scholarly journals Evaluation of niche adaptation features by genome data mining approach of Escherichia coli urinary and gastrointestinal strains

2019 ◽  
Author(s):  
Thiago GS Paim ◽  
Gustavo E Sambrano ◽  
Keli C Reiter ◽  
Fernando H Sant'Anna ◽  
Renata Soares ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Data Mining ◽  
Urinary Tract ◽  
Resistance Genes ◽  
Primary Metabolism ◽  
Great Density ◽  
E Coli ◽  
Data Mining Approach ◽  
Niche Adaptation ◽  
Tract Infections

Background. Urinary Tract Infections (UTIs) are among most common infections in humans. The vast majority are caused by Escherichia coli, occasionally responsible for severe clinical manifestations. Although the species frequently adheres and colonizes the bladder mucosa, its reservoir is the host gastrointestinal tract. Therefore, the study was designed to evaluate genomic features for niche adaptation of urinary and gastrointestinal strains of E. coli by data mining approach. Results. In the E. coli strains, the repertoire of genes was higher than those found in previous studies, and the majority of genes associated to primary metabolism did not depend of bacteria niche, with exception of cell cycle-division, cell motility and secondary metabolite metabolism. Urinary tract isolates of E. coli had great density of virulence and resistance genes carried by prophages. Conclusion. The urinary and gastrointestinal strains of E. coli evaluated in the study presented an open pan-genome, with groups of functional annotation genes associated to specific niches. In addition, gastrointestinal isolates of E. coli were demonstrated as important reservoir of resistance genes.

scholarly journals Evaluation of niche adaptation features by genome data mining approach of Escherichia coli urinary and gastrointestinal strains

2019 ◽  
Author(s):  
Thiago GS Paim ◽  
Gustavo E Sambrano ◽  
Keli C Reiter ◽  
Fernando H Sant'Anna ◽  
Renata Soares ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Data Mining ◽  
Urinary Tract ◽  
Resistance Genes ◽  
Primary Metabolism ◽  
Great Density ◽  
E Coli ◽  
Data Mining Approach ◽  
Niche Adaptation ◽  
Tract Infections

Background. Urinary Tract Infections (UTIs) are among most common infections in humans. The vast majority are caused by Escherichia coli, occasionally responsible for severe clinical manifestations. Although the species frequently adheres and colonizes the bladder mucosa, its reservoir is the host gastrointestinal tract. Therefore, the study was designed to evaluate genomic features for niche adaptation of urinary and gastrointestinal strains of E. coli by data mining approach. Results. In the E. coli strains, the repertoire of genes was higher than those found in previous studies, and the majority of genes associated to primary metabolism did not depend of bacteria niche, with exception of cell cycle-division, cell motility and secondary metabolite metabolism. Urinary tract isolates of E. coli had great density of virulence and resistance genes carried by prophages. Conclusion. The urinary and gastrointestinal strains of E. coli evaluated in the study presented an open pan-genome, with groups of functional annotation genes associated to specific niches. In addition, gastrointestinal isolates of E. coli were demonstrated as important reservoir of resistance genes.

scholarly journals Phenotypic and Molecular Detection of Resistance Genes from Multi-drug Resistant Escherichia coli Isolated from Patients Attending Selected Hospitals in Damaturu, Yobe State, Nigeria

2021 ◽  
Vol 8 (9) ◽  
pp. 396-407
Author(s):  
Sheriff Wakil ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapa
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Resistance Genes ◽  
Molecular Detection ◽  
Multidrug Resistant ◽  
Clinical Samples ◽  
E Coli ◽  
Resistant Genes ◽  
Tract Infections

