A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups

Termination of DNA replication, the final stage of genome duplication, is surprisingly complex, and failures to bring DNA synthesis to an accurate conclusion can impact genome stability and cell viability. In Escherichia coli, termination takes place in a specialised termination area opposite the origin. A ‘replication fork trap’ is formed by unidirectional fork barriers via the binding of Tus protein to genomic ter sites. Such a fork trap system is found in some bacterial species, but it appears not to be a general feature of bacterial chromosomes. The biochemical properties of fork trap systems have been extensively characterised, but little is known about their precise physiological roles. In this study, we compare locations and distributions of ter terminator sites in E. coli genomes across all phylogenetic groups, including Shigella. Our analysis shows that all ter sites are highly conserved in E. coli, with slightly more variability in the Shigella genomes. Our sequence analysis of ter sites and Tus proteins shows that the fork trap is likely to be active in all strains investigated. In addition, our analysis shows that the dif chromosome dimer resolution site is consistently located between the innermost ter sites, even if rearrangements have changed the location of the innermost termination area. Our data further support the idea that the replication fork trap has an important physiological role that provides an evolutionary advantage.

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Growth of Escherichia coli in Model Distribution System Biofilms Exposed to Hypochlorous Acid or Monochloramine

Applied and Environmental Microbiology ◽

10.1128/aem.69.9.5463-5471.2003 ◽

2003 ◽

Vol 69 (9) ◽

pp. 5463-5471 ◽

Cited By ~ 67

Author(s):

Margaret M. Williams ◽

Ellen B. Braun-Howland

Keyword(s):

Escherichia Coli ◽

Legionella Pneumophila ◽

Distribution System ◽

Distribution Systems ◽

Hypochlorous Acid ◽

Bacterial Species ◽

Phylogenetic Groups ◽

Bacterial Populations ◽

E Coli ◽

Model Distribution

ABSTRACT Bacteria indigenous to water distribution systems were used to grow multispecies biofilms within continuous-flow slide chambers. Six flow chambers were also inoculated with an Escherichia coli isolate obtained from potable water. The effect of disinfectants on bacterial populations was determined after exposure of established biofilms to 1 ppm of hypochlorous acid (ClOH) for 67 min or 4 ppm of monochloramine (NH2Cl) for 155 min. To test the ability of bacterial populations to initiate biofilm formation in the presence of disinfectants, we assessed the biofilms after 2 weeks of exposure to residual concentrations of 0.2 ppm of ClOH or 4 ppm of NH2Cl. Lastly, to determine the effect of recommended residual concentrations on newly established biofilms, we treated systems with 0.2 ppm of ClOH after 5 days of growth in the absence of disinfectant. Whole-cell in situ hybridizations using fluorescently tagged, 16S rRNA-targeted oligonucleotide probes performed on cryosectioned biofilms permitted the direct observation of metabolically active bacterial populations, including certain phylogenetic groups and species. The results of these studies confirmed the resistance of established bacterial biofilms to treatment with recommended levels of disinfectants. Specifically, Legionella pneumophila, E. coli, and β and δ proteobacteria were identified within biofilms both before and after treatment. Furthermore, although it was undetected using routine monitoring techniques, the observation of rRNA-containing E. coli within biofilms demonstrated not only survival but also metabolic activity of this organism within the model distribution systems. The persistence of diverse bacterial species within disinfectant-treated biofilms suggests that current testing practices underestimate the risk to immunocompromised individuals of contracting waterborne disease.

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Single-Nucleotide Polymorphism Phylotyping of Escherichia coli

Applied and Environmental Microbiology ◽

10.1128/aem.71.8.4784-4792.2005 ◽

2005 ◽

Vol 71 (8) ◽

pp. 4784-4792 ◽

Cited By ~ 39

Author(s):

Florence Hommais ◽

Sabrina Pereira ◽

Cécile Acquaviva ◽

Patricia Escobar-Páramo ◽

Erick Denamur

Keyword(s):

