Complete Genome Sequences of Seven Uropathogenic Escherichia coli Strains Isolated from Postmenopausal Women with Recurrent Urinary Tract Infection

Sharon, Belle M.; Nguyen, Amber; Arute, Amanda P.; Hulyalkar, Neha V.; Nguyen, Vivian; Nisco, Nicole J. De

doi:10.1128/mra.00700-20

Cited by 6 publications

(7 citation statements)

References 23 publications

(26 reference statements)

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“…The isolate belongs to the ST2279 lineage (owing to the combination of adk -53, fumC -40, gyrB -47, icd -13, mdh -36, purA -8, and recA -29), which is closely related to the ST131 high-risk clone. It has been reported that the only difference between these two groups is a single nucleotide at position 263 of the purA gene [57] . Few studies have associated ST2279 with isolates from human samples, such as tracheal secretions, urine, and blood [58] , [59] , in accordance with the phylogenetic analysis performed in the present study.…”

Section: Discussionmentioning

confidence: 99%

Genomic characterization of a multidrug-resistant uropathogenic Escherichia coli and evaluation of Echeveria plant extracts as antibacterials

Castañeda-Meléndrez,

Magaña-Lizárraga,

Martínez-Valenzuela

et al. 2024

AIMSMICRO

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<abstract> Uropathogenic <italic>Escherichia coli</italic> (UPEC) is the most common bacterial agent associated with urinary tract infections, threatening public health systems with elevated medical costs and high morbidity rates. The successful establishment of the infection is associated with virulence factors encoded in its genome, in addition to antibacterial resistance genes, which could limit the treatment and resolution of the infection. In this sense, plant extracts from the genus <italic>Echeveria</italic> have traditionally been used to treat diverse infectious diseases. However, little is known about the effects of these extracts on bacteria and their potential mechanisms of action. This study aims to sequence a multidrug-resistant UPEC isolate (UTI-U7) and assess the multilocus sequence typing (MLST), virulence factors, antimicrobial resistance profile, genes, serotype, and plasmid content. Antimicrobial susceptibility profiling was performed using the Kirby-Bauer disk diffusion. The antibacterial and anti-adherent effects of the methanol extracts (ME) of <italic>Echeveria</italic> (<italic>E. craigiana</italic>, <italic>E. kimnachii</italic>, and <italic>E. subrigida</italic>) against UTI-U7 were determined. The isolate was characterized as an O25:H4-B2-ST2279-CH40 subclone and had resistant determinants to aminoglycosides, β-lactams, fluoroquinolones/quinolones, amphenicols, and tetracyclines, which matched with the antimicrobial resistance profile. The virulence genes identified encode adherence factors, iron uptake, protectins/serum resistance, and toxins. Identified plasmids belonged to the IncF group (IncFIA, IncFIB, and IncFII), alongside several prophage-like elements. After an extensive genome analysis that confirmed the pathogenic status of UTI-U7 isolate, <italic>Echeveria</italic> extracts were tested to determine their antibacterial effects; as an extract, <italic>E. subrigida</italic> (MIC, 5 mg/mL) displayed the best inhibitory effect. However, the adherence between UTI-U7 and HeLa cells was unaffected by the ME of the <italic>E. subrigida</italic> extract. </abstract>

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Section: Discussionmentioning

confidence: 99%

Genomic characterization of a multidrug-resistant uropathogenic Escherichia coli and evaluation of Echeveria plant extracts as antibacterials

Castañeda-Meléndrez,

Magaña-Lizárraga,

Martínez-Valenzuela

et al. 2024

AIMSMICRO

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“…The results suggest that clonal lineages related to uncomplicated and community-based UTIs may have pathogenic characteristics to adapt to recurrent urinary strains if the appropriate environmental and host factors are present. Interestingly, UTI-1_774U and UTI-3_455U were related to the clinical cUTI strain named EcPF40 in the database, reported by Sharon et al (2020) to be associated with RUTI. Our work supports the proposal to monitor ST1193 as a new clone at the same level of importance as ST131 ( Pitout et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection

Flores-Oropeza,

Ochoa,

Cruz-Córdova

et al. 2024

Front. Microbiol.