Multidrug resistance among Escherichia coli causing urinary tract infections (UTIs) and diarrhea are major public health problem worldwide which cause difficulty in treating the infections caused by Escherichia coli due to the high resistances. The study is aimed to determine the phenotypic and molecular detection of multidrug resistant E. coli isolated from clinical samples of patients attending selected Hospitals in Damaturu, Yobe State-Nigeria. Methods: Two hundred (200) clinical samples were collected aseptically from patient diagnosed with (100 stool samples) and UTI’s (100 urine samples) using sterile universal container. The samples were processed using standard microbiological methods for identification of E. coli. Samples were cultured on MacConkey agar (stool) and Cystine lactose electrolyte deficient agar (urine). The resulting colonies of isolates were further subculture on Eosin methylene blue agar for confirmatory and followed by gram stain, biochemical identification at Microbiology laboratory unit of Yobe State Specialist and Yobe State Teaching Hospital respectively. The antimicrobial susceptibility patterns were determined using Kirby-Bauer disc diffusion techniques and the phenotypic expression of extended spectrum beta-lactamases (ESBLs) were determined using modified double disc synergy test (MDDST) and also the three (3) resistance genes (blaTEM, accC1 and qnrA) were detected using polymerase chain reaction. Results: One hundred and twenty-two (122) isolates were resistant to antibiotics. The highest level of resistance was against amoxicillin (90.2%) while the least resistance was against sparfloxacin (24.3%). Thirty-seven (37) E. coli isolates shows MDR; the highest MDR was (24.3%) while least MDR was (5.4%). The PCR amplification of resistant genes (blaTEM, accC1 and qnrA) were detected on E. coli that shows positive ESBL and the bands were separated using agarose gel electrophoresis. Conclusion: The findings of this study show augmentin, ciprofloxacin and sparfloxacin are the most effective antibiotics against E. coli isolated from patients attending the two hospitals in Damaturu; who are diagnose with UTI and diarrheic infection. The resistant genes include; blaTEM, accC1 and qnrA coding for beta-lactam, aminoglycoside and quinolones were present in E. coli isolated from patients attending selected Hospitals in Yobe State, Nigeria. Keywords: Multidrug resistant, Escherichia coli, extended spectrum beta lactamase, resistance-associated genes, urinary tract infections, diarrheic.

scholarly journals Detection of Phylogenetic Groups and Drug Resistance Genes of Escherichia coli Causing Urinary Tract Infection in Southwest Iran

2021 ◽  
Vol 14 (2) ◽  
Author(s):  
Mostafa Boroumand Boroumand ◽  
Mohsen Naghmachi ◽  
Mohammad Amin Ghatee
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Phylogenetic Group ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Pcr Method ◽  
Tract Infections

Background: Many bacteria can cause urinary tract infections (UTIs), among which Escherichia coli is the most common causative agent. E. coli strains are divided into eight phylogenetic groups based on the new Quadroplex-PCR method, which are different in terms of patterns of resistance to antibiotics, virulence, and environmental characteristics. Objectives: This study aimed to determine the phylogenetic groups and the prevalence of drug resistance genes in E. coli strains causing UTIs. Methods: In this descriptive cross-sectional study, 129 E. coli isolates obtained from the culture of patients with UTIs were evaluated for phylogenetic groups using the new method of Clermont et al. The identification of phylogenetic groups and antibiotic resistance genes was performed using the multiplex polymerase chain reaction (PCR) method. Results: In this study, concerning the distribution of phylogenetic groups among E. coli isolates, the phylogenetic group B2 (36.4%) was the most common phylogenetic group, followed by phylogroups C (13.2%), clade I (10.1%), D (9.3%), and A (3.1%) while groups B1 and F were not observed in any of the isolates, and 20.2% had an unknown state. Also, out of 129 E. coli isolates, the total frequency of tetA, tetB, sul1, sul2, CITM, DfrA, and qnr resistance genes was 59.7%, 66.7, 69, 62, 30.2, 23.3, and 20.2%, respectively. In this study, there was a significant relationship between antibiotics (P = 0.026), cefotaxime (P = 0.003), and nalidixic acid (P = 0.044) and E. coli phylogenetic groups. No significant relationship was observed between E. coli phylogenetic groups and antibiotic resistance genes. Conclusions: The results of this study showed that strains belonging to group B2 had the highest prevalence among other phylogroups, and also, the frequency of antibiotic resistance genes and drug-resistant isolates had a higher prevalence in this phylogroup. These results show that phylogroup B2 has a more effective role in causing urinary tract infections compared to other phylogroups, and this phylogroup can be considered a genetic reservoir of antibiotic resistance.

