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Extraintestinal Pathogenic Escherichia coli

Extraintestinal Pathogenic Escherichia coli (ExPEC) are a subgroup of E. coli bacteria that can cause infections outside the intestinal tract, such as urinary tract infections, sepsis, and meningitis.
These pathogenic strains have acquired virulence factors that enable them to invade and colonize extraintestinal sites.
Resarchers studying ExPEC can optimize their work using PubCompare.ai, a tool that helps locate relevant protocols from literature, preprints, and patents, while leveraging AI-driven comparisons to identify the best protocols and products.
This can enhance the reproducibility and accuracy of ExPEC studies, leading to more reliable results.
With PubCompare.ai's powerful features, scientists can streamline their ExPEC research and gain valuable insights more efficiently.

Most cited protocols related to «Extraintestinal Pathogenic Escherichia coli»

1
Validation of ExPEC Virulence Markers
The initial proof of concept analysis used nine strains—hereafter termed control strains—that had previously been classified by multiplex PCR as representing ExPECJJ. They were included for validation of 18 singleton genes and genes representing two operons (foc-sfa and afa-dra-daa) in the VirulenceFinder ExPEC database (6 (link)). Of the nine control strains, five (BioProject accession numbers PRJNA169903, PRJNA475142, PRJNA479435, PRJNA475142, PRJNA16235) had publicly available genomes that, for this study, were collected from NCBI, whereas two (11A and 31A) underwent WGS within this study. One of the nine control strains (L31) ultimately was excluded for reasons described in Text S1 in the supplemental material. Additionally, strain JJ055 (positive for fimH and ompT) was replaced by K-12 strain MG1655 (GenBank accession number U00096.3) as a non-ExPEC negative control.
Malberg Tetzschner A.M., Johnson J.R., Johnston B.D., Lund O, & Scheutz F. (2020). In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. Journal of Clinical Microbiology, 58(10), e01269-20.
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Publication 2020
Extraintestinal Pathogenic Escherichia coli Genes Genome Multiplex Polymerase Chain Reaction Operon Strains
2
Expanding E. coli Virulence Database
To supplement VirulenceFinder's existing E. coli virulence gene database as of study onset (101 genes, 936 alleles), a supplemental ExPEC FASTA database containing a selection of diverse ExPEC-associated genes was constructed. Genes were identified as candidates for inclusion based on the genes used in the two main established operational definitions for ExPEC and UPEC (4 (link), 5 (link)) and recommendations from expert colleagues (authors J. R. Johnson and B. D. Johnston as well as Erick Denamur [INSERM, Universités Paris Diderot et Paris Nord, France] and David M. Gordon [Ecology and Evolution, Research School of Biology, the Australian National University, Acton, Australia]). As a proof of concept, the database was validated first by comparing PCR virulence genotyping results obtained in previous studies for nine control strains (6 (link)) with the virulence genes predicted here in silico for the same nine strains by using the revised VirulenceFinder to analyze the WGS data of these strain. A second evaluation was done by comparing (previous and new) PCR virulence genotyping results for 288 clinical and fecal strains of human origin that had been classified previously as ExPECJJ versus non-ExPECJJ (11 (link)) with the virulence genes predicted here by applying the revised VirulenceFinder to the WGS data of these strains. Finally, using WGS-based pathotype classifications as derived using the revised VirulenceFinder, the ExPECJJ/non-ExPECJJ status of these 288 strains was compared with their UPECHM/non-UPECHM status.
Malberg Tetzschner A.M., Johnson J.R., Johnston B.D., Lund O, & Scheutz F. (2020). In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. Journal of Clinical Microbiology, 58(10), e01269-20.
