scholarly journals Comparative Genomic and Morphological Analyses of Listeria Phages Isolated from Farm Environments

2014 ◽  
Vol 80 (15) ◽  
pp. 4616-4625 ◽  
Author(s):  
Thomas Denes ◽  
Kitiya Vongkamjan ◽  
Hans-Wolfgang Ackermann ◽  
Andrea I. Moreno Switt ◽  
Martin Wiedmann ◽  
...  
Keyword(s):  
New York ◽  
Dairy Farm ◽  
Morphological Diversity ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
The Novel ◽  
Important Food ◽  
Content Type ◽  
Small Genome ◽  
Food Borne

ABSTRACTThe genusListeriais ubiquitous in the environment and includes the globally important food-borne pathogenListeria monocytogenes. While the genomic diversity ofListeriahas been well studied, considerably less is known about the genomic and morphological diversity ofListeriabacteriophages. In this study, we sequenced and analyzed the genomes of 14Listeriaphages isolated mostly from New York dairy farm environments as well as one relatedEnterococcus faecalisphage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. TheseListeriaphages, based on gene orthology and morphology, together with previously sequencedListeriaphages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large-genome (∼135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (∼66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) ofE. faecalisphages, with medium-sized genomes (∼56 kb), was identified, which grouped together and shares morphological features with the novelListeriaphage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.

scholarly journals Silage Collected from Dairy Farms Harbors an Abundance of Listeriaphages with Considerable Host Range and Genome Size Diversity

2012 ◽  
Vol 78 (24) ◽  
pp. 8666-8675 ◽  
Author(s):  
Kitiya Vongkamjan ◽  
Andrea Moreno Switt ◽  
Henk C. den Bakker ◽  
Esther D. Fortes ◽  
Martin Wiedmann
Keyword(s):  
Host Range ◽  
Dairy Farm ◽  
Dairy Farms ◽  
Genomic Diversity ◽  
Broad Host Range ◽  
Content Type ◽  
Narrow Host Range ◽  
Food Borne ◽  
Size Diversity ◽  
Range Characterization

ABSTRACTSince the food-borne pathogenListeria monocytogenesis common in dairy farm environments, it is likely that phages infecting this bacterium (“listeriaphages”) are abundant on dairy farms. To better understand the ecology and diversity of listeriaphages on dairy farms and to develop a diverse phage collection for further studies, silage samples collected on two dairy farms were screened forL. monocytogenesand listeriaphages. While only 4.5% of silage samples tested positive forL. monocytogenes, 47.8% of samples were positive for listeriaphages, containing up to >1.5 × 104PFU/g. Host range characterization of the 114 phage isolates obtained, with a reference set of 13L. monocytogenesstrains representing the nine major serotypes and four lineages, revealed considerable host range diversity; phage isolates were classified into nine lysis groups. While one serotype 3c strain was not lysed by any phage isolates, serotype 4 strains were highly susceptible to phages and were lysed by 63.2 to 88.6% of phages tested. Overall, 12.3% of phage isolates showed a narrow host range (lysing 1 to 5 strains), while 28.9% of phages represented broad host range (lysing ≥11 strains). Genome sizes of the phage isolates were estimated to range from approximately 26 to 140 kb. The extensive host range and genomic diversity of phages observed here suggest an important role of phages in the ecology ofL. monocytogeneson dairy farms. In addition, the phage collection developed here has the potential to facilitate further development of phage-based biocontrol strategies (e.g., in silage) and other phage-based tools.

scholarly journals Genomic Diversity and Virulence Profiles of Historical Escherichia coli O157 Strains Isolated from Clinical and Environmental Sources

2014 ◽  
Vol 81 (2) ◽  
pp. 569-577 ◽  
Author(s):  
Lydia V. Rump ◽  
Narjol Gonzalez-Escalona ◽  
Wenting Ju ◽  
Fei Wang ◽  
Guojie Cao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
The United States ◽  
Genomic Diversity ◽  
Severe Illness ◽  
Pathogenic Potential ◽  
Content Type ◽  
E Coli ◽  
Virulence Markers ◽  
Virulence Potential ◽  
Food Borne

