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Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology – A systematic literature review

Clinical microbiology and infection, 2019-09, Vol.25 (9), p.1086-1095

2019

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Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

Antimicrobial agents and chemotherapy, 2019-01, Vol.63 (1)

2019

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Occurrence of Campylobacter spp. in Swedish calves, common sequence types and antibiotic resistance patterns

Journal of applied microbiology, 2021-06, Vol.130 (6), p.2111-2122

2021

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Adaptive evolution of engineered yeast for squalene production improvement and its genome‐wide analysis

Yeast (Chichester, England), 2021-07, Vol.38 (7), p.424-437

2021

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Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

mBio, 2017-12, Vol.8 (6), p.e01941-17

2017

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Cryptic Resistance Mutations Associated With Misdiagnoses of Multidrug-Resistant Tuberculosis

The Journal of infectious diseases, 2019-06, Vol.220 (2), p.316-320

2019

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Whole-Genome Sequencing Characterization of Virulence Profiles of Listeria monocytogenes Food and Human Isolates and In Vitro Adhesion/Invasion Assessment

Microorganisms (Basel), 2021-12, Vol.10 (1), p.62

2021

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Implementation of a high-throughput whole genome sequencing approach with the goal of maximizing efficiency and cost effectiveness to improve public health

Microbiology spectrum, 2024-04, Vol.12 (4), p.e0388523-e0388523

2024

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Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

Pathogens (Basel), 2022-05, Vol.11 (5), p.545

2022

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Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov

Microorganisms (Basel), 2022-03, Vol.10 (4), p.704

2022

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Whole-genome sequencing enables molecular characterization of non-clonal group 258 high-risk clones (ST13, ST17, ST147 and ST307) among Carbapenem-resistant Klebsiella pneumoniae from a tertiary university hospital centre in Portugal

Microorganisms (Basel), 2022-02, Vol.10 (2), p.416

2022

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Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture

BMC microbiology, 2020-05, Vol.20 (1), p.120-120, Article 120

2020

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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

Nature reviews. Microbiology, 2019-09, Vol.17 (9), p.533-545

2019

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Prediction of Minimum Inhibitory Concentrations of Antimicrobials for Neisseria gonorrhoeae Using Whole-Genome Sequencing

Methods in molecular biology (Clifton, N.J.), 2019-01, Vol.1997, p.59

2019

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Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study

The Lancet infectious diseases, 2021-11, Vol.21 (11), p.1507-1517

2021

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Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection

Clinical infectious diseases, 2022-08, Vol.75 (3), p.476-482

2022

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Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?

Clinical microbiology and infection, 2018-06, Vol.24 (6), p.604-609

2018

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Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome

The Journal of infectious diseases, 2022-04, Vol.225 (7), p.1227-1237

2022

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From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

Trends in microbiology (Regular ed.), 2018-12, Vol.26 (12), p.1035-1048

2018

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Evolution of Listeria monocytogenes in a Food Processing Plant Involves Limited Single-Nucleotide Substitutions but Considerable Diversification by Gain and Loss of Prophages

Applied and environmental microbiology, 2020-03, Vol.86 (6)

2020

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Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing

Journal of clinical microbiology, 2018-08, Vol.56 (8)

2018

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Mutational change of CTX‐M‐15 to CTX‐M‐127 resulting in mecillinam resistant Escherichia coli during pivmecillinam treatment of a patient

MicrobiologyOpen (Weinheim), 2019-12, Vol.8 (12), p.e941-n/a

2019

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Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward

Microbiology and molecular biology reviews, 2019-06, Vol.83 (2)

2019

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Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

Clinical microbiology and infection, 2021-07, Vol.27 (7), p.1036.e1-1036.e8

2021

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Time Required for Nanopore Whole-Genome Sequencing of Neisseria gonorrhoeae for Identification of Phylogenetic Relationships

The Journal of infectious diseases, 2023-11, Vol.228 (9), p.1179-1188

2023

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Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology – A systematic literature review

Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

Occurrence of Campylobacter spp. in Swedish calves, common sequence types and antibiotic resistance patterns

Adaptive evolution of engineered yeast for squalene production improvement and its genome‐wide analysis

Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

Cryptic Resistance Mutations Associated With Misdiagnoses of Multidrug-Resistant Tuberculosis

Whole-Genome Sequencing Characterization of Virulence Profiles of Listeria monocytogenes Food and Human Isolates and In Vitro Adhesion/Invasion Assessment

Implementation of a high-throughput whole genome sequencing approach with the goal of maximizing efficiency and cost effectiveness to improve public health

Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov

Whole-genome sequencing enables molecular characterization of non-clonal group 258 high-risk clones (ST13, ST17, ST147 and ST307) among Carbapenem-resistant Klebsiella pneumoniae from a tertiary university hospital centre in Portugal

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

Prediction of Minimum Inhibitory Concentrations of Antimicrobials for Neisseria gonorrhoeae Using Whole-Genome Sequencing

Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study

Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection

Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?

Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

Evolution of Listeria monocytogenes in a Food Processing Plant Involves Limited Single-Nucleotide Substitutions but Considerable Diversification by Gain and Loss of Prophages

Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing

Mutational change of CTX‐M‐15 to CTX‐M‐127 resulting in mecillinam resistant Escherichia coli during pivmecillinam treatment of a patient

Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward

Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

Time Required for Nanopore Whole-Genome Sequencing of Neisseria gonorrhoeae for Identification of Phylogenetic Relationships

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