scholarly journals Selection of unique Escherichia coli clones by random amplified polymorphic DNA (RAPD): Evaluation by whole genome sequencing

2014 ◽  
Vol 103 ◽  
pp. 101-103 ◽  
Author(s):  
Karen L. Nielsen ◽  
Paul A. Godfrey ◽  
Marc Stegger ◽  
Paal S. Andersen ◽  
Michael Feldgarden ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Random Amplified Polymorphic Dna ◽  
Whole Genome ◽  
Selection Of

scholarly journals Experimental evolution of gallium resistance in Escherichia coli

2019 ◽  
Vol 2019 (1) ◽  
pp. 169-180
Author(s):  
Joseph L Graves ◽  
Akamu J Ewunkem ◽  
Jason Ward ◽  
Constance Staley ◽  
Misty D Thomas ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Experimental Evolution ◽  
Molecular Mechanisms ◽  
Gallium Nitrate ◽  
Whole Genome ◽  
Mechanisms Of Resistance ◽  
Genomic Changes ◽  
K 12

Abstract Background and Objectives Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. Methodology Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. Results By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies > 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. Conclusions This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. Lay summary We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

scholarly journals Clinical Characteristics of Patients and Whole Genome Sequencing-Based Surveillance of Escherichia coli Community-Onset Bloodstream Infections at a Non-tertiary Hospital in CHINA

2021 ◽  
Vol 12 ◽  
Author(s):  
Fenghong Chen ◽  
Tao Lv ◽  
Yupeng Xiao ◽  
Aizhi Chen ◽  
Yonghong Xiao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Mortality Rate ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Agents ◽  
Bloodstream Infections ◽  
Tertiary Hospital ◽  
Living Environment ◽  
Whole Genome ◽  
Community Onset

Background:Escherichia coli is the most common pathogens in patients with community-onset blood stream infections (COBSI). Knowledge of the epidemiology of this disease is crucial to improve allocation of health resources, formulate isolation strategies that prevent transmission, and guide empirical antibiotic therapy.Methods: This retrospective observational study examined patients with E. coli COBSI (EC-COBSI) at a non-tertiary hospital in China. Whole-genome sequencing and analysis of the isolates was performed. The relationships of clinical variables with antimicrobial resistance and the genetic background of the isolates were examined.Results: There were 148 isolates in patients with EC-COBSI. All isolates were susceptible to ceftazidime/avibactam, carbapenems, and tigecycline; 35.1% were positive for extended spectrum β-lactamase (ESBL+); and blaCTX–M–14 was the most common ESBL gene. Patients with ESBL- isolates were more likely to receive appropriate empiric treatment than those with ESBL+ isolates (61.5% vs. 91.4%, p < 0.001), but these two groups had similar mortality rates. The overall 30-day mortality rate was 9.5%. Phylogenetic analysis showed that the isolates were diverse, and that the main sequence types (STs) were ST95, ST131, and ST69. Intra-abdominal infection was the primary source of disease, and isolates from these patients had lower frequencies of virulence genes.Conclusion: The mortality rate of patients with EC-COBSI was unrelated to ESBL status of the isolates. Most isolates had low resistance to most of the tested antimicrobial agents. The isolates were diverse, and multiple strains were related. Prevention and control of EC-COBSI should target prevention of patient colonization and the living environment.

scholarly journals Evaluating coverage bias in next-generation sequencing of Escherichia coli

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253440
Author(s):  
Samantha Gunasekera ◽  
Sam Abraham ◽  
Marc Stegger ◽  
Stanley Pang ◽  
Penghao Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
De Novo ◽  
Fragment Size ◽  
Gc Content ◽  
Main Concern ◽  
Whole Genome ◽  
Assembly Quality ◽  
Coverage Bias

Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.

scholarly journals Isolation and Identification of Kidney-derived Pathogenic Escherichia coli from Red Panda (Ailurus fulgens)

2020 ◽  
Author(s):  
Songrui Liu ◽  
Yunli Li ◽  
Chanjuan Yue ◽  
Dongsheng Zhang ◽  
Xiaoyan Su ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Infection ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Ex Situ ◽  
Type I ◽  
Pathogenicity Test ◽  
Whole Genome ◽  
Red Panda ◽  
Ailurus Fulgens

Abstract Background Disease prevention and control is a significant part during the ex-situ conservation of the red panda (Ailurus fulgens) with bacterial infection being one of the important threats to the health of the captive population. So far, there was no systematic and detailed publications about the red panda-related E. coli disease. This study was conducted for the purpose of determining the cause of death, etiology and pathogenesis on a red panda through clinical symptoms, complete blood count, biochemical analysis, pathological diagnosis, antimicrobial susceptibility test, mouse pathogenicity test, and bacterial whole genome sequencing.Results A bacterial strain confirmed as Uropathogenic Escherichia coli (UPEC) was isolated from one captive dead red panda, which is resistant to most of the β-lactam drugs and a small number of aminoglycoside medications. The mouse pathogenicity test results showed the strains isolated postmortem from mice were the same as from the dead red panda, and the pathological findings were similar to the red panda while they were not completely the same. These pathological differences between red panda and mice may be related to the routes of infection and perhaps species differences and tolerance. The whole genome sequencing results showed that the isolated strain contained P pili, type I pili and iron uptake system related factors, which were closely related to its nephrotoxicity. Conclusion The red panda died of bacterial infection which was identified as Uropathogenic Escherichia coli. The pathogenic mechanisms of the strain are closely related to the expression of specific virulence genes.

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