scholarly journals Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach

2016 ◽  
Vol 55 (2) ◽  
pp. 81-90 ◽  
Author(s):  
M.A. Prieto-Calvo ◽  
M.K. Omer ◽  
O. Alvseike ◽  
M. López ◽  
A. Alvarez-Ordóñez ◽  
...  

AbstractPhenotypic, chemotaxonomic and genotypic data from 12 strains ofEscherichia coli werecollected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems forE. coliand to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing ofE. colito species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification ofE. coli. The results showed that identification ofE. colistrains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Madeline Tong ◽  
Shawn French ◽  
Sara S. El Zahed ◽  
Wai kit Ong ◽  
Peter D. Karp ◽  
...  

ABSTRACT Central metabolism is a topic that has been studied for decades, and yet, this process is still not fully understood in Escherichia coli, perhaps the most amenable and well-studied model organism in biology. To further our understanding, we used a high-throughput method to measure the growth kinetics of each of 3,796 E. coli single-gene deletion mutants in 30 different carbon sources. In total, there were 342 genes (9.01%) encompassing a breadth of biological functions that showed a growth phenotype on at least 1 carbon source, demonstrating that carbon metabolism is closely linked to a large number of processes in the cell. We identified 74 genes that showed low growth in 90% of conditions, defining a set of genes which are essential in nutrient-limited media, regardless of the carbon source. The data are compiled into a Web application, Carbon Phenotype Explorer (CarPE), to facilitate easy visualization of growth curves for each mutant strain in each carbon source. Our experimental data matched closely with the predictions from the EcoCyc metabolic model which uses flux balance analysis to predict growth phenotypes. From our comparisons to the model, we found that, unexpectedly, phosphoenolpyruvate carboxylase (ppc) was required for robust growth in most carbon sources other than most trichloroacetic acid (TCA) cycle intermediates. We also identified 51 poorly annotated genes that showed a low growth phenotype in at least 1 carbon source, which allowed us to form hypotheses about the functions of these genes. From this list, we further characterized the ydhC gene and demonstrated its role in adenosine efflux. IMPORTANCE While there has been much study of bacterial gene dispensability, there is a lack of comprehensive genome-scale examinations of the impact of gene deletion on growth in different carbon sources. In this context, a lot can be learned from such experiments in the model microbe Escherichia coli where much is already understood and there are existing tools for the investigation of carbon metabolism and physiology (1). Gene deletion studies have practical potential in the field of antibiotic drug discovery where there is emerging interest in bacterial central metabolism as a target for new antibiotics (2). Furthermore, some carbon utilization pathways have been shown to be critical for initiating and maintaining infection for certain pathogens and sites of infection (3–5). Here, with the use of high-throughput solid medium phenotyping methods, we have generated kinetic growth measurements for 3,796 genes under 30 different carbon source conditions. This data set provides a foundation for research that will improve our understanding of genes with unknown function, aid in predicting potential antibiotic targets, validate and advance metabolic models, and help to develop our understanding of E. coli metabolism.


2005 ◽  
Vol 49 (1) ◽  
pp. 281-288 ◽  
Author(s):  
Liqun Xiong ◽  
Yakov Korkhin ◽  
Alexander S. Mankin

ABSTRACT Ketolides represent the latest group of macrolide antibiotics. Tight binding of ketolides to the ribosome appears to correlate with the presence of an extended alkyl-aryl side chain. Recently developed 6,11-bridged bicyclic ketolides extend the spectrum of platforms used to generate new potent macrolides with extended alkyl-aryl side chains. The purpose of the present study was to characterize the site of binding and the action of bridged macrolides in the ribosomes of Escherichia coli. All the bridged macrolides investigated efficiently protected A2058 and A2059 in domain V of 23S rRNA from modification by dimethyl sulfate and U2609 from modification by carbodiimide. In addition, bridged macrolides that carry extended alkyl-aryl side chains protruding from the 6,11 bridge protected A752 in helix 35 of domain II of 23S rRNA from modification by dimethyl sulfate. Bridged macrolides efficiently displaced erythromycin from the ribosome in a competition binding assay. The A2058G mutation in 23S rRNA conferred resistance to the bridged macrolides. The U2609C mutation, which renders E. coli resistant to the previously studied ketolides telithromycin and cethromycin, barely affected cell susceptibility to the bridged macrolides used in this study. The results of the biochemical and genetic studies indicate that in the E. coli ribosome, bridged macrolides bind in the nascent peptide exit tunnel at the site previously described for other macrolide antibiotics. The presence of the side chain promotes the formation of specific interactions with the helix 35 of 23S rRNA.


