Uropathogenic E. coli and Hybrid Pathotypes in Mexican Women with Urinary Tract Infections: A Comprehensive Molecular and Phenotypic Overview

Uropathogenic Escherichia coli (UPEC) is the main cause of urinary tract infections (UTIs) and carries virulence and resistance factors often found in mobilizable genetic elements, such as plasmids or pathogenicity islands (PAIs). UPEC is part of the extraintestinal pathogenic E. coli (ExPEC), but hybrid strains possessing both diarrheagenic E. coli (DEC) and ExPEC traits, termed "hypervirulent", present a significant health threat. This study assessed the prevalence of UPEC PAIs, ExPEC sequence types (ST), DEC genes, carbapenemase and extended-spectrum β-lactamase (ESBL) phenotypes, resistance genotypes, and plasmids in 40 clinical isolates of UPEC. Results showed that 72.5% of isolates had PAIs, mainly PAI IV536 (53%). ESBL phenotypes were found in 65% of β-lactam-resistant isolates, with 100% of carbapenem-resistant isolates producing carbapenemase. The predominant ESBL gene was blaCTX-M-2 (60%), and the most common resistance gene in fluoroquinolone and aminoglycoside-resistant isolates was aac(6')Ib (93%). Plasmids were present in 57% of isolates, and 70% belonged to the ST131 clonal group. Molecular markers for DEC pathotypes were detected in 20 isolates, with 60% classified as hybrid pathotypes. These findings indicate significant pathogenic potential and the presence of hybrid pathotypes in E. coli UTI clinical isolates in the Mexican population.

Phylotypic Profiling, Distribution of Pathogenicity Island Markers, and Antimicrobial Susceptibility of Escherichia coli Isolated from Retail Chicken Meat and Humans

Escherichia coli (E.coli) found in retail chicken meat could be causing a wide range of infections in humans and constitute a potential risk. This study aimed to evaluate 60 E. coli isolates from retail chicken meat (n = 34) and human urinary tract infections (UTIs, n = 26) for phylogenetic diversity, presence of pathogenicity island (PAI) markers, antimicrobial susceptibility phenotypes, and antimicrobial resistance genes, and to evaluate their biofilm formation capacity. In that context, confirmed E.coli isolates were subjected to phylogrouping analysis using triplex PCR, antimicrobial susceptibility testing using the Kirby–Bauer disc diffusion method; PAI distribution was investigated by using two multiplex PCRs. Most of the chicken isolates (22/34, 64.7%) were identified as commensal E. coli (A and B1), while 12 isolates (35.3%) were classified as pathogenic virulent E. coli (B2 and D). Similarly, the commensal group dominated in human isolates. Overall, 23 PAIs were detected in the chicken isolates; among them, 39.1% (9/23) were assigned to group B1, 34.8% (8/23) to group A, 4.34% (1/23) to group B2, and 21.7% (5/23) to group D. However, 25 PAIs were identified from the human isolates. PAI IV536 was the most prevalent (55.9%, 69.2%) PAI detected in both sources. In total, 37 (61.7%) isolates of the chicken and human isolates were biofilm producers. Noticeably, 100% of E. coli isolates were resistant to penicillin and rifamycin. Markedly, all E. coli isolates displayed multiple antibiotic resistance (MAR) phenotypes, and the multiple antibiotic resistance index (MARI) among E. coli isolates ranged between 0.5 and 1. Several antibiotic resistance genes (ARGs) were identified by a PCR assay; the sul2 gene was the most prevalent (38/60, 63.3%) from both sources. Interestingly, a significant positive association (r = 0.31) between biofilm production and resistance to quinolones by the qnr gene was found by the correlation analysis. These findings were suggestive of the transmission of PAI markers and antibiotic resistance genes from poultry to humans or humans to humans through the food chain. To avoid the spread of virulent and multidrug-resistant E. coli, intensive surveillance of retail chicken meat markets is required.

Distribution of Pathogenicity Island Markers and Virulence Factors Genes of Extraintestinal Pathogenic Escherichia coli Isolates

Background: Extraintestinal pathogenic Escherichia coli (ExPEC) can colonize the urinary system with various virulence factors. Escaping from the host defense, can lead to serious infections, such as bacteremia and sepsis. Objectives: This study aimed to investigate the presence of phylogenetic groups, various virulence factor genes, and pathogenicity island (PAI) markers of extraintestinal and commensal E. coli isolates. Methods: Within January 2016 and December 2017, 50 E. coli isolates were isolated from simultaneous blood and urine samples of 25 patients hospitalized in Mersin University Faculty of Medicine, Turkey, and 50 commensal E. coli isolates were isolated from fecal 18 samples of healthy volunteers as the control group was included in the study. Phylogenetic groups, virulence factors genes, and PAI markers were determined by the multiplex polymerase chain reaction method. Results: The majority of ExPEC isolates were observed to be in phylogenetic group B2. All of the commensal E. coli isolates were detected in phylogenetic group A. The most predominant virulence factor gene was traT (80%). The most prevalent PAI marker was PAI IV536 (86%). However, the PAI I536, IJ96, and IIJ96 markers were not detected in any isolates. Only PAI IV536 was detected in commensal E. coli isolates. Conclusions: It was determined that E. coli isolates that cause uropathogenic and bloodstream infections contain a higher frequency of PAI than commensal isolates.

