Salmonella serotype prediction using the GalaxyTrakr SeqSero2 workflow v1

Salmonella serotypes are defined by two surface structures, O antigen and two H antigens. Traditional serotype determination is performed with the Salmonella serological somatic (O) and flagellar (H) tests and paired with biochemical confirmation. More than 2,600 Salmonella serotypes have been described in the White-Kauffmann-Le Minor scheme. Molecular methods for serotype determination have been developed based on genes responsible for serotype antigens. These genes are encoded in the rfb gene cluster, fliC, and fljB. SeqSero2 is a bioinformatic pipeline that uses whole genome sequence (WGS) data from pure-culture isolates to perform in silico analysis to determine the antigenic formula, including somatic (O) antigens and both flagellar (H) antigens. This provides continuity with the well-established scheme for phenotypic Salmonella serotypes. PURPOSE: This document outlines the steps required to run SeqSero2 v1.1.1 on a collection of isolates in the GalaxyTrakr environment. This is performed by utilizing a custom workflow called “SeqSero2 v1.1.1 collection workflow” and downloading the resulting table. SCOPE: This protocol covers the following tasks: 1. set up an account in GalaxyTrakr 2. Create a new history/workspace 3. Upload data 4. Execute the SeqSero2 workflow 5. Download the results

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Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

European Journal of Plant Pathology ◽

10.1007/s10658-020-02190-8 ◽

2021 ◽

Author(s):

Viola Kurm ◽

Ilse Houwers ◽

Claudia E. Coipan ◽

Peter Bonants ◽

Cees Waalwijk ◽

...

Keyword(s):

Ralstonia Solanacearum ◽

In Silico ◽

Species Complex ◽

Sequence Data ◽

In Silico Analysis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

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NCBI submission protocol for microbial pathogen surveillance v2

10.17504/protocols.io.bz7cp9iw ◽

2021 ◽

Author(s):

Ruth E Timme ◽

Maria Balkey ◽

Robyn Randolph ◽

Julie Haendiges ◽

Sai Laxmi Gubbala Venkata ◽

...

Keyword(s):

Active Surveillance ◽

Genome Sequence ◽

Large Volume ◽

Pathogen Detection ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Web Interface ◽

Data Submission ◽

Set Up

PURPOSE: Step-by-step instructions for submitting pathogen whole genome sequence data to NCBI and to the NCBI Pathogen Detection portal. This protocol covers the steps needed to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. SCOPE: for use by any laboratory submitting WGS data for species under active surveillance within NCBI’s Pathogen Detection. (This includes US laboratories in GenomeTrakr, NARMS, Vet-LIRN, PulseNet, and other non-US networks and submitters). For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. This protocol covers submission using NCBI's Submission Portal web-interface. Version history: V5: Linking directly to the metadata template guidance instead of including duplicate copies of the files in this protocol. Updated screenshot for choosing the pathogen template to reflect changes at NCBI. V4: updated screenshots to reflect NCBI submission portal changes. Updated custom BioSample template.

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High-Throughput Crystallization Pipeline at the Crystallography Core Facility of the Institut Pasteur

Molecules ◽

10.3390/molecules24244451 ◽

2019 ◽

Vol 24 (24) ◽

pp. 4451 ◽

Cited By ~ 6

Author(s):

Patrick Weber ◽

Cédric Pissis ◽

Rafael Navaza ◽

Ariel E. Mechaly ◽

Frederick Saul ◽

...

Keyword(s):

High Throughput ◽

Sequence Data ◽

Data Bank ◽

Whole Genome Sequence ◽

Whole Genome ◽

X Ray Diffraction ◽

Sequencing Technology ◽

X Ray ◽

Set Up ◽

General User

The availability of whole-genome sequence data, made possible by significant advances in DNA sequencing technology, led to the emergence of structural genomics projects in the late 1990s. These projects not only significantly increased the number of 3D structures deposited in the Protein Data Bank in the last two decades, but also influenced present crystallographic strategies by introducing automation and high-throughput approaches in the structure-determination pipeline. Today, dedicated crystallization facilities, many of which are open to the general user community, routinely set up and track thousands of crystallization screening trials per day. Here, we review the current methods for high-throughput crystallization and procedures to obtain crystals suitable for X-ray diffraction studies, and we describe the crystallization pipeline implemented in the medium-scale crystallography platform at the Institut Pasteur (Paris) as an example.

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The role of mobile genetic elements in evolution of cyanobacteria

Ecological genetics ◽

10.17816/ecogen9452-62 ◽

2011 ◽

Vol 9 (4) ◽

pp. 52-62

Author(s):

Lidia E Mikheeva ◽

Elena A Karbysheva ◽

Sergey V Shestakov

Keyword(s):

Gene Regulation ◽

Significant Role ◽

In Silico ◽

In Silico Analysis ◽

Whole Genome ◽

Number Of Genes ◽

Genes Encoding ◽

Adaptation Processes ◽

Silico Analysis

Possible pathways of cyanobacterial evolution are discussed on the basis of in silico analysis of fully sequenced genomes of 45 species/strains of cyanobacteria. The information on quantity and functions of different mobile elements (IS, MITE elements and group II introns) was reviewed. Positive correlation between whole genome sizes and number of genes, encoding transposases has been revealed. It is suggested that transpositions play significant role in genome rearrangements taking part in gene regulation and adaptation processes determining the directions of microevolution processes in cyanobacterial populations.

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Evaluation of applicability of DNA microarray–based characterization of bovine Shiga toxin–producing Escherichia coli isolates using whole genome sequence analysis

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638717700689 ◽

2017 ◽

Vol 29 (5) ◽

pp. 721-724 ◽

Cited By ~ 2

Author(s):

Stefanie A. Barth ◽

Christian Menge ◽

Inga Eichhorn ◽

Torsten Semmler ◽

Derek Pickard ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Microarray ◽

Shiga Toxin ◽

In Silico ◽

Whole Genome Sequence ◽

Whole Genome ◽

Molecular Surveillance ◽

Antimicrobial Resistance Genes ◽

O Antigens

We assessed the ability of a commercial DNA microarray to characterize bovine Shiga toxin–producing Escherichia coli (STEC) isolates and evaluated the results using in silico hybridization of the microarray probes within whole genome sequencing scaffolds. From a total of 69,954 reactions (393 probes with 178 isolates), 68,706 (98.2%) gave identical results by DNA microarray and in silico probe hybridization. Results were more congruent when detecting the genoserotype (209 differing results from 19,758 in total; 1.1%) or antimicrobial resistance genes (AMRGs; 141 of 26,878; 0.5%) than when detecting virulence-associated genes (VAGs; 876 of 22,072; 4.0%). Owing to the limited coverage of O-antigens by the microarray, only 37.2% of the isolates could be genoserotyped. However, the microarray proved suitable to rapidly screen bovine STEC strains for the occurrence of high numbers of VAGs and AMRGs and is suitable for molecular surveillance workflows.

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