Bacteriophages against Vibrio coralliilyticus and Vibrio tubiashii: Isolation, Characterization, and Remediation of Larval Oyster Mortalities.

and are pathogens responsible for high larval oyster mortality rates in shellfish hatcheries. Bacteriophage therapy was evaluated to determine its potential to remediate these mortalities. Sixteen phages against and were isolated and characterized from Hawaiian seawater.

A Targeted Sequencing Assay for Serotyping Using AgriSeq Technology.

The gold standard method for serotyping has relied on antisera-based typing of the O- and H-antigens, which is labor intensive and often unreliable. In the post-genomic era, sequence-based assays are potentially faster to provide results, could combine O-serogrouping and H-typing in a single test, and could simultaneously screen for the presence of other genetic markers of interest such as virulence factors. Whole genome sequencing is one approach; however, this method has limited multiplexing capabilities, and only a small fraction of the sequence is informative for subtyping or identifying virulence potential.

Complete Genome Sequences of Bacteriocin-Producing Streptococcus thermophilus Strains ST106 and ST109.

Streptococcus thermophilus strains ST106 and ST109 produce broad-spectrum bacteriocins encoded within a bacteriocin-like peptide () gene cluster. This study reports the complete genome sequences for both strains, with the ST109 chromosome containing 1,788,866 nucleotides (nt) and 1,572 predicted genes, and ST106 having 1,856,083 nt and 1,601 predicted genes.

Whole-Genome Sequences of Two Pseudoalteromonas piscicida Strains, DE1-A and DE2-A, with Strong Antibacterial Activity against Vibrio vulnificus.

Highly vesiculated Pseudoalteromonas piscicida strains DE1-A and DE2-A were isolated from seawater and show bactericidal properties toward Vibrio vulnificus and other Gram-positive and Gram-negative bacteria. Here, we report the complete genome sequences of these two P. piscicida strains and identify proteolytic enzymes potentially involved in their antibacterial properties.

Complete Genome Sequence of Vibrio coralliilyticus RE22, a Marine Bacterium Pathogenic toward Larval Shellfish.

Vibrio coralliilyticus RE22 is an indigenous marine pathogen that infects larval bivalve shellfish. This strain is particularly problematic in oyster hatcheries, where it causes high larval mortality. It contains two circular chromosomes and one megaplasmid.

Draft Genomic Sequencing of Six Potential Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Meat.

Potential extraintestinal pathogenic strains DP254, WH333, WH398, F356, FEX675, and FEX725 were isolated from retail chicken meat products. Here, we report the draft genome sequences for these six isolates, which are currently being used in food safety research.

Draft Genome Sequences of Four Uropathogenic Escherichia coli Serotype O4:H5 Isolates (ATCC 700414, 700415, 700416, and 700417).

Uropathogenic serotype O4:H5 isolates (ATCC 700414, 700415, 700416, and 700417) were recovered from women with first-time urinary tract infections. Here, we report the draft genome sequences for these four isolates, which are currently being used to validate food safety processing technologies.

Complete Genome Sequence of Strain B59671, Which Naturally Produces the Broad-Spectrum Bacteriocin Thermophilin 110.

strain B59671 is a Gram-positive lactic acid bacterium that naturally produces a broad-spectrum bacteriocin, thermophilin 110, and is capable of producing gamma-aminobutyric acid (GABA). The complete genome sequence for this strain contains 1,821,173 nucleotides, 1,936 predicted genes, and an average G+C content of 39.1%.

Complete Genome Sequence of Strain DE2-B, a Bacterium with Broad Inhibitory Activity toward Human and Fish Pathogens.

strain DE2-B is a halophilic bacterium which has broad inhibitory activity toward vibrios and other human and fish pathogens. We report the first closed genome sequence for this species, which consists of two chromosomes (4,128,210 and 1,188,838 bp). Annotation revealed multiple genes encoding proteases with potential antibacterial properties.

Mechanisms for Pseudoalteromonas piscicida-Induced Killing of Vibrios and Other Bacterial Pathogens.

is a Gram-negative gammaproteobacterium found in the marine environment. Three strains of pigmented were isolated from seawater and partially characterized by inhibition studies, electron microscopy, and analysis for proteolytic enzymes. Growth inhibition and death occurred around colonies of on lawns of the naturally occurring marine pathogens , , , , and Inhibition also occurred on lawns of but not on O157:H7 or serovar Typhimurium.

Advances in Molecular Serotyping and Subtyping of Escherichia coli.

Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract.

Correction: Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing.

[This corrects the article DOI: 10.1371/journal.pone.

Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing.

Escherichia coli strains are classified based on O-antigens that are components of the lipopolysaccharide (LPS) in the cell envelope. O-antigens are important virulence factors, targets of both the innate and adaptive immune system, and play a role in host-pathogen interactions. Because they are highly immunogenic and display antigenic specificity unique for each strain, O-antigens are the biomarkers for designating O-types.

Complete Genome Sequence of Campylobacter jejuni RM1285, a Rod-Shaped Morphological Variant.

Campylobacter jejuni is a spiral shaped Gram-negative food-borne bacterial pathogen of humans found on poultry products. Strain RM1285 is a rod-shaped variant of this species. The genome of RM1285 was determined to be 1,635,803 bp, with a G+C content of 30.

