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Microbiology Spectrum Dec 2020is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and... (Review)
Review
is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of that cause diarrhea are often described as intestinal pathogenic (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of or pathovars. While IPEC can be distinguished from commensal based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by . *This article is part of a curated collection.
Topics: Animals; Escherichia coli; Escherichia coli Infections; Escherichia coli Proteins; Extraintestinal Pathogenic Escherichia coli; Genotype; Humans; Molecular Epidemiology; Phylogeny; Sepsis; Urinary Tract Infections; Virulence; Virulence Factors; Whole Genome Sequencing
PubMed: 33385193
DOI: 10.1128/microbiolspec.AME-0014-2020 -
Polish Journal of Microbiology Dec 2019Urinary tract infections (UTIs) belong to the most common community-acquired and nosocomial infections. A main etiological factor of UTIs is uropathogenic (UPEC). This... (Review)
Review
Urinary tract infections (UTIs) belong to the most common community-acquired and nosocomial infections. A main etiological factor of UTIs is uropathogenic (UPEC). This review describes the current state of knowledge on the resistance of UPEC to antibiotics recommended for the treatment of UTIs based on the available literature data. Nitrofurantoin and fosfomycin are recommended as first-line therapy in the treatment of uncomplicated cystitis, and the resistance to these antimicrobial agents remains low between UPEC. Recently, in many countries, the increasing resistance is observed to trimethoprim-sulfamethoxazole, which is widely used as the first-line antimicrobial in the treatment of uncomplicated UTIs. In European countries, the resistance of UPEC to this antimicrobial agent ranges from 14.6% to 60%. The widespread use of fluoroquinolones (FQs), especially ciprofloxacin, in the outpatients is the cause of a continuous increase in resistance to these drugs. The resistance of UPEC to FQs is significantly higher in developing countries (55.5-85.5%) than in developed countries (5.1-32.0%). Amoxicillin-clavulanic acid is recommended as first line-therapy for pyelonephritis or complicated UTI. Resistance rates of UPEC to amoxicillin-clavulanic acid are regionally variable. In European countries the level of resistance to this antimicrobial ranges from 5.3% (Germany) to 37.6% (France). Increasing rates of UPEC resistance to antimicrobials indicate that careful monitoring of their use for UTI treatment is necessary. Urinary tract infections (UTIs) belong to the most common community-acquired and nosocomial infections. A main etiological factor of UTIs is uropathogenic (UPEC). This review describes the current state of knowledge on the resistance of UPEC to antibiotics recommended for the treatment of UTIs based on the available literature data. Nitrofurantoin and fosfomycin are recommended as first-line therapy in the treatment of uncomplicated cystitis, and the resistance to these antimicrobial agents remains low between UPEC. Recently, in many countries, the increasing resistance is observed to trimethoprim-sulfamethoxazole, which is widely used as the first-line antimicrobial in the treatment of uncomplicated UTIs. In European countries, the resistance of UPEC to this antimicrobial agent ranges from 14.6% to 60%. The widespread use of fluoroquinolones (FQs), especially ciprofloxacin, in the outpatients is the cause of a continuous increase in resistance to these drugs. The resistance of UPEC to FQs is significantly higher in developing countries (55.5–85.5%) than in developed countries (5.1–32.0%). Amoxicillin-clavulanic acid is recommended as first line-therapy for pyelonephritis or complicated UTI. Resistance rates of UPEC to amoxicillin-clavulanic acid are regionally variable. In European countries the level of resistance to this antimicrobial ranges from 5.3% (Germany) to 37.6% (France). Increasing rates of UPEC resistance to antimicrobials indicate that careful monitoring of their use for UTI treatment is necessary.
Topics: Animals; Anti-Bacterial Agents; Drug Resistance, Bacterial; Escherichia coli Infections; Humans; Urinary Tract Infections; Uropathogenic Escherichia coli
PubMed: 31880885
DOI: 10.33073/pjm-2019-048 -
Current Opinion in Infectious Diseases Oct 2020Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize... (Review)
Review
PURPOSE OF REVIEW
Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize diarrheagenic Escherichia coli (DEC) pathotype definitions and discuss existing and emerging molecular, genomic, and gut microbiome methods to detect, define, and study DEC pathotypes.
RECENT FINDINGS
DEC pathotypes are currently diagnosed by molecular detection of unique virulence genes. However, some pathotypes have defied coherent molecular definitions because of imperfect gene targets, and pathotype categories are complicated by hybrid strains and isolation of pathotypes from asymptomatic individuals. Recent progress toward more efficient, sensitive, and multiplex DEC pathotype detection has been made using emerging PCR-based technologies. Genomics and gut microbiome detection methods continue to advance rapidly and are contributing to a better understanding of DEC pathotype diversity and functional potential.
SUMMARY
DEC pathotype categorizations and detection methods are useful but imperfect. The implementation of molecular and sequence-based methods and well designed epidemiological studies will continue to advance understanding of DEC pathotypes. Additional emphasis is needed on sequencing DEC genomes from regions of the world where they cause the most disease and from the pathotypes that cause the greatest burden of disease globally.