scholarly journals Antibiotic Susceptibility and Molecular Characterization of Uropathogenic Escherichia coli Associated with Community-Acquired Urinary Tract Infections in Urban and Rural Settings in South Africa

2020 ◽  
Vol 5 (4) ◽  
pp. 176
Author(s):  
Purity Z. Kubone ◽  
Koleka P. Mlisana ◽  
Usha Govinden ◽  
Akebe Luther King Abia ◽  
Sabiha Y. Essack
Keyword(s):  
Escherichia Coli ◽  
South Africa ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Uropathogenic Escherichia Coli ◽  
Diffusion Method ◽  
E Coli ◽  
Tract Infections

We investigated the phenotypic and genotypic antibiotic resistance, and clonality of uropathogenic Escherichia coli (UPEC) implicated in community-acquired urinary tract infections (CA-UTIs) in KwaZulu-Natal, South Africa. Mid-stream urine samples (n = 143) were cultured on selective media. Isolates were identified using the API 20E kit and their susceptibility to 17 antibiotics tested using the disk diffusion method. Extended-spectrum β-lactamases (ESBLs) were detected using ROSCO kits. Polymerase chain reaction (PCR) was used to detect uropathogenic E. coli (targeting the papC gene), and β-lactam (blaTEM/blaSHV-like and blaCTX-M) and fluoroquinolone (qnrA, qnrB, qnrS, gyrA, parC, aac(6’)-Ib-cr, and qepA) resistance genes. Clonality was ascertained using ERIC-PCR. The prevalence of UTIs of Gram-negative etiology among adults 18–60 years of age in the uMgungundlovu District was 19.6%. Twenty-six E. coli isolates were obtained from 28 positive UTI samples. All E. coli isolates were papC-positive. The highest resistance was to ampicillin (76.9%) and the lowest (7.7%) to amoxicillin/clavulanic acid and gentamycin. Four isolates were multidrug-resistant and three were ESBL-positive, all being CTX-M-positive but SHV-negative. The aac(6’)-Ib-cr and gyrA were the most detected fluoroquinolone resistance genes (75%). Isolates were clonally distinct, suggesting the spread of genetically diverse UPEC clones within the three communities. This study highlights the spread of genetically diverse antibiotic-resistant CA-UTI aetiologic agents, including multidrug-resistant ones, and suggests a revision of current treatment options for CA-UTIs in rural and urban settings.

scholarly journals Iron Acquisition of Urinary Tract Infection Escherichia coli Involves Pathogenicity in Caenorhabditis elegans

2021 ◽  
Vol 9 (2) ◽  
pp. 310
Author(s):  
Masayuki Hashimoto ◽  
Yi-Fen Ma ◽  
Sin-Tian Wang ◽  
Chang-Shi Chen ◽  
Ching-Hao Teng
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Caenorhabditis Elegans ◽  
Large Scale ◽  
Iron Acquisition ◽  
Infection Model ◽  
High Throughput Analysis ◽  
E Coli ◽  
C Elegans ◽  
Tract Infections

Uropathogenic Escherichia coli (UPEC) is a major bacterial pathogen that causes urinary tract infections (UTIs). The mouse is an available UTI model for studying the pathogenicity; however, Caenorhabditis elegans represents as an alternative surrogate host with the capacity for high-throughput analysis. Then, we established a simple assay for a UPEC infection model with C. elegans for large-scale screening. A total of 133 clinically isolated E. coli strains, which included UTI-associated and fecal isolates, were applied to demonstrate the simple pathogenicity assay. From the screening, several virulence factors (VFs) involved with iron acquisition (chuA, fyuA, and irp2) were significantly associated with high pathogenicity. We then evaluated whether the VFs in UPEC were involved in the pathogenicity. Mutants of E. coli UTI89 with defective iron acquisition systems were applied to a solid killing assay with C. elegans. As a result, the survival rate of C. elegans fed with the mutants significantly increased compared to when fed with the parent strain. The results demonstrated, the simple assay with C. elegans was useful as a UPEC infectious model. To our knowledge, this is the first report of the involvement of iron acquisition in the pathogenicity of UPEC in a C. elegans model.

