Michael R. Weigand
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View article: No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis
No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis Open
Pathogens adapting to the human host and to vaccination-induced immunity may follow parallel evolutionary paths. Bordetella parapertussis ( Bpp ) contributes significantly to the burden of whooping cough (pertussis) and shares vaccine anti…
View article: Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States
Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States Open
View article: Variation in virulence between three representative <i>Bordetella pertussis</i> pertactin-negative clinical isolates
Variation in virulence between three representative <i>Bordetella pertussis</i> pertactin-negative clinical isolates Open
Pertussis is a respiratory disease caused by the bacterium Bordetella pertussis . Acellular pertussis (aP) vaccines replaced more reactogenic whole-cell pertussis (wP) vaccines in the United States in the 1990s. Despite high rates of vacci…
View article: <i>Bordetella pertussis</i> exhibits genomic diversity within patients and laboratory culture
<i>Bordetella pertussis</i> exhibits genomic diversity within patients and laboratory culture Open
Over the past decade, genomic characterization of Bordetella pertussis isolates recovered from US pertussis patients has unveiled noteworthy structural gene order variations. Whole-genome sequencing (WGS) shows that although B. pertussis e…
View article: Complete genome sequences of four representative <i>Corynebacterium belfantii</i> strains
Complete genome sequences of four representative <i>Corynebacterium belfantii</i> strains Open
This report describes the complete genome sequence assemblies from four representative isolates of the human pathogen Corynebacterium belfantii . These data provide necessary references to aid accurate sequence-based species discrimination…
View article: No innocent bystanders: pertussis vaccination epitomizes evolutionary parallelisms between<i>Bordetella parapertussis</i>and<i>B. pertussis</i>
No innocent bystanders: pertussis vaccination epitomizes evolutionary parallelisms between<i>Bordetella parapertussis</i>and<i>B. pertussis</i> Open
Pathogens adapting to the human host and to vaccination-induced immunity may follow parallel evolutionary paths. Bordetella parapertussis ( Bpp ) contributes significantly to the burden of whooping cough (pertussis), shares vaccine antigen…
View article: Strengthening <i>Bordetella pertussis</i> genomic surveillance by direct sequencing of residual positive specimens
Strengthening <i>Bordetella pertussis</i> genomic surveillance by direct sequencing of residual positive specimens Open
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent method…
View article: Genomic characterization of Bordetella pertussis in South Africa, 2015–2019
Genomic characterization of Bordetella pertussis in South Africa, 2015–2019 Open
Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillanc…
View article: Strengthening<i>Bordetella pertussis</i>genomic surveillance by direct sequencing of residual positive specimens
Strengthening<i>Bordetella pertussis</i>genomic surveillance by direct sequencing of residual positive specimens Open
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent method…
View article: Genome-based prediction of cross-protective, HLA-DR-presented epitopes as putative vaccine antigens for multiple <i>Bordetella</i> species
Genome-based prediction of cross-protective, HLA-DR-presented epitopes as putative vaccine antigens for multiple <i>Bordetella</i> species Open
Acellular pertussis vaccines protect against severe pertussis, but vaccine-induced immunity wanes over time. Prior animal studies showed that T-cell responses are integral to long-lasting immunity. Current pertussis vaccines also do not pr…
View article: Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019 Open
Respiratory diphtheria is a serious infection caused by toxigenic Corynebacterium diphtheriae , and disease transmission mainly occurs through respiratory droplets. Between 2017 and 2019, a large diphtheria outbreak among forcibly displace…
View article: Genomic deletions and rearrangements in monkeypox virus from the 2022 outbreak, USA
Genomic deletions and rearrangements in monkeypox virus from the 2022 outbreak, USA Open
Genomic surveillance of monkeypox virus (MPXV) during the 2022 outbreak has been mainly focused on single nucleotide polymorphism (SNP) changes. DNA viruses, including MPXV, have a lower SNP mutation rate than RNA viruses due to higher fid…
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: Complete Genome Sequences of Four Macrolide-Resistant Nondiphtheritic <i>Corynebacterium</i> Isolates
Complete Genome Sequences of Four Macrolide-Resistant Nondiphtheritic <i>Corynebacterium</i> Isolates Open
This report describes the complete genome sequences of four isolates of the nondiphtheritic Corynebacterium (NDC) species Corynebacterium pseudodiphtheriticum and Corynebacterium propinquum , recovered during investigation of a large dipht…
View article: Toxigenic <i>Corynebacterium diphtheriae</i> Infection in Cat, Texas, USA
Toxigenic <i>Corynebacterium diphtheriae</i> Infection in Cat, Texas, USA Open