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Publication 2020
Alleles Biological Evolution Escherichia coli Extraintestinal Pathogenic Escherichia coli Feces Genes Genes, vif Strains Virulence
3
Classifying ExPEC and UPEC Strains
The final ExPEC virulence gene database was added to the existing E. coli VirulenceFinder database (https://bitbucket.org/genomicepidemiology/virulencefinder_db/src/master/) (9 (link)). WGS sequences were uploaded to VirulenceFinder as either assembled genomes (control strains) or raw reads (evaluation strains) using a threshold of 80% identity and a minimum length of 60%. Strains were classified as ExPECJJ if positive for ≥2 of the following: papAH and/or papC (P fimbriae), sfa-focDE (S and F1C fimbriae), afa-draBC (Dr-binding adhesins), iutA (aerobactin siderophore system), and kpsM II (group 2 capsules) (6 (link)). Strains were considered positive for afa-draBC if a combination of afaB or nfaE and also afaC was identified and for the sfa-focDE operon by WGS if a combination of focC or sfaE and also focI or sfaD was identified. Strains were classified as UPECHM if positive for two or more of the following: chuA (heme uptake), fyuA (yersiniabactin siderophore system), vat (vacuolating toxin), and yfcV (adhesin) (5 (link)).
Malberg Tetzschner A.M., Johnson J.R., Johnston B.D., Lund O, & Scheutz F. (2020). In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. Journal of Clinical Microbiology, 58(10), e01269-20.
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Publication 2020
Adhesins, Bacterial aerobactin Bacterial Fimbria Capsule Escherichia coli Extraintestinal Pathogenic Escherichia coli Genome Heme Operon Siderophores Strains Toxins, Biological Virulence yersiniabactin
4
Extraintestinal Pathogenic E. coli Protocol
All ExPEC strains used in this study were isolated from extraintestinal tissues, among which PCN033 was a swine cerebrospinal fluid isolate [27 (link)]. E. coli strain RS218 (O18:K1:H7) was obtained also as a cerebrospinal fluid isolate from a case of neonate meningitis, which used as the positive control strain, and E. coli K12 strain HB101 was as the negative strain [13 (link), 55 (link)]. All E. coli strains were grown aerobically at 37°C in Luria–Bertani (LB) medium unless other specified.
The hBMEC cell line was kindly provided by Prof. Kwang Sik Kim in Johns Hopkins University School of Medicine [56 (link), 57 (link)], and was routinely cultured in RPMI1640 supplemented with 10% heat-inactivated fetal bovine serum, 10% Nu-Serum, 2 mM L-glutamine, 1 mM Sodium pyruvate, nonessential amino acids, vitamins, and penicillin and streptomycin (100 U/mL) in 37°C incubator under 5% CO2 until monolayer confluence. In some experiments, confluent hBMEC was washed thrice with Hanks' Balanced Salt Solution (Corning Cellgro, Manassas, VA, USA) and starved in serum-free medium (1:1 mixture of Ham's F-12 and M-199) for 16–18 h before further treatment. As specified in some assays, cells were pretreated with various inhibitors prior to addition of the bacteria.
Yang R., Liu W., Miao L., Yang X., Fu J., Dou B., Cai A., Zong X., Tan C., Chen H, & Wang X. (2016). Induction of VEGFA and Snail-1 by meningitic Escherichia coli mediates disruption of the blood-brain barrier. Oncotarget, 7(39), 63839-63855.
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Publication 2016
Amino Acids Bacteria Biological Assay Cell Lines Cells Cerebrospinal Fluid Escherichia coli Escherichia coli K12 Extraintestinal Pathogenic Escherichia coli Fetal Bovine Serum Glutamine Hanks Balanced Salt Solution Infant, Newborn inhibitors Meningitis Penicillins Pyruvate Serum Sodium Strains Streptomycin Sus scrofa Tissues Vitamins
5
Transposon Mutagenesis of ExPEC F11
A detailed protocol for the transposon mutagenesis of ExPEC strain F11 using the E. coli donor strain EcS17 carrying pSAM-Ec and the methods to verify and sequence mutant libraries is provided in Protocol S1. Briefly, EcS17/pSAM-Ec and F11 were mixed 2∶1 (donor∶recipient), deposited onto nitrocellulose 0.45 µm filter discs (Millipore) and incubated for 5 h on agar plates at 37°C. Because the Plac promoter allows for constitutive low-level expression of the himar1C9 transposase, no induction was required. Bacteria from individual mating discs were recovered in 2 ml of 1× M9 salts by vortexing. A 100 µl aliquot was serially diluted and plated on selective agar plates to determine mutagenesis frequency. The remaining 1.9 ml of mating mixture was added to 20 ml of selective media and allowed to grow shaking at 37°C until an optical density at 600 nm (OD600) of ∼0.5 was reached. One ml aliquots from individual matings were then store at −80°C until used in selection screening. In the event a mutant library did not contain a satisfactory number of mutants, for example, <50,000 mutants, frozen axillary stocks were briefly thawed, combined and refrozen.
