Characteristics of lytic phage vB_EcoM-ECP26 and reduction of shiga-toxin producing Escherichia coli on produce romaine

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Abstract

Foodborne Shiga toxin-producing Escherichia coli (STEC) cause severe diarrhea and hemolytic uremic syndrome (HUS) in humans. However, traditional methods for STEC sterilization are difficult to apply to fresh food. To control the pathogen, phage infecting E. coli O157:H7 were isolated and characterized. The isolated phage vB_EcoM-ECP26 had an icosahedral head and a contractile tail, and was classified as belonging to the Myoviridae family. The phage showed a broad host range against STEC and exhibited a large burst size of 1914 PFU/cell. The phage was highly stable at high temperatures (65 °C) and wide ranges of pH (4–10). The genome of vB_EcoM-ECP26 consists of 136,993 nucleotides, 214 open reading frames, and does not contain lysogenicity-related genes. Phylogenetic analysis showed that vB_EcoM-ECP26 is a V5-like species. STEC O157 growth was inhibited by vB_EcoM-ECP26 for 8 h. Furthermore, this phage not only significantly decreased the STEC population (p < 0.05), but also persisted in fresh lettuce at 4 °C for 5 days. Therefore, these results reveal that the novel lytic phage vB_EcoM-ECP26 could be a useful agent for the control of foodborne STEC.

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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.

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The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.