The Experts below are selected from a list of 177 Experts worldwide ranked by ideXlab platform
Paul D. Ebner - One of the best experts on this subject based on the ideXlab platform.
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Genome Sequence of a Salmonella Phage Used To Control Salmonella Transmission in Swine
Genome announcements, 2014Co-Authors: Jiayi Zhang, Yingying Hong, Nicholas J. Harman, Archana Das, Paul D. EbnerAbstract:Salmonella shedding in swine often increases in response to transportation and lairage. We previously demonstrated that such increases can be limited by directly feeding microencapsulated Salmonella bacterioPhages. Here we present the genome sequence of vB_SalM_SJ_3, a broader spectrum Viuna-like Salmonella Phage used in those studies.
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Development of an anti-Salmonella Phage cocktail with increased host range.
Foodborne pathogens and disease, 2010Co-Authors: Jiayi Zhang, Brittany L. Kraft, Yanying Pan, Samantha K. Wall, Anthea C. Saez, Paul D. EbnerAbstract:Salmonella shedding in many livestock species can increase significantly after transport and lairage. Preprocessing increases in shedding can amplify the amount of Salmonella that enters the processing facility and the likelihood of end-product contamination. We previously produced an anti-Salmonella Phage cocktail that reduced colonization in swine when the pigs were exposed to an environment heavily contaminated with Salmonella, similar to what might be seen in a transport trailer or processing facility holding pen. The aim of this study was to increase the efficacy of the Phage treatment by (1) expanding the host-range of the cocktail and (2) developing a more cost-effective microencapsulation technique. We collected samples from wastewater treatment facilities and isolated 20 distinct Phages belonging to either the Siphoviridae or Myoviridae families. From this library we identified 10 Phages that together lysed a mixed culture of Salmonella enterica Typhimurium, Enteriditis, and Kentucky--three serovars commonly associated with meat and poultry products. The Phages were microencapsulated using two sodium-alginate-based methods that only reduced the cocktail titer by 1.0-1.5 logs (premicroencapsulation: 10.4 log(10) PFU/mL; postmicroencapsulation method one: 9.2 log(10) PFU/mL; postmicroencapsulation method two: 8.9 log(10) PFU/mL). Microencapsulated Phages remained stable at both 4°C and 22°C for up to 14 days with no appreciable drop in titer (mean titer: 8.9 log(10) PFU/mL). These data indicate that Phage cocktails with wider host ranges are possible and a cost-effective microencapsulation process can protect the Phages over an extended period, making simultaneous treatment of large numbers of animals with feed- or water-based delivery possible.
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Phage therapy to reduce preprocessing Salmonella infections in market-weight swine.
Applied and environmental microbiology, 2009Co-Authors: Samantha K. Wall, Jiayi Zhang, M. H. Rostagno, Paul D. EbnerAbstract:Contamination of meat products with food-borne pathogens usually results from the carcass coming in contact with the feces of an infected animal during processing. In the case of Salmonella, pigs can become colonized with the organism during transport and lairage from contaminated trailers and holding pens, resulting in increased pathogen shedding just prior to processing. Increased shedding, in turn, amplifies the likelihood of carcass contamination by magnifying the amount of bacteria that enters the processing facility. We conducted a series of experiments to test whether Phage therapy could limit Salmonella infections at this crucial period. In a preliminary experiment done with small pigs (3 to 4 weeks old; 30 to 40 lb), administration of an anti-Salmonella Phage cocktail at the time of inoculation with Salmonella enterica serovar Typhimurium reduced Salmonella colonization by 99.0 to 99.9% (2- to 3-log reduction) in the tonsils, ileum, and cecum. To test the efficacy of Phage therapy in a production-like setting, we inoculated four market-weight pigs (in three replicates) with Salmonella enterica serovar Typhimurium and allowed the challenged pigs to contaminate a holding pen for 48 h. Sixteen naive pigs were randomly split into two groups which received either the anti-Salmonella Phage cocktail or a mock treatment. Both groups of pigs were comingled with the challenged pigs in the contaminated pen. Treatment with the anti-Salmonella Phage cocktail significantly reduced cecal Salmonella concentrations (95%; P < 0.05) while also reducing (numerically) ileal Salmonella concentrations (90%; P = 0.06). Additional in vitro studies showed that the Phage cocktail was also lytic against several non-Typhimurium serovars.
