Escherichia coli EHEC Germany outbreak preliminary functional annotation using BG7 system

Manrique, Marina; Pareja-Tobes, Pablo; Pareja-Tobes, Eduardo; Pareja, Eduardo; Tobes, Raquel

doi:10.1038/npre.2011.6001.1

Cited by 4 publications

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“…This information is relevant to understanding of the role that the horizontal gene exchange plays in evolution of new pathogens. The analysis of the complete genome sequence of the strain E. coli TY-2482 isolated from the latest outbreak of entero-aggregative-haemorrhagic (EAHEC) infection in Europe in 2011 showed that its extraordinary virulence and lethality are associated with the virulence determinants located in horizontally transferred GIs (Brzuszkiewicz, 2011); (Manrique, 2011). Enterobacteria (Escherichia, Shigella and Salmonella) share multiple GIs shown in Fig.…”

Section: Discussionmentioning

confidence: 99%

APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange

Bezuidt¹,

Mncube²,

Reva³

2012

Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms

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With more sequences of complete bacterial genomes getting public availability the approaches of genome comparison by frequencies of oligonucleotides (k-mers) known also as the genome linguistics are becoming popular and practical to resolve problems which can not be tackled by the traditional sequence comparison tools. In this work we present several innovative approaches based on k-mer statistics for detection of inserts of genomic islands and tracing down the ontological links and origins of mobile genetic elements. 637 bacterial genomes were analyzed by SeqWord Sniffer program that has detected 2,622 putative genomic islands. These genomic islands were clustered by DNA compositional similarity. A stratigraphic analysis was introduced that allows distinguishing between new and old genomic inserts. A method of reconstruction of donor-recipient relations between microorganisms was proposed. The strain E. coli TY-2,482 isolated from the latest deadly outbreak of a haemorrhagic infection in Europe in 2011 was used for the case study. It was shown that this strain appeared on an intersection of two independent fluxes of horizontal gene exchange, one of which is a conventional for Enterobacteria stream of vectors generated in marine gamma-Proteobacteria; and the second is a new channel of antibiotic resistance genomic islands originated from environmental beta-Proteobacteria.

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Section: Discussionmentioning

confidence: 99%

APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange

Bezuidt¹,

Mncube²,

Reva³

2012

Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms

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“…The efficacy, speed and specificity of BG7 for NGS projects were proved in a real case, the 2011 Germany E. coli outbreak [17]. BG7 annotations for all the sequenced isolates can be found at: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains.…”

Section: Introductionmentioning

confidence: 99%

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

Pareja-Tobes¹,

Manrique²,

Pareja-Tobes³

et al. 2012

PLoS One

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BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version – which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future.

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Infected insect gut reveals differentially expressed proteins for cellular redox, metal resistance and secretion system in Yersinia enterocolitica-Helicoverpa armigera pathogenic model

et al. 2021

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Escherichia coli EHEC Germany outbreak preliminary functional annotation using BG7 system

Cited by 4 publications

References 0 publications

APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange

APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

Infected insect gut reveals differentially expressed proteins for cellular redox, metal resistance and secretion system in Yersinia enterocolitica-Helicoverpa armigera pathogenic model

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