scholarly journals In Silico Prediction and Prioritisation of Novel Selective Antimicrobial Drug Targets in Escherichia Coli

2021 ◽  
Author(s):  
Frida Svanberg Frisinger ◽  
Bimal Jana ◽  
Stefano Donadio ◽  
Luca Guardabassi
Keyword(s):  
Escherichia Coli ◽  
Gut Microbiota ◽  
In Silico ◽  
Drug Targets ◽  
Biological Processes ◽  
Opportunistic Pathogens ◽  
Antimicrobial Drugs ◽  
E Coli ◽  
Outer Membrane Biogenesis ◽  
Gut Microbiota Dysbiosis

Abstract Treatment of infections caused by Escherichia coli and other Enterobacteriaceae often requires broad-spectrum antimicrobials, which cause perturbations of the gut microbiota (dysbiosis). Novel antimicrobial drugs interfering with pathogen-specific targets would minimize the risk of such dysbiosis. Here, we employed an in silico approach to identify essential proteins in E. coli, including pathogenic ST131, that are either absent or have low homology to humans and beneficial taxa of the gut microbiota. We identified 37 potential new targets with little or no homology to the proteomes seven taxa representative of the healthy gut microbiota. The suitability of these proteins as drug targets was further analysed through essentiality and conservation in the closely related pathogen Klebsiella pneumoniae. None of them are targets of commercially used antibiotics. Eighteen proteins are involved in four functionally connected essential biological processes (replication, chromosome segregation, cell division, and outer membrane biogenesis). Our results indicate that it may be possible to selectively interfere with essential biological processes in Enterobacteriaceae that are absent or mediated by unrelated proteins in beneficial bacterial taxa residing in the gut. The identified targets can be used to discover antimicrobial drugs that are effective against these opportunistic pathogens with a decreased potential of causing dysbiosis.

scholarly journals In silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli

Antibiotics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 632
Author(s):  
Frida Svanberg Frisinger ◽  
Bimal Jana ◽  
Stefano Donadio ◽  
Luca Guardabassi
Keyword(s):  
Escherichia Coli ◽  
Gut Microbiota ◽  
In Silico ◽  
Drug Targets ◽  
3D Structure ◽  
Opportunistic Pathogens ◽  
Antimicrobial Drugs ◽  
E Coli ◽  
Essential Proteins ◽  
Alignment Length

Novel antimicrobials interfering with pathogen-specific targets can minimize the risk of perturbations of the gut microbiota (dysbiosis) during therapy. We employed an in silico approach to identify essential proteins in Escherichia coli that are either absent or have low sequence identity in seven beneficial taxa of the gut microbiota: Faecalibacterium, Prevotella, Ruminococcus, Bacteroides, Lactobacillus, Lachnospiraceae and Bifidobacterium. We identified 36 essential proteins that are present in hyper-virulent E. coli ST131 and have low similarity (bitscore < 50 or identity < 30% and alignment length < 25%) to proteins in mammalian hosts and beneficial taxa. Of these, 35 are also present in Klebsiella pneumoniae. None of the proteins are targets of clinically used antibiotics, and 3D structure is available for 23 of them. Four proteins (LptD, LptE, LolB and BamD) are easily accessible as drug targets due to their location in the outer membrane, especially LptD, which contains extracellular domains. Our results indicate that it may be possible to selectively interfere with essential biological processes in Enterobacteriaceae that are absent or mediated by unrelated proteins in beneficial taxa residing in the gut. The identified targets can be used to discover antimicrobial drugs effective against these opportunistic pathogens with a decreased risk of causing dysbiosis.

scholarly journals Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation

2005 ◽  
Vol 71 (12) ◽  
pp. 7880-7887 ◽  
Author(s):  
Sang Jun Lee ◽  
Dong-Yup Lee ◽  
Tae Yong Kim ◽  
Byung Hun Kim ◽  
Jinwon Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Succinic Acid ◽  
In Silico ◽  
Acid Production ◽  
Gene Knockout ◽  
Fermentation Products ◽  
E Coli ◽  
Metabolic Analysis ◽  
Enhanced Production ◽  
Succinic Acid Production