Andrew M Kropinski - One of the best experts on this subject based on the ideXlab platform.
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a shigella boydii bacterioPhage which resembles Salmonella Phage vii
Virology Journal, 2011Co-Authors: Hany Anany, Erika J Lingohr, Andre Villegas, Hanswolfgang Ackermann, Yimin She, Mansel W Griffiths, Andrew M KropinskiAbstract:Background: Lytic bacterioPhages have been applied successfully to control the growth of various foodborne pathogens. Sequencing of their genomes is considered as an important preliminary step to ensure their safety prior to food applications. Results: The lytic bacterioPhage, FSboM-AG3, targets the important foodborne pathogen, Shigella .I t is morphologically similar to Phage ViI of Salmonella enterica serovar Typhi and a series of Phages of Acinetobacter calcoaceticus and Rhizobium meliloti. The complete genome of FSboM-AG3 was determined to be 158 kb and was terminally redundant and circularly permuted. Two hundred and sixteen open reading frames (ORFs) were identified and annotated, most of which displayed homology to proteins of Salmonella Phage ViI. The genome also included four genes specifying tRNAs. Conclusions: This is the first time that a Vi-specific Phage for Shigella has been described. There is no evidence for the presence of virulence and lysogeny-associated genes. In conclusion, the genome analysis of FSboM-AG3 indicates that this Phage can be safely used for biocontrol purposes.
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The genome and proteome of a virulent Escherichia coli O157:H7 bacterioPhage closely resembling Salmonella Phage Felix O1.
Virology journal, 2009Co-Authors: Andre Villegas, Erika J Lingohr, Hanswolfgang Ackermann, Yimin She, Andrew M Kropinski, Amanda Mazzocco, Shivani Ojha, Thomas E. Waddell, Dianne M. Moyles, Rafiq AhmedAbstract:Based upon whole genome and proteome analysis, Escherichia coli O157:H7-specific bacterioPhage (Phage) wV8 belongs to the new myoviral genus, "the Felix O1-like viruses" along with Salmonella Phage Felix O1 and Erwinia amylovora Phage φEa21-4. The genome characteristics of Phage wV8 (size 88.49 kb, mol%G+C 38.9, 138 ORFs, 23 tRNAs) are very similar to those of Phage Felix O1 (86.16 kb, 39.0 mol%G+C, 131 ORFs and 22 tRNAs) and, indeed most of the proteins have their closest homologs within Felix O1. Approximately one-half of the Escherichia coli O157:H7 mutants resistant to Phage wV8 still serotype as O157:H7 indicating that this Phage may recognize, like coliPhage T4, two different surface receptors: lipopolysaccharide and, perhaps, an outer membrane protein.
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Complete Genome of the Broad-Host-Range Erwinia amylovora Phage ΦEa21-4 and Its Relationship to Salmonella Phage Felix O1
Applied and environmental microbiology, 2009Co-Authors: Susan M. Lehman, Andrew M Kropinski, Alan J. Castle, Antonet M. SvircevAbstract:ABSTRACT The first complete genome sequence for a myoviridal bacterioPhage, ΦEa21-4, infecting Erwinia amylovora, Erwinia pyrifoliae, and Pantoea agglomerans strains has been determined. The unique sequence of this terminally redundant, circularly permuted genome is 84,576 bp. The ΦEa21-4 genome has a GC content of 43.8% and contains 117 putative protein-coding genes and 26 tRNA genes. ΦEa21-4 is the first Phage in which a precisely conserved rho-independent terminator has been found dispersed throughout the genome, with 24 copies in all. Also notable in the ΦEa21-4 genome are the presence of tRNAs with six- and nine-base anticodon loops, the absence of a small packaging terminase subunit, and the presence of nadV, a principle component of the NAD+ salvage pathway, which has been found in only a few Phage genomes to date. ΦEa21-4 is the first reported Felix O1-like Phage genome; 56% of the predicted ΦEa21-4 proteins share homology with those of the Salmonella Phage. Apart from this similarity to Felix O1, the ΦEa21-4 genome appears to be substantially different, both globally and locally, from previously reported sequences. A total of 43 of the 117 genes are unique to ΦEa21-4, and 32 of the Felix O1-like genes do not appear in any Phage genome sequences other than ΦEa21-4 and Felix O1. N-terminal sequencing and matrix-assisted laser desorption ionization-time of flight analysis resulted in the identification of five ΦEa21-4 genes coding for virion structural proteins, including the major capsid protein.
