K. pneumoniae KpQ3 was isolated from a blood culture from a burn unit patient in the context of a small outbreak at Hospital Universitario La Paz. Oh no sequences team from Era7 Bioinformatics did the assembly and the annotation of the genome. Assembly was done with Newbler and manually refined. The KpQ3 genome was submitted to GenBank (AMSU00000000) with 73 contigs assembled in 18 scaffolds with a genome global length of 5,401,505 bp. Genome annotation was done using the Era7 Bioinformatics' Bacterial Genome Annotation system BG7.
This work, published in the journal Genome Announcements from the American Association of Microbiology, is a new success of Era7 Bioinformatics related to its project NEXTMICRO. The goal of this project is the development of a platform able to manage all the NGS sequence data and related data important in an outbreak. The NEXTMICRO project includes the BG7 annotation system and new Cloud Computing pipelines and services specially designed or adapted to manage NGS outbreak data from hospital and community outbreaks.
]]>In this article Dr. Fernando Baquero and Dr. Raquel Tobes discuss how "as in a crowdsourcing software project, the evolution of O104:H4 starts with an initial plastic bacterium project onto which new elements, including pathogenicity genes, are anonymously contributed by similar bacteria. At the end, we have different combinations of elements that develop and grow continuously within the crowdsourcing community. How to follow that process is the aim of predicting risks for future outbreaks.
Surveilling a reduced number of conserved genes can produce deceiving results, because pathogenicity genes are frequently allocated to mobile modules with little sequence conservation. The availability of next-generation sequencing (NGS) technologies allows us to reveal the complete gene landscape of a bacterium and, moreover, of a community of bacteria. This new perspective on outbreaks circumvents the old bias of looking only at specific conserved genes belonging to the causative agents. NGS enables scientists to trace the importance of gene units that move freely between strains and to analyze the flux of these genes between bacterial communities. In the postgenomics era, NGS technologies are providing public health efforts with advanced and quick tools that allow researchers not only to retrospectively analyze the epidemiological evolution of an outbreak but also to predict its future evolution."
]]>BG7, the Era7 Bioinformatics bacterial genome annotation recently published in PLOS ONE, will be a solid foundation from which to grow the Bacterial genomics and comparative genomics services that Era7 Bioinformatics will commercialize in the USA during 2013.
MG7, the core method in Era7 Bioinformatics for Microbial diversity analysis using cloud computing, is the other innovative service that we offer to researches interest in microbiology and related fields like microbiome.
“When we first thought about expanding our company outside of Spain, we felt that the USA would be the first foreign market for us and that Massachusetts was the best option for our business,” said Era7 CEO, Eduardo Pareja. “Massachusetts will offer our company two important pieces: The most innovative and advanced public and private research activities around genomics, biomedicine and biotechnology, and the best place to attract talented people to grow and extend our bacterial genomics-based business.”
“Thanks to our growth strategy of investing in education, innovation and infrastructure, Massachusetts continues to lead the world in life sciences,” said Governor Deval Patrick. “We welcome Era7 Bioinformatics to Massachusetts and look forward to their contributions to our thriving life sciences community.”
“On behalf of the Center, I would like to extend our warmest congratulations to the team at Era7 as they open their first U.S. office here in Massachusetts,” said Susan Windham-Bannister, Ph.D., President & CEO of the Massachusetts Life Sciences Center, the agency charged with implementing Governor Patrick’s 10-year, $1 billion Life Sciences Initiative. “The Commonwealth has emerged as a stand-out leader in the field of bioinformatics, with a strong, technology-oriented workforce that will provide a depth of talent for Era7 as they grow their business here.”
Era7 worked closely with the Massachusetts Life Sciences Center as they developed their plans for their first U.S. office.
“Congratulations to Eduardo and the Era7 team on the opening of their first U.S. office; it is an achievement not just for the company, but for the Massachusetts supercluster, which continues to grow as the U.S. base for international life sciences companies,” said Robert K. Coughlin, President & CEO of MassBio, a biotechnology trade association representing 600+ member organizations. “We are excited to be a destination for innovative companies like Era7.”
More than one-half of all the genomic information available today, globally, comes from bacteria. Next Generation Sequencing technologies have radically changed the scenario of genomic data acquisition by means of lowering the sequencing prices by a factor of more than one-thousand over the past five years. Era7’s BG7 bacterial genome annotation system was specially designed for Next Generation Sequencing data for a bacterial genome. The open source BG7 system, which was successfully used last year to obtain one of the first annotations of the E. coli German outbreak genome, was recently published in the open access journal, PLOS ONE.
Founded in 2004, Era7 has become a leading company in Next Generation Sequencing and bacterial genomics in Spain. Era7 is headquartered in Granada, with offices in Madrid, and currently employs 16 people, the majority of whom are researchers investigating new approaches for Genomics data analysis based in Cloud Computing.
Era7’s new U.S. office is based at:
Era7 Bioinformatics
Cambridge Innovation Center
14th floor
Cambridge, MA 02142
USA
About Era7 Bioinformatics
Era7 Bioinformatics is a Next Generation Sequencing service provider that specializes in Microbial genomics. Its business model is based on offering complete and integrated solutions, from project design to deep bioinformatics analysis and reporting. Era7 Bioinformatics is based in Research, Cloud Computing, Open Source and bacterial genomics specialization.