ABSTRACTEscherichia coliO157:H7 is, to date, the majorE. coliserotype causing food-borne human disease worldwide. Strains of O157 with other H antigens also have been recovered. We analyzed a collection of historic O157 strains (n= 400) isolated in the late 1980s to early 1990s in the United States. Strains were predominantly serotype O157:H7 (55%), and various O157:non-H7 (41%) serotypes were not previously reported regarding their pathogenic potential. Although lacking Shiga toxin (stx) andeaegenes, serotypes O157:H1, O157:H2, O157:H11, O157:H42, and O157:H43 carried several virulence factors (iha,terD, andhlyA) also found in virulent serotypeE. coliO157:H7. Pulsed-field gel electrophoresis (PFGE) showed the O157 serogroup was diverse, with strains with the same H type clustering together closely. Among non-H7 isolates, serotype O157:H43 was highly prevalent (65%) and carried important enterohemorrhagicE. coli(EHEC) virulence markers (iha,terD,hlyA, andespP). Isolates from two particular H types, H2 and H11, among the most commonly found non-O157 EHEC serotypes (O26:H11, O111:H11, O103:H2/H11, and O45:H2), unexpectedly clustered more closely with O157:H7 than other H types and carried several virulence genes. This suggests an early divergence of the O157 serogroup to clades with different pathogenic potentials. The appearance of important EHEC virulence markers in closely related H types suggests their virulence potential and suggests further monitoring of those serotypes not implicated in severe illness thus far.

scholarly journals Novel IncR/IncP6 Hybrid Plasmid pCRE3-KPC Recovered from a Clinical KPC-2-Producing Citrobacter braakii Isolate

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Dandan Dong ◽  
Ziqiang Mi ◽  
Dujun Li ◽  
Mingming Gao ◽  
Nan Jia ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Multidrug Resistant ◽  
Genomic Diversity ◽  
Hybrid Plasmid ◽  
The Novel ◽  
Antimicrobial Susceptibility Test ◽  
Genetic Characteristics ◽  
Content Type ◽  
Carbapenemase Gene ◽  
Insight Into

ABSTRACT Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae have become widespread in hospitals and the environment. Here, we describe a blaKPC-2-carrying plasmid called pCRE3-KPC, which was recovered from a clinical multidrug-resistant Citrobacter braakii CRE3 strain in China. The complete nucleotide sequence of pCRE3-KPC was determined by combining MiSeq and MinION sequencing and then compared with those of three related plasmids. Plasmid conjugal transfer and electroporation tests, modified carbapenem inactivation method, and bacterial antimicrobial susceptibility test were carried out. We compared this plasmid with three related plasmids to verify that the backbone of pCRE3-KPC was composed of the backbones of the IncR plasmid and IncP6 plasmid. Further bioinformatics analysis showed that pCRE3-KPC carried two resistance-related regions (the blaKPC-2 gene cluster and the aacC2-tmrB-related region). The aacC2-tmrB-related region included two novel insertion sequences (ISCfr28 and ISCfr16). IMPORTANCE Reports of human-pathogenic C. braakii strains, especially of strains showing resistance to carbapenems, are rare. To the best of our knowledge, our results represent the first detection of carbapenemase gene blaKPC-2 in C. braakii strains. In addition, we have studied detailed genetic characteristics of the novel IncR/IncP6 hybrid plasmid pCRE3-KPC, which was isolated from a clinical multidrug-resistant Citrobacter braakii CRE3 strain. Our results may provide further insight into the horizontal transfer of multidrug resistance genes in bacteria and into the genomic diversity and molecular evolution of plasmids.

County road 23

2014 ◽  
Author(s):  
◽  
Meagan Ciesla
Keyword(s):  
New York ◽  
New England ◽  
Interest Rates ◽  
Land Development ◽  
Dairy Farm ◽  
Fourth Generation ◽  
The Novel ◽  
Family Farms ◽  
Late 20Th Century ◽  
Moral Culpability