Escherichia Coli ◽

Bacterial Species ◽

Bacterial Genome ◽

The Other ◽

Enzyme Electrophoresis ◽

Phylogenetic Groups ◽

Single Nucleotide ◽

E Coli ◽

Base Extension ◽

Typing Methods

ABSTRACT We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30 Escherichia coli strains representing the genetic diversity of the species. The 13 SNPs were localized in five genes, trpA, trpB, putP, icdA, and polB, and were selected to allow recovery of the main phylogenetic groups (groups A, B1, E, D, and B2) and subgroups of the species. In the first step, we validated the SNP approach in silico by extracting SNP data from the complete sequences of the five genes for a panel of 65 pathogenic strains belonging to different E. coli pathovars, which were previously analyzed by MLST. In the second step, we determined these SNPs by dideoxy single-base extension of unlabeled oligonucleotide primers for a collection of 183 commensal and extraintestinal clinical E. coli isolates and compared the SNP phylotyping method to previous well-established typing methods. This SNP phylotyping method proved to be consistent with the other methods for assigning phylogenetic groups to the different E. coli strains. In contrast to the other typing methods, such as multilocus enzyme electrophoresis, ribotyping, or PCR phylotyping using the presence/absence of three genomic DNA fragments, the SNP typing method described here is derived from a solid phylogenetic analysis, and the results obtained by this method are more meaningful. Our results indicate that similar approaches may be used for a wide variety of bacterial species.

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Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli

Nature Communications ◽

10.1038/ncomms12984 ◽

2016 ◽

Vol 7 (1) ◽

Cited By ~ 56

Author(s):

Leanid Laganenka ◽

Remy Colin ◽

Victor Sourjik

Keyword(s):

Escherichia Coli ◽

Quorum Sensing ◽

Biofilm Formation ◽

Bacterial Species ◽

Physiological Role ◽

Growth Conditions ◽

Signal Molecules ◽

E Coli ◽

Autoinducer 2 ◽

Cell Densities

Abstract Bacteria communicate by producing and sensing extracellular signal molecules called autoinducers. Such intercellular signalling, known as quorum sensing, allows bacteria to coordinate and synchronize behavioural responses at high cell densities. Autoinducer 2 (AI-2) is the only known quorum-sensing molecule produced by Escherichia coli but its physiological role remains elusive, although it is known to regulate biofilm formation and virulence in other bacterial species. Here we show that chemotaxis towards self-produced AI-2 can mediate collective behaviour—autoaggregation—of E. coli. Autoaggregation requires motility and is strongly enhanced by chemotaxis to AI-2 at physiological cell densities. These effects are observed regardless whether cell–cell interactions under particular growth conditions are mediated by the major E. coli adhesin (antigen 43) or by curli fibres. Furthermore, AI-2-dependent autoaggregation enhances bacterial stress resistance and promotes biofilm formation.

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Replacement of GroEL in Escherichia coli by the Group II Chaperonin from the Archaeon Methanococcus maripaludis

Journal of Bacteriology ◽

10.1128/jb.00317-16 ◽

2016 ◽

Vol 198 (19) ◽

pp. 2692-2700 ◽

Cited By ~ 5

Author(s):

Riddhi Shah ◽

Andrew T. Large ◽

Astrid Ursinus ◽

Bevan Lin ◽

Preethy Gowrinathan ◽

...

Keyword(s):

Escherichia Coli ◽

Single Point ◽

Biochemical Properties ◽

Phylogenetic Groups ◽

Methanococcus Maripaludis ◽

Content Type ◽

E Coli ◽

Group I ◽

Group Ii ◽

Group Ii Chaperonin

ABSTRACTChaperonins are required for correct folding of many proteins. They exist in two phylogenetic groups: group I, found in bacteria and eukaryotic organelles, and group II, found in archaea and eukaryotic cytoplasm. The two groups, while homologous, differ significantly in structure and mechanism. The evolution of group II chaperonins has been proposed to have been crucial in enabling the expansion of the proteome required for eukaryotic evolution. In an archaeal species that expresses both groups of chaperonins, client selection is determined by structural and biochemical properties rather than phylogenetic origin. It is thus predicted that group II chaperonins will be poor at replacing group I chaperonins. We have tested this hypothesis and report here that the group II chaperonin fromMethanococcus maripaludis(Mm-cpn) can partially functionally replace GroEL, the group I chaperonin ofEscherichia coli. Furthermore, we identify and characterize two single point mutations in Mm-cpn that have an enhanced ability to replace GroEL function, including one that allowsE. coligrowth after deletion of thegroELgene. The biochemical properties of the wild-type and mutant Mm-cpn proteins are reported. These data show that the two groups are not as functionally diverse as has been thought and provide a novel platform for genetic dissection of group II chaperonins.IMPORTANCEThe two phylogenetic groups of the essential and ubiquitous chaperonins diverged approximately 3.7 billion years ago. They have similar structures, with two rings of multiple subunits, and their major role is to assist protein folding. However, they differ with regard to the details of their structure, their cofactor requirements, and their reaction cycles. Despite this, we show here that a group II chaperonin from a methanogenic archaeon can partially substitute for the essential group I chaperonin GroEL inE. coliand that we can easily isolate mutant forms of this chaperonin with further improved functionality. This is the first demonstration that these two groups, despite the long time since they diverged, still overlap significantly in their functional properties.