Contacts:
Eduardo Pareja
CEO
Era7 Bioinformatics
[email protected]
Phone: 617-401-3340
Angus G. McQuilken
Vice President for Communications & Marketing
Massachusetts Life Sciences Center
[email protected]
617-921-7749
MLSC Disclaimer: This announcement is not intended to be a commercial endorsement of any products or services provided or developed by the entities referenced in this release.
BG7 bacterial genome annotation system from Era7 Bioinformatics is specially designed for Next Generation Sequencing data. BG7 is tolerant for the typical errors of NGS data and able to get a good functional annotation for a bacterial genome in the draft stage even when the genome is fragmented in thousands of contigs. An original approach that integrates, in only one step, gene prediction and functional annotation, makes possible this optimal performance for NGS bacterial genome data.
The open source BG7 system that was successfully used last year to get one of the first annotations of the E. coli German outbreak genome ( https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki) has just been published in the open access journal PLOS ONE: http://dx.plos.org/10.1371/journal.pone.0049239.
Era7 Bioinformatics (www.era7bioinformatics.com ) is a Next Generation Sequencing service provider specialized in Microbial genomics. Its business model is based in offering complete and integrated solutions, from project design to deep bioinformatics analysis and reporting. Era7 bioinformatics is based in Research, Cloud Computing, Open Source and knowledge area specialization.
Klebsiella pneumoniae is a bacterium frequently found in the mouth and gut of healthy humans. In most instances, it does not lead to disease but it can mutate opportunistically and cause diverse types of infections. The bacterium also has a significant capacity to acquire antibiotic resistance. Three closely related isolates of a pathogenic strain of K. pneumonia with increasing degrees of antibiotic resistance were obtained in the Microbiology department at Hospital Universitario La Paz and sequenced at LifeSequencing in Valencia, Spain using the long read GS FLX+ System, developed by 454 Life Sciences, a Roche Company
The sequencing data was assembled using the GS De Novo Assembler software and functional annotation was performed to identify the relevant genes codified in the three genomes with BG7, the optimized system developed by Era 7 Bioinformatics, providing rich functional annotation of 454 Sequencing data.
The researchers found that the three bacteria strains showed an increasing resistance pattern to a wide range of the antibiotics most commonly used at the hospital. Comparison of the genomes will give insights regarding how antibiotic resistance evolves within K. pneumonia and will aid in efforts to reduce the increasing prevalence of antibiotic resistance worldwide. In addition, the comparison of these genomes with other previously studied bacteria will help to understand how a microorganism that is part of our normal microbiome can become a dangerous pathogen.
“Fast and affordable sequencing of pathogenic bacteria is a huge qualitative and quantitative advance that is radically changing the way researchers and clinicians view the infectious disease process,” said Dr. Jesús Mingorance lead researcher at the Hospital Universitario La Paz. The GS FLX+ and GS Junior Systems from Roche are aiding in these pathogen detection and bacterial comparative genomics efforts worldwide.
About Roche
Headquartered in Basel, Switzerland, Roche is a leader in research-focused healthcare with combined strengths in pharmaceuticals and diagnostics. Roche is the world’s largest biotech company with truly differentiated medicines in oncology, virology, inflammation, metabolism and CNS. Roche is also the world leader in in-vitro diagnostics, tissue-based cancer diagnostics and a pioneer in diabetes management. Roche’s personalized healthcare strategy aims at providing medicines and diagnostic tools that enable tangible improvements in the health, quality of life and survival of patients. In 2011, Roche had over 80,000 employees worldwide and invested over 8 billion Swiss francs in R&D. The Group posted sales of 42.5 billion Swiss francs. Genentech, United States, is a wholly owned member of the Roche Group. Roche has a majority stake in Chugai Pharmaceutical, Japan. For more information: www.roche.com.
About IdiPAZ
The IdiPAZ Institute for Health Research was created as a place for biomedical research, as a result of the relationship that has been forged over the years between La Paz University Hospital (HULP) and the Autonomous University of Madrid (UAM). This strategic alliance has enabled multidisciplinary teams belonging to the above institutions to be set up in order to take on joint research projects, making the most of the human and material research resources at their disposal and promoting fundraising for research. For more information: www.idipaz.es.
About Era7 Bioinformatics
Era7 bioinformatics is the leading Spanish Next Generation Sequencing bioinformatics company with a business model based on Research, Open Source and the use of Amazon Cloud Computing. Its focus on bacterial genomics has led to the development of BG7, an innovative pipeline for bacterial genome annotation designed for Next Generation Sequencing data. For more information: www.era7bioinformatics.com.
About LifeSequencing
LifeSequencing is based in Valencia, Spain. It is the leading Spanish company in Next Generation Sequencing data generation and interpretation. Lifesequencing is specialized in developing Taylor made massive sequencing solutions for answering any question that researchers and private companies may arise. For further information: www.lifesequencing.com.
Reports and Deliverables
What do you get at the end?
Annotation files in standard formarts: gff, genbank, xml...