2019
Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles
Emerging Microbes & Infections
2019
The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid
Frontiers in Microbiology
2019
Revolutionizing Tropical Medicine
2019
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
Nature Reviews Microbiology
2018
Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics
Frontiers in Public Health
2018
Tuberculosis
2018
Molecular diagnosis of suspected tuberculosis from archived smear slides from the Balimo region, Papua New Guinea
International Journal of Infectious Diseases
2018
Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice
Clinical Infectious Diseases
2017
Genotypic characterization directly applied to sputum improves the detection of Mycobacterium africanum West African 1, under-represented in positive cultures
PLOS Neglected Tropical Diseases
2017
Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples
Journal of Clinical Microbiology
2017
Translational metagenomics and the human resistome: confronting the menace of the new millennium
Journal of Molecular Medicine
2017
Advances in Experimental Medicine and Biology
2017
Real-Time Sequencing of Mycobacterium tuberculosis: Are We There Yet?
Journal of Clinical Microbiology
2017
Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review
European Journal of Clinical Microbiology & Infectious Diseases
2017
Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action
International Journal of Infectious Diseases
2017
Advances in Experimental Medicine and Biology
2017
The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee
Clinical Microbiology and Infection
2017
Whole genome sequencing for the management of drug-resistant TB in low income high TB burden settings: Challenges and implications
Tuberculosis
2017
Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis
PLOS ONE
2017
A brief primer on genomic epidemiology: lessons learned fromMycobacterium tuberculosis
Annals of the New York Academy of Sciences
2016
Recent developments in genomics, bioinformatics and drug discovery to combat emerging drug-resistant tuberculosis
Tuberculosis
2016
Diagnostic ‘omics’ for active tuberculosis
BMC Medicine
2016
Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
Microbial Genomics
2016
Discrimination between bacterial species by ratiometric analysis of their carbohydrate binding profile
Molecular BioSystems
2016
Microbial bioinformatics 2020
Microbial Biotechnology
2016
Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology
Journal of Clinical Microbiology
2016
The implications of whole-genome sequencing in the control of tuberculosis
Therapeutic Advances in Infectious Disease
2016
Metagenomic Analysis of Sputum Microbiome as a Tool toward Culture-Independent Pathogen Detection of Patients with Ventilator-associated Pneumonia
American Journal of Respiratory and Critical Care Medicine
2016
Next-generation sequencing diagnostics of bacteremia in septic patients
Genome Medicine
2016
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Nature Methods
2016
Personalizing therapy for multidrug resistant TB: the potential of Rapid Whole Genome Sequencing
Expert Review of Anti-infective Therapy
2016
Recent and emerging innovations inSalmonelladetection: a food and environmental perspective
Microbial Biotechnology
2016
Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria
Clinical Microbiology Reviews
2016
Diagnosing tuberculosis in the 21st century – Dawn of a genomics revolution?
International Journal of Mycobacteriology
2015
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
Genome Biology
2015
Methods in Microbiology
2015
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study
The Lancet Infectious Diseases
2015
Mycobacterial DNA Extraction for Whole-Genome Sequencing from Early Positive Liquid (MGIT) Cultures
Journal of Clinical Microbiology
2015
Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples
Journal of Clinical Microbiology
2015
Diversity and disease pathogenesis in Mycobacterium tuberculosis
Trends in Microbiology
2015
Methods in Microbiology
2015
Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission
Nature Communications
2015
A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics
Clinical Microbiology Reviews
2015
Clinical value of whole-genome sequencing of Mycobacterium tuberculosis
The Lancet Infectious Diseases
2015
ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data
BMC Genomics
2015
Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
Nature Communications
2015
Advances in Tuberculosis Diagnostics
Current Tropical Medicine Reports
2015
Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data
Genome Medicine
2014
Technology comes to typing
Nature Biotechnology
2014
Translating genomics research into control of tuberculosis: lessons learned and future prospects
Genome Biology
2014
The road to drug resistance in Mycobacterium tuberculosis
Genome Biology
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