Project description:Various species of the intestinal microbiota have been associated with the
development of colorectal cancer (CRC), yet a direct role of bacteria in the
occurrence of oncogenic mutations has not been established. Escherichia coli can
carry the pathogenicity island pks, which encodes a set of enzymes that
synthesize colibactin. This compound alkylates DNA on adenine residues and
induces double strand breaks in cultured cells. Here, we exposed human intestinal
organoids to genotoxic pks+ Escherichia coli by repeated luminal injection over a
period of 5 months. Whole genome sequencing (WGS) of clonal organoids before
and after this exposure reveals a distinct mutational signature, absent from
organoids injected with isogenic pks-mutant bacteria. The same mutational
signature is detected in a subset of 3668 human metastatic cancer genomes,
predominantly in a subset of CRC cases. Our study describes a distinct mutational
signature in CRC and implies that the underlying mutational process directly
results from past exposure to bacteria carrying the colibactin-producing pks
pathogenicity island.
Project description:To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.
Project description:Antibiotic resistance associated with the expression of the clinically significant carbapenemases, IMP, KPC, and NDM and OXA-48 in Enterobacteriaceae is emerging as a worldwide calamity to health care. In Australia, IMP-producing Enterobacteriaceae is the most prevalent carbapenemase-producing Enterobacteriaceae (CPE). Genomic characteristics of such carbapenemase-producing Enterobacteriaceae (CPE) are well described, but the corresponding proteome is poorly characterised. We have thus developed a method to analyse dynamic changes in the proteome of CPE under antibiotic pressure. Specifically, we have investigated the effect of meropenem at sub-lethal concentrations to develop a better understanding of how antibiotic pressure leads to resistance. Escherichia coli, producing either NDM, IMP or KPC type carbapenemase were included in this study, and their proteomes were analysed in growth conditions with or without meropenem.
Project description:We performed evolution of Escherichia coli K12 MG1655 to study how the system adapt to iron toxicity. RNA-Seq was performed to examine the underlying transcriptional rewiring.
Project description:Avian Pathogenic Escherichia coli (APEC) are a group of extra-intestinal E. coli that infect poultry, and are able to cause a variety of diseases, systemic or localized, collectively designated as colibacillosis. Colibacillosis is the most common bacterial illness in poultry production, resulting in significant economic losses world-wide. Despite of its importance, pathogenicity mechanisms of APEC strains remain not completelly elucidated and available vaccines are not fully effectives. In order to better understand which genes could be related to pathogenicity in different APEC isolated, a microarray analyses of two APEC strains representing: Swollen Head Syndrome and Omphalitis was carried out.
2013-06-18 | GSE48015 | GEO
Project description:NDM producing mcr-1 positive E. coli
Project description:Primary objectives: The study investigates whether a Escherichia coli Nissle-suspenison has a (preventive) antidiarrheal effect in patients with tumors who are treated with chemotherapeutic schemes which are associated with increased occurances of diarrhea. Diarrhea caused by treatment are thought to be reduced in intensity and/or frequency by the treatment with Escherichia coli Nissle-Suspension.
Primary endpoints: Common toxicity criteria (CTC) for diarrhea
Project description:We performed evolution of Escherichia coli K12 MG1655 to study how the system adapts to loss of ubiC gene involved in ubiquinone biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring.