2006 ◽  
Vol 396 (3) ◽  
pp. 565-571 ◽  
Author(s):  
Takaomi Nomura ◽  
Kohji Nakano ◽  
Yasushi Maki ◽  
Takao Naganuma ◽  
Takashi Nakashima ◽  
...  

We cloned the genes encoding the ribosomal proteins Ph (Pyrococcus horikoshii)-P0, Ph-L12 and Ph-L11, which constitute the GTPase-associated centre of the archaebacterium Pyrococcus horikoshii. These proteins are homologues of the eukaryotic P0, P1/P2 and eL12 proteins, and correspond to Escherichia coli L10, L7/L12 and L11 proteins respectively. The proteins and the truncation mutants of Ph-P0 were overexpressed in E. coli cells and used for in vitro assembly on to the conserved domain around position 1070 of 23S rRNA (E. coli numbering). Ph-L12 tightly associated as a homodimer and bound to the C-terminal half of Ph-P0. The Ph-P0·Ph-L12 complex and Ph-L11 bound to the 1070 rRNA fragments from the three biological kingdoms in the same manner as the equivalent proteins of eukaryotic and eubacterial ribosomes. The Ph-P0·Ph-L12 complex and Ph-L11 could replace L10·L7/L12 and L11 respectively, on the E. coli 50S subunit in vitro. The resultant hybrid ribosome was accessible for eukaryotic, as well as archaebacterial elongation factors, but not for prokaryotic elongation factors. The GTPase and polyphenylalanine-synthetic activity that is dependent on eukaryotic elongation factors was comparable with that of the hybrid ribosomes carrying the eukaryotic ribosomal proteins. The results suggest that the archaebacterial proteins, including the Ph-L12 homodimer, are functionally accessible to eukaryotic translation factors.


2016 ◽  
Vol 9 (2) ◽  
pp. 15
Author(s):  
Emil Salim ◽  
Hasnirwan ◽  
Sanusi Ibrahim ◽  
Afrizal

Kitooligosakarida-2,5-anhidro-D-mannofuranosa (KOSamf) dipersiapkan dengan derajat polimerisasi tertentu melalui reaksi nitrous deaminasi dari kitosan parsial N-deasetilasi. KOSamf kemudian diubah menjadi turunan KOSamf dengan mengkopling gugus aldehid yang terdapat pada unit 2,5-anhidro-D-mannofuranosa (amf). KOSamf dengan 3,5-dikloroanilin dan NaBH3CN dalam pelarut buffer ammonium asetat direaksikan melalui metoda one-pot aminasi reduktif untuk menghasilkan turunan KOSamf yang berpotensi sebagai senyawa antibakteri dan antijamur. Struktur kimia dari turunan KOSamf yang telah disintesis dikarakterisasi dengan Spektroskopi FT-IR dan NMR. Senyawa turunan KOSamf memiliki aktivitas sebagai antibakteri terhadap bakteri Staphylococcus aureus dengan zona inhibisi 12,5 mm dan bakteri E. coli dengan zona inhibisi 10,5 mm.


Metabolites ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 228
Author(s):  
R. Axayacatl Gonzalez-Garcia ◽  
Lars K. Nielsen ◽  
Esteban Marcellin

Polyketides are a remarkable class of natural products with diverse functional and structural diversity. The class includes many medicinally important molecules with antiviral, antimicrobial, antifungal and anticancer properties. Native bacterial, fungal and plant hosts are often difficult to cultivate and coax into producing the desired product. As a result, Escherichia coli has been used for the heterologous production of polyketides, with the production of 6-deoxyerythronolide B (6-dEB) being the first example. Current strategies for production in E. coli require feeding of exogenous propionate as a source for the precursors propionyl-CoA and S-methylmalonyl-CoA. Here, we show that heterologous polyketide production is possible from glucose as the sole carbon source. The heterologous expression of eight genes from the Wood-Werkman cycle found in Propionibacteria, in combination with expression of the 6-dEB synthases DEBS1, DEBS2 and DEBS3 resulted in 6-dEB formation from glucose as the sole carbon source. Our results show that the Wood-Werkman cycle provides the required propionyl-CoA and the extender unit S-methylmalonyl-CoA to produce up to 0.81 mg/L of 6-dEB in a chemically defined media.


