scholarly journals Plasmids Shape the Diverse Accessory Resistomes of Escherichia coli ST131

2020 ◽  
Author(s):  
Arun G. Decano ◽  
Nghia Tran ◽  
Hawriya Al-Foori ◽  
Buthaina Al-Awadi ◽  
Leigh Campbell ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pathogenic Bacteria ◽  
Gene Diversity ◽  
Gastrointestinal Microbiome ◽  
E Coli ◽  
Type Iv ◽  
Genes Encoding ◽  
Clade C ◽  
Gene Sharing

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host adhesion like type 1 fimbriae. The extent to which non-pathogenic gut E. coli and infectious ST131 share AMR genes and key associated plasmids remains understudied at a genomic level. Here, we examined AMR gene sharing between gut E. coli and ST131 to discover an extensive shared preterm infant resistome. In addition, individual ST131 show extensive AMR gene diversity highlighting that analyses restricted to the core genome may be limiting and could miss AMR gene transfer patterns. We show that pEK499-like segments are ancestral to most ST131 Clade C isolates, contrasting with a minority with substantial pEK204-like regions encoding a type IV fimbriae operon. Moreover, ST131 possess extensive diversity at genes encoding type 1, type IV, P and F17-like fimbriae, particular within subclade C2. The type, structure and composition of AMR genes, plasmids and fimbriae varies widely in ST131 and this may mediate pathogenicity and infection outcomes.

scholarly journals Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

2020 ◽  
Author(s):  
Arun Gonzales Decano ◽  
Nghia Tran ◽  
Hawriya Al-Foori ◽  
Buthaina Al-Awadi ◽  
Leigh Campbell ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Pathogenic Bacteria ◽  
Gastrointestinal Microbiome ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Type Iv ◽  
Clade C

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and we examined this here using a preterm infant resistome. We found that individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.

scholarly journals Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

2020 ◽  
Author(s):  
Arun Gonzales Decano ◽  
Nghia Tran ◽  
Hawriya Al-Foori ◽  
Buthaina Al-Awadi ◽  
Leigh Campbell ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pathogenic Bacteria ◽  
Sequence Similarity ◽  
List Type ◽  
E Coli ◽  
Type Iv ◽  
Gene Profiles ◽  
Clade C ◽  
Genome Assemblies

AbstractThe human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes that exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and here we examined this using a preterm infant resistome. Here, individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.Data SummaryThe following files are available on the FigShare project “Plasmids_ST131_resistome_2020” : The set of 794 AMR genes derived from [74] are available (with their protein sequence translation) at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961402. The AMR gene profiles per sample determined by their BLAST sequence similarity results against CARD are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961612. This dataset includes the PlasmidFinder results. It also includes other AMR database comparisons (ARG-ANNOT, ResFinder, MegaRes, VFDB and VirulenceFinder). The BLAST sequence similarity results for the fim, pil, pap and ucl operons’ genes versus 4,071 E. coli ST131 assemblies from Decano & Downing (2019) are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961711. The genome sequences and annotation files for reference genomes NCTC13441, EC958 and SE15, along with the assembled contigs for 83972 and 3_2_53FAA are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961813. The 4,071 E. coli ST131 genome assemblies from Decano & Downing (2019) are available at FigShare at doi: 10.6084/m9.figshare.11962278 (the first 1,680 assemblies) and at doi: dx.doi.org/10.6084/m9.figshare.11962557 (the second 2,391 assemblies).

scholarly journals Detection and Quantification of Superoxide Formed within the Periplasm of Escherichia coli

2006 ◽  
Vol 188 (17) ◽  
pp. 6326-6334 ◽  
Author(s):  
Sergei Korshunov ◽  
James A. Imlay
Keyword(s):  
Escherichia Coli ◽  
Pathogenic Bacteria ◽  
Phagocytic Cells ◽  
Free Living ◽  
E Coli ◽  
Superoxide Formation ◽  
Genes Encoding ◽  
Copper Zinc ◽  
Primary Substrate