Wiles T.J., Norton J.P., Russell C.W., Dalley B.K., Fischer K.F, & Mulvey M.A. (2013). Combining Quantitative Genetic Footprinting and Trait Enrichment Analysis to Identify Fitness Determinants of a Bacterial Pathogen. PLoS Genetics, 9(8), e1003716.
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Publication 2013
5'-palmitoyl cytarabine Agar Axilla Bacteria DNA Library Escherichia coli Extraintestinal Pathogenic Escherichia coli Freezing Jumping Genes Mutagenesis Nitrocellulose Salts Tissue Donors Transposase Vision

Most recents protocols related to «Extraintestinal Pathogenic Escherichia coli»

1
Bacterial Strain Characterization and Genetic Manipulation
Bacterial strains and plasmids used in this study were listed in Table S1. PU-1 is an O2:K1 ExPEC strain (isolated from the blood of a piglet) causing acute sepsis in mouse infection model (Ma et al., 2020 (link); Ma et al., 2021 (link)). All strains were grown on Luria-Bertani (LB) broth medium at 37°C with 180 rpm, supplemented with corresponding antibiotics, or isopropyl–D-thiogalactopyranoside (IPTG) when necessary. DNA amplification, ligation and electroporation were performed as previously described (Ma et al., 2018 (link)) unless otherwise indicated. Deletion mutants were constructed using the λ red mutagenesis method (Datsenko and Wanner, 2000 (link)), and the details of primers, restriction enzymes and fragments’ deletion have been listed in Table S2. All restriction and DNA-modifying enzymes were purchased from Thermo Fisher Scientific (Waltham, MA, USA) and performed according to the supplier instruction.
Pan X., Chen R., Zhang Y., Zhu Y., Zhao J., Yao H, & Ma J. (2023). Porcine extraintestinal pathogenic Escherichia coli delivers two serine protease autotransporters coordinately optimizing the bloodstream infection. Frontiers in Cellular and Infection Microbiology, 13, 1138801.
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Publication 2023
Antibiotics Bacteria Blood Deletion Mutation DNA Restriction Enzymes Electroporation Therapy Enzymes Extraintestinal Pathogenic Escherichia coli Infection Ligation Mice, House Mutagenesis Oligonucleotide Primers Plasmids Sepsis Strains
2
Monolithic Catalysts for VOC Oxidation
The dichloromethane, ethyl acetate (EA) and ethanol (EtOH) catalytic activities of as-prepared monolithic catalysts were tested in a conventional fixed-bed reactor, and the monolithic catalysts were placed in the constant temperature zone of the reactor. The reactor was continuously heated and the temperature of the reactor was maintained at the set temperature before analysing the VOCs concentration. The gaseous reactants (DCM, EA and EtOH) were generated by air stream through the liquid reactants in a saturator, and then diluted by another air stream. Here, the indoor air without any purification was used. The liquid reactants were maintained at 0 °C in an ice-water bath during the experiments, respectively. The mass flow controllers (Sevenstar Electronics) were applied to regulate the air intake flow. The total flow was about 6.05 L min−1 and the gas hourly space velocity (GHSV) was kept at 15 000 h−1 with an initial gaseous reactant concentration of about 1000 ppm that was tested at 250 °C in inlet. The DCM concentration in both inlet and outlet of the reactor was monitored by the gas chromatograph (Fuli, China) with flame ionization detector (FID). The schematic diagram of experimental set-up is displayed in Fig. S1.† Additionally, the ethyl acetate and ethanol concentration in both inlet and outlet of reactor was analyzed by the EXPEC 3200 portable gas chromatograph (Hangzhou PuYu Technology Development Co., Ltd. China) with flame ionization detector. The CO2 was analysed by the GC with a Ni convertor furnace. The DCM conversion (%) and CO2 yield (%) were calculated by using the following equation:where [DCM]in denotes the DCM concentration in the inlet gas. [DCM]out denotes the DCM concentration in the outlet gas.where [CO2]in is the CO2 concentration in the inlet. [CO2]out is the CO2 concentration in the outlet. [DCM]in is the DCM concentration in the inlet gas.