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] This dissertation is composed of a critical introduction and a creative manuscript. The critical introduction "Deindustrial Half-life: Decayed Whiteness in Postcards and Affliction," contributes to whiteness studies scholarship by arguing that the deindustrial shift from local to global economies in the late 20th century results in the representation of poor white rural New England characters as decayed bodies. The creative manuscript is County Road 23, a novel narrated by an omniscient voice that details the lives of the disenfranchised in rural 1980s Upstate New York. The narrative follows the Savages, a family of three impoverished middle-aged brothers who manage their fourth-generation dairy farm. The brothers' livelihood is threatened by low milk prices, high loan interest rates, and the impending development of a landfill used for surplus garbage shipped westward from the New York City boroughs. The novel leaps across time to reveal the conflict between the Savages and their neighbors, the Keegans, who live in a bordering trailer town. A deal between the Keegans' son and a land developer leads to a drowning as well as the death of the eldest Savage brother. While the novel is interested in the ramifications of disappearing family farms in the face of corporate land development, primarily it questions moral culpability, family allegiance, and the social stigmas regarding work, property, and land ownership in the impoverished rural community.

scholarly journals The Genome of the Nucleopolyhedrosis-Causing Virus from Tipula oleracea Sheds New Light on the Nudiviridae Family

2014 ◽  
Vol 89 (6) ◽  
pp. 3008-3025 ◽  
Author(s):  
Annie Bézier ◽  
Julien Thézé ◽  
Frederick Gavory ◽  
Julien Gaillard ◽  
Julie Poulain ◽  
...  
Keyword(s):  
New Genus ◽  
Brown Planthopper ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Body Protein ◽  
Content Type ◽  
Occlusion Bodies ◽  
Phylogenomic Analyses ◽  
Dsdna Viruses ◽  
Core Genes

ABSTRACTA large double-stranded DNA (dsDNA) virus that produces occlusion bodies, typical of baculoviruses, has been described to infect crane fly larvae of the genusTipula(Diptera, Tipulidae). Because of a lack of genomic data, this virus has remained unclassified. Electron microscopy of an archival virus isolated fromTipula oleracea,T. oleraceanudivirus (ToNV), showed irregularly shaped occlusion bodies measuring from 2 to 5 μm in length and 2 μm in middiameter, filled with rod-shape virions containing single nucleocapsids within a bilayer envelope. Whole-genome amplification and Roche 454 sequencing revealed a complete circular genome sequence of 145.7 kb, containing five direct repeat regions. We predicted 131 open reading frames, including a homolog of the polyhedrin gene encoding the major occlusion body protein ofT. paludosanucleopolyhedrovirus (NPV). BLAST searches demonstrated that ToNV had 21 of the 37 baculovirus core genes but shared 52 genes with nudiviruses (NVs). Phylogenomic analyses indicated that ToNV clearly belongs to theNudiviridaefamily but should probably be assigned to a new genus. Among nudiviruses, ToNV was most closely related to thePenaeus monodonNV andHeliothis zeaNV clade but distantly related toDrosophila innubiaNV, the other nudivirus infecting a Diptera. Lastly, ToNV was found to be most closely related to the nuvidirus ancestor of bracoviruses. This was also reflected in terms of gene content, as ToNV was the only known exogenous virus harboring homologs of theCc50C22.6and27b(Cc50C22.7) genes found in the nudiviral genomic cluster involved in bracovirus particle production.IMPORTANCETheNudiviridaeis a family of arthropod dsDNA viruses from which striking cases of endogenization have been reported (i.e., symbiotic bracoviruses deriving from a nudivirus and the endogenous nudivirus of the brown planthopper). Although related to baculoviruses, relatively little is known about the genomic diversity of exogenous nudiviruses. Here, we characterized, morphologically and genetically, an archival sample of theTipula oleraceanudivirus (ToNV), which has the particularity of forming occlusion bodies. Comparative genomic and phylogenomic analyses showed ToNV to be to date the closest known relative of the exogenous ancestor of bracoviruses and that ToNV should be assigned to a new genus. Moreover, we revised the homology relationships of nudiviral genes and identified a new set of 32 core genes for theNudiviridae, of which 21 were also baculovirus core genes. These findings provide important insights into the evolutionary history of large arthropod dsDNA viruses.

scholarly journals Leptospire Genomic Diversity Revealed by Microarray-Based Comparative Genomic Hybridization

2012 ◽  
Vol 78 (9) ◽  
pp. 3045-3050 ◽  
Author(s):  
Broderick Eribo ◽  
Sirima Mingmongkolchai ◽  
Tingfen Yan ◽  
Padunsri Dubbs ◽  
Karen E. Nelson
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Comparative Genomic Hybridization ◽  
Virulence Factors ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Leptospira Interrogans ◽  
Genomic Hybridization ◽  
Content Type ◽  
Reference Genomes

