Zoe A. Dyson
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View article: Temporal genome dynamics of ST39 <i>Klebsiella pneumoniae</i> in a neonatal unit in Blantyre, Malawi
Temporal genome dynamics of ST39 <i>Klebsiella pneumoniae</i> in a neonatal unit in Blantyre, Malawi Open
Background Klebsiella pneumoniae ( Kpn ) is an important cause of healthcare-associated infections (HAI). In low and middle-income countries, HAI due to Kpn disproportionally affects neonates. In this study, we investigated the genomic cha…
View article: AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance
AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance Open
Antimicrobial resistance (AMR) poses a substantial threat to global public health. Whole genome sequencing is increasingly used as a core method for pathogen characterization to support AMR surveillance. As a result, a vast amount of bacte…
View article: AmpliconTyper – a tool for analysing ONT multiplex PCR data from environmental and other complex samples
AmpliconTyper – a tool for analysing ONT multiplex PCR data from environmental and other complex samples Open
Amplicon sequencing is a popular method for understanding the diversity of bacterial communities in samples containing multiple organisms as exemplified by 16S rRNA sequencing. Another application of amplicon sequencing includes multiplexi…
View article: Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing.
Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing. Open
In this study, we provide proof of concept data for amplicon sequencing of S. Typhi in wastewater which with further optimisation could be used to complement clinical surveillance data or provide data on S. Typhi presence in the absence of…
View article: Tools and challenges in the use of routine clinical data for antimicrobial resistance surveillance
Tools and challenges in the use of routine clinical data for antimicrobial resistance surveillance Open
View article: The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health Open
Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR)…
View article: EnviroAmpDesigner – a tool for designing high specificity multiplex PCR primer panels for detecting and subtyping a target organism in environmental surveillance samples
EnviroAmpDesigner – a tool for designing high specificity multiplex PCR primer panels for detecting and subtyping a target organism in environmental surveillance samples Open
Background Amplicon sequencing is a popular method for understanding the diversity of bacterial communities in environmental or similar samples as exemplified by 16S rRNA sequencing. This approach has been extended into multiplex amplicon …
View article: AmpliconTyper – tool for analysing ONT multiplex PCR data from environmental and other mixed sources
AmpliconTyper – tool for analysing ONT multiplex PCR data from environmental and other mixed sources Open
Amplicon sequencing is a popular method for understanding the diversity of bacterial communities in mixed samples as exemplified by 16S rRNA metagenome sequencing. This approach has been extended into multiplex amplicon sequencing in which…
View article: Conference report of the 2024 Antimicrobial Resistance Meeting
Conference report of the 2024 Antimicrobial Resistance Meeting Open
View article: Amplicon sequencing for Salmonella Paratyphi A detection v1
Amplicon sequencing for Salmonella Paratyphi A detection v1 Open
This protocol is for direct detection of Salmonella Paratyphi A in wastewater. The wastewater extract can be pre-screened by qPCR for possible presence of Salmonella using triplex qPCR as described in https://doi.org/10.1093/infdis/jiad427
View article: Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent <i>Salmonella</i> Typhi
Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent <i>Salmonella</i> Typhi Open
Background Typhoid fever results from systemic infection with Salmonella enterica serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccina…
View article: Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study
Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study Open
View article: The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi
The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi Open
Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi ( S . Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becomin…
View article: The TyphiNET data visualisation dashboard: Unlocking<i>Salmonella</i>Typhi genomics data to support public health
The TyphiNET data visualisation dashboard: Unlocking<i>Salmonella</i>Typhi genomics data to support public health Open
Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR)…
View article: The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi
The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi Open
Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming …
View article: Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study
Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study Open
Wellcome Trust, Bill & Melinda Gates Foundation, and National Institute for Health and Care Research (UK).
