scholarly journals Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 454 ◽  
Author(s):  
Imke H. E. Korf ◽  
Jan P. Meier-Kolthoff ◽  
Evelien M. Adriaenssens ◽  
Andrew M. Kropinski ◽  
Manfred Nimtz ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Taxonomic Classification ◽  
New Genera ◽  
E Coli ◽  
Transmission Electron ◽  
Poultry Farms ◽  
Genomic Characterization ◽  
Escherichia Coli Phage ◽  
Insight Into

The aim of this study was to gain further insight into the diversity of Escherichia coli phages followed by enhanced work on taxonomic issues in that field. Therefore, we present the genomic characterization and taxonomic classification of 50 bacteriophages against E. coli isolated from various sources, such as manure or sewage. All phages were examined for their host range on a set of different E. coli strains, originating, e.g., from human diagnostic laboratories or poultry farms. Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and 8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb. Annotation and comparison with databases showed similarities in particular to T4- and T5-like phages, but also to less-known groups. Though various phages against E. coli are already described in literature and databases, we still isolated phages that showed no or only few similarities to other phages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny and classification of the newly isolated phages using VICTOR resulted in the proposal of new genera and led to an enhanced taxonomic classification of E. coli phages.

scholarly journals A Review of the Taxonomy, Genetics and Biology of the Genus Escherichia and the Type Species Escherichia coli

2021 ◽  
Author(s):  
Daniel Yu ◽  
Graham Banting ◽  
Norman Neumann
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Natural Waters ◽  
Distinct Species ◽  
Taxonomic Classification ◽  
Natural Environments ◽  
Microbial World ◽  
E Coli ◽  
Wide Range

Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics has led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as Escherichia coli. The extraordinary genetic diversity in E. coli recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last several years, a growing body of evidence suggests that many E. coli strains appear to be very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggests that E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype and ecotype recapitulate our understanding of the biology of this remarkable bacterium.

scholarly journals Mechanically Ventilated Broiler Sheds: a Possible Source of Aerosolized Salmonella, Campylobacter, and Escherichia coli

2009 ◽  
Vol 75 (23) ◽  
pp. 7417-7425 ◽  
Author(s):  
H. N. Chinivasagam ◽  
T. Tran ◽  
L. Maddock ◽  
A. Gale ◽  
P. J. Blackall
Keyword(s):  
Escherichia Coli ◽  
Most Probable Number ◽  
Production Cycle ◽  
Airborne Bacteria ◽  
Probable Number ◽  
Mechanically Ventilated ◽  
The Public ◽  
E Coli ◽  
Poultry Farms ◽  
Low Levels

ABSTRACT This study assessed the levels of two key pathogens, Salmonella and Campylobacter, along with the indicator organism Escherichia coli in aerosols within and outside poultry sheds. The study ranged over a 3-year period on four poultry farms and consisted of six trials across the boiler production cycle of around 55 days. Weekly testing of litter and aerosols was carried out through the cycle. A key point that emerged is that the levels of airborne bacteria are linked to the levels of these bacteria in litter. This hypothesis was demonstrated by E. coli. The typical levels of E. coli in litter were ∼108 CFU g−1 and, as a consequence, were in the range of 102 to 104 CFU m−3 in aerosols, both inside and outside the shed. The external levels were always lower than the internal levels. Salmonella was only present intermittently in litter and at lower levels (103 to 105 most probable number [MPN] g−1) and consequently present only intermittently and at low levels in air inside (range of 0.65 to 4.4 MPN m−3) and once outside (2.3 MPN m−3). The Salmonella serovars isolated in litter were generally also isolated from aerosols and dust, with the Salmonella serovars Chester and Sofia being the dominant serovars across these interfaces. Campylobacter was detected late in the production cycle, in litter at levels of around 107 MPN g−1. Campylobacter was detected only once inside the shed and then at low levels of 2.2 MPN m−3. Thus, the public health risk from these organisms in poultry environments via the aerosol pathway is minimal.

scholarly journals Susceptibility of Escherichia coli and Clostridium perfringens to sucrose monoesters of capric and lauric acid

