Publications by authors named "Lori A Rowe"

The effects of immunodeficiency associated with chronic HIV infection on COVID-19 disease and viral persistence have not been directly addressed in a controlled setting. In this pilot study, we exposed two pigtail macaques (PTMs) chronically infected with SIVmac239, exhibiting from very low to no CD4 T cells across all compartments, to SARS-CoV-2. We monitored the disease progression, viral replication, and evolution, and compared these outcomes with SIV-naïve PTMs infected with SARS-CoV-2.

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Article Synopsis
  • HIV and malaria often occur together in the same regions, leading to co-infection that worsens the symptoms of both diseases, but the mechanisms behind this increase in severity are not well understood.
  • A pilot study in rhesus macaques treated with antiretroviral therapy (ART) aimed to explore the effects of co-infection, revealing persistent viral loads and decreased CD4+ T-cells despite treatment, along with signs of anemia and parasitemia.
  • The study also found that co-infection increased inflammatory markers and altered neutrophil behavior, suggesting that inflammation and gastrointestinal dysfunction could play key roles in the aggravated disease pathology seen in HIV and malaria co-infection.
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Ten isolates representing the top 10 ribotypes collected in 2016 through the Emerging Infections Program underwent long-read sequencing to obtain high-quality reference genome assemblies. These isolates are publicly available through the CDC & FDA Antibiotic Resistance Isolate Bank.

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Group A streptococcal strains potentially acquire new M protein gene types through genetic recombination (emm switching). To detect such variants, we screened 12,596 invasive GAS genomes for strains of differing emm types that shared the same multilocus sequence type (ST). Through this screening we detected a variant consisting of 16 serum opacity factor (SOF)-positive, emm pattern E, emm82 isolates that were ST36, previously only associated with SOF-negative, emm pattern A, emm12.

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  • * A pilot study involved two pigtail macaques infected with SIV (a simian version of HIV), which were exposed to SARS-CoV-2 and monitored to observe clinical disease and viral behavior over six weeks, compared to non-SIV-infected macaques.
  • * Despite lacking robust immune responses, the SIV-infected macaques showed similar patterns of viral replication and clearance as non-infected macaques, suggesting that their immunodeficiency didn't affect the progression or evolution of SARS-CoV-2. *
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The ability of each new SARS-CoV-2 variant to evade host humoral immunity is the focus of intense research. Each variant may also harbor unique replication capabilities relevant for disease and transmission. Here, we demonstrate a new approach to assessing viral replication kinetics using real-time cell analysis (RTCA).

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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 associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period.

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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; overall, the average read length of these sequences was 2,869,880 bp, with an average GC content of 37%.

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Naturally occurring human infections by zoonotic Plasmodium species have been documented for P. knowlesi, P. cynomolgi, P.

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Breakthrough gastrointestinal COVID-19 was observed after experimental SARS-CoV-2 upper mucosal infection in a rhesus macaque undergoing low-dose monoclonal antibody prophylaxis. High levels of viral RNA were detected in intestinal sites contrasting with minimal viral replication in upper respiratory mucosa. Sequencing of virus recovered from tissue in 3 gastrointestinal sites and rectal swab revealed loss of furin cleavage site deletions present in the inoculating virus stock and 2 amino acid changes in spike that were detected in 2 colon sites but not elsewhere, suggesting compartmentalized replication and intestinal viral evolution.

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Article Synopsis
  • Recent SARS-CoV-2 variants are more transmissible and can evade immune responses, making tracking their evolution essential.
  • A study sequenced viral RNA from rectal swabs of African green monkeys infected with SARS-CoV-2 to understand its evolution in nonhuman primate models.
  • Two key findings emerged: mutations in the furin cleavage site were absent in the monkeys, indicating its importance for infection, and three specific amino acid changes were consistently found in all samples, suggesting a possible host-adapted variant for future research.
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  • - A new bacterial species was discovered from ticks collected in Oregon in 1967 and was found to cause mild symptoms in guinea pigs, but it took 30 years for it to be formally identified and characterized using modern techniques.
  • - Whole-genome sequencing showed that this new isolate is distinct from known species and has a relatively small genome, positioning it in a transitional group among similar bacteria with low similarity scores to existing species.
  • - The new strain, named sp. nov. and designated Tillamook 23, has been made available in several research collections for further study, highlighting its potential significance in understanding tick-borne diseases.
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PacBio and Illumina MiSeq platforms were used for genomic sequencing of a strain isolated from a patient infected in Pakistan. PacBio assemblies were generated using Flye v2.4 and polished with MiSeq data.

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We present the chromosome sequences of a isolate from a human primary amebic meningoencephalitis (PAM) case. The genome sequences were assembled from Illumina HiSeq and PacBio sequencing data and verified with the optical mapping data. This led to the identification of 37 contigs representing 37 chromosomes in .

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Candida auris is an emerging fungal pathogen of rising concern due to global spread, the ability to cause healthcare-associated outbreaks, and antifungal resistance. Genomic analyses revealed that early contemporaneously detected cases of C. auris were geographically stratified into four major clades.

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sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with NBRC 100433 as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.

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DSM 45196 and W9323 are aerobic, Gram-positive, filamentous, chemoorganotrophic thermoactinomycetes. Here, we report on the complete and circular genome assemblies generated using Illumina MiSeq and Oxford Nanopore Technologies MinION reads. Putative gene clusters predicted to be involved in the production of secondary metabolites were also identified.

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The genus in the family is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species.

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Background: Antibiotic resistance is often spread through bacterial populations via conjugative plasmids. However, plasmid transfer is not well recognized in clinical settings because of technical limitations, and health care-associated infections are usually caused by clonal transmission of a single pathogen. In 2015, multiple species of carbapenem-resistant Enterobacteriaceae (CRE), all producing a rare carbapenemase, were identified among patients in an intensive care unit.

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  • Whooping cough, primarily caused by Bordetella pertussis, has seen a resurgence in the U.S., highlighting the need to study the chromosome structural fluidity of its strains, which involves rearrangement and deletion.
  • Researchers analyzed complete genome sequences from 167 species isolates and 469 other isolates to understand the patterns of chromosome rearrangement among related pathogens in the Bordetella genus.
  • The study found that large inversions in gene order are mainly observed in species with multiple insertion sequence (IS) elements, indicating that while some species show less chromosomal diversity, they still experience similar mutations in gene order.
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We present here the draft genome sequences of () , () , and () , potential etiological agents of diffuse cutaneous leishmaniasis (DCL). Sequence data were obtained using PacBio and MiSeq platforms. The PacBio assemblies generated using Canu v1.

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Escherichia albertii is an emerging pathogen that is closely related to Escherichia coli and can carry some of the same virulence genes as E. coli. Here, we report the release of Illumina-corrected PacBio sequences for eight E.

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We present here the first draft genome sequence of Leishmania (Viannia) lainsoni strain 216-34, sequenced using PacBio and MiSeq platforms. PacBio contigs were generated from assemblies using CANU version 1.6 and polished using Illumina reads.

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