Lee S. Katz
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View article: Validation of Core and Whole-Genome Multi-Locus Sequence Typing Schemes for Shiga-Toxin-Producing E. coli (STEC) Outbreak Detection in a National Surveillance Network, PulseNet 2.0, USA
Validation of Core and Whole-Genome Multi-Locus Sequence Typing Schemes for Shiga-Toxin-Producing E. coli (STEC) Outbreak Detection in a National Surveillance Network, PulseNet 2.0, USA Open
Shiga-toxin-producing E. coli (STEC) is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Whole-genome sequencing (WGS) is a powerful tool used in public health and microbiology for the detection, surveillance, an…
View article: Genomic Characterization of <i>Escherichia coli</i> O157:H7 Associated with Multiple Sources, United States
Genomic Characterization of <i>Escherichia coli</i> O157:H7 Associated with Multiple Sources, United States Open
In the United States, Shiga toxin-producing Escherichia coli (STEC) outbreaks cause >265,000 infections and cost $280 million annually. We investigated REPEXH01, a persistent strain of STEC O157:H7 associated with multiple sources, includi…
View article: Kalamari: a representative set of genomes of public health concern
Kalamari: a representative set of genomes of public health concern Open
Kalamari is a resource that supports genomic epidemiology and pathogen surveillance. It consists of representative genomes and common contaminants. Kalamari also contains a custom taxonomy and software for downloading and formatting the da…
View article: Mashpit: sketching out genomic epidemiology
Mashpit: sketching out genomic epidemiology Open
View article: primerForge: a Python program for identifying primerpairs capable of distinguishing groups of genomes from eachother
primerForge: a Python program for identifying primerpairs capable of distinguishing groups of genomes from eachother Open
In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest f…
View article: PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training Open
As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achiev…
View article: hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling
hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling Open
The detection of antimicrobial resistance (AMR) markers directly from genomic or metagenomic data is becoming a standard clinical and public health procedure. This has resulted in the development of a number of different bioinformatic AMR …
View article: Fasten: a toolkit for streaming operations on fastqfiles
Fasten: a toolkit for streaming operations on fastqfiles Open
There are still many gaps in basic command line tools for the handling of standard file formats in the field of bioinformatics.Bioinformaticians have been able to use many tools to manipulate sequence data files in the fastq format, such a…
View article: Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics
Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics Open
Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calcula…
View article: Fasten with Pipes
Fasten with Pipes Open
Fasten is a versatile bioinformatics tool suite developed to address gaps in the manipulation of sequence data files in the fastq format. Existing tools often lack support for interleaved fastq files and Unix-style pipe file control. Faste…
View article: Reoccurring <i>Escherichia coli</i> O157:H7 Strain Linked to Leafy Greens–Associated Outbreaks, 2016–2019
Reoccurring <i>Escherichia coli</i> O157:H7 Strain Linked to Leafy Greens–Associated Outbreaks, 2016–2019 Open
Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively ass…
View article: Characterization of a Nonagglutinating Toxigenic Vibrio cholerae Isolate
Characterization of a Nonagglutinating Toxigenic Vibrio cholerae Isolate Open
Clinical cases of vibriosis are on the rise due to climate events and ocean warming (1, 2), and increased surveillance of toxigenic Vibrio cholerae strains is now more crucial than ever. While traditional phenotyping using antisera against…
View article: Genome Sequences from a Reemergence of Vibrio cholerae in Haiti, 2022 Reveal Relatedness to Previously Circulating Strains
Genome Sequences from a Reemergence of Vibrio cholerae in Haiti, 2022 Reveal Relatedness to Previously Circulating Strains Open
After more than 3 years without a documented cholera case, the Republic of Haiti reported its first resurgent case on 30 September 2022 (1–3). As of 18 February 2023, more than 27,000 cholera cases have been hospitalized and 594 deaths con…
View article: <i>Cronobacter sakazakii</i> Infections in Two Infants Linked to Powdered Infant Formula and Breast Pump Equipment — United States, 2021 and 2022
<i>Cronobacter sakazakii</i> Infections in Two Infants Linked to Powdered Infant Formula and Breast Pump Equipment — United States, 2021 and 2022 Open
Cronobacter sakazakii, a species of gram-negative bacteria belonging to the Enterobacteriaceae family, is known to cause severe and often fatal meningitis and sepsis in young infants. C. sakazakii is ubiquitous in the environment, and most…