1973 ◽  
Vol 133 (4) ◽  
pp. 739-747 ◽  
Author(s):  
A. Robinson ◽  
J. Sykes

1. The behaviour of the large ribosomal subunit from Rhodopseudomonas spheroides (45S) has been compared with the 50S ribosome from Escherichia coli M.R.E. 600 (and E. coli M.R.E. 162) during unfolding by removal of Mg2+ and detachment of ribosomal proteins by high univalent cation concentrations. The extent to which these processes are reversible with these ribosomes has also been examined. 2. The R. spheroides 45S ribosome unfolds relatively slowly but then gives rise directly to two ribonucleoprotein particles (16.6S and 13.7S); the former contains the intact primary structure of the 16.25S rRNA species and the latter the 15.00S rRNA species of the original ribosome. No detectable protein loss occurs during unfolding. The E. coli ribosome unfolds via a series of discrete intermediates to a single, unfolded ribonucleoprotein unit (19.1S) containing the 23S rRNA and all the protein of the original ribosome. 3. The two unfolded R. spheroides ribonucleoproteins did not recombine when the original conditions were restored but each simply assumed a more compact configuration. Similar treatments reversed the unfolding of the E. coli 50S ribosomes; replacement of Mg2+ caused the refolding of the initial products of unfolding and in the presence of Ni2+ the completely unfolded species (19.1S) again sedimented at the same rate as the original ribosomes (44S). 4. Ribosomal proteins (25%) were dissociated from R. spheroides 45S ribosomes by dialysis against a solution with a Na+/Mg2+ ratio of 250:1. During this process two core particles were formed (21.2S and 14.2S) and the primary structures of the two original rRNA species were conserved. This dissociation was not reversed. With E. coli 50S approximately 15% of the original ribosomal protein was dissociated, a single 37.6S core particle was formed, the 23S rRNA remained intact and the ribosomal proteins would reassociate with the core particle to give a 50S ribosome. 5. The ribonuclease activities in R. spheroides 45S and E. coli M.R.E. 600 and E. coli M.R.E. 162 50S ribosomes are compared. 6. The observations concerning unfolding and dissociation are consistent with previous reports showing the unusual rRNA complement of the mature R. spheroides 45S ribosome and show the dependence of these events upon the rRNA and the importance of protein–protein interactions in the structure of the R. spheroides ribosome.


Molbank ◽  
10.3390/m1058 ◽  
2019 ◽  
Vol 2019 (2) ◽  
pp. M1058
Author(s):  
Vinuta Kamat ◽  
Rangappa Santosh ◽  
Suresh Nayak

5-methyl-2-(pyridin-3-yl)-1,3-thiazole-4-carbohydrazide (1) on treatment with 4-fluorobenzaldehyde in presence of catalytic amount of acetic acid, accessed the target compound (2) with the yield of 79%. The target compound was confirmed by 1H-NMR, 13C-NMR, FT-IR and LCMS. In vitro antibacterial activity against Staphylococcus aureus (S. Aureus), Bacillus subtilis (B. subtilis), Escherichia coli (E. coli), and Pseudomonas aeruginosa (P. aeruginosa) were carried out and compound 2 showed promising activity against B. subtilis. In addition, compound 2 was analyzed for DNA binding study. It revealed that compound 2 has a promising affinity towards DNA double helix.


