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Posts Tagged ‘Next Generation Sequencing’

Extended scope for Gut Pathogens

December 19, 2013 Leave a comment

Gut Pathogens is pleased to announce an extended scope for the journal. This scope reflects a broad range of topics, including metagenomics, new genome sequences, microbiota profiling and systems biology, as well as the biological and clinical aspects of gut microbes.

Topical areas include, but are not limited to:

  • Microbial etiology of gut ailments
  • Gut invasion mechanisms
  • Microbial toxins and virulence factors in infections of the gut and associated glands – liver, pancreas
  • Bacterial adaptation to gut niches and evolution of pathogenicity
  • Biology and ecology of gut commensals and microbiota in health and disease
  • Biology and ecology of probiotic organisms
  • Host susceptibility or resistance to gut pathogens
  • Immune mechanisms of gut infections
  • Etiology of inflammatory bowel diseases
  • Molecular and serological diagnosis
  • Treatment and drug resistance mechanisms
  • Molecular epidemiology, transmission dynamics and evolutionary genetics
  • Vaccines for gut pathogens
  • Comparative and veterinary infectious diseases of the gut
  • Pathogenesis of bacterial, parasitic and viral infections of the gut
  • Genome sequencing, comparative genomics and systems biology
  • Microbiota analysis, metagenomics and gut microbiomes

Please visit the Gut Pathogens website to view the full journal scope.

We will be happy to answer any pre-submission enquiries at editorial@gutpathogens.com.

Gut Pathogens

Prospective genomics in epidemics – lessons from the German E. coli outbreak

July 23, 2011 Leave a comment

The Open Access biomedical journal, PLoS ONE  recently published an article by Mellmann et al. entitled, Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. The following is an opinion piece by Dr. Niyaz Ahmed, who works as a section editor for PLoS ONE and the academic editor of this paper. He is an expert in the area of molecular epidemiology and genomics of bacterial pathogens at the University of Hyderabad, India. As the subject of this blog is also of significant interest to the audience of Gut Pathogens, we are reproducing Dr Ahmed’s blog post hereunder [with thanks to PLoS ONE community blog, EveryONE) where the blog was originally posted.

When a monstrously virulent strain of never-before-seen E. coli suddenly appeared in Germany last month, the rush to decode became an immediate focus. Several groups became engaged simultaneously to crack the genome of the underlying bug and then followed a huge crowd-sourcing effort on the internet as soon as the genome sequences were made available. Given that reasonable data were made available by these authors within 60 hours of the outbreak, not much of the evolutionary history of the organism had been dissected and a great deal of the interpretation remained vague. An informed, scientific treatise was needed to help health control authorities and policy makers launch a serious mitigation campaign; this work, in that sense, constitutes the first official report on the genomic footprint of the underlying E. coli strain. The authors report chronological (step-wise) recombination of the genome in the outbreak strains over a period of ten years. This reveals the extraordinary capability of certain pathogens to recombine so that a devastating phenotype finally emerges with a multi-dimensional fitness advantage. Further, the study of Mellmann et al. demonstrates the might of present-day sequencing technologies such as Ion Torrent in enabling genome-guided epidemiology, diagnostics, and interventions.

I have no hesitation to say that the study carried out by Mellmann et al. is truly a technical masterpiece, a first time proof-of-principle, whereby, next generation sequencing could be harnessed in real-time when certain ‘gold standards’ such as serotyping failed miserably. This report has an important bearing on the new proposed field of ‘epidemic forecasting’ in which the spread potentials of a pathogen could be predicted based on genomic fingerprints – in other words, predicting if the infection will assume pandemic proportions.  The finding that the E. coli strains analyzed were enteroaggregative (EAEC) could explain this. EAECs could persist in recovered or subclinical cases and that they could be carried by the latter on travel routes worldwide.

One of the possible shortcomings of the study could be that it is silent on the mechanistic details of ‘adornment’ of these bacteria with several layers of fitness – multiple antibiotic resistance, acid tolerance, enteroaggregative capacity and shigatoxin production all bundled up in one ‘naturally’ chimeric strain in just 10 years is extremely dramatic!  The pace of evolution of the German outbreak strains has surpassed even Helicobacter pylori, an organism notorious for its speed of recombination, recasting its entire genome every forty years. We recently had an opportunity to sequence and look at H. pylori genomes hierarchically obtained across ten years. We did not find major insertion, deletion and substitution events.

Technology helped with the dissection of the E. coli epidemic in hours and days, but the editorial process also was seamless and prompt enough to enable rapid dissemination of results. Open and early access is very important for the dissemination of findings during epidemic times because much of the control and mitigation measures need planning in the light of latest research findings.