2014 ◽  
Vol 59 (No. 8) ◽  
pp. 374-380
Author(s):  
E. Skřivanová ◽  
Š. Pražáková ◽  
O. Benada ◽  
P. Hovorková ◽  
MarounekM
Keyword(s):  
Escherichia Coli ◽  
Antibacterial Activity ◽  
Clostridium Perfringens ◽  
Lauric Acid ◽  
Cytoplasmic Membrane ◽  
E Coli ◽  
Enteropathogenic Bacteria ◽  
Viable Cells ◽  
Transmission Electron ◽  
Cytoplasmic Structures

The sucrose monoesters of capric and lauric acid were tested for their antibacterial activity towards two foodborne enteropathogenic bacteria &ndash; Escherichia coli (CCM 3954 &ndash; serotype O6 and E22 &ndash; serotype O103) and Clostridium perfringens (CNCTC 5459 and CIP 105178). Antibacterial activity was evaluated by the plating technique. Sucrose monocaprate significantly decreased the number of viable cells of E. coli at all tested concentrations (0.1&ndash;5 mg/ml). The overnight incubation of C. perfringens with the sucrose ester of lauric acid at 0.1&ndash;5 mg/ml reduced the number of viable cells below the detection limit (2 log<sub>10</sub> CFU/ml). Incubating E. coli CCM 3954 and C. perfringens CNCTC 5459 with monoesters (0.1 and 2 mg/ml) did not influence the K<sup>+</sup> permeability of the cytoplasmic membrane in cells during a 2.5-minute treatment. A 30-minute incubation of E. coli CCM 3954 and C. perfringens CNCTC 5459 with esters (0.1 and 2 mg/ml) revealed damage to cytoplasmic structures, as observed by transmission electron microscopy. &nbsp;

scholarly journals New Bacteriocins from Lacticaseibacillus paracasei CNCM I-5369 Adsorbed on Alginate Nanoparticles Are Very Active against Escherichia coli

2020 ◽  
Vol 21 (22) ◽  
pp. 8654
Author(s):  
Yanath Belguesmia ◽  
Noura Hazime ◽  
Isabelle Kempf ◽  
Rabah Boukherroub ◽  
Djamel Drider
Keyword(s):  
Escherichia Coli ◽  
High Performance ◽  
Hplc Analysis ◽  
Inhibitory Concentration ◽  
Culture Supernatant ◽  
Gram Negative Bacteria ◽  
E Coli ◽  
Highly Active ◽  
Transmission Electron ◽  
Intracellular Proteins

Lacticaseibacillus paracasei CNCM I-5369, formerly Lactobacillus paracasei CNCM I-5369, produces bacteriocins that are remarkably active against Gram-negative bacteria, among which is the Escherichia coli-carrying mcr-1 gene that is involved in resistance to colistin. These bacteriocins present in the culture supernatant of the producing strain were extracted and semi-purified. The fraction containing these active bacteriocins was designated as E20. Further, E20 was loaded onto alginate nanoparticles (Alg NPs), leading to a highly active nano-antibiotics formulation named hereafter Alg NPs/E20. The amount of E20 adsorbed on the alginate nanoparticles was 12 wt.%, according to high-performance liquid chromatography (HPLC) analysis. The minimal inhibitory concentration (MIC) values obtained with E20 ranged from 250 to 2000 μg/mL, whilst those recorded for Alg NPs/E20 were comprised between 2 and 4 μg/mL, which allowed them to gain up to 500-fold in the anti-E. coli activity. The damages caused by E20 and/or Alg NPs/E20 on the cytology of the target bacteria were characterized by transmission electron microscopy (TEM) imaging and the quantification of intracellular proteins released following treatment of the target bacteria with these antimicrobials. Thus, loading these bacteriocins on Alg NPs appeared to improve their activity, and the resulting nano-antibiotics stand as a promising drug delivery system.

scholarly journals Using a Chemical Genetic Screen to Enhance Our Understanding of the Antimicrobial Properties of Gallium against Escherichia coli

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 34 ◽  
Author(s):  
Natalie Gugala ◽  
Kate Chatfield-Reed ◽  
Raymond J. Turner ◽  
Gordon Chua
Keyword(s):  
Escherichia Coli ◽  
Cell Envelope ◽  
Antimicrobial Properties ◽  
Iron Sulfur Cluster ◽  
Nucleotide Biosynthesis ◽  
E Coli ◽  
Chemical Genetic ◽  
Iron Sulfur ◽  
Insight Into ◽  
Mutant Collection

