Jeff Knaggs
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View article: An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach Open
Bedaquiline (BDQ) has only been approved for use for just over a decade and is a key drug for treating multidrug-resistant tuberculosis; however, rising levels of resistance threaten to reduce its effectiveness. Catalogues of mutations ass…
View article: An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in <i>M. tuberculosis</i> using a reproducible algorithmic approach
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in <i>M. tuberculosis</i> using a reproducible algorithmic approach Open
Objectives Bedaquiline (BDQ) has only been approved for use for a little over a decade yet is a key drug for treating multi-drug resistant tuberculosis. Rising levels of resistance threaten, however, to reduce its effec-tiveness. Catalogue…
View article: Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 <i>Mycobacterium tuberculosis</i> samples
Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 <i>Mycobacterium tuberculosis</i> samples Open
Tuberculosis remains a global health problem. Making it easier and quicker to identify which antibiotics an infection is likely to be susceptible to will be a key part of the solution. Whilst whole-genome sequencing offers many advantages,…
View article: MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis
MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis Open
US Centers for Disease Control and Prevention.
View article: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny Open
The SARS-CoV-2 genome occupies a unique place in infection biology – it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has bee…
View article: Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses Open
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has ac…
View article: Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach
Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach Open
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary m…
View article: A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology
A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology Open
Background Viral sequencing has made critical contributions to our understanding of and response to the COVID-19 pandemic, but sequencing capacity and bioinformatic expertise remain limited in many settings. This proof-of-principle study a…
View article: Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses Open
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has ac…
View article: Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis
Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis Open
View article: Repeated evolution of bedaquiline resistance in<i>Mycobacterium tuberculosis</i>is driven by truncation of<i>mmpR5</i>
Repeated evolution of bedaquiline resistance in<i>Mycobacterium tuberculosis</i>is driven by truncation of<i>mmpR5</i> Open
The antibiotic Bedaquiline (BDQ) is a key component of new WHO regimens for drug resistant tuberculosis (TB) but predicting BDQ resistance (BDQ-R) from genotypes remains challenging. We analysed a collection (n=505) of Mycobacterium tuberc…
View article: High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region Open
View article: A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics
A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics Open
The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all of which have undergone whole-genome sequenc…
View article: The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis Open
View article: Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance
Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance Open
View article: Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of <i>M. tuberculosis</i>
Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of <i>M. tuberculosis</i> Open
Drug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm. Whilst there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate it i…
View article: The 2021 WHO Catalogue of <i>Mycobacterium Tuberculosis</i> Complex Mutations Associated with Drug Resistance: A New Global Standard for Molecular Diagnostics
The 2021 WHO Catalogue of <i>Mycobacterium Tuberculosis</i> Complex Mutations Associated with Drug Resistance: A New Global Standard for Molecular Diagnostics Open
View article: Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing
Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing Open
Next generation sequencing (NGS) is a trending new standard for genotypic HIV-1 drug resistance (HIVDR) testing. Many NGS HIVDR data analysis pipelines have been independently developed, each with variable outputs and data management proto…
View article: Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice
Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice Open
Genomic analysis of cancer tissues is an essential aspect of personalized oncology treatment. Though it has been suggested that formalin fixation of patient tissues may be suboptimal for molecular studies, this tissue processing approach r…