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  1. Article ; Online: Domestic pigs are susceptible to experimental infection with non-human primate-derived Reston virus without the need for adaptation

    Charles E. Lewis / Mathieu M. Pinette / Steven M. Lakin / Greg Smith / Mathew Fisher / Estella Moffat / Carissa Embury-Hyatt / Brad S. Pickering

    Scientific Reports, Vol 14, Iss 1, Pp 1-

    2024  Volume 16

    Abstract: Abstract Domestic pigs are a critical component of the food supply and one of the most commonly raised production animals. Pork consumption has driven the intensification of pig production expanding into environments conducive to increased emergence and ... ...

    Abstract Abstract Domestic pigs are a critical component of the food supply and one of the most commonly raised production animals. Pork consumption has driven the intensification of pig production expanding into environments conducive to increased emergence and spread of infectious diseases, including the spillover of pathogens into human populations. One of these emerging viruses, Reston virus (RESTV), is an enigma among the Orthoebolavirus genus in that its lack of human pathogenicity is in stark contrast to the high virulence associated with most other ebolaviruses. RESTV is, however, associated with outbreaks of highly lethal hemorrhagic disease in non-human primates (NHP), as well as poorly understood clinical manifestations of mixed virulence and lethality in naturally and experimentally infected domestic pigs. Our results show it is possible for RESTV derived from an NHP to infect domestic pigs resulting in a spectrum of disease, from asymptomatic to severe respiratory distress. Further, we report on the first experimental transmission of RESTV between infected pigs and a co-housed, naïve animal, as well as the first report of the successful use of group oral fluids for the detection of RESTV RNA and virus-specific IgA antibodies.
    Keywords Medicine ; R ; Science ; Q
    Subject code 630
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences

    Steven M. Lakin / Alan Kuhnle / Bahar Alipanahi / Noelle R. Noyes / Chris Dean / Martin Muggli / Rob Raymond / Zaid Abdo / Mattia Prosperi / Keith E. Belk / Paul S. Morley / Christina Boucher

    Communications Biology, Vol 2, Iss 1, Pp 1-

    2019  Volume 11

    Abstract: Steven Lakin et al. present Meta-MARC, a computational method for identifying antimicrobial resistance sequences using DNA-based Hidden Markov Models. Because of its increased sensitivity, Meta-MARC is able to detect novel antimicrobial resistance ... ...

    Abstract Steven Lakin et al. present Meta-MARC, a computational method for identifying antimicrobial resistance sequences using DNA-based Hidden Markov Models. Because of its increased sensitivity, Meta-MARC is able to detect novel antimicrobial resistance sequences that are divergent from all known sequences.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  3. Article ; Online: Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics

    Katherine L. Huebner / Jennifer N. Martin / Carla J. Weissend / Katlyn L. Holzer / Jennifer K. Parker / Steven M. Lakin / Enrique Doster / Margaret D. Weinroth / Zaid Abdo / Dale R. Woerner / Jessica L. Metcalf / Ifigenia Geornaras / Tony C. Bryant / Paul S. Morley / Keith E. Belk

    Scientific Reports, Vol 9, Iss 1, Pp 1-

    2019  Volume 11

    Abstract: Abstract Liver abscesses in feedlot cattle form secondary to high concentrate feeds and rumen acidosis. Antimicrobial drugs are commonly included in cattle feed for prevention of liver abscesses, but concerns regarding antimicrobial resistance have ... ...

    Abstract Abstract Liver abscesses in feedlot cattle form secondary to high concentrate feeds and rumen acidosis. Antimicrobial drugs are commonly included in cattle feed for prevention of liver abscesses, but concerns regarding antimicrobial resistance have increased the need for alternative treatments. A block randomized clinical trial was conducted to evaluate the effects of a Saccharomyces cerevisiae fermentation product (SCFP) on liver abscesses, fecal microbiomes, and resistomes in cattle raised without antibiotics in a Colorado feedlot. At enrollment, steers (n = 4,689) were sorted, by weight and source, into 2 pens comprising a block (n = 14 blocks, 28 pens); pens were randomly allocated to either the control group or the treatment group, where the diet was supplemented with SCFP. Prior to harvest, composited feces were collected for characterization of the microbiome and resistome using 16S rRNA gene and shotgun sequencing. At harvest, liver abscess severity was quantified for individual cattle. There were no statistical differences detected by treatment group in animal health, liver abscess prevalence or severity. Organisms classified to phylum, Elusimicrobia were more abundant in the feces of treated cattle, however, there were no differences in the resistome by treatment group. Both microbiome and resistome varied significantly among enrollment blocks.
    Keywords Medicine ; R ; Science ; Q
    Subject code 630
    Language English
    Publishing date 2019-02-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

    Noelle R. Noyes / Maggie E. Weinroth / Jennifer K. Parker / Chris J. Dean / Steven M. Lakin / Robert A. Raymond / Pablo Rovira / Enrique Doster / Zaid Abdo / Jennifer N. Martin / Kenneth L. Jones / Jaime Ruiz / Christina A. Boucher / Keith E. Belk / Paul S. Morley

    Microbiome, Vol 5, Iss 1, Pp 1-

    2017  Volume 13

    Abstract: Abstract Background Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for ... ...

    Abstract Abstract Background Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. Results The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. Conclusions These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.
    Keywords Resistome ; Antimicrobial resistance ; Molecular enrichment ; Microbial ecology ; Rare microbiome ; QR100-130
    Language English
    Publishing date 2017-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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