The diagnostic and therapeutic agent gallium offers multiple clinical and commercial uses including the treatment of cancer and the localization of tumors, among others. Further, this metal has been proven to be an effective antimicrobial agent against a number of microbes. Despite the latter, the fundamental mechanisms of gallium action have yet to be fully identified and understood. To further the development of this antimicrobial, it is imperative that we understand the mechanisms by which gallium interacts with cells. As a result, we screened the Escherichia coli Keio mutant collection as a means of identifying the genes that are implicated in prolonged gallium toxicity or resistance and mapped their biological processes to their respective cellular system. We discovered that the deletion of genes functioning in response to oxidative stress, DNA or iron–sulfur cluster repair, and nucleotide biosynthesis were sensitive to gallium, while Ga resistance comprised of genes involved in iron/siderophore import, amino acid biosynthesis and cell envelope maintenance. Altogether, our explanations of these findings offer further insight into the mechanisms of gallium toxicity and resistance in E. coli.

scholarly journals Genomic characterization of asymptomatic Escherichia coli isolated from the neobladder

Microbiology ◽  
2011 ◽  
Vol 157 (4) ◽  
pp. 1088-1102 ◽  
Author(s):  
Jason W. Sahl ◽  
Amanda L. Lloyd ◽  
Julia C. Redman ◽  
Thomas A. Cebula ◽  
David P. Wood ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Severe Disease ◽  
Comparative Genomic ◽  
Trauma Studies ◽  
Ileal Neobladder ◽  
E Coli ◽  
Genomic Characterization ◽  
Tract Infections ◽  
Ileal Tissue

The replacement of the bladder with a neobladder made from ileal tissue is the prescribed treatment in some cases of bladder cancer or trauma. Studies have demonstrated that individuals with an ileal neobladder have recurrent colonization by Escherichia coli and other species that are commonly associated with urinary tract infections; however, pyelonephritis and complicated symptomatic infections with ileal neobladders are relatively rare. This study examines the genomic content of two E. coli isolates from individuals with neobladders using comparative genomic hybridization (CGH) with a pan-E. coli/Shigella microarray. Comparisons of the neobladder genome hybridization patterns with reference genomes demonstrate that the neobladder isolates are more similar to the commensal, laboratory-adapted E. coli and a subset of enteroaggregative E. coli than they are to uropathogenic E. coli isolates. Genes identified by CGH as exclusively present in the neobladder isolates among the 30 examined isolates were primarily from large enteric isolate plasmids. Isolations identified a large plasmid in each isolate, and sequencing confirmed similarity to previously identified plasmids of enteric species. Screening, via PCR, of more than 100 isolates of E. coli from environmental, diarrhoeagenic and urinary tract sources did not identify neobladder-specific genes that were widely distributed in these populations. These results taken together demonstrate that the neobladder isolates, while distinct, are genomically more similar to gastrointestinal or commensal E. coli, suggesting why they can colonize the transplanted intestinal tissue but rarely progress to acute pyelonephritis or more severe disease.

scholarly journals Isolation and Characterization of Potentially Pathogenic Antimicrobial-Resistant Escherichia coli Strains from Chicken and Pig Farms in Spain

2010 ◽  
Vol 76 (9) ◽  
pp. 2799-2805 ◽  
Author(s):  
Pilar Cortés ◽  
Vanessa Blanc ◽  
Azucena Mora ◽  
Ghizlane Dahbi ◽  
Jesús E. Blanco ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Phylogenetic Analyses ◽  
Virulence Gene ◽  
E Coli ◽  
Isolation And Characterization ◽  
Zoonotic Risk ◽  
Poultry Farms ◽  
Pig Farms ◽  
Genes Encoding