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Genomic analysis of bacterioPhage ε34 of Salmonella enterica serovar Anatum (15
BMC microbiology, 2008Co-Authors: Robert Villafane, Milka Zayas, Andrew M Kropinski, Eddie B. Gilcrease, Sherwood R CasjensAbstract:Background The presence of proPhages has been an important variable in genetic exchange and divergence in most bacteria. This study reports the determination of the genomic sequence of Salmonella Phage e34, a temperate bacterioPhage that was important in the early study of proPhages that modify their hosts' cell surface and is of a type (P22-like) that is common in Salmonella genomes.
Sherwood R Casjens - One of the best experts on this subject based on the ideXlab platform.
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Genome Sequence of Salmonella Phage χ
Genome Announcements, 2015Co-Authors: Roger W. Hendrix, Ching Chung Ko, Marc Erhardt, Kelly T Hughes, Deborah Jacobs-sera, Graham F. Hatfull, Sherwood R CasjensAbstract:ABSTRACT Salmonella bacterioPhage χ is a member of the Siphoviridae family that gains entry into its host cells by adsorbing to their flagella. We report the complete 59,578-bp sequence of the genome of Phage χ, which together with its relatives, exemplifies a largely unexplored type of tailed bacterioPhage.
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Genome Sequence of Salmonella Phage 9NA.
Genome announcements, 2014Co-Authors: Sherwood R Casjens, Graham F. Hatfull, Justin C Leavitt, Roger W. HendrixAbstract:The virulent double-stranded DNA (dsDNA) bacterioPhage 9NA infects Salmonella enterica serovar Typhimurium and has a long noncontractile tail. We report its complete 52,869-bp genome sequence. Phage 9NA and two closely related S. enterica serovar Newport Phages represent a tailed Phage type whose molecular lifestyle has not yet been studied in detail.
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Genomic analysis of bacterioPhage ε34 of Salmonella enterica serovar Anatum (15
BMC microbiology, 2008Co-Authors: Robert Villafane, Milka Zayas, Andrew M Kropinski, Eddie B. Gilcrease, Sherwood R CasjensAbstract:Background The presence of proPhages has been an important variable in genetic exchange and divergence in most bacteria. This study reports the determination of the genomic sequence of Salmonella Phage e34, a temperate bacterioPhage that was important in the early study of proPhages that modify their hosts' cell surface and is of a type (P22-like) that is common in Salmonella genomes.
Susan T. Weintraub - One of the best experts on this subject based on the ideXlab platform.