ABSTRACT Many gram-negative bacteria harbor a copper/zinc-containing superoxide dismutase (CuZnSOD) in their periplasms. In pathogenic bacteria, one role of this enzyme may be to protect periplasmic biomolecules from superoxide that is released by host phagocytic cells. However, the enzyme is also present in many nonpathogens and/or free-living bacteria, including Escherichia coli. In this study we were able to detect superoxide being released into the medium from growing cultures of E. coli. Exponential-phase cells do not normally synthesize CuZnSOD, which is specifically induced in stationary phase. However, the engineered expression of CuZnSOD in growing cells eliminated superoxide release, confirming that this superoxide was formed within the periplasm. The rate of periplasmic superoxide production was surprisingly high and approximated the estimated rate of cytoplasmic superoxide formation when both were normalized to the volume of the compartment. The rate increased in proportion to oxygen concentration, suggesting that the superoxide is generated by the adventitious oxidation of an electron carrier. Mutations that eliminated menaquinone synthesis eradicated the superoxide formation, while mutations in genes encoding respiratory complexes affected it only insofar as they are likely to affect the redox state of menaquinone. We infer that the adventitious autoxidation of dihydromenaquinone in the cytoplasmic membrane releases a steady flux of superoxide into the periplasm of E. coli. This endogenous superoxide may create oxidative stress in that compartment and be a primary substrate of CuZnSOD.

scholarly journals Adhesion of enteropathogenic, enterotoxigenic and commensal Escherichia coli to the Major Zymogen Granule Membrane Glycoprotein 2

2022 ◽  
Author(s):  
Christin Bartlitz ◽  
Rafał Kolenda ◽  
Jarosław Chilimoniuk ◽  
Krzysztof Grzymajło ◽  
Stefan Rödiger ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Host Specificity ◽  
Pathogenic Bacteria ◽  
Cell Receptor ◽  
Membrane Glycoprotein ◽  
Zymogen Granule ◽  
E Coli ◽  
Type 1 Fimbriae ◽  
Granule Membrane

Pathogenic bacteria, such as enteropathogenic (EPEC) and enterotoxigenic Escherichia coli (ETEC), cause diarrhea in mammals. In particular, E. coli colonize and infect the gastrointestinal tract via type 1 fimbriae (T1F). Here the major zymogen granule membrane glycoprotein 2 (GP2) acts as host cell receptor. GP2 is also secreted by the pancreas and various mucous glands, interacting with luminal type 1 fimbriae-positive E. coli . It is unknown whether GP2 isoforms demonstrate specific E. coli pathotype binding. In this study, we investigated interactions of human, porcine and bovine EPEC, ETEC as well as commensal E. coli isolates with human, porcine and bovine GP2. We first defined pathotype- and host-associated FimH variants. Secondly, we could prove that GP2 isoforms bound to FimH variants to varying degrees. However, the GP2-FimH interactions did not seem to be influenced by the host specificity of E. coli . In contrast, soluble GP2 affected ETEC infection and phagocytosis rates of macrophages. Pre-incubation of ETEC pathotype with GP2 reduced infection of cell lines. Furthermore, pre-incubation of E. coli with GP2 improved the phagocytosis rate of macrophages. Our findings suggest that GP2 plays a role in the defense against E. coli infection and in the corresponding host immune response. IMPORTANCE Infection by pathogenic bacteria such as certain Escherichia coli pathotypes results in diarrhea in mammals. Pathogens, including zoonotic agents, can infect different hosts or show host-specificity. There are Escherichia coli strains which are frequently transmitted between humans and animals, whereas other Escherichia coli strains tend to colonize only one host. This host-specificity is still not fully understood. We show that glycoprotein 2 is a selective receptor for particular Escherichia coli strains or variants of the adhesin FimH but not a selector for a species-specific Escherichia coli group. We demonstrate that GP2 is involved in the regulation of colonization and infection and thus represents a molecule of interest for the prevention or treatment of disease.

