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Genomic data of an environmental Escherichia coli isolate shows high resemblance to E. coli K-12 reference strain MG1655.

ABSTRACT: Escherichia coli species exhibits a high genomic diversification from evolution, mobile genetic elements and recombination. An environmental E. coli isolate, 'JHI_5025' from a crop trial appeared to be clonally related to the historical reference isolate E. coli K-12 strain 'MG1655', warranting further genomic analysis. Their genomes share an average nucleotide identity of 99.74% and whole genome alignment showed little rearrangement of the JHI_5025 sequence compared to the reference. Five genomic islands not in the reference aligned to other sequences in the Enterobacteriaceae. Isolate JHI_5025 contained E. coli K-12 F plasmid sequence and at least one complete prophage sequence. The genome and comparison dataset provides utility of E. coli JHI_5025 as a representative contemporary genetic mimic of a well-known and much used workhorse strain.

SUBMITTER: Holden N

PROVIDER: S-EPMC8609132 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Genomic data of an environmental Escherichia coli isolate shows high resemblance to E. coli K-12 reference strain MG1655.

Holden Nicola N

Data in brief 20211118

Escherichia coli species exhibits a high genomic diversification from evolution, mobile genetic elements and recombination. An environmental E. coli isolate, 'JHI_5025' from a crop trial appeared to be clonally related to the historical reference isolate E. coli K-12 strain 'MG1655', warranting further genomic analysis. Their genomes share an average nucleotide identity of 99.74% and whole genome alignment showed little rearrangement of the JHI_5025 sequence compared to the ...[more]

PMID: 34849384

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Project description:Escherichia coli EDL933, an O157:H7 strain, is known to colonize the streptomycin-treated CD-1 mouse intestine by growing in intestinal mucus (E. A. Wadolkowski, J. A. Burris, and A. D. O'Brien, Infect. Immun. 58:2438-2445, 1990), but what nutrients and metabolic pathways are employed during colonization has not been determined. In this study, when the wild-type EDL933 strain was fed to mice along with an EDL933 DeltappsA DeltapckA mutant, which is unable to utilize tricarboxylic acid cycle intermediates and gluconeogenic substrates for growth, both strains colonized the mouse intestine equally well. Therefore, EDL933 utilizes a glycolytic substrate(s) for both initial growth and maintenance when it is the only E. coli strain fed to the mice. However, in the presence of large numbers of MG1655, a K-12 strain, it is shown that EDL933 utilizes a glycolytic substrate(s) for initial growth in the mouse intestine but appears to utilize both glycolytic and gluconeogenic substrates in an attempt to maintain colonization. It is further shown that MG1655 predominantly utilizes glycolytic substrates for growth in the mouse intestine whether growing in the presence or absence of large numbers of EDL933. Data are presented showing that although small numbers of EDL933 grow to large numbers in the intestine in the presence of large numbers of MG1655 when both strains are fed to mice simultaneously, precolonization with MG1655 affords protection against subsequent colonization by EDL933. Moreover, in mice that are precolonized with EDL933, small numbers of MG1655 are able to grow rapidly in the intestine and EDL933 is eliminated. In situ hybridization experiments using E. coli-specific rRNA probes showed that while MG1655 is found only in mucus, EDL933 is found both in mucus and closely associated with intestinal epithelial cells. The data are discussed with respect to competition for nutrients and to the protection that some intestinal commensal E. coli strains might afford against infection by O157:H7 strains.

Project description:The use of antibiotics leads to strong stresses to bacteria, leading to profound impact on cellular physiology. Elucidating how bacteria respond to antibiotic stresses not only helps us to decipher bacteria's strategies to resistant antibiotics but also assists in proposing targets for antibiotic development. In this work, a comprehensive comparative transcriptomic analysis on how Escherichia coli responds to nine representative classes of antibiotics (tetracycline, mitomycin C, imipenem, ceftazidime, kanamycin, ciprofloxacin, polymyxin E, erythromycin, and chloramphenicol) was performed, aimed at determining and comparing the responses of this model organism to antibiotics at the transcriptional level. On average, 39.71% of genes were differentially regulated by antibiotics at concentrations that inhibit 50% growth. Kanamycin leads to the strongest transcriptomic response (76.4% of genes regulated), whereas polymyxin E led to minimal transcriptomic response (4.7% of genes regulated). Further GO, KEGG, and EcoCyc enrichment analysis found significant transcriptomic changes in carbon metabolism, amino acid metabolism, nutrient assimilation, transport, stress response, nucleotide metabolism, protein biosynthesis, cell wall biosynthesis, energy conservation, mobility, and cell-environmental communications. Analysis of coregulated genes led to the finding of significant reduction of sulfur metabolism by all antibiotics, and analysis of transcription factor-coding genes suggested clustered regulatory patterns implying coregulation. In-depth analysis of regulated pathways revealed shared and unique strategies of E. coli resisting antibiotics, leading to the proposal of four different strategies (the pessimistic, the ignorant, the defensive, and the invasive). In conclusion, this work provides a comprehensive analysis of E. coli's transcriptomic response to antibiotics, which paves the road for further physiological investigation. IMPORTANCE Antibiotics are among the most important inventions in the history of humankind. They are the ultimate reason why bacterial infections are no longer the number one threat to people's lives. However, the wide application of antibiotics in the last half a century has led to aggravating antibiotic resistance, weakening the efficacy of antibiotics. To better comprehend the ways bacteria deal with antibiotics that may eventually turn into resistance mechanisms, and to identify good targets for potential antibiotics, knowledge on how bacteria regulate their physiology in response to different classes of antibiotics is needed. This work aimed to fill this knowledge gap by identifying changes of bacterial functions at the transcription level and suggesting strategies of bacteria to resist antibiotics.

Dataset Information

Genomic data of an environmental Escherichia coli isolate shows high resemblance to E. coli K-12 reference strain MG1655.

Publications

Genomic data of an environmental <i>Escherichia coli</i> isolate shows high resemblance to <i>E. coli</i> K-12 reference strain MG1655.

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