scholarly journals Characterization of Anti-Bacterial Effect of the Two New Phages against Uropathogenic Escherichia coli

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1348
Author(s):  
Lívia Slobodníková ◽  
Barbora Markusková ◽  
Michal Kajsík ◽  
Michal Andrezál ◽  
Marek Straka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Therapeutic Potential ◽  
Medical Intervention ◽  
Uropathogenic Escherichia Coli ◽  
E Coli ◽  
Phage Cocktail ◽  
Causative Agents ◽  
Tract Infections

Urinary tract infections (UTIs) are among the events that most frequently need medical intervention. Uropathogenic Escherichia coli are frequently their causative agents and the infections are sometimes complicated by the presence of polyresistant nosocomial strains. Phage therapy is a tool that has good prospects for the treatment of these infections. In the present study, we isolated and characterized two bacteriophages with broad host specificity against a panel of local uropathogenic E. coli strains and combined them into a phage cocktail. According to genome sequencing, these phages were closely related and belonged to the Tequatrovirus genus. The newly isolated phages showed very good activity on a panel of local clinical E. coli strains from urinary tract infections. In the form of a two-phage cocktail, they were active on E. coli strains belonging to phylogroups B2 and D, with relatively lower activity in B1 and no response in phylogroup A. Our study is a preliminary step toward the establishment of a national phage bank containing local, well-characterized phages with therapeutic potential for patients in Slovakia.

Viability and survival capability of quinolone-resistant uropathogenic Escherichia coli

2010 ◽  
Vol 5 (6) ◽  
pp. 827-830
Author(s):  
Georgi Slavchev ◽  
Nadya Markova
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Expression System ◽  
Antibiotic Sensitivity ◽  
Uropathogenic Escherichia Coli ◽  
Resistant Bacteria ◽  
E Coli ◽  
Serum Bactericidal Assay ◽  
Tract Infections ◽  
Macrophage Killing

AbstractUropathogenic strains of E. coli isolated from urine of patients with urinary tract infections were tested for antibiotic sensitivity using bio-Merieux kits and ATB-UR 5 expression system. The virulence of strains was evaluated by serum bactericidal assay, macrophage “killing” and bacterial adhesive tests. Survival capability of strains was assessed under starvation in saline. The results showed that quinolone-resistant uropathogenic strains of E. coli exhibit significantly reduced adhesive potential but relatively high resistance to serum and macrophage bactericidity. In contrast to laboratory strains, the quinolone-resistant uropathogenic clinical isolate demonstrated increased viability during starvation in saline. Our study suggests that quinolone-resistant uropathogenic strains are highly adaptable clones of E. coli, which can exhibit compensatory viability potential under unfavorable conditions. The clinical occurrence of such phenotypes is likely to contribute to the survival, persistence and spread strategy of resistant bacteria.

scholarly journals Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Dana Willner ◽  
Serene Low ◽  
Jason A. Steen ◽  
Narelle George ◽  
Graeme R. Nimmo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Clinical Isolates ◽  
Content Type ◽  
E Coli ◽  
Strain Diversity ◽  
Amplicon Pyrosequencing ◽  
Culture Independent ◽  
Tract Infections

ABSTRACTUrinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenicEscherichia colistrains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typedEscherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene,fimH. There were nine highly abundantfimHtypes, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eightE. coliurine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicatedE. coli-mediated UTIs, single cultured isolates are diagnostic of the infection.IMPORTANCEIn clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods.Escherichia coliwas the most common organism identified, and analysis ofE. colidominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.