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global proteomic profiling of Salmonella infection by a giant Phage
Journal of Virology, 2018Co-Authors: Susan T. Weintraub, Nurul Humaira Mohd Redzuan, Melissa K Barton, Nur Amira Md Amin, Maxim I Desmond, Lily E Adams, Bazla Ali, Sammy Pardo, Dana Molleur, William W NewcombAbstract:The 240-kb Salmonella Phage SPN3US genome encodes 264 gene products, many of which are functionally uncharacterized. We have previously used mass spectrometry to define the proteomes of wild-type and mutant forms of the SPN3US virion. In this study, we sought to determine whether this technique was suitable for the characterization of the SPN3US proteome during liquid infection. Mass spectrometry of SPN3US-infected cells identified 232 SPN3US and 1,994 Salmonella proteins. SPN3US proteins with related functions, such as proteins with roles in DNA replication, transcription, and virion formation, were coordinately expressed in a temporal manner. Mass spectral counts showed the four most abundant SPN3US proteins to be the major capsid protein, two head ejection proteins, and the functionally unassigned protein gp22. This high abundance of gp22 in infected bacteria contrasted with its absence from mature virions, suggesting that it might be the scaffold protein, an essential head morphogenesis protein yet to be identified in giant Phages. We identified homologs to SPN3US gp22 in 45 related giant Phages, including ϕKZ, whose counterpart is also abundant in infected bacteria but absent in the virion. We determined the ϕKZ counterpart to be cleaved in vitro by its prohead protease, an event that has been observed to promote head maturation of some other Phages. Our findings are consistent with a scaffold protein assignment for SPN3US gp22, although direct evidence is required for its confirmation. These studies demonstrate the power of mass spectral analyses for facilitating the acquisition of new knowledge into the molecular events of viral infection. IMPORTANCE “Giant” Phages with genomes >200 kb are being isolated in increasing numbers from a range of environments. With hosts such as Salmonella enterica, Pseudomonas aeruginosa, and Erwinia amylovora, these Phages are of interest for Phage therapy of multidrug-resistant pathogens. However, our understanding of how these complex Phages interact with their hosts is impeded by the proportion (∼80%) of their gene products that are functionally uncharacterized. To develop the repertoire of techniques for analysis of Phages, we analyzed a liquid infection of Salmonella Phage SPN3US (240-kb genome) using third-generation mass spectrometry. We observed the temporal production of Phage proteins whose genes collectively represent 96% of the SPN3US genome. These findings demonstrate the sensitivity of mass spectrometry for global proteomic profiling of virus-infected cells, and the identification of a candidate for a major head morphogenesis protein will facilitate further studies into giant Phage head assembly.
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Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly
Journal of virology, 2016Co-Authors: Julie A. Thomas, Andrea Denisse Benítez Quintana, Martine A. Bosch, Adriana Coll De Peña, Elizabeth Aguilera, Assitan Coulibaly, Michael V. Osier, André O. Hudson, Susan T. WeintraubAbstract:ABSTRACT Giant tailed bacterial viruses, or Phages, such as Pseudomonas aeruginosa Phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related Phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica Phage SPN3US could be a useful model Phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related Phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant Phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related Phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241 , which encodes an RNA polymerase β subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a “missing” β′ subunit domain. These findings support SPN3US as an excellent model for giant Phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution. IMPORTANCE In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant Phages) can be found in many environments. A group of Phages related to the prototype giant Phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for biocontrol and Phage therapy applications. Our understanding of the biology of these Phages is limited, as a large proportion of their proteins have not been characterized and/or have been deemed putative without any experimental verification. In this study, we analyzed Salmonella Phage SPN3US using a combination of genomics, genetics, and proteomics and in doing so revealed new information regarding giant Phage head structure and assembly and virion RNA polymerase composition. Our findings demonstrate the suitability of SPN3US as a model Phage for the growing group of Phages related to ϕKZ.
Martin Wiedmann - One of the best experts on this subject based on the ideXlab platform.
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Salmonella Phages isolated from dairy farms in Thailand show wider host range than a comparable set of Phages isolated from U.S. dairy farms
Veterinary Microbiology, 2014Co-Authors: Sarach Wongsuntornpoj, Andrea I. Moreno Switt, Martin Wiedmann, Peter W. Bergholz, Soraya ChaturongakulAbstract:Salmonella is a zoonotic pathogen with globally distributed serovars as well as serovars predominantly found in certain regions; for example, serovar Weltevreden is rarely isolated in the U.S., but is common in Thailand. Relative to our understanding of Salmonella diversity, our understanding of the global diversity of Salmonella Phages is limited. We hypothesized that the serovar diversity in a given environment and farming system will affect the Salmonella Phage diversity associated with animal hosts. We thus isolated and characterized Salmonella Phages from 15 small-scale dairy farms in Thailand and compared the host ranges of the 62 Salmonella Phage isolates obtained with host range diversity for 129 Phage isolates obtained from dairy farms in the U.S. The 62 Phage isolates from Thailand represented genome sizes ranging from 40 to 200 kb and showed lysis of 6-25 of the 26 host strains tested (mean number of strain lysed=19). By comparison, Phage isolates previously obtained in a survey of 15 U.S. dairy farms showed a narrow host range (lysis of 1-17; mean number of strains lysed=4); principal coordinate analysis also confirmed U.S. and Thai Phages had distinct host lysis profiles. Our data indicate that dairy farms that differ in management practices and are located on different continents can yield Phage isolates that differ in their host ranges, providing an avenue for isolation of Phages with desirable host range characteristics for commercial applications. Farming systems characterized by coexistence of different animals may facilitate presence of Salmonella Phages with wide host ranges.