ABSTRACTComparative genomic hybridization was used to compare genetic diversity of five strains ofLeptospira(Leptospira interrogansserovars Bratislava, Canicola, and Hebdomadis andLeptospira kirschneriserovars Cynopteri and Grippotyphosa). The array was designed based on two available sequencedLeptospirareference genomes, those ofL. interrogansserovar Copenhageni andL. interrogansserovar Lai. A comparison of genetic contents showed thatL. interrogansserovar Bratislava was closest to the reference genomes whileL. kirschneriserovar Grippotyphosa had the least similarity to the reference genomes. Cluster analysis indicated thatL. interrogansserovars Bratislava and Hebdomadis clustered together first, followed byL. interrogansserovar Canicola, before the twoL. kirschneristrains. Confirmed/potential virulence factors identified in previous research were also detected in the tested strains.

scholarly journals Biodegradation of Ephedrine Isomers by Arthrobacter sp. Strain TS-15: Discovery of Novel Ephedrine and Pseudoephedrine Dehydrogenases

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Tarek Shanati ◽  
Marion B. Ansorge-Schumacher
Keyword(s):  
Genome Mining ◽  
Genomic Analysis ◽  
Sole Source ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Arthrobacter Aurescens

ABSTRACT The Gram-positive soil bacterium Arthrobacter sp. strain TS-15 (DSM 32400), which is capable of metabolizing ephedrine as a sole source of carbon and energy, was isolated. According to 16S rRNA gene sequences and comparative genomic analysis, Arthrobacter sp. TS-15 is closely related to Arthrobacter aurescens. Distinct from all known physiological paths, ephedrine metabolism by Arthrobacter sp. TS-15 is initiated by the selective oxidation of the hydroxyl function at the α-C atom, yielding methcathinone as the primary degradation product. Rational genome mining revealed a gene cluster potentially encoding the novel pathway. Two genes from the cluster, which encoded putative short-chain dehydrogenases, were cloned and expressed in Escherichia coli. The obtained enzymes were strictly NAD+ dependent and catalyzed the oxidation of ephedrine to methcathinone. Pseudoephedrine dehydrogenase (PseDH) selectively converted (S,S)-(+)-pseudoephedrine and (S,R)-(+)-ephedrine to (S)- and (R)-methcathinone, respectively. Ephedrine dehydrogenase (EDH) exhibited strict selectivity for the oxidation of the diastereomers (R,S)-(–)-ephedrine and (R,R)-(–)-pseudoephedrine. IMPORTANCE Arthrobacter sp. TS-15 is a newly isolated bacterium with the unique ability to degrade ephedrine isomers. The initiating steps of the novel metabolic pathway are described. Arthrobacter sp. TS-15 and its isolated ephedrine-oxidizing enzymes have potential for use in decontamination and synthetic applications.

scholarly journals Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars ofSalmonella entericasubsp.enterica

2011 ◽  
Vol 77 (6) ◽  
pp. 1946-1956 ◽  
Author(s):  
Fenyun Liu ◽  
Rodolphe Barrangou ◽  
Peter Gerner-Smidt ◽  
Efrain M. Ribot ◽  
Stephen J. Knabel ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Virulence Genes ◽  
Virulence Gene ◽  
The United States ◽  
Pulsed Field Gel Electrophoresis ◽  
The Novel ◽  
Important Food ◽  
Mlst Scheme ◽  
Food Borne ◽  
Short Palindromic Repeat

ABSTRACTSalmonella entericasubsp.entericais the leading cause of bacterial food-borne disease in the United States. Molecular subtyping methods are powerful tools for tracking the farm-to-fork spread of food-borne pathogens during outbreaks. In order to develop a novel multilocus sequence typing (MLST) scheme for subtyping the major serovars ofS. entericasubsp.enterica, the virulence genessseLandfimHand clustered regularly interspaced short palindromic repeat (CRISPR) loci were sequenced from 171 clinical isolates from nineSalmonellaserovars,Salmonellaserovars Typhimurium, Enteritidis, Newport, Heidelberg, Javiana, I 4,[5],12:i:−, Montevideo, Muenchen, and Saintpaul. The MLST scheme using only virulence genes was congruent with serotyping and identified epidemic clones but could not differentiate outbreaks. The addition of CRISPR sequences dramatically improved discriminatory power by differentiating individual outbreak strains/clones. Of particular note, the present MLST scheme provided better discrimination ofSalmonellaserovar Enteritidis strains than pulsed-field gel electrophoresis (PFGE). This method showed high epidemiologic concordance for all serovars screened except forSalmonellaserovar Muenchen. In conclusion, the novel MLST scheme described in the present study accurately differentiated outbreak strains/clones of the major serovars ofSalmonella, and therefore, it shows promise for subtyping this important food-borne pathogen during investigations of outbreaks.