View article: Amplicon Sequencing for Genotyping S. Typhi v2
Amplicon Sequencing for Genotyping S. Typhi v2 Open
The following protocol is for amplifying and sequencing amplicons targeting Salmonella Typhi. It is primarily for use with samples that are already suspected to be positive for S. Typhi and has been designed for use with DNA extracted from…
View article: Amplicon Sequencing for Genotyping S. Typhi v2
Amplicon Sequencing for Genotyping S. Typhi v2 Open
The following protocol is for amplifying and sequencing amplicons targeting Salmonella Typhi. It is primarily for use with samples that are already suspected to be positive for S. Typhi and has been designed for use with DNA extracted from…
View article: Amplicon Sequencing for Genotyping S. Typhi v2
Amplicon Sequencing for Genotyping S. Typhi v2 Open
The following protocol is for amplifying and sequencing amplicons targeting Salmonella enterica serovar Typhi (S. Typhi). It is primarily for use with samples that are already suspected to be positive for S. Typhi and has been designed for…
View article: Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes Open
Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analys…
View article: Author response: Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Author response: Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes Open
Full text Figures and data Side by side Abstract Editor's evaluation eLife digest Introduction Methods Results Discussion Data availability References Decision letter Author response Article and author information Metrics Abstract Backgrou…
View article: Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive <i>Escherichia coli</i>
Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive <i>Escherichia coli</i> Open
Enteroinvasive Escherichia coli (EIEC) and Shigella are closely related agents of bacillary dysentery. It is widely viewed that EIEC and Shigella species evolved from E. coli via independent acquisitions of a large virulence plasmid (pINV)…
View article: Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization
Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization Open
The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spr…
View article: The rapid emergence of<i>Salmonella</i>Typhi with decreased ciprofloxacin susceptibility following an increase in ciprofloxacin prescriptions in Blantyre, Malawi
The rapid emergence of<i>Salmonella</i>Typhi with decreased ciprofloxacin susceptibility following an increase in ciprofloxacin prescriptions in Blantyre, Malawi Open
Ciprofloxacin is the first-line drug for treating typhoid fever in many high burden countries in Africa, but the emergence of non-susceptibility poses a grave challenge to public health programmes. Through enhanced surveillance as part of …
View article: Genomic epidemiology and antimicrobial resistance transmission of<i>Salmonella</i>Typhi and Paratyphi A at three urban sites in Africa and Asia
Genomic epidemiology and antimicrobial resistance transmission of<i>Salmonella</i>Typhi and Paratyphi A at three urban sites in Africa and Asia Open
Background Enteric fever is a serious public health concern. The causative agents, Salmonella enterica serovars Typhi and Paratyphi A, are frequently antimicrobial resistant (AMR), leading to limited treatment options and poorer clinical o…
View article: The genomic characterization of Salmonella Paratyphi A from an outbreak of enteric fever in Vadodara, India
The genomic characterization of Salmonella Paratyphi A from an outbreak of enteric fever in Vadodara, India Open
Salmonella enterica Typhi ( S . Typhi) and Paratyphi A ( S . Paratyphi A) are the causative agents of enteric fever, a systemic human disease with a burden of 300 000 cases per year in India. The majority of enteric fever cases are associa…
View article: Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000<i>Salmonella</i>Typhi genomes
Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000<i>Salmonella</i>Typhi genomes Open
The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which ma…
View article: Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity
Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity Open
View article: Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive<i>Escherichia coli</i>
Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive<i>Escherichia coli</i> Open
Enteroinvasive Escherichia coli (EIEC) and Shigella are closely related agents of bacillary dysentery. It is widely viewed that EIEC and Shigella species evolved from E. coli via independent acquisitions of a large virulence plasmid (pINV)…
View article: The origins of haplotype 58 (H58) <i>Salmonella enterica</i> serovar Typhi
The origins of haplotype 58 (H58) <i>Salmonella enterica</i> serovar Typhi Open
Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi ( S . Typhi) is associated with the H58 lineage, which arose comparatively recently before becoming globally dissemi…