Zhao Y., Xi C., Gao S., Wang Y., Wang H., Sun P, & Wu Z. (2023). Ru-based monolithic catalysts for the catalytic oxidation of chlorinated volatile organic compounds. RSC Advances, 13(10), 7037-7044.
Publication 2023
Bath enzyme activity Ethanol ethyl acetate Extraintestinal Pathogenic Escherichia coli Flame Ionization Gas Chromatography Ice Methylene Chloride
3
Identification and Characterization of Pathogenic E. coli
Potential pathogenic E. coli isolates were identified by screening for the presence of some characteristic virulence genes (eae, aggR, elt, estp, and ipaH) by multiplex PCR (modified from Persson 2007, Boisen 2012 and Fujioka 2013 [16 (link),17 (link),18 (link)]) and for the presence of Shiga toxins stx1 and stx2 [19 (link)], as previously described [20 (link)]. An E. coli isolate was classified as potentially pathogenic (STEC; EPEC, Enteropathogenic E. coli; EAEC, Enteroaggregative E. coli; ETEC, Enterotoxigenic E. coli; EIEC, Enteroinvasive E. coli) when at least one of the pathotype-specific genes was detected.
E. coli pathogenicity was also defined after sequence analysis (some of the presumptive non-pathogenic E. coli isolates were sequenced because were multidrug resistant (MDR) or presented hemolytic activity). In this case, the presence of two or more Extraintestinal pathogenic E. coli (ExPEC) typical virulence genes were used for this pathotype classification [21 (link)].
The Kirby–Bauer method was followed for the Antimicrobial Susceptibility Testing (AST), in 55 presumptive non-pathogenic E. coli isolates, following the European Committee on Antimicrobial Susceptibility Testing [22 ] recommendations. A panel of 18 antimicrobials were used: Trimethoprim (TMP), Tigecycline (TGC), Tetracycline (TET), Sulfamethoxazole (SMX), Ciprofloxacin (CIP), Nalidixic Acid (NAL), Meropenem (MEM), Gentamicin (GMN), Erythromycin (ERY), Chloramphenicol (CHL), Ceftriaxone (CRO), Ceftazidime (CZD), Cefoxitin (FOX), Cefotaxime (COX), Cefepime (FEP), Azithromycin (AZM), Amoxicillin-Clavulanic Acid (AMC) and Ampicillin (AMP). The results were interpreted according to the EUCAST epidemiological cut-off values (ECOFFs) [22 ]. An isolate was classified as multidrug-resistant (MDR) when it presented resistance to three or more antimicrobial classes.
Praça J., Furtado R., Coelho A., Correia C.B., Borges V., Gomes J.P., Pista A, & Batista R. (2023). Listeria monocytogenes, Escherichia coli and Coagulase Positive Staphylococci in Cured Raw Milk Cheese from Alentejo Region, Portugal. Microorganisms, 11(2), 322.