Escherichia coli O-Antigen Gene Clusters of Serogroups O62, O68, O131, O140, O142, and O163: DNA Sequences and Similarity between O62 and O68, and PCR-Based Serogrouping.

The DNA sequence of the O-antigen gene clusters of Escherichia coli serogroups O62, O68, O131, O140, O142, and O163 was determined, and primers based on the wzx (O-antigen flippase) and/or wzy (O-antigen polymerase) genes within the O-antigen gene clusters were designed and used in PCR assays to identify each serogroup. Specificity was tested with E. coli reference strains, field isolates belonging to the target serogroups, and non-E.

Complete Genome Sequence for the Shellfish Pathogen Vibrio coralliilyticus RE98 Isolated from a Shellfish Hatchery.

Vibrio coralliilyticus is a pathogen of corals and larval shellfish. Publications on strain RE98 list it as a Vibrio tubiashii; however, whole genome sequencing confirms RE98 as V. coralliilyticus containing a total of 6,037,824 bp consisting of two chromosomes (3,420,228 and 1,917,482 bp) and two megaplasmids (380,714 and 319,400 bp).

Complete Genome Sequence of the Larval Shellfish Pathogen Vibrio tubiashii Type Strain ATCC 19109.

Vibrio tubiashii is a larval shellfish pathogen. Here, we report the first closed genome sequence for this species (ATCC type strain 19109), which consists of two chromosomes (3,294,490 and 1,766,582 bp), two megaplasmids (251,408 and 122,808 bp), and two plasmids (57,076 and 47,973 bp).

Mortalities of Eastern and Pacific oyster Larvae caused by the pathogens Vibrio coralliilyticus and Vibrio tubiashii.

Vibrio tubiashii is reported to be a bacterial pathogen of larval Eastern oysters (Crassostrea virginica) and Pacific oysters (Crassostrea gigas) and has been associated with major hatchery crashes, causing shortages in seed oysters for commercial shellfish producers. Another bacterium, Vibrio coralliilyticus, a well-known coral pathogen, has recently been shown to elicit mortality in fish and shellfish. Several strains of V.

Cloning, sequencing, and characterization of lipase genes from a polyhydroxyalkanoate (PHA)-synthesizing Pseudomonas resinovorans.

Lipase (lip) and lipase-specific foldase (lif) genes of a biodegradable polyhydroxyalkanoate (PHA)-synthesizing Pseudomonas resinovorans NRRL B-2649 were cloned using primers based on consensus sequences, followed by polymerase chain reaction-based genome walking. Sequence analyses showed a putative Lip gene product (314 amino acids, a.a.

DNA sequence and analysis of a 90.1-kb plasmid in Shiga toxin-producing Escherichia coli (STEC) O145:NM 83-75.

Shiga toxin-producing Escherichia coli (STEC) strains belonging to serogroup O145 are important emerging food-borne pathogens responsible for sporadic cases and outbreaks of hemorrhagic colitis and hemolytic uremic syndrome. A large plasmid carried by STEC O145:NM strain 83-75 and named pO145-NM was sequenced, and the genes were annotated. pO145-NM is 90,103bp in size and carries 89 open reading frames.

From ontology selection and semantic web to an integrated information system for food-borne diseases and food safety.

Several factors have hindered effective use of information and resources related to food safety due to inconsistency among semantically heterogeneous data resources, lack of knowledge on profiling of food-borne pathogens, and knowledge gaps among research communities, government risk assessors/managers, and end-users of the information. This paper discusses technical aspects in the establishment of a comprehensive food safety information system consisting of the following steps: (a) computational collection and compiling publicly available information, including published pathogen genomic, proteomic, and metabolomic data; (b) development of ontology libraries on food-borne pathogens and design automatic algorithms with formal inference and fuzzy and probabilistic reasoning to address the consistency and accuracy of distributed information resources (e.g.

Identification of optimal protocols for sequencing difficult templates: results of the 2008 ABRF DNA Sequencing Research Group difficult template study 2008.

The 2008 ABRF DNA Sequencing Research Group (DSRG) difficult template sequencing study was designed to identify a general set of guidelines that would constitute the best approaches for sequencing difficult templates. This was a continuation of previous DSRG difficult template studies performed in 1996, 1997, and 2003. The distinguishing factors in the present study were the number of DNA templates used, the number of different types of difficult regions tested, and the inclusion of a follow-up phase of the study to identify optimal protocols for each type of difficult template.

Broiler Campylobacter contamination and human campylobacteriosis in Iceland.

To examine whether there is a relationship between the degree of Campylobacter contamination observed in product lots of retail Icelandic broiler chicken carcasses and the incidence of human disease, 1,617 isolates from 327 individual product lots were genetically matched (using the flaA short variable region [SVR[) to 289 isolates from cases of human campylobacteriosis whose onset was within approximately 2 weeks from the date of processing. When there was genetic identity between broiler isolates and human isolates within the appropriate time frame, a retail product lot was classified as implicated in human disease. According to the results of this analysis, there were multiple clusters of human disease linked to the same process lot or lots.