ABSTRACT Comparative analysis of the genomes of mixed-acid-fermenting Escherichia coli and succinic acid-overproducing Mannheimia succiniciproducens was carried out to identify candidate genes to be manipulated for overproducing succinic acid in E. coli. This resulted in the identification of five genes or operons, including ptsG, pykF, sdhA, mqo, and aceBA, which may drive metabolic fluxes away from succinic acid formation in the central metabolic pathway of E. coli. However, combinatorial disruption of these rationally selected genes did not allow enhanced succinic acid production in E. coli. Therefore, in silico metabolic analysis based on linear programming was carried out to evaluate the correlation between the maximum biomass and succinic acid production for various combinatorial knockout strains. This in silico analysis predicted that disrupting the genes for three pyruvate forming enzymes, ptsG, pykF, and pykA, allows enhanced succinic acid production. Indeed, this triple mutation increased the succinic acid production by more than sevenfold and the ratio of succinic acid to fermentation products by ninefold. It could be concluded that reducing the metabolic flux to pyruvate is crucial to achieve efficient succinic acid production in E. coli. These results suggest that the comparative genome analysis combined with in silico metabolic analysis can be an efficient way of developing strategies for strain improvement.

scholarly journals Impact of Ceftiofur Injection on Gut Microbiota and Escherichia coli Resistance in Pigs

2015 ◽  
Vol 59 (9) ◽  
pp. 5171-5180 ◽  
Author(s):  
M. A. Fleury ◽  
G. Mourand ◽  
E. Jouy ◽  
F. Touzain ◽  
L. Le Devendec ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gut Microbiota ◽  
Treated Group ◽  
Conjugative Plasmid ◽  
Health Concern ◽  
Pcr Analysis ◽  
Contamination Level ◽  
Content Type ◽  
E Coli ◽  
The Impact

ABSTRACTResistance to extended-spectrum cephalosporins (ESCs) is an important health concern. Here, we studied the impact of the administration of a long-acting form of ceftiofur on the pig gut microbiota and ESC resistance inEscherichia coli. Pigs were orally inoculated with an ESC-resistantE. coliM63 strain harboring a conjugative plasmid carrying a gene conferring resistance,blaCTX-M-1. On the same day, they were given or not a unique injection of ceftiofur. Fecal microbiota were studied using quantitative PCR analysis of the main bacterial groups and quantification of short-chain fatty acids.E. coliand ESC-resistantE. coliwere determined by culture methods, and the ESC-resistantE. coliisolates were characterized. The copies of theblaCTX-M-1gene were quantified. After ceftiofur injection, the main change in gut microbiota was the significant but transitory decrease in theE. colipopulation. Acetate and butyrate levels were significantly lower in the treated group. In all inoculated groups,E. coliM63 persisted in most pigs, and theblaCTX-M-1gene was transferred to otherE. coli. Culture and PCR results showed that the ceftiofur-treated group shed significantly more resistant strains 1 and 3 days after ESC injection. Thereafter, on most dates, there were no differences between the groups, but notably, one pig in the nontreated group regularly excreted very high numbers of ESC-resistantE. coli, probably leading to a higher contamination level in its pen. In conclusion, the use of ESCs, and also the presence of high-shedding animals, are important features in the spread of ESC resistance.

scholarly journals A Comparative Study of the Adherent-Invasive Escherichia coli Population and Gut Microbiota of Healthy Vegans versus Omnivores

2020 ◽  
Vol 8 (8) ◽  
pp. 1165
Author(s):  
Rebecca Veca ◽  
Christian O’Dea ◽  
Jarred Burke ◽  
Eva Hatje ◽  
Anna Kuballa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gut Microbiota ◽  
Random Amplified Polymorphic Dna ◽  
Fecal Microbiota ◽  
Vegan Diet ◽  
Rrna Gene ◽  
E Coli ◽  
Abundance And Diversity ◽  
The Individual ◽  
Diversity Profiles

