Jordan D. Zehr

Dynamics of natural selection preceding human viral epidemics and pandemics

Jennifer L. Havens, Sergei L. Kosakovsky Pond, Jordan D. Zehr, Jonathan E. Pekar et autres

Using a phylogenetic framework to characterize natural selection, we investigate the hypothesis that zoonotic viruses require adaptation prior to zoonosis to sustain human-to-human transmission. Examining the zoonotic emergence of Ebola virus, Marburg virus, mpox virus, influenza A virus, and SARS-CoV-2, we find …

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Analyzing multidrug resistance patterns across the food supply chain using association rule mining

J. Colin Glass, Gayatri Anil, Jordan D. Zehr, Kristina Ceres et autres

We used the machine learning method association rule mining to analyze multidrug resistance (MDR) among cattle-associated Escherichia coli along the food supply chain in the USA. All datasets were stratified by year, source, and resistance indicator (genotypic/phenotypic). Pruned rulesets were compared by …

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WITHDRAWN: A Comprehensive Hybrid Capture Sequencing Platform for Tick-borne Disease Detection Reveals Zoonotic Emerging Pathogens in a Weather and Vector Transition Zone

Chloe M. Murrell, Ximena A. Olarte‐Castillo, X.-D. Wang, Aiman Sabaawy et autres

Withdrawal Statement The authors have withdrawn this manuscript because this preprint was merged with the preprint BIORXIV/2025/658355. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding …

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A Comprehensive Hybrid Capture Sequencing Platform for Tick-borne Disease Detection Reveals Zoonotic Emerging Pathogens in a Weather and Vector Transition Zone

Chloe M. Murrell, Ximena A. Olarte‐Castillo, Xiyu Wang, Aiman Sabaawy et autres

Ticks are vectors of many debilitating pathogens that are transmitted during blood meal acquisition. As both vector and pathogen species continue to emerge, there is a critical need for improved pathogen diagnostic and host remnant identification methods to develop interventions. Current pathogen …

us, Sénégal, Afrique du Sud (code pays fourni par la source)

Population and pan-genomic analyses of Staphylococcus pseudintermedius identify geographic distinctions in accessory gene content and novel loci associated with AMR

Jordan D. Zehr, Qi Sun, Kristina Ceres, Amy Merrill et autres

ABSTRACT Staphylococcus pseudintermedius is a common representative of the normal skin microbiota of dogs and cats but is also a causative agent of a variety of infections. Although primarily a canine/feline bacterium, recent studies suggest an expanded host range including humans. This …

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Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin

Yining Sun, Y. Tina Yu, Ximena Olarte Castillo, Renee Anderson et autres

BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction. OBJECTIVES: This case-control study aimed …

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Dynamics of natural selection preceding human viral epidemics and pandemics

Jennifer L. Havens, Sergei L. Kosakovsky Pond, Jordan D. Zehr, Jonathan E. Pekar et autres

Using a phylogenetic framework to characterize natural selection, we investigate the hypothesis that zoonotic viruses require adaptation prior to zoonosis to sustain human-to-human transmission. Examining the zoonotic emergence of Ebola virus, Marburg virus, influenza A virus, SARS-CoV, and SARS-CoV-2, we find no …

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Genome sequence of Equine Erythroparvovirus 1 , identified in the United States

Y. Tina Yu, Ximena Olarte Castillo, Guillaume Reboul, Jordan D. Zehr et autres

ABSTRACT Equine Erythroparvovirus 1 is a parvovirus that was identified in the blood of four horses in the United States. Here, we report one genome from a horse in New York State. This genome may represent a new species within the genus …

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Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus

Jordan D. Zehr, Sergei L. Kosakovsky Pond, Stephen D. Shank, Holly McQueary et autres

ABSTRACT There are several examples of coronaviruses in the Betacoronavirus subgenus Embecovirus that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the coronavirus host-switching potential. Equids, such as …

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Evolutionary genomic analyses of canine E. coli infections identify a relic capsular locus associated with resistance to multiple classes of antimicrobials

Kristina Ceres, Jordan D. Zehr, Chloe Murrell, Jean K. Millet et autres

ABSTRACT Infections caused by antimicrobial-resistant Escherichia coli are the leading cause of death attributed to antimicrobial resistance (AMR) worldwide, and the known AMR mechanisms involve a range of functional proteins. Here, we employed a pan-genome wide association study (GWAS) approach on over …

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Temporal changes in antibiotic resistance and population structure of methicillin-resistant Staphylococcus pseudintermedius between 2010 and 2021 in the United States

Lufuno Phophi, Mohamed A. Abouelkhair, Rebekah D. Jones, Jordan D. Zehr et autres

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Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses

Alexander G. Lucaci, Jordan D. Zehr, David Enard, Joseph W. Thornton et autres

Inference and interpretation of evolutionary processes, in particular of the types and targets of natural selection affecting coding sequences, are critically influenced by the assumptions built into statistical models and tests. If certain aspects of the substitution process (even when they are …

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