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Genetic and Phylogenetic Diversity of Escherichia coli Strains Collected From Fecal Specimens of Patients Admitted to Zabol Hospitals

International journal of basic science in medicine ◽

10.15171/ijbsm.2018.27 ◽

2018 ◽

Vol 3 (4) ◽

pp. 154-158

Author(s):

Aliyeh Firoozkoohi ◽

Zahra Rashki Ghalehnoo

Keyword(s):

Escherichia Coli ◽

Bacterial Species ◽

Genotypic Diversity ◽

Biochemical Tests ◽

Phylogenetic Groups ◽

E Coli ◽

Random Amplification ◽

Group A ◽

The Difference ◽

Tract Infections

Introduction: Escherichia coli is one of the most prevalent bacterial species which cause gastrointestinal and digestive tract infections in humans and livestock. This study examined genotypic diversity of the E. coli isolates taken from fecal specimens in Zabol using random amplification of polymorphic DNA (RAPD) method and phylogenetic background.Materials and Methods: In this study, 100 isolates were collected from human samples and identified by the common biochemical tests. The isolates were categorized into four main phylogenetic groups including group A (28 isolates), group B1 (7 isolates), group B2 (48 isolates), and group D (17 isolates). Two primers (H1 & H2) were used to study the genetic variation of E. coli and the electrophoresis band pattern was analyzed by the NTSYS.Results: The analysis of the difference in isolates using the RAPD technique showed a genetic similarity between 14% and 100%.Conclusion: The phylogenetic groups B2 and A were more frequent in fecal isolates. In addition, the number of isolates related to phylogenetic groups B1 and D was significantly lower than that of the other groups.

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Antimicrobial Resistance Genes and Diversity of Clones among ESBL- and Acquired AmpC-Producing Escherichia coli Isolated from Fecal Samples of Healthy and Sick Cats in Portugal

Antibiotics ◽

10.3390/antibiotics10030262 ◽

2021 ◽

Vol 10 (3) ◽

pp. 262

Author(s):

Isabel Carvalho ◽

Nadia Safia Chenouf ◽

Rita Cunha ◽

Carla Martins ◽

Paulo Pimenta ◽

...

Keyword(s):

Escherichia Coli ◽

Public Health Problem ◽

Phylogenetic Groups ◽

Disk Diffusion Test ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Specific Pcr ◽

Flight Mass Spectrometry ◽

Antimicrobial Resistance Genes ◽

Esbl Producers

The aim of the study was to analyze the mechanisms of resistance in extended-spectrum beta-lactamase (ESBL)- and acquired AmpC (qAmpC)-producing Escherichia coli isolates from healthy and sick cats in Portugal. A total of 141 rectal swabs recovered from 98 sick and 43 healthy cats were processed for cefotaxime-resistant (CTXR) E. coli recovery (in MacConkey agar supplemented with 2 µg/mL cefotaxime). The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method was used for E. coli identification and antimicrobial susceptibility was performed by a disk diffusion test. The presence of resistance/virulence genes was tested by PCR sequencing. The phylogenetic typing and multilocus sequence typing (MLST) were determined by specific PCR sequencing. CTXRE. coli isolates were detected in seven sick and six healthy cats (7.1% and 13.9%, respectively). Based on the synergy tests, 11 of 13 CTXRE. coli isolates (one/sample) were ESBL-producers (ESBL total rate: 7.8%) carrying the following ESBL genes: blaCTX-M-1 (n = 3), blaCTX-M-15 (n = 3), blaCTX-M-55 (n = 2), blaCTX-M-27 (n = 2) and blaCTX-M-9 (n = 1). Six different sequence types were identified among ESBL-producers (sequence type/associated ESBLs): ST847/CTX-M-9, CTX-M-27, CTX-M-1; ST10/CTX-M-15, CTX-M-27; ST6448/CTX-M-15, CTX-M-55; ST429/CTX-M-15; ST101/CTX-M-1 and ST40/CTX-M-1. Three of the CTXR isolates were CMY-2-producers (qAmpC rate: 2.1%); two of them were ESBL-positive and one ESBL-negative. These isolates were typed as ST429 and ST6448 and were obtained in healthy or sick cats. The phylogenetic groups A/B1/D/clade 1 were detected among ESBL- and qAmpC-producing isolates. Cats are carriers of qAmpC (CMY-2)- and ESBL-producing E. coli isolates (mostly of variants of CTX-M group 1) of diverse clonal lineages, which might represent a public health problem due to the proximity of cats with humans regarding a One Health perspective.