We report a toxigenic strain of Corynebacterium diphtheriae isolated from an oozing dermal wound in a pet cat in Texas, USA. We also describe the epidemiologic public health efforts conducted to identify potential sources of infection and …
View article: Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis
Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis Open
Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but…
View article: Genomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLST
Genomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLST Open
Multilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis , the causative agent of whooping cough, seldom reveal di…
View article: Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019
Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019 Open
Between July 2018 and May 2019, Corynebacterium diphtheriae was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were micr…
View article: Genomic surveillance and improved molecular typing of<i>Bordetella pertussis</i>using wgMLST
Genomic surveillance and improved molecular typing of<i>Bordetella pertussis</i>using wgMLST Open
Multi-Locus Sequence Typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, current MLST schemes for Bordetella pertussis , the causative agent of whooping cough, seldom reveal div…
View article: Detection and Characterization of Diphtheria Toxin Gene-Bearing <i>Corynebacterium</i> Species through a New Real-Time PCR Assay
Detection and Characterization of Diphtheria Toxin Gene-Bearing <i>Corynebacterium</i> Species through a New Real-Time PCR Assay Open
Respiratory diphtheria, characterized by a firmly adherent pseudomembrane, is caused by toxin-producing strains of Corynebacterium diphtheriae , with similar illness produced occasionally by toxigenic Corynebacterium ulcerans or, rarely, C…
View article: Duplications drive diversity in<i>Bordetella pertussis</i>on an underestimated scale
Duplications drive diversity in<i>Bordetella pertussis</i>on an underestimated scale Open
Bacterial genetic diversity is often described using solely base pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplications of genomic loci are thought to be widespread among bacteria b…
View article: Conserved Patterns of Symmetric Inversion in the Genome Evolution of <i>Bordetella</i> Respiratory Pathogens
Conserved Patterns of Symmetric Inversion in the Genome Evolution of <i>Bordetella</i> Respiratory Pathogens Open
Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis…
View article: imGLAD: accurate detection and quantification of target organisms in metagenomes
imGLAD: accurate detection and quantification of target organisms in metagenomes Open
Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting f…
View article: Widely Used Benzalkonium Chloride Disinfectants Can Promote Antibiotic Resistance
Widely Used Benzalkonium Chloride Disinfectants Can Promote Antibiotic Resistance Open
Benzalkonium chlorides (BAC) are biocides broadly used in disinfectant solutions. Disinfectants are widely used in food processing lines, domestic households, and pharmaceutical products and are typically designed to have a different mode …
View article: Genomic and Transcriptomic Insights into How Bacteria Withstand High Concentrations of Benzalkonium Chloride Biocides
Genomic and Transcriptomic Insights into How Bacteria Withstand High Concentrations of Benzalkonium Chloride Biocides Open
Benzalkonium chlorides (BAC) are commonly used biocides in broad-spectrum disinfectant solutions. How microorganisms cope with BAC exposure remains poorly understood, despite its importance for disinfection and disinfectant-induced antibio…
View article: Genomic Survey of<i>Bordetella pertussis</i>Diversity, United States, 2000–2013
Genomic Survey of<i>Bordetella pertussis</i>Diversity, United States, 2000–2013 Open
We characterized 170 complete genome assemblies from clinical Bordetella pertussis isolates representing geographic and temporal diversity in the United States. These data capture genotypic shifts, including increased pertactin deficiency,…
View article: imGLAD: Accurate detection and quantification of target organisms in metagenomes
imGLAD: Accurate detection and quantification of target organisms in metagenomes Open
Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting f…
View article: imGLAD: Accurate detection and quantification of target organisms in metagenomes
imGLAD: Accurate detection and quantification of target organisms in metagenomes Open
Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting f…
View article: Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis
Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis Open
Despite high vaccine coverage, pertussis cases in the United States have increased over the last decade. Growing evidence suggests that disease resurgence results, in part, from genetic divergence of circulating strain populations away fro…
View article: Complete Genome Sequences of Bordetella pertussis Isolates with Novel Pertactin-Deficient Deletions
Complete Genome Sequences of Bordetella pertussis Isolates with Novel Pertactin-Deficient Deletions Open
Clinical isolates of the respiratory pathogen Bordetella pertussis in the United States have become predominantly deficient for the acellular vaccine immunogen pertactin through various independent mutations. Here, we report the complete g…