Adherent-invasive Escherichia coli (AIEC) strains carry virulence genes (VGs) which are rarely found in strains other than E. coli. These strains are abundantly found in gut mucosa of patients with inflammatory bowel disease (IBD); however, it is not clear whether their prevalence in the gut is affected by the diet of the individual. Therefore, in this study, we compared the population structure of E. coli and the prevalence of AIEC as well as the composition of gut microbiota in fecal samples of healthy participants (n = 61) on either a vegan (n = 34) or omnivore (n = 27) diet to determine whether diet is associated with the presence of AIEC. From each participant, 28 colonies of E. coli were typed using Random Amplified Polymorphic DNA (RAPD)–PCR. A representative of each common type within an individual was tested for the presence of six AIEC-associated VGs. Whole genomic DNA of the gut microbiota was also analyzed for its diversity profiles, utilizing the V5-V6 region of the16S rRNA gene sequence. There were no significant differences in the abundance and diversity of E. coli between the two diet groups. The occurrence of AIEC-associated VGs was also similar among the two groups. However, the diversity of fecal microbiota in vegans was generally higher than omnivores, with Prevotella and Bacteroides dominant in both groups. Whilst 88 microbial taxa were present in both diet groups, 28 taxa were unique to vegans, compared to seven unique taxa in the omnivores. Our results indicate that a vegan diet may not affect the number and diversity of E. coli populations and AIEC prevalence compared to omnivores. The dominance of Prevotella and Bacteroides among omnivores might be accounted for the effect of diet in these groups.

scholarly journals No evidence for a bovine mastitis Escherichia coli pathotype

2016 ◽  
Author(s):  
Andreas Leimbach ◽  
Anja Poehlein ◽  
John Vollmers ◽  
Dennis Göerlich ◽  
Rolf Daniel ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bovine Mastitis ◽  
Gene Families ◽  
Opportunistic Pathogens ◽  
Gastrointestinal Microbiota ◽  
E Coli ◽  
History Of ◽  
Definition Of ◽  
Selection Of

AbstractBackgroundEscherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result in the identification of common traits. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype has been proposed suggesting virulence traits that differentiate MAEC from commensal E. coli. The present study was designed to investigate the MPEC pathotype hypothesis by comparing the genomes of MAEC and commensal bovine E. coli.ResultsWe sequenced the genomes of eight E. coli isolated from bovine mastitis cases and six fecal commensal isolates from udder-healthy cows. We analyzed the phylogenetic history of bovine E. coli genomes by supplementing this strain panel with eleven bovine-associated E. coli from public databases. The majority of the isolates originate from phylogroups A and B1, but neither MAEC nor commensal strains could be unambiguously distinguished by phylogenetic lineage. The gene content of both MAEC and commensal strains is highly diverse and dominated by their phylogenetic background. Although individual strains carry some typical E. coli virulence-associated genes, no traits important for pathogenicity could be specifically attributed to MAEC. Instead, both commensal strains and MAEC have very few gene families enriched in either pathotype. Only the aerobactin siderophore gene cluster was enriched in commensal E. coli within our strain panel.ConclusionsThis is the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates. With our comparative genomics approach we could not confirm previous studies that argue for a positive selection of specific traits enabling MAEC to elicit bovine mastitis. Instead, MAEC are facultative and opportunistic pathogens recruited from the highly diverse bovine gastrointestinal microbiota. Virulence-associated genes implicated in mastitis are a by-product of commensalism with the primary function to enhance fitness in the bovine gastrointestinal tract. Therefore, we put the definition of the MPEC pathotype into question and suggest to designate corresponding isolates as MAEC.

scholarly journals Antimicrobial Activity of Wine in Relation to Bacterial Resistance to Medicinal Antibiotics

OENO One ◽  
2021 ◽  
Vol 55 (1) ◽  
pp. 45-48
Author(s):  
Mladen Boban ◽  
Nataša Boban ◽  
Marija Tonkić ◽  
Mia Grga ◽  
Ana Marija Milat ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Activity ◽  
Salmonella Enteritidis ◽  
Bacterial Resistance ◽  
Bacterial Suspension ◽  
Antimicrobial Drugs ◽  
Principal Mechanism ◽  
E Coli ◽  
Resistance To Antibiotics ◽  
Time Kill