Topics: Diarrhea; Enteropathogenic Escherichia coli; Enterotoxigenic Escherichia coli; Escherichia coli; Escherichia coli Infections; Gastrointestinal Microbiome; Genes, Bacterial; Genomics; Humans; Polymerase Chain Reaction; Virulence; Virulence Factors
PubMed: 32773499
DOI: 10.1097/QCO.0000000000000665 -
Protein Science : a Publication of the... Aug 2019The production of proteins in sufficient amounts is key for their study or use as biotherapeutic agents. Escherichia coli is the host of choice for recombinant protein... (Review)
Review
The production of proteins in sufficient amounts is key for their study or use as biotherapeutic agents. Escherichia coli is the host of choice for recombinant protein production given its fast growth, easy manipulation, and cost-effectiveness. As such, its protein production capabilities are continuously being improved. Also, the associated tools (such as plasmids and cultivation conditions) are subject of ongoing research to optimize product yield. In this work, we review the latest advances in recombinant protein production in E. coli.
Topics: Escherichia coli; Recombinant Proteins
PubMed: 31219641
DOI: 10.1002/pro.3668 -
Trends in Pharmacological Sciences Sep 2022Engineered microbes are rapidly being developed for the delivery of therapeutic modalities to sites of disease. Escherichia coli Nissle 1917 (EcN), a genetically... (Review)
Review
Engineered microbes are rapidly being developed for the delivery of therapeutic modalities to sites of disease. Escherichia coli Nissle 1917 (EcN), a genetically tractable probiotic with a well-established human safety record, is emerging as a favored chassis. Here, we summarize the latest progress in rationally engineered variants of EcN for the treatment of infectious diseases, metabolic disorders, and inflammatory bowel diseases (IBDs) when administered orally, as well as cancers when injected directly into tumors or the systemic circulation. We also discuss emerging studies that raise potential safety concerns regarding these EcN-based strains as therapeutics due to their secretion of a genotoxic colibactin that can promote the formation of DNA double-stranded breaks in mammalian DNA.
Topics: Animals; Escherichia coli; Humans; Inflammatory Bowel Diseases; Mammals; Probiotics
PubMed: 35232591
DOI: 10.1016/j.tips.2022.02.002 -
Microbiology Spectrum Dec 2021The causative agents of recurrent Escherichia coli bacteremia can be genetically identical or discordant, but the differences between them remain unclear. This study...
The causative agents of recurrent Escherichia coli bacteremia can be genetically identical or discordant, but the differences between them remain unclear. This study aimed to explore these differences, with regard to their clinical and microbiological features. Patients were recruited from a Japanese tertiary teaching hospital based on blood culture data and the incidence of recurrent E. coli bacteremia. We compared the patients' clinical and microbiological characteristics between the two groups (those with identical or discordant E. coli bacteremia) divided by the result of enterobacterial repetitive intergenic consensus PCR. Among 70 pairs of recurrent E. coli bacteremia strains, 49 pairs (70%) were genetically identical. Patients with genetically identical or discordant E. coli bacteremia were more likely to have renal failure or neoplasms, respectively. The virulence factor (VF) scores of genetically identical E. coli strains were significantly higher than those of genetically discordant strains, with the prevalence of eight VF genes being significantly higher in genetically identical E. coli strains. No significant differences were found between the two groups regarding antimicrobial susceptibility and biofilm formation potential. This study showed that genetically identical E. coli bacteremia strains have more VF genes than genetically discordant strains in recurrent E. coli bacteremia. Escherichia coli causes bloodstream infection, although not all strains are pathogenic to humans. In some cases, this infection reoccurs, and several reports have described the clinical characteristics and/or molecular microbiology of recurrent Escherichia coli bacteremia. However, these studies focused on patients with specific characteristics, and they included cases caused by microorganisms other than Escherichia coli. Hence, little is known about the pathogenicity of Escherichia coli isolated from the recurrent one. The significance of our study is in evaluating the largest cohorts to date, as no cohort studies have been conducted on this topic.