ABSTRACT To ascertain whether on animal farms there reside extended-spectrum β-lactamase (ESBL) and plasmidic class C β-lactamase-producing Escherichia coli isolates potentially pathogenic for humans, phylogenetic analyses, pulsed-field gel electrophoresis (PFGE) typing, serotyping, and virulence genotyping were performed for 86 isolates from poultry (57 isolates) and pig (29 isolates) farms. E. coli isolates from poultry farms carried genes encoding enzymes of the CTX-M-9 group as well as CMY-2, whereas those from pig farms mainly carried genes encoding CTX-M-1 enzymes. Poultry and pig isolates differed significantly in their phylogenetic group assignments, with phylogroup A predominating in pig isolates and phylogroup D predominating in avian isolates. Among the 86 farm isolates, 23 (26.7%) carried two or more virulence genes typical of extraintestinal pathogenic E. coli (ExPEC). Of these, 20 were isolated from poultry farms and only 3 from pig farms. Ten of the 23 isolates belonged to the classic human ExPEC serotypes O2:H6, O2:HNM, O2:H7, O15:H1, and O25:H4. Despite the high diversity of serotypes and pulsotypes detected among the 86 farm isolates, 13 PFGE clusters were identified. Four of these clusters contained isolates with two or more virulence genes, and two clusters exhibited the classic human ExPEC serotypes O2:HNM (ST10) and O2:H6 (ST115). Although O2:HNM and O2:H6 isolates of human and animal origins differed with respect to their virulence genes and PFGE pulsotypes, the O2:HNM isolates from pigs showed the same sequence type (ST10) as those from humans. The single avian O15:H1 isolate was compared with human clinical isolates of this serotype. Although all were found to belong to phylogroup D and shared the same virulence gene profile, they differed in their sequence types (ST362-avian and ST393-human) and PFGE pulsotypes. Noteworthy was the detection, for the first time, in poultry farms of the clonal groups O25b:H4-ST131-B2, producing CTX-M-9, and O25a-ST648-D, producing CTX-M-32. The virulence genes and PFGE profiles of these two groups were very similar to those of clinical human isolates. While further studies are required to determine the true zoonotic potential of these clonal groups, our results emphasize the zoonotic risk posed especially by poultry farms, but also by pig farms, as reservoirs of ESBL- and CMY-2-encoding E. coli.

scholarly journals Classification of Avian Pathogenic Escherichia coli by a Novel Pathogenicity Index Based on an Animal Model

2018 ◽  
Vol 44 (1) ◽  
pp. 6
Author(s):  
Guilherme Fonseca de Souza ◽  
Silvio Luís da Silveira Rocha ◽  
Thales Quedi Furian ◽  
Karen Apellanis Borges ◽  
Felipe De Oliveira Salle ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Brain Heart Infusion ◽  
Brain Heart Infusion Broth ◽  
Bedding Material ◽  
Avian Pathogenic Escherichia Coli ◽  
E Coli ◽  
Death Time ◽  
A Value ◽  
Pathogenic Escherichia Coli

Background: Avian Pathogenic Escherichia coli is the main agent of colibacillosis, a systemic disease that causes considerable economic losses to the poultry industry. In vivo experiments are used to measure the ability of E. coli to be pathogenic. Generally, these experiments have proposed different criteria for results interpretation and did not take into account the death time. The aim of this study was to propose a new methodology for the classification of E. coli pathogenicity by the establishment of a pathogenicity index based in the lethality, death time and the ability of the strain to cause colibacillosis lesions in challenged animals.Materials, Methods & Results: A total of 293 isolates of E. coli were randomly selected to this study. The strains were isolated from cellulitis lesions, broiler bedding material or respiratory diseases and were previously confirmed through biochemical profile. The bacterial isolates were kept frozen at -20°C. The strains were retrieved from stocks and cultured in brain-heart infusion broth overnight at 37°C to obtain a final concentration of 109 UFC/mL. A total of 2940 one-dayold chicks from commercial breeding hens were randomly assigned to groups containing 10 animals and each group was subcutaneously inoculated in the abdominal region with 0.1 mL of the standard inoculum solution containing each of the strains. A control group of 10 broilers were inoculated with 0.1 mL of brain-heart infusion broth by the same route. The chicks were kept for seven days. They were observed at intervals of 6, 12 and 24 h post-inoculation during the first days. From the second day on, the chicks were observed at intervals of 12 h. According to the death time and to the scores of each lesion (aerosaculitis, pericarditis, perihepatitis, peritonitis and cellulitis), a formula to determine the Individual Pathogenicity Index was established. A value of 10 was established as the maximum pathogenicity rate for an inoculated bird. From this rate, 5 points corresponded to scores for gross lesions present at necropsy. For each lesion present, it represents 1 point. The remaining 5 points corresponded to the death time. To obtain the death time value, an index of 1, corresponding to the maximum value assigned to a death on the first day, was divided by the number of days that the birds were evaluated, resulting in a value of 0.1428, which corresponded to a survival bonus factor. It was possible to classify E. coli strains into four pathogenicity groups according to the pathogenicity index: high pathogenicity (pathogenicity index ranging from 7 to 10), intermediate pathogenicity (pathogenicity index ranging from 4 to 6.99), low pathogenicity (pathogenicity index ranging from 1 to 3.99) and apathogenic (pathogenicity index ranging from 0 to 0.99). The analysis of the strains according to their origin revealed that isolates from broiler bedding material presented a lower pathogenicity index.Discussion: It is possible that the source of isolation implies in different results, depending on the criteria adopted. This data reinforces the importance of use a more accurate mathematical model to represents the biological phenomenon. In the study, all avian pathogenic Escherichia coli strains were classified based on a pathogenicity index and the concept of the death time represents an interesting parameter to measure the ability of the strain to promote acute and septicemic manifestation. The use of a support method for poultry veterinary diagnostic accompanying the fluctuation of the bacteria pathogenicity inside the farms may indicate a rational use of antimicrobial in poultry industry.