Although antimicrobial properties of wine have been extensively studied, antimicrobial effects of wine in relation to bacterial resistance to medicinal antibiotics have not been examined. Therefore, our aim was to determine whether bacterial resistance to antibiotics can be related to their resistance to red wine as an unspecific antimicrobial medium. The organisms studied were Salmonella enteritidis (ATCC 13076), Escherichia coli (ATCC 25922), and two clinical isolates which exhibited different resistance to antibiotics, ESBL - producing Escherichia coli UR 3612 and Salmonella enteritidis KK 962. The time-kill curves method was used. The minimal incubation time of the bacterial suspension with wine, necessary for prevention of bacterial growth, was 3 and 20 min for E. coli ATCC and ESBL E. coli respectively. This was associated with susceptibility testing in which E. coli ATCC proved highly sensitive in contrast to ESBL-producing E. coli, which exhibited resistance to a spectrum of antimicrobial drugs of different classes regarding their principal mechanism of action. In the case of S. enteritidis strains, they were similar in their susceptibility against test antibiotics and time-kill curves following exposure to wine. Bacterial resistance to wine is closely associated with bacterial resistance to antimicrobial drugs. The exact mechanisms of antimicrobial activity of wine are still a matter of debate. However, wine might be less susceptible to bacterial resistance development and may include mechanisms different from those of medicinal antibiotics. The present study represents an initial contribution to this important subject which has been practically unexplored.

scholarly journals Data for Molecular Dynamics Simulations of Escherichia Coli Cytochrome Bd Oxidase with the Amber Force Field

2021 ◽  
Author(s):  
Surl-Hee Ahn ◽  
Christian Seitz ◽  
Vinicius Cruzeiro ◽  
James McCammon ◽  
Andreas Goetz
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Force Field ◽  
Drug Targets ◽  
Food Poisoning ◽  
Md Simulations ◽  
Data Bank ◽  
Low Oxygen ◽  
Amber Force Field ◽  
E Coli

<div> <div> <div> <div> <p>Cytochrome <i>bd</i>-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the <i>Mycobacterium tuberculosis (Mtb)</i> bacterium that causes tuberculosis (TB) in humans, the <i>Vibrio cholerae</i> bacterium that causes cholera, the <i>Pseudomonas aeruginosa</i> bacterium that contributes to antibiotic resistance and sepsis, and the <i>Campylobacter jejuni</i> bacterium that causes food poisoning. <i>Escherichia coli (E. coli)</i> is another organism exhibiting the cytochrome <i>bd</i> oxidase. Since it has the highest sequence identity to <i>Mtb</i> (36 %) and we are ultimately interested in finding drug targets for TB, we have built parameters for the <i>E. coli bd </i>oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome <i>bd</i>-type oxidases (heme b<sub>558</sub>, heme b<sub>595</sub>, and heme d) along with their axial ligands. This data report includes the parameter files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions. </p> </div> </div> </div> </div>

scholarly journals In Silico Design for Systems-Based Metabolic Engineering In Escherichia Coli for The Bioconversion of Aerobic Glycerol to Succinic Acid

2020 ◽  
Author(s):  
Albert Enrique Tafur Rangel ◽  
Wendy Lorena Rios Guzman ◽  
Carmen Elvira Ojeda Cuella ◽  
Daissy Esther Mejia Perez ◽  
Ross Carlson ◽  
...  
Keyword(s):  
Machine Learning ◽  
Escherichia Coli ◽  
Metabolic Engineering ◽  
Succinic Acid ◽  
In Silico ◽  
Rational Design ◽  
Industrial Biotechnology ◽  
E Coli ◽  
Cell Factories ◽  
Transcriptomics Data

Abstract BackgroundGlycerol has become an interesting carbon source for industrial processes as consequence of the biodiesel business growth since it has shown promising results in terms of biomass/substrate yields. Selecting the appropriate metabolic targets to build efficient cell factories and maximize the desired chemical production in as little time as possible is a major challenge in industrial biotechnology. The engineering of microbial metabolism following rational design has been widely studied. However, it is a cost-, time-, and laborious-intensive process because of the cell network complexity; thus, to be proficient is needed known in advance the effects of gene deletions.ResultsAn in silico experiment was performed to model and understand the effects of metabolic engineering over the metabolism by transcriptomics data integration. In this study, systems-based metabolic engineering to predict the metabolic engineering targets was used in order to increase the bioconversion of glycerol to succinic acid by Escherichia coli. Transcriptomics analysis suggest insights of how increase the glycerol utilization of the cell for further design efficient cell factories. Three models were used; an E. coli core model, a model obtained after the integration of transcriptomics data obtained from E. coli growing in an optimized culture media, and a third one obtained after integration of transcriptomics data obtained from E. coli after adaptive laboratory evolution experiments. A total of 2402 strains were obtained from these three models. Fumarase and pyruvate dehydrogenase were frequently predicted in all the models, suggesting that these reactions are essential to increasing succinic acid production from glycerol. Finally, using flux balance analysis results for all the mutants predicted, a machine learning method was developed to predict new mutants as well as to propose optimal metabolic engineering targets and mutants based on the measurement of importance of each knockout’s (feature’s) contribution.ConclusionsThe combination of transcriptome, systems metabolic modeling, and machine learning analyses revealed versatile molecular mechanisms involved in the utilization of glycerol. These data provide a platform to improve the prediction of metabolic engineering targets to design efficient cell factories. Our results may also work a guide platform for the selection/engineering of microorganisms for production of interesting chemical compounds.