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Characterization of Escherichia coli Strains Derived from Cow Milk of Subclinical and Clinical Cases of Mastitis

Applied Sciences ◽

10.3390/app11020541 ◽

2021 ◽

Vol 11 (2) ◽

pp. 541

Author(s):

Katarzyna Grudlewska-Buda ◽

Krzysztof Skowron ◽

Ewa Wałecka-Zacharska ◽

Natalia Wiktorczyk-Kapischke ◽

Jarosław Bystroń ◽

...

Keyword(s):

Escherichia Coli ◽

Bacterial Species ◽

Subclinical Mastitis ◽

Clinical Mastitis ◽

Economic Problem ◽

Cow Milk ◽

P Value ◽

Dairy Herds ◽

E Coli ◽

Bonferroni Test

Mastitis is a major economic problem in dairy herds, as it might decrease fertility, and negatively affect milk quality and milk yield. Out of over 150 bacterial species responsible for the udder inflammation, Escherichia coli is one of the most notable. This study aimed to assess antimicrobial susceptibility, resistance to dipping agents and biofilm formation of 150 E. coli strains isolated from milk of cows with subclinical and clinical mastitis. The strains came from three dairy herds located in Northern and Central Poland. The statistical analyses were performed with post-hoc Bonferroni test and chi-square test (including Yates correction). The data with a p value of <0.05 were considered significant. We found that the tested strains were mostly sensitive to antimicrobials and dipping agents. It was shown that 37.33% and 4.67% of strains were resistant and moderately resistant to at least one antimicrobial agent, respectively. No extended-spectrum beta-lactamases (ESBL)-producing E. coli were detected. The majority of strains did not possess the ability to form biofilm or formed a weak biofilm. The strong biofilm formers were found only among strains derived from cows with subclinical mastitis. The lowest bacteria number was noted for subclinical mastitis cows’ strains, after stabilization with iodine (3.77 log CFU × cm−2) and chlorhexidine (3.96 log CFU × cm−2) treatment. In the present study, no statistically significant differences in susceptibility to antibiotics and the ability to form biofilm were found among the strains isolated from cows with subclinical and clinical mastitis. Despite this, infections in dairy herds should be monitored. Limiting the spread of bacteria and characterizing the most common etiological factors would allow proper treatment.

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Phylogenetic Grouping and Virulence Potential of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains in Cattle

Applied and Environmental Microbiology ◽

10.1128/aem.00351-12 ◽

2012 ◽

Vol 78 (13) ◽

pp. 4677-4682 ◽

Cited By ~ 38

Author(s):