scholarly journals Patterns of Variations in Escherichia coli Strains That Produce Cytolethal Distending Toxin

2004 ◽  
Vol 72 (2) ◽  
pp. 684-690 ◽  
Author(s):  
Carol L. Pickett ◽  
Robert B. Lee ◽  
Aysegul Eyigor ◽  
Ben Elitzur ◽  
Emily M. Fox ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Pcr Primers ◽  
Pcr Analysis ◽  
Cytolethal Distending Toxin ◽  
E Coli ◽  
Heat Stable ◽  
Genes Encoding ◽  
Factor Type

ABSTRACT A collection of 20 Escherichia coli strains that produce cytolethal distending toxin (CDT) were analyzed for their virulence-associated genes. All of these strains were serotyped, and multiplex PCR analysis was used to ascertain the presence of genes encoding other virulence factors, including Shiga toxin, intimin, enterohemolysin, cytotoxic necrotizing factor type 1 (CNF1) and CNF2, heat-stable toxin, and heat-labile toxin. These CDT-producing strains possessed various combinations of known virulence genes, some of which have not been noted before. Partial cdtB sequences were obtained from 10 of these strains, and their predicted CdtB sequences were compared to known E. coli CdtB sequences; some of the sequences were identical to known CdtB sequences, but two were not. PCR primers based on sequence differences between the known cdt sequences were tested for their ability to detect CDT producers and to determine CDT type. Correlations between the type of CDT produced, the presence of other virulence properties, and overall strain relatedness revealed that the CDT producers studied here can be divided into three general groups, with distinct differences in CDT type and in their complement of virulence-associated genes.

scholarly journals Prevalence of Quinolone Resistance of Extended-Spectrum β-Lactamase-Producing Escherichia coli with ST131-fimH30 in a City Hospital in Hyogo, Japan

2019 ◽  
Vol 20 (20) ◽  
pp. 5162 ◽  
Author(s):  
Masazumi Teramae ◽  
Kayo Osawa ◽  
Katsumi Shigemura ◽  
Koichi Kitagawa ◽  
Toshiro Shirakawa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibacterial Agents ◽  
City Hospital ◽  
Antimicrobial Susceptibility Test ◽  
E Coli ◽  
Specific Pcr ◽  
Extended Spectrum ◽  
Type 1 Pili ◽  
Genes Encoding

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates are known to tolerate superior quinolone antimicrobials compared with other antibacterial agents. Among the clones belonging to sequence type (ST) 131 by multilocus sequence typing, the involvement of the H30-Rx subclone has been reported worldwide with various fimH genes encoding type 1 pili. We investigated 83 isolates of ESBL-producing E. coli and performed antimicrobial susceptibility test, CH (fumC/fimH) ST131 by typing the specific PCR. Moreover, mutation analysis of genes involved in quinolone antibiotic resistance (gyrA and parC) and ESBL genotypes were determined. As a result, 54 of 83 isolates (65.1%) of CH40-30 clones corresponding to ST131-fimH30 were detected, and all were resistant to levofloxacin. Mutations associated with this resistance were common, and included S83L and D87N of gyrA and S80I and E84V of parC. Subclone analysis revealed a high proportion of fimH30-non-Rx (40 isolates, 74.1%). Each subclone was characterized by ESBL genotype, and the CTX-M-15 type was mainly seen for fimH30-Rx, with the CTX-M-14 type or CTX-M-27 type seen for fimH30-non-Rx. This study suggests that an increase in ESBL-producing quinolone-resistant E. coli in a city hospital in Hyogo, Japan, was caused by the spread of subclones belonging to fimH30-non-Rx of ST131.

scholarly journals Development of a Set of Primers for Drug-Resistance Genes Detection in the Agents of Dangerous Bacterial Infections as Exemplified by Yersinia pestis, Vibrio cholerae, Escherichia coli Strains