2020 ◽  
Vol 21 (2) ◽  
pp. 106-113
Author(s):  
D.K. Adeyemi ◽  
A.O. Adeluola ◽  
M.J. Akinbile ◽  
O.O. Johnson ◽  
G.A. Ayoola

Background: Nanotechnology offers an advantage as a green route for synthesis of metal nanoparticles (NPs) with plant extracts as capping agent. Spondias mombin is a fruit-bearing tree and its leaf extracts have been reported to possess anxiolytic, hypoglycaemic, antiepileptic, antipsychotic, sedative, antioxidant, and antimicrobial properties. The objective of the study is to determine the antibacterial potential of a simple non-toxic product of green synthesis of metallic (Ag, Zn and Cu) nanoparticles using the leaf of Spondias mombin aqueous extracts (SMAE) as a reducing and capping agents of the metal ions.Methodology: Nanoparticles were characterized by UV visible spectrophotometeric analysis, Fourier Transform Infra-Red (FT-IR) spectrophotometer and scanning electron microscope (SEM). Antimicrobial activities of synthesized NPs against Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa were determined by agar well diffusion technique.Results: The synthesized NPs varied in colour from dark brown to green and appears dominantly spherical, occasionally rod or triangular shaped with size ranging from 65-90 nm. UV spectroscopy absorption spectra of Ag, Zn and Cu NPs had absorbance peak at 267, 262 and 765 nm respectively. FT-IR spectrometry of Zn NP, Cu NP, and SMAE gave wave number ranging from 895.71-3320.67, 747.02-3225.45 and 658.25-3674.49 respectively. FT-IR analysis showed that SMAE acted as reducing and stabilizing agent while the NPs exhibited lower energy absorption band when compared to the plant extract. The NPs demonstrated higher antimicrobial activities against S. aureus than Ps. aeruginosa and E. coli. The antimicrobial activity was higher with copper NP than Ag and Zn NPs, and also higher than SMAE.Conclusion: The result from this study presents an indication for an alternative means for development of novel antimicrobial agents for clinical and biotechnological applications.Keywords: synthesis, nanoparticles, FT-IR, UV-visible spectrophotometry, antibacterial activitiesFrench Title: Synthèse verte de nanoparticules d'Ag, de Zn et de Cu à partir d'extrait aqueux de feuilles de Spondias mombin et évaluation de leur activité antibactérienneContexte: La nanotechnologie offre un avantage en tant que voie verte pour la synthèse de nanoparticules métalliques (NP) avec des extraits de plantes comme agent de coiffage. Spondias mombin est un arbre fruitier et ses extraits de feuilles possèdent des propriétés anxiolytiques,  hypoglycémiques, antiépileptiques, antipsychotiques, sédatives,  antioxydantes et antimicrobiennes. L’objectif de l’étude est de déterminer le potentiel antibactérien d’un simple produit non toxique de synthèse verte de nanoparticules métalliques (Ag, Zn et Cu) à l’aide de la feuille d’extraits aqueux de Spondias mombin (SMAE) en tant qu’agent réducteur et coiffant de la ions métalliques.Méthodologie: Les nanoparticules ont été caractérisées par analyse  spectrophotométrique UV visible, spectrophotomètre à transformée de Fourier infrarouge (FT-IR) et microscope électronique à balayage (MEB). Lesactivités antimicrobiennes de NP synthétisées contre Escherichia coli, Staphylococcus aureus et Pseudomonas aeruginosa ont été déterminées par une technique de diffusion sur puits d’agar.Résultats: Les NP synthétisés ont une couleur allant du brun foncé au vert et apparaissent principalement sphériques, parfois en bâtonnets ou en triangles, avec des tailles allant de 65 à 90 nm. Les spectres  d'absorption par spectroscopie UV des NP Ag, Zn et Cu présentaient des pics  d'absorbance à 267, 262 et 765 nm respectivement. La spectrométrie FT-IR de Zn NP, Cu NP et SMAE a donné un nombre d'onde allant de 895,71 à 3320,67, 747,02 à 3225,45 et 658,25 à 3674,49 respectivement. L'analyse FT-IR a montré que le SMAE agissait en tant qu'agent réducteur et  stabilisant, alors que les NP présentaient une bande d'absorption d'énergie inférieure à celle de l'extrait de plante. Les NP ont démontré des activités antimicrobiennes plus élevées contre S. aureus que Ps. aeruginosa et E. coli. L'activité antimicrobienne était plus élevée avec les NP en cuivre que dans les NP Ag et Zn, et également supérieure à celle du SMAE.Conclusion: le résultat de cette étude présente une indication d'un autre moyen de développement de nouveaux agents antimicrobiens pour des applications cliniques et biotechnologiques.Mots-clés: synthèse, nanoparticules, FT-IR, spectrophotométrie UV-visible, activités antibactériennes 