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IntroductionRecurrent urinary tract infections (RUTIs) caused by uropathogenic Escherichia coli are costly public health problems impacting patients’ quality of life.AimIn this work, a comparative genomics analysis of three clinical RUTI strains isolated from bladder biopsy specimens was performed.Materials and methodsOne hundred seventy-two whole genomes of urinary tract E. coli strains were selected from the NCBI database. The search for virulence factors, fitness genes, regions of interest, and genetic elements associated with resistance was manually carried out. The phenotypic characterization of antibiotic resistance, haemolysis, motility, and biofilm formation was performed. Moreover, adherence and invasion assays with human bladder HTB-5 cells, and transmission electron microscopy (TEM) were performed.ResultsThe UTI-1_774U and UTI-3_455U/ST1193 strains were associated with the extraintestinal pathotypes, and the UTI-2_245U/ST295 strain was associated with the intestinal pathotype, according to a phylogenetic analysis of 172 E. coli urinary strains. The three RUTI strains were of clinical, epidemiological, and zoonotic relevance. Several resistance genes were found within the plasmids of these strains, and a multidrug resistance phenotype was revealed. Other virulence genes associated with CFT073 were not identified in the three RUTI strains (genes for type 1 and P fimbriae, haemolysin hlyA, and sat toxin). Quantitative adherence analysis showed that UTI-1_774U was significantly (p < 0.0001) more adherent to human bladder HTB-5 cells. Quantitative invasion analysis showed that UTI-2_245U was significantly more invasive than the control strains. No haemolysis or biofilm activity was detected in the three RUTI strains. The TEM micrographs showed the presence of short and thin fimbriae only in the UTI-2_245U strain.ConclusionThe high variability and genetic diversity of the RUTI strains indicate that are a mosaic of virulence, resistance, and fitness genes that could promote recurrence in susceptible patients.

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“…Genomic DNA (gDNA) was extracted using Qiagen Blood & Tissue kit and assessed for quality using 260/280nm absorbance ratio, fluorometry, and agarose gel electrophoresis. High quality gDNA libraries were prepared for short-read Illumina and long-read MinION sequencing as described previously (56,60). See detailed methods in Supplemental Materials.…”

Section: Genomic Dna Isolation and Sequencingmentioning

confidence: 99%

Functional and genetic adaptations contributing toEnterococcus faecalispersistence in the female urinary tract

Sharon,

Arute,

Nguyen

et al. 2023

Preprint

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Enterococcus faecalisis the leading Gram-positive bacterial species implicated in urinary tract infection (UTI). An opportunistic pathogen,E. faecalisis a commensal of the human gastrointestinal tract (GIT) and its presence in the GIT is a predisposing factor for UTI. The mechanisms by whichE. faecaliscolonizes and survives in the urinary tract (UT) are poorly understood, especially in uncomplicated or recurrent UTI. The UT is distinct from the GIT and is characterized by a sparse nutrient landscape and unique environmental stressors. In this study, we isolated and sequenced a collection of 37 clinicalE. faecalis strainsfrom the urine of primarily postmenopausal women. We generated 33 closed genome assemblies and four highly contiguous draft assemblies and conducted a comparative genomics to identify genetic features enriched in urinaryE. faecaliswith respect toE. faecalisisolated from the human GIT and blood. Phylogenetic analysis revealed high diversity among urinary strains and a closer relatedness between urine and gut isolates than blood isolates. Plasmid replicon (rep) typing further underscored possible UT-GIT interconnection identifying nine shared rep types between urine and gutE. faecalis. Both genotypic and phenotypic analysis of antimicrobial resistance among urinaryE. faecalisrevealed infrequent resistance to front-line UTI antibiotics nitrofurantoin and fluoroquinolones and no vancomycin resistance. Finally, we identified 19 candidate genes enriched among urinary strains that may play a role in adaptation to the UT. These genes are involved in the core processes of sugar transport, cobalamin import, glucose metabolism, and post-transcriptional regulation of gene expression.

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Complete Genome Sequences of Seven Uropathogenic Escherichia coli Strains Isolated from Postmenopausal Women with Recurrent Urinary Tract Infection

Cited by 6 publications

References 23 publications

Genomic characterization of a multidrug-resistant uropathogenic <i>Escherichia coli</i> and evaluation of <i>Echeveria</i> plant extracts as antibacterials

Genomic characterization of a multidrug-resistant uropathogenic <i>Escherichia coli</i> and evaluation of <i>Echeveria</i> plant extracts as antibacterials

Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection

Functional and genetic adaptations contributing toEnterococcus faecalispersistence in the female urinary tract

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