scholarly journals Microorganisms Resistant to Antimicrobials in Wild Canarian Egyptian Vultures (Neophron percnopterus majorensis)

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 970
Author(s):  
Alejandro Suárez-Pérez ◽  
Juan Alberto Corbera ◽  
Margarita González-Martín ◽  
José Antonio Donázar ◽  
Rubén Sebastián Rosales ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Human Population ◽  
Resistant Bacteria ◽  
Livestock Waste ◽  
Antimicrobial Drugs ◽  
E Coli ◽  
Bird Of Prey ◽  
Neophron Percnopterus ◽  
Low Levels

Due to their predatory habits, raptors may serve as indicators of the presence of antimicrobial-resistant bacteria in the environment, but they also represent a public health risk for livestock and humans because they can act as reservoirs, sources and spreaders of these bacteria. Our objective was to determine the presence of antimicrobial-resistant bacteria in cloacal samples of Canarian Egyptian vultures (Neophron percnopterus majorensis), an endemic bird of prey. One hundred and forty-two cloacal swabs were obtained; Escherichia coli was isolated from 80.28% and Salmonella from 6.3% of these samples. Low levels of susceptibility to ampicillin, tetracycline and trimethoprim/sulfamethoxazole were found. About 20% of the isolates were resistant or presented intermediate susceptibility to fluoroquinolones. Surprisingly, we found isolates resistant to imipenem (6.96%). Isolates from chicks were more susceptible to antimicrobial drugs than adult and immature birds. About 50% of E. coli isolates were resistant to ampicillin, tetracycline and trimethoprim/sulfamethoxazole, and about 20% to piperacillin, enrofloxacin and marbofloxacin. High percentages of isolates of Salmonella were found to be resistant to cephalexin (88%) and aminoglycosides (greater than 77%). Our results support the idea that raptors could act as reservoirs of Salmonella and antimicrobial-resistant bacteria, posing a risk not only to wildlife but also to livestock and the human population, thus reinforcing the need to minimize the exposure of wildlife to antimicrobial agent through human and livestock waste.

scholarly journals Estabelecimento de sistema bacteriano de expressão de peptídeos derivados da enzima vegetal RuBisCO

2019 ◽  
Vol 22 ◽  
Author(s):  
Jessica Audrey Feijó Corrêa ◽  
Svetlana Yurgel ◽  
Chibuike Udenigwe ◽  
Fernando Bittencourt Luciano
Keyword(s):  
Escherichia Coli ◽  
In Silico ◽  
E Coli

Resumo O objetivo do presente estudo foi estabelecer um sistema bacteriano de expressão de peptídeos derivados da proteólise simulada in silico da enzima ribulose-1,5-bisfosfato carboxilase oxigenase (RuBisCO), proveniente de soja, visando viabilizar um método sustentável de produção dessas moléculas para futura aplicação industrial. Inicialmente, foi conferida à cepa Escherichia coli S17-1 cálcio-competência para propagação do plasmídeo de expressão pET-30a(+) contendo o inserto codificante da sequência peptídica GSIKAFKEATKVDKVVVLWTALVPR. Após extração de DNA plasmidial, o material foi transformado em células de alto rendimento E. coli Rosetta™(DE3)pLysS. As células Rosetta portando o plasmídeo de expressão foram induzidas e a produção dos peptídeos foi verificada por meio de eletroforese em gel vertical, confirmando o estabelecimento de um sistema de expressão viável para peptídeos heterólogos. Assim, a produção em maior escala de peptídeos derivados de RuBisCO – associando-se futuramente etapas de purificação e ativação – torna-se possível. Além disso, o método aqui estabelecido pode também ser aplicado utilizando diferentes sequências peptídicas com atividade antimicrobiana.

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