Topics: Aged; Aged, 80 and over; Anti-Bacterial Agents; Bacteremia; Biofilms; Escherichia coli; Escherichia coli Infections; Female; Humans; Japan; Male; Microbial Sensitivity Tests; Middle Aged; Recurrence; Tertiary Care Centers; Virulence; Virulence Factors
PubMed: 34878318
DOI: 10.1128/Spectrum.01399-21 -
Archives of Microbiology Apr 2023The production of recombinant proteins is one of the most significant achievements of biotechnology in the last century. These proteins are produced in the eukaryotic or... (Review)
Review
The production of recombinant proteins is one of the most significant achievements of biotechnology in the last century. These proteins are produced in the eukaryotic or prokaryotic heterologous hosts. By increasing the omics data especially related to different heterologous hosts as well as the presence of new amenable genetic engineering tools, we can artificially engineer heterologous hosts to produce recombinant proteins in sufficient quantities. Numerous recombinant proteins have been produced and applied in various industries, and the global recombinant proteins market size is expected to be cast to reach USD 2.4 billion by 2027. Therefore, identifying the weakness and strengths of heterologous hosts is critical to optimize the large-scale biosynthesis of recombinant proteins. E. coli is one of the popular hosts to produce recombinant proteins. Scientists reported some bottlenecks in this host, and due to the increasing demand for the production of recombinant proteins, there is an urgent need to improve this host. In this review, we first provide general information about the E. coli host and compare it with other hosts. In the next step, we describe the factors involved in the expression of the recombinant proteins in E. coli. Successful expression of recombinant proteins in E. coli requires a complete elucidation of these factors. Here, the characteristics of each factor will be fully described, and this information can help to improve the heterologous expression of recombinant proteins in E. coli.
Topics: Escherichia coli; Recombinant Proteins; Biotechnology; Genetic Engineering
PubMed: 37120438
DOI: 10.1007/s00203-023-03541-9 -
Nature Biotechnology Aug 2022Living bacteria therapies have been proposed as an alternative approach to treating a broad array of cancers. In this study, we developed a genetically encoded microbial...
Living bacteria therapies have been proposed as an alternative approach to treating a broad array of cancers. In this study, we developed a genetically encoded microbial encapsulation system with tunable and dynamic expression of surface capsular polysaccharides that enhances systemic delivery. Based on a small RNA screen of capsular biosynthesis pathways, we constructed inducible synthetic gene circuits that regulate bacterial encapsulation in Escherichia coli Nissle 1917. These bacteria are capable of temporarily evading immune attack, whereas subsequent loss of encapsulation results in effective clearance in vivo. This dynamic delivery strategy enabled a ten-fold increase in maximum tolerated dose of bacteria and improved anti-tumor efficacy in murine models of cancer. Furthermore, in situ encapsulation increased the fraction of microbial translocation among mouse tumors, leading to efficacy in distal tumors. The programmable encapsulation system promises to enhance the therapeutic utility of living engineered bacteria for cancer.
Topics: Animals; Escherichia coli; Immunotherapy; Mice; Neoplasms
PubMed: 35301496
DOI: 10.1038/s41587-022-01244-y -
EcoSal Plus Dec 2023EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the... (Review)
Review
EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of . EcoCyc is an electronic reference source for biologists and for biologists who work with related microorganisms. The database includes information pages on each gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on the regulation of gene expression, gene essentiality, and nutrient conditions that do or do not support the growth of . The website and downloadable software contain tools for the analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed online. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. Data generated from a whole-cell model that is parameterized from the latest data on EcoCyc are also available. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
Topics: Escherichia coli; Escherichia coli K12; Databases, Genetic; Software; Computational Biology; Escherichia coli Proteins
PubMed: 37220074
DOI: 10.1128/ecosalplus.esp-0002-2023 -
International Journal of Molecular... Dec 2022The bacterial archetypal adaptive immune system, CRISPR-Cas, is thought to be repressed in the best-studied bacterium, K-12. We show here that the CRISPR-Cas system is...
The bacterial archetypal adaptive immune system, CRISPR-Cas, is thought to be repressed in the best-studied bacterium, K-12. We show here that the CRISPR-Cas system is active and serves to inhibit its nine defective (i.e., cryptic) prophages. Specifically, compared to the wild-type strain, reducing the amounts of specific interfering RNAs (crRNA) decreases growth by 40%, increases cell death by 700%, and prevents persister cell resuscitation. Similar results were obtained by inactivating CRISPR-Cas by deleting the entire 13 spacer region (CRISPR array); hence, CRISPR-Cas serves to inhibit the remaining deleterious effects of these cryptic prophages, most likely through CRISPR array-derived crRNA binding to cryptic prophage mRNA rather than through cleavage of cryptic prophage DNA, i.e., self-targeting. Consistently, four of the 13 spacers contain complementary regions to the mRNA sequences of seven cryptic prophages, and inactivation of CRISPR-Cas increases the level of mRNA for lysis protein YdfD of cryptic prophage Qin and lysis protein RzoD of cryptic prophage DLP-12. In addition, lysis is clearly seen via transmission electron microscopy when the whole CRISPR-Cas array is deleted, and eliminating spacer #12, which encodes crRNA with complementary regions for DLP-12 (including ), Rac, Qin (including ), and CP4-57 cryptic prophages, also results in growth inhibition and cell lysis. Therefore, we report the novel results that (i) CRISPR-Cas is active in and (ii) CRISPR-Cas is used to tame cryptic prophages, likely through RNAi, i.e., unlike with active lysogens, active CRISPR-Cas and cryptic prophages may stably co-exist.
Topics: Prophages; Escherichia coli; CRISPR-Cas Systems; Escherichia coli K12; Bacteria
PubMed: 36555835
DOI: 10.3390/ijms232416195