2014 ◽  
pp. 57-60 ◽  
Author(s):  
K. A. Nikiforov ◽  
L. V. Anisimova ◽  
G. N. Odinokov ◽  
A. V. Fadeeva ◽  
L. A. Novichkova ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Yersinia Pestis ◽  
Vibrio Cholerae ◽  
Resistance Genes ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
E Coli ◽  
Genes Encoding ◽  
Drug Resistant Strains

A set of primers for detection of genes encoding resistance to streptomycin ( strA, strB ), tetracyclin ( tetA, tetR ), chloramphenicol ( catА ), kanamycin ( npt , aphA ), vankomycin ( sanA ), polymyxin ( pmrD ) has been developed with the aim of rapid and effective detection of drug-resistant strains of dangerous bacterial infections agents. Efficacy of constructed primers has been confirmed against a panel of 40 Yersinia pestis, 49 Vibrio cholerae, and 2 Escherichia coli strains from the State collection of pathogenic bacteria of the RAPI “Microbe”. Drug-resistance genes ntp and catA have been detected in plague agent strains , strA, strB , npt , aphA , tetA and tetR - in cholera agent; strA , tetR , ntp and aphA - in pathogenic strain E. coli О157:H7. Determined is universal character of the designed primers for drug-resistance genes detection in these pathogenic bacteria species.

scholarly journals The Escherichia coli Protein YfeX Functions as a Porphyrinogen Oxidase, Not a Heme Dechelatase

mBio ◽  
2011 ◽  
Vol 2 (6) ◽  
Author(s):  
Harry A. Dailey ◽  
Alecia N. Septer ◽  
Lauren Daugherty ◽  
Daniel Thames ◽  
Svetlana Gerdes ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pathogenic Bacteria ◽  
Iron Removal ◽  
Anaerobic Growth ◽  
Limiting Factor ◽  
Alizarin Red ◽  
Content Type ◽  
E Coli ◽  
Genes Encoding

ABSTRACT The protein YfeX from Escherichia coli has been proposed to be essential for the process of iron removal from heme by carrying out a dechelation of heme without cleavage of the porphyrin macrocycle. Since this proposed reaction is unique and would represent the first instance of the biological dechelation of heme, we undertook to characterize YfeX. Our data reveal that YfeX effectively decolorizes the dyes alizarin red and Cibacron blue F3GA and has peroxidase activity with pyrogallal but not guiacol. YfeX oxidizes protoporphyrinogen to protoporphyrin in vitro. However, we were unable to detect any dechelation of heme to free porphyrin with purified YfeX or in cellular extracts of E. coli overexpressing YfeX. Additionally, Vibrio fischeri, an organism that can utilize heme as an iron source when grown under iron limitation, is able to grow with heme as the sole source of iron when its YfeX homolog is absent. Plasmid-driven expression of YfeX in V. fischeri grown with heme did not result in accumulation of protoporphyrin. We propose that YfeX is a typical dye-decolorizing peroxidase (or DyP) and not a dechelatase. The protoporphyrin reported to accumulate when YfeX is overexpressed in E. coli likely arises from the intracellular oxidation of endogenously synthesized protoporphyrinogen and not from dechelation of exogenously supplied heme. Bioinformatic analysis of bacterial YfeX homologs does not identify any connection with iron acquisition but does suggest links to anaerobic-growth-related respiratory pathways. Additionally, some genes encoding homologs of YfeX have tight association with genes encoding a bacterial cytoplasmic encapsulating protein. IMPORTANCE Acquisition of iron from the host during infection is a limiting factor for growth and survival of pathogens. Host heme is the major source of iron in infections, and pathogenic bacteria have evolved complex mechanisms to acquire heme and abstract the iron from heme. Recently Létoffé et al. (Proc. Natl. Acad. Sci. U. S. A. 106:11719–11724, 2009) reported that the protein YfeX from E. coli is able to dechelate heme to remove iron and leave an intact tetrapyrrole. This is totally unlike any other described biological system for iron removal from heme and, thus, would represent a dramatically new feature with potentially profound implications for our understanding of bacterial pathogenesis. Given that this reaction has no precedent in biological systems, we characterized YfeX and a related protein. Our data clearly demonstrate that YfeX is not a dechelatase as reported but is a peroxidase that oxidizes endogenous porphyrinogens to porphyrins.