scholarly journals Biological Cost of Single and Multiple Norfloxacin Resistance Mutations in Escherichia coli Implicated in Urinary Tract Infections

2005 ◽  
Vol 49 (6) ◽  
pp. 2343-2351 ◽  
Author(s):  
Patricia Komp Lindgren ◽  
Linda L. Marcusson ◽  
Dorthe Sandvang ◽  
Niels Frimodt-Møller ◽  
Diarmaid Hughes
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Infection Model ◽  
Resistance Mutations ◽  
Topoisomerase Iv ◽  
E Coli ◽  
Tract Infections ◽  
Subsequent Selection

ABSTRACT Resistance to fluoroquinolones in urinary tract infection (UTIs) caused by Escherichia coli is associated with multiple mutations, typically those that alter DNA gyrase and DNA topoisomerase IV and those that regulate AcrAB-TolC-mediated efflux. We asked whether a fitness cost is associated with the accumulation of these multiple mutations. Mutants of the susceptible E. coli UTI isolate Nu14 were selected through three to five successive steps with norfloxacin. Each selection was performed with the MIC of the selected strain. After each selection the MIC was measured; and the regions of gyrA, gyrB, parC, and parE, previously associated with resistance mutations, and all of marOR and acrR were sequenced. The first selection step yielded mutations in gyrA, gyrB, and marOR. Subsequent selection steps yielded mutations in gyrA, parE, and marOR but not in gyrB, parC, or acrR. Resistance-associated mutations were identified in almost all isolates after selection steps 1 and 2 but in less than 50% of isolates after subsequent selection steps. Selected strains were competed in vitro, in urine, and in a mouse UTI infection model against the starting strain, Nu14. First-step mutations were not associated with significant fitness costs. However, the accumulation of three or more resistance-associated mutations was usually associated with a large reduction in biological fitness, both in vitro and in vivo. Interestingly, in some lineages a partial restoration of fitness was associated with the accumulation of additional mutations in late selection steps. We suggest that the relative biological costs of multiple mutations may influence the evolution of E. coli strains that develop resistance to fluoroquinolones.

scholarly journals The Repeat-In-Toxin Family Member TosA Mediates Adherence of Uropathogenic Escherichia coli and Survival during Bacteremia

2011 ◽  
Vol 80 (2) ◽  
pp. 493-505 ◽  
Author(s):  
Patrick D. Vigil ◽  
Travis J. Wiles ◽  
Michael D. Engstrom ◽  
Lev Prasov ◽  
Matthew A. Mulvey ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Virulence Factors ◽  
Upper Urinary Tract ◽  
Host Cells ◽  
Content Type ◽  
E Coli ◽  
Wide Range ◽  
Novel Target ◽  
Tract Infections

ABSTRACTUropathogenicEscherichia coli(UPEC) is responsible for the majority of uncomplicated urinary tract infections (UTI) and represents the most common bacterial infection in adults. UPEC utilizes a wide range of virulence factors to colonize the host, including the novel repeat-in-toxin (RTX) protein TosA, which is specifically expressed in the host urinary tract and contributes significantly to the virulence and survival of UPEC.tosA, found in strains within the B2 phylogenetic subgroup ofE. coli, serves as a marker for strains that also contain a large number of well-characterized UPEC virulence factors. The presence oftosAin anE. coliisolate predicts successful colonization of the murine model of ascending UTI, regardless of the source of the isolate. Here, a detailed analysis of the function oftosArevealed that this gene is transcriptionally linked to genes encoding a conserved type 1 secretion system similar to other RTX family members. TosA localized to the cell surface and was found to mediate (i) adherence to host cells derived from the upper urinary tract and (ii) survival in disseminated infections and (iii) to enhance lethality during sepsis (as assessed in two different animal models of infection). An experimental vaccine, using purified TosA, protected vaccinated animals against urosepsis. From this work, it was concluded that TosA belongs to a novel group of RTX proteins that mediate adherence and host damage during UTI and urosepsis and could be a novel target for the development of therapeutics to treat ascending UTIs.

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