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Publication 2023
Amox clav Ampicillin Azithromycin Cefepime Cefotaxime Cefoxitin Ceftazidime Ceftriaxone Chloramphenicol Ciprofloxacin Enteroaggregative Escherichia coli Enteroinvasive Escherichia coli Enteropathogenic Escherichia coli Enterotoxigenic Escherichia coli Erythromycin Escherichia coli Europeans Extraintestinal Pathogenic Escherichia coli Genes Gentamicin Hemolysis Meropenem Microbicides Multiplex Polymerase Chain Reaction Nalidixic Acid Pathogenicity Sequence Analysis Shiga-Toxigenic Escherichia coli Shiga Toxins STX2 protein, human Sulfamethoxazole Susceptibility, Disease Tetracycline Tigecycline Trimethoprim Virulence
4
Comprehensive Virulence Gene Analysis
An extended virulence-associated gene analysis was carried out. The sequences were scanned (i.e., BLAST search) against a custom database previously used for characterizing environmental isolates (Finton et al., 2020 (link)) now expanded to include 1,191 genes/gene variants or genetic markers. The database contains genes related to both ExPEC and IPEC as well as loci suspected to contribute to virulence, e.g., the ETT2 locus. Only matches with 95% or more nucleotide identity with 60% or more query coverage were included in the results.
Buberg M.L., Wasteson Y., Lindstedt B.A, & Witsø I.L. (2023). In vitro digestion of ESC-resistant Escherichia coli from poultry meat and evaluation of human health risk. Frontiers in Microbiology, 14, 1050143.
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Publication 2023
Extraintestinal Pathogenic Escherichia coli Genes Genetic Diversity Genetic Markers Nucleotides Virulence
5
Isoniazid Dosage for LTBI Treatment
The sample size was calculated based on the primary outcome of the completion of treatment of LTBI. Non-completion rates vary between 20 and 40%, with most studies reporting 30% of the treatment abandonment of LTBI [11 –14 (link)].
For the sample calculation, we used an expec abandonment reduction rate is expected to be around 11%. Abandonment in the intervention group (INH 300 mg) would be 19% and in the control group (INH 100 mg) 30%. With a power of 80% to detect differences, a 5% significance level, using Pearson’s chi-square test, two-sided, about 478 individuals would be needed. Besides using the STATA 14.0 program, a 15% loss was also considered, and the number was corrected to 548 study individuals.
Cola J.P., do Prado T.N., Campos B.A., Borges B.J., Alves B.M., de Jezus S.V., Sales C.M., de Araújo W.N., Tavares N.U, & Noia Maciel E.L. (2023). Protocol for pragmatic randomized clinical trial to evaluate the completion of treatment of latent Mycobacterium tuberculosis infection with Isoniazid in the 300 mg formulation. PLOS ONE, 18(2), e0281638.
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Publication 2023
Extraintestinal Pathogenic Escherichia coli

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More about "Extraintestinal Pathogenic Escherichia coli"

Extraintestinal Pathogenic Escherichia coli (ExPEC) are a group of E. coli bacteria that can cause infections outside the intestinal tract, such as urinary tract infections, sepsis, and meningitis.
These pathogenic strains have acquired virulence factors that enable them to invade and colonize extraintestinal sites.
Researchers studying ExPEC can utilize PubCompare.ai, a powerful tool that helps locate relevant protocols from literature, preprints, and patents, while leveraging AI-driven comparisons to identify the best protocols and products.
This can enhance the reproducibility and accuracy of ExPEC studies, leading to more reliable results.
PubCompare.ai's features can streamline ExPEC research and provide valuable insights more efficiently.
Scientists can use the tool to locate protocols related to ExPEC, including those involving GelRed, Newton 7.0, Taq DNA polymerase, Streptavidin agarose resin, and other relevant techniques and materials.
The AI-driven comparisons can help researchers identify the most effective protocols and products, improving the quality and consistency of their ExPEC studies.
Additionally, the tool can be useful for researchers studying other pathogens, such as Streptococcus agalactiae (Group B Streptococcus) and Streptococcus pneumoniae, which can also cause extraintestinal infections.
The ability to compare protocols and products across different studies and research areas can lead to greater insights and advancements in the field of infectious disease research.
By leveraging PubCompare.ai, scientists can enhance the reproducibility and accuracy of their ExPEC studies, ultimately leading to more reliable and impactful results.
The tool's ease of use and powerful features make it an invaluable resource for researchers working to understand and combat these problematic E. coli strains.