scholarly journals P fimbriae, capsule and aerobactin characterize colonic resident Escherichia coli

2001 ◽  
Vol 126 (1) ◽  
pp. 11-18 ◽  
Author(s):  
F. NOWROUZIAN ◽  
I. ADLERBERTH ◽  
A. E. WOLD
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Large Intestine ◽  
Class Ii ◽  
E Coli ◽  
Colonic Microflora ◽  
Genes Encoding ◽  
P Type ◽  
Fimbrial Adhesin

Resident and transient Escherichia coli strains from the colonic microflora of 13 Swedish schoolgirls were analysed for carriage of genes encoding a range of adhesins (P, type 1 and S fimbriae, Dr haemagglutinin and three varieties of the P fimbrial papG adhesin) and other virulence traits (K1 and K5 capsule, haemolysin and aerobactin) using multiplex PCR. Forty-four percent of the resident clones carried genes for P fimbriae, K1 or K5 capsule, and aerobactin, compared with only 3% of transient clones (P<0·0001). The P-fimbriated clones most often had the class II variety of the P-fimbrial adhesin gene papG and this adhesin was significantly associated with persistence of a strain. S fimbriae and type 1 fimbriae were equally common in resident and transient strains. The results indicate that not only P fimbriae, but also, certain capsules and the ability to produce the siderophore aerobactin might contribute to persistence of E. coli in the large intestine.

scholarly journals Differential Stability and Trade-Off Effects of Pathoadaptive Mutations in the Escherichia coli FimH Adhesin

2007 ◽  
Vol 75 (7) ◽  
pp. 3548-3555 ◽  
Author(s):  
Scott J. Weissman ◽  
Viktoriya Beskhlebnaya ◽  
Veronika Chesnokova ◽  
Sujay Chattopadhyay ◽  
Walter E. Stamm ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acute Cystitis ◽  
E Coli ◽  
Trade Offs ◽  
Genes Encoding ◽  
Differential Stability ◽  
Rolling Mode ◽  
Tract Infections ◽  
Pathoadaptive Mutations

ABSTRACT FimH is the tip adhesin of mannose-specific type 1 fimbriae of Escherichia coli, which are critical to the pathogenesis of urinary tract infections. Point FimH mutations increasing monomannose (1M)-specific uroepithelial adhesion are commonly found in uropathogenic strains of E. coli. Here, we demonstrate the emergence of a mixed population of clonally identical E. coli strains in the urine of a patient with acute cystitis, where half of the isolates carried a glycine-to-arginine substitution at position 66 of the mature FimH. The R66 mutation induced an unusually strong 1M-binding phenotype and a 20-fold advantage in mouse bladder colonization. However, E. coli strains carrying FimH-R66, but not the parental FimH-G66, had disappeared from the patient's rectal and urine samples collected from 29 to 44 days later, demonstrating within-host instability of the R66 mutation. No FimH variants with R66 were identified in a large (>600 strains) sequence database of fimH-positive E. coli strains. However, several strains carrying genes encoding FimH with either S66 or C66 mutations appeared to be relatively stable in the E. coli population. Relative to FimH-R66, the FimH-S66 and FimH-C66 variants mediated only moderate increases in 1M binding but preserved the ability to enhance binding under flow-induced shear conditions. In contrast, FimH-R66 completely lost shear-enhanced binding properties, with bacterial adhesion being inhibited by shear forces and lacking a rolling mode of binding. These functional trade-offs may determine the natural populational instability of this mutation or other pathoadaptive FimH mutations that confer dramatic increases in 1M binding strength.

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