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Genomic characterization provides new insight into Salmonella Phage diversity.
BMC genomics, 2013Co-Authors: Andrea I. Moreno Switt, Renato H. Orsi, Henk C. Den Bakker, Kitiya Vongkamjan, Craig Altier, Martin WiedmannAbstract:Salmonella is a widely distributed foodborne pathogen that causes tens of millions of salmonellosis cases globally every year. While the genomic diversity of Salmonella is increasingly well studied, our knowledge of Salmonella Phage genomic diversity is still rather limited, despite the contributions of both lysogenic and lytic Phages to Salmonella virulence, diversity and ecology (e.g., through horizontal gene transfer and Salmonella lysis). To gain a better understanding of Phage diversity in a specific ecological niche, we sequenced 22 Salmonella Phages isolated from a number of dairy farms from New York State (United States) and analyzed them using a comparative genomics approach. Classification of the 22 Phages according to the presence/absence of orthologous genes allowed for classification into 8 well supported clusters. In addition to two Phage clusters that represent novel virulent Salmonella Phages, we also identified four Phage clusters that each contained previously characterized Phages from multiple continents. Our analyses also identified two clusters of Phages that carry putative virulence (e.g., adhesins) and antimicrobial resistance (tellurite and bicyclomycin) genes as well as virulent and temperate transducing Phages. Insights into Phage evolution from our analyses include (i) identification of DNA metabolism genes that may facilitate nucleotide synthesis in Phages with a G+C % distinct from Salmonella, and (ii) evidence of Salmonella Phage tailspike and fiber diversity due to both single nucleotide polymorphisms and major re-arrangements, which may affect the host specificity of Salmonella Phages. Genomics-based characterization of 22 Salmonella Phages isolated from dairy farms allowed for identification of a number of novel Salmonella Phages. While the comparative genomics analyses of these Phages provide a number of new insights in the evolution and diversity of Salmonella Phages, they only represent a first glimpse into the diversity of Salmonella Phages that is likely to be discovered when Phages from different environments are characterized.
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Salmonella bacterioPhage diversity reflects host diversity on dairy farms
Food microbiology, 2013Co-Authors: Andrea I. Moreno Switt, Henk C. Den Bakker, Kitiya Vongkamjan, Karin Hoelzer, Lorin D. Warnick, Kevin J. Cummings, Martin WiedmannAbstract:Salmonella is an animal and human pathogen of worldwide concern. Surveillance programs indicate that the incidence of Salmonella serovars fluctuates over time. While bacterioPhages are likely to play a role in driving microbial diversity, our understanding of the ecology and diversity of Salmonella Phages is limited. Here we report the isolation of Salmonella Phages from manure samples from 13 dairy farms with a history of Salmonella presence. Salmonella Phages were isolated from 10 of the 13 farms; overall 108 Phage isolates were obtained on serovar Newport, Typhimurium, Dublin, Kentucky, Anatum, Mbandaka, and Cerro hosts. Host range characterization found that 51% of Phage isolates had a narrow host range, while 49% showed a broad host range. The Phage isolates represented 65 lysis profiles; genome size profiling of 94 Phage isolates allowed for classification of Phage isolates into 11 groups with subsequent restriction fragment length polymorphism analysis showing considerable variation within a given group. Our data not only show an abundance of diverse Salmonella Phage isolates in dairy farms, but also show that Phage isolates that lyse the most common serovars causing salmonellosis in cattle are frequently obtained, suggesting that Phages may play an important role in the ecology of Salmonella on dairy farms.