scholarly journals Environmental inactivation and irrigation-mediated regrowth of Escherichia coli O157:H7 on romaine lettuce when inoculated in a fecal slurry matrix

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6591 ◽  
Author(s):  
Jennifer A. Chase ◽  
Melissa L. Partyka ◽  
Ronald F. Bond ◽  
Edward R. Atwill
Keyword(s):  
Escherichia Coli ◽  
Field Trials ◽  
Inactivation Rate ◽  
Bacterial Inactivation ◽  
Romaine Lettuce ◽  
E Coli ◽  
Log Reduction ◽  
Salinas Valley ◽  
Kinetics Of ◽  
Insight Into

Field trials were conducted in July–August and October 2012 to quantify the inactivation rate of Escherichia coli O157:H7 when mixed with fecal slurry and applied to romaine lettuce leaves. Lettuce was grown under commercial conditions in Salinas Valley, California. One-half milliliter of rabbit, chicken, or pig fecal slurry, containing an average of 4.05 × 107 CFU E. coli O157:H7 (C0), was inoculated onto the upper (adaxial) surface of a lower leaf on 288 heads of lettuce per trial immediately following a 2.5 h irrigation event. To estimate the bacterial inactivation rate as a function of time, fecal matrix, irrigation and seasonal climate effects, sets of lettuce heads (n = 28) were sampled each day over 10 days and the concentration of E. coli O157:H7 (Ct) determined. E. coli O157:H7 was detected on 100% of heads during the 10-day duration, with concentrations ranging from ≤340 MPN/head (∼5-log reduction) to >3.45 × 1012 MPN/head (∼5-log growth). Relative to C0, on day 10 (Ct = 12) we observed an overall 2.6-log and 3.2-log mean reduction of E. coli O157:H7 in July and October, respectively. However, we observed relative maximum concentrations due to bacterial growth on day 6 (maximum Ct = 8) apparently stimulated by foliar irrigation on day 5. From this maximum there was a mean 5.3-log and 5.1-log reduction by day 10 (Ct = 12) for the July and October trials, respectively. This study provides insight into the inactivation and growth kinetics of E. coli O157:H7 on romaine lettuce leaves under natural field conditions. This study provides evidence that harvesting within 24 h post irrigation has the potential to increase the concentration of E. coli O157:H7 contamination, if present on heads of romaine lettuce; foliar irrigation can temporarily stimulate substantial regrowth of E. coli O157:H7.

scholarly journals The Complete Genome Sequence of Escherichia coli phage Eco_BIFF

2018 ◽  
Author(s):  
Lauren Cooper ◽  
Erica Lasek-Nesselquist ◽  
Joseph Wade
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Genome Annotation ◽  
Complete Genome ◽  
Lytic Phage ◽  
E Coli ◽  
K 12 ◽  
Escherichia Coli Phage ◽  
Effective Growth

Escherichia coli phage Eco_BIFF was isolated from several laboratory stocks of E. coli K-12 MG1655 derivatives. The source of the contamination is unknown. Eco_BIFF is a lytic phage that shows effective growth inhibition of E. coli K-12. Here, we announce the complete genome sequence of Eco_BIFF, and major findings from its genome annotation.

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