Uropathogenic Escherichia coli pathogenicity islands and other ExPEC virulence genes may contribute to the genome variability of enteroinvasive E. coli

BACKGROUND

Enteroinvasive Escherichia coli (EIEC) may be the causative agent of part of those million cases of diarrhea illness reported worldwide every year and attributable to Shigella. That is because both enteropathogens have many common characteristics that difficult their identification either by traditional microbiological methods or by molecular tools used in the clinical laboratory settings. While Shigella has been extensively studied, EIEC remains barely characterized at the molecular level. Recent EIEC important outbreaks, apparently generating more life-threatening cases, have prompted us to screen EIEC for virulence traits usually related to extraintestinal pathogenic E. coli (ExPEC). That could explain the appearance of EIEC strains presenting higher virulence potential.

RESULTS

EIEC strains were distributed mainly in three phylogroups in a serogroup-dependent manner. Serogroups O124, O136, O144, and O152 were exclusively classified in phylogroup A; O143 in group E; and O28ac and O29 in group B1. Only two serogroups showed diverse phylogenetic origin as follows: O164 was assigned to groups A, B1, C, and B2 (one strain each), and O167 in groups E (five strains), and A (one strain) (Table 1). Eleven of 20 virulence genes (VGs) searched were detected, and the majority of the 19 different VGs combinations found were serogroup-specific. Uropathogenic E. coli (UPEC) PAI genetic markers were detected in all EIEC strains. PAIs I_J96 and II_CFT073 were the most frequent (92.1 and 80.4%, respectively). PAI IV₅₃₆ was restricted to some serogroups from phylogroups A, B1 and E. PAI I_CFT073 was uniquely detected in phylogroups B2 and E. A total of 45 (88%) strains presented multiple PAI markers (two to four). PAIs I_J96 and II_CFT073 were found together in 80% of strains.

CONCLUSIONS

EIEC is a DEC pathovar that presents VGs and pathogenicity island genetic markers typically associated with ExPEC, especially UPEC. These features are distributed in a phylogenetic and serogroup-dependent manner suggesting the existence of stable EIEC subclones. The presence of phylogroups B2 and E strains allied to the presence of UPEC virulence-associated genes may underscore the ongoing evolution of EIEC towards a hypervirulent pathotype.

Distribution of pathogenicity island markers in commensal and uropathogenic Escherichia coli isolates

Uropathogenic Escherichia coli (UPEC) isolates contain large genomic segments, termed pathogenicity islands (PAIs), that contribute to their virulence. A total of 150 UPEC and 50 commensal E. coli isolates from outpatients were investigated for antimicrobial susceptibility and the presence of eight PAI markers. One hundred ninety (95 %) isolates were resistant to one or more antimicrobial agents. The most frequent resistance found against amoxicillin (68 %), amoxicillin/clavulanic acid (55 %), aztreonam (50 %), trimethoprim/sulfamethoxazole (46 %) and tetracycline (43.5 %). Antimicrobial resistance among UPEC isolates was higher than that of commensals. PAI markers were detected in substantial percentage of commensal (88 %) and UPEC isolates (98.6 %) (P > 0.05). The most prevalent PAI marker among UPEC and commensal isolates was PAI IV536 (98.7 % UPEC vs. 84 % commensal). We found a high number of PAI markers such as PAI ICFT073, PAI IICFT073, PAI I536, PAI II536, PAI III536 and PAI IIJ96 significantly associated with UPEC. PAI III536 (21.3 %) and PAI IIJ96 (8 %) were detected only in the uropathogenic isolates. Several different combinations of PAIs were found among UPEC isolates. Comparison of PAIs among UPEC and commensal isolates showed that many UPEC isolates (79.3 %) carried two or more PAI markers, while 6 % of commensals had two PAI markers (P < 0.05). The most frequent combinations of PAI markers in UPEC isolates were PAI IV536 + PAI IICFT073 (18 %) and PAI IV536 + PAI ICFT073 + PAI IICFT073 (18 %). These results indicate that PAI markers are widespread among commensal and UPEC isolates and these commensal isolates may be reservoirs for transmission of these markers.

Virulence Genes and Antimicrobial Resistance Pattern in Uropathogenic Escherichia coli Isolated From Hospitalized Patients in Kashan, Iran

Background:

Urinary tract infection (UTI) is one of the most prevalent infectious diseases. Uropathogenic Escherichia coli (UPEC), as the most important cause of UTI, are associated with a number of virulence factors.

Objectives:

The current study aimed to investigate the virulence associated determinants as well as their patterns of antibiotic resistance in UPEC isolated from hospitalized patients with UTI.

Materials and Methods:

A total of 150 E. coli isolates were collected from patients with UTI from December 2012 to June 2013 in Kashan, Iran. Antimicrobial susceptibility screening of 12 antibiotics was determined using disk diffusion method. Polymerase Chain Reaction (PCR) assay was used to detect virulence-related genes in UPEC strains. The purified PCR products were sequenced.

Results:

Of the total 150 UPEC isolates, 111 (74%) were multidrug-resistant. High resistance was observed against ampicillin (81.3%), nalidixic acid (71.3%), cotrimoxazole (64.7%) and ciprofloxacin (61.3%), respectively. Eighty-four out of the 150 isolates showed resistance against the extended spectrum cephalosporins. Totally, virulence genes were detected in 126 (84%) UPEC isolates .The PCR results identified the traT gene in (74%), PAIs markers in (61.3%) and the pap gene in (16.6%) of the isolates.

Conclusions:

The traT gene and PAI markers were highly prevalent among UPEC strains isolated from patients in Kashan, Iran; therefore these determinants could be used as targets for prophylactic interventions. Also there was a high level of resistance against the antibiotics commonly used for urinary tract infection treatment. To reach better therapeutic outcomes, treatment regimens have to be modified.