View article: Genome Sequences of Hemolytic and Nonhemolytic Listeria innocua Strains from Human, Food, and Environmental Sources
Genome Sequences of Hemolytic and Nonhemolytic Listeria innocua Strains from Human, Food, and Environmental Sources Open
This report describes genome sequences for nine Listeria innocua strains that varied in hemolytic phenotypes on sheep blood agar. All strains were sequenced using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) chemistry; ove…
View article: Benchmark datasets for SARS-CoV-2 surveillance bioinformatics
Benchmark datasets for SARS-CoV-2 surveillance bioinformatics Open
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of…
View article: Peer Review #3 of "Benchmark datasets for SARS-CoV-2 surveillance bioinformatics (v0.2)"
Peer Review #3 of "Benchmark datasets for SARS-CoV-2 surveillance bioinformatics (v0.2)" Open
one unique dataset representing common sequence failures was obtained by rigorously scrutinizing
View article: Peer Review #3 of "Benchmark datasets for SARS-CoV-2 surveillance bioinformatics (v0.1)"
Peer Review #3 of "Benchmark datasets for SARS-CoV-2 surveillance bioinformatics (v0.1)" Open
one unique dataset representing common sequence failures was obtained by rigorously scrutinizing
View article: Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya
Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya Open
A high burden of Salmonella enterica subspecies enterica serovar Typhi ( S . Typhi) bacteremia has been reported from urban informal settlements in sub-Saharan Africa, yet little is known about the introduction of these strains to the regi…
View article: Software testing in microbial bioinformatics: a call to action
Software testing in microbial bioinformatics: a call to action Open
Computational algorithms have become an essential component of research, with great efforts by the scientific community to raise standards on development and distribution of code. Despite these efforts, sustainability and reproducibility a…
View article: Overview of NCBI&#39;s SARS-CoV-2 submission process and the metadata required v5
Overview of NCBI's SARS-CoV-2 submission process and the metadata required v5 Open
PURPOSE: This protocol explains the metadata requirements for the following two protocols: 1. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission a…
View article: Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package Open
Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of cr…
View article: SARS-CoV-2 NCBI consensus submission protocol: GenBank v3
SARS-CoV-2 NCBI consensus submission protocol: GenBank v3 Open
This is a SARS-CoV-2 specific protocol that covers the steps needed to submit SARS-CoV-2 consensus sequence to GenBank. If you need a pipeline for frequent or large volume submissions, follow Step 1 in the SARS-CoV-2 NCBI submission protoc…
View article: Sepia, a taxonomy oriented read classifier in Rust
Sepia, a taxonomy oriented read classifier in Rust Open
Here we present Sepia, a fast and accurate read classifier. It is implemented in Rust, has the ability to switch between different taxonomies, can detect inconsistencies in taxonomies, and can estimate similarities between organisms in a q…
View article: Overview of NCBI&#39;s SARS-CoV-2 submission process and the metadata required v4
Overview of NCBI's SARS-CoV-2 submission process and the metadata required v4 Open
PURPOSE: This protocol explains the metadata requirements for the following two protocols: 1. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission a…
View article: Peer Review #1 of "Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks (v0.1)"
Peer Review #1 of "Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks (v0.1)" Open
Background.Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks.Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon…
View article: Peer Review #2 of "Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks (v0.1)"
Peer Review #2 of "Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks (v0.1)" Open
Background.Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks.Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon…
View article: Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks
Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks Open
Background Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks. Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upo…
View article: Peer Review #1 of "Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks (v0.2)"
Peer Review #1 of "Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks (v0.2)" Open
Background.Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks.Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon…
View article: SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject v4
SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject v4 Open
PURPOSE: This is a SARS-CoV-2 specific protocol that covers the steps needed to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the…