scholarly journals Landscape and Meteorological Factors Affecting Prevalence of Three Food-Borne Pathogens in Fruit and Vegetable Farms

2012 ◽  
Vol 79 (2) ◽  
pp. 588-600 ◽  
Author(s):  
Laura K. Strawn ◽  
Esther D. Fortes ◽  
Elizabeth A. Bihn ◽  
Kendra K. Nightingale ◽  
Yrjö T. Gröhn ◽  
...  
Keyword(s):  
New York ◽  
Water Samples ◽  
Meteorological Factors ◽  
New York State ◽  
Environmental Constraints ◽  
Content Type ◽  
Factors Affecting ◽  
Drainage Class ◽  
Food Borne Pathogens ◽  
Food Borne

ABSTRACTProduce-related outbreaks have been traced back to the preharvest environment. A longitudinal study was conducted on five farms in New York State to characterize the prevalence, persistence, and diversity of food-borne pathogens in fresh produce fields and to determine landscape and meteorological factors that predict their presence. Produce fields were sampled four times per year for 2 years. A total of 588 samples were analyzed forListeria monocytogenes,Salmonella, and Shiga toxin-producingEscherichia coli(STEC). The prevalence measures ofL. monocytogenes,Salmonella, and STEC were 15.0, 4.6, and 2.7%, respectively.L. monocytogenesandSalmonellawere detected more frequently in water samples, while STEC was detected with equal frequency across all sample types (soil, water, feces, and drag swabs).L. monocytogenes sigBgene allelic types 57, 58, and 61 andSalmonella entericaserovar Cerro were repeatedly isolated from water samples. Soil available water storage (AWS), temperature, and proximity to three land cover classes (water, roads and urban development, and pasture/hay grass) influenced the likelihood of detectingL. monocytogenes. Drainage class, AWS, and precipitation were identified as important factors inSalmonelladetection. This information was used in a geographic information system framework to hypothesize locations of environmental reservoirs where the prevalence of food-borne pathogens may be elevated. The map indicated that not all croplands are equally likely to contain environmental reservoirs ofL. monocytogenes. These findings advance recommendations to minimize the risk of preharvest contamination by enhancing models of the environmental constraints on the survival and persistence of food-borne pathogens in fields.

scholarly journals The US shale oil production, market forces and the US export ban

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Ilayda Taneri ◽  
Nukhet Dogan ◽  
M. Hakan Berument
Keyword(s):  
New York ◽  
Interest Rates ◽  
Empirical Evidence ◽  
Oil Production ◽  
Shale Oil ◽  
The Novel ◽  
Content Type ◽  
Dynamic Relationship ◽  
The Us ◽  
Positive Shock

Purpose The purpose of this paper is to use the novel data from the primary vision to determine the main financial and economic drivers of this revolutionary shale oil production and how these drivers changed after 2016 when the US removed its oil-exporting ban. Design/methodology/approach In this paper, the authors use the vector autoregressive model to assess the dynamic relationships among the Frac Count (FSCN) from the primary vision and the set of financial/macro-economic variables and how this dynamic relationship is altered with the effects of the US export ban before and after the lifting of the export ban. Findings The empirical evidence reveals that a positive shock to New York Mercantile Exchange, Standard and Poor’s 500, rig count, West Texas Intermediate or the US ending oil stocks increase the FSCN but higher interest rates and oil production decrease the FSCN. After the US became one of the major oil producers, it removed its crude export ban in December 2015. The empirical evidence suggests that the shale oil industry gets more integrated with the financial system and becomes more efficient in its production process in the post-2016 era after the export ban was removed. Originality/value The purpose of this paper is to use the novel data from the primary vision to determine the main financial and economic drivers of this revolutionary shale oil production and how these drivers changed after 2016 when the US removed its oil-exporting ban.

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