2019 ◽  
Vol 74 (11) ◽  
pp. 3179-3183 ◽  
Author(s):  
Katrine Hartung Hansen ◽  
Minna Rud Andreasen ◽  
Martin Schou Pedersen ◽  
Henrik Westh ◽  
Lotte Jelsbak ◽  
...  

Abstract Background bla TEM-1 encodes a narrow-spectrum β-lactamase that is inhibited by β-lactamase inhibitors and commonly present in Escherichia coli. Hyperproduction of blaTEM-1 may cause resistance to penicillin/β-lactamase inhibitor (P/BLI) combinations. Objectives To characterize EC78, an E. coli bloodstream isolate, resistant to P/BLI combinations, which contains extensive amplification of blaTEM-1 within the chromosome. Methods EC78 was sequenced using Illumina and Oxford Nanopore Technology (ONT) methodology. Configuration of blaTEM-1 amplification was probed using PCR. Expression of blaTEM-1 mRNA was determined using quantitative PCR and β-lactamase activity was determined spectrophotometrically in a nitrocefin conversion assay. Growth rate was assessed to determine fitness and stability of the gene amplification was assessed by passage in the absence of antibiotics. Results Illumina sequencing of EC78 identified blaTEM-1B as the only acquired β-lactamase preceded by the WT P3 promoter and present at a copy number of 182.6 with blaTEM-1B bracketed by IS26 elements. The chromosomal location of the IS26-blaTEM-1B amplification was confirmed by ONT sequencing. Hyperproduction of blaTEM-1 was confirmed by increased transcription of blaTEM-1 and β-lactamase activity and associated with a significant fitness cost; however, the array was maintained at a relatively high copy number for 150 generations. PCR screening for blaTEM amplification of isolates resistant to P/BLI combinations identified an additional strain containing an IS26-associated amplification of a blaTEM gene. Conclusions IS26-associated amplification of blaTEM can cause resistance to P/BLI combinations. This adaptive mechanism of resistance may be overlooked if simple methods of genotypic prediction (e.g. gene presence/absence) are used to predict antimicrobial susceptibility from sequencing data.


2010 ◽  
Vol 73 (2) ◽  
pp. 212-220 ◽  
Author(s):  
ROWAIDA K. KHALIL ◽  
JOSEPH F. FRANK

Recent foodborne illness outbreaks associated with the consumption of leafy green produce indicates a need for additional information on the behavior of pathogenic bacteria on these products. Previous research indicates that pathogen growth and survival is enhanced by leaf damage. The objective of this study was to compare the behavior of Escherichia coli O157:H7 on damaged leaves of baby Romaine lettuce, spinach, cilantro, and parsley stored at three abusive temperatures (8, 12, and 15°C). The damaged portions of leaves were inoculated with approximately 105 CFU E. coli O157:H7 per leaf. The pathogen grew on damaged spinach leaves held for 3 days at 8 and 12°C (P < 0.05), with the population increasing by 1.18 and 2.08 log CFU per leaf, respectively. E. coli O157:H7 did not grow on damaged Romaine leaves at 8 or 12°C, but growth was observed after 8 h of storage at 15°C, with an increase of less than 1.0 log. Growth of E. coli O157:H7 on Romaine lettuce held at 8 or 12°C was enhanced when inocula were suspended in 0.05% ascorbic acid, indicating the possibility of inhibition by oxidation reactions associated with tissue damage. Damaged cilantro and Italian parsley leaves held at 8°C for 4 days did not support the growth of E. coli O157:H7. Behavior of the pathogen in leaf extracts differed from behavior on the damaged tissue. This study provides evidence that the damaged portion of a leafy green is a distinct growth niche that elicits different microbial responses in the various types of leafy greens.


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