Charlotte Valat ◽

Frédéric Auvray ◽

Karine Forest ◽

Véronique Métayer ◽

Emilie Gay ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Determinants ◽

Phylogenetic Groups ◽

Content Type ◽

E Coli ◽

Extended Spectrum ◽

Specific Distribution ◽

Extended Spectrum Beta Lactamases ◽

Phylogenetic Grouping ◽

Almost All

ABSTRACTIn line with recent reports of extended-spectrum beta-lactamases (ESBLs) inEscherichia coliisolates of highly virulent serotypes, such as O104:H4, we investigated the distribution of phylogroups (A, B1, B2, D) and virulence factor (VF)-encoding genes in 204 ESBL-producingE. coliisolates from diarrheic cattle. ESBL genes, VFs, and phylogroups were identified by PCR and a commercial DNA array (Alere, France). ESBL genes belonged mostly to the CTX-M-1 (65.7%) and CTX-M-9 (27.0%) groups, whereas those of the CTX-M-2 and TEM groups were much less represented (3.9% and 3.4%, respectively). One ESBL isolate wasstx1andeaepositive and belonged to a major enterohemorrhagicE. coli(EHEC) serotype (O111:H8). Two other isolates wereeaepositive butstxnegative; one of these had serotype O26:H11. ESBL isolates belonged mainly to phylogroup A (55.4%) and, to lesser extents, to phylogroups D (25.5%) and B1 (15.6%), whereas B2 strains were quasi-absent (1/204). The number of VFs was significantly higher in phylogroup B1 than in phylogroups A (P= 0.04) and D (P= 0.02). Almost all of the VFs detected were found in CTX-M-1 isolates, whereas only 64.3% and 33.3% of them were found in CTX-M-9 and CTX-M-2 isolates, respectively. These results indicated that the widespread dissemination of theblaCTX-Mgenes within theE. colipopulation from cattle still spared the subpopulation of EHEC/Shiga-toxigenicE. coli(STEC) isolates. In contrast to other reports on non-ESBL-producing isolates from domestic animals, B1 was not the main phylogroup identified. However, B1 was found to be the most virulent phylogroup, suggesting host-specific distribution of virulence determinants among phylogenetic groups.

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Toxicity of the First Ten MEIC Chemicals to Bacteria

Alternatives to Laboratory Animals ◽

10.1177/026119299302100205 ◽

1993 ◽

Vol 21 (2) ◽

pp. 151-155

Author(s):

Gustaw Kerszman

Keyword(s):

Escherichia Coli ◽

Bacillus Subtilis ◽

Linear Regression ◽

Minimal Inhibitory Concentration ◽

Blood Concentration ◽

Inhibitory Concentration ◽

Human Lymphocytes ◽

Bacterial Species ◽

E Coli ◽

Mild Toxicity

The toxicity of the first ten MEIC chemicals to Escherichia coli and Bacillus subtilis was examined. Nine of the chemicals were toxic to the bacteria, with the minimal inhibitory concentration (MIC) ranging from 10-3 to 4.4M. The sensitivities of both organisms were similar, but the effect on E. coli was often bactericidal, while it was bacteriostatic for B. subtilis. Digoxin was not detectably toxic to either bacterial species. Amitriptyline and FeSO4 were relatively less toxic to the bacteria than to human cells. For seven chemicals, a highly significant linear regression was established between log MIC in bacteria and log of blood concentration, giving lethal and moderate/mild toxicity in humans, as well as with toxicity to human lymphocytes.

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The HiPIP from the acidophilic Acidithiobacillus ferrooxidans is correctly processed and translocated in Escherichia coli, in spite of the periplasm pH difference between these two micro-organisms

Microbiology ◽

10.1099/mic.0.27476-0 ◽

2005 ◽

Vol 151 (5) ◽

pp. 1421-1431 ◽

Cited By ~ 34

Author(s):

Patrice Bruscella ◽

Laure Cassagnaud ◽

Jeanine Ratouchniak ◽

Gaël Brasseur ◽

Elisabeth Lojou ◽

...

Keyword(s):

Escherichia Coli ◽

Acidithiobacillus Ferrooxidans ◽

Biochemical Properties ◽

Gene Encoding ◽

Iron Sulfur Cluster ◽

E Coli ◽

Iron Sulfur ◽

Sulfur Protein ◽

Tat System ◽

Micro Organisms

The gene encoding a putative high-potential iron–sulfur protein (HiPIP) from the strictly acidophilic and chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 33020 has been cloned and sequenced. This potential HiPIP was overproduced in the periplasm of the neutrophile and heterotroph Escherichia coli. As shown by optical and EPR spectra and by electrochemical studies, the recombinant protein has all the biochemical properties of a HiPIP, indicating that the iron–sulfur cluster was correctly inserted. Translocation of this protein in the periplasm of E. coli was not detected in a ΔtatC mutant, indicating that it is dependent on the Tat system. The genetic organization of the iro locus in strains ATCC 23270 and ATCC 33020 is different from that found in strains Fe-1 and BRGM. Indeed, in A. ferrooxidans ATCC 33020 and ATCC 23270 (the type strain), iro was not located downstream from purA but was instead downstream from petC2, encoding cytochrome c 1 from the second A. ferrooxidans cytochrome bc 1 complex. These findings underline the genotypic heterogeneity within the A. ferrooxidans species. The results suggest that Iro transfers electrons from a cytochrome bc 1 complex to a terminal oxidase, as proposed for the HiPIP in photosynthetic bacteria.

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