Phylogenetic Group/Subgroups Distributions, Virulence Factors, and Antimicrobial Susceptibility of Escherichia coli Strains from Urinary Tract Infections in Hatay

High Carriage of tetA, sul1, sul2 and bla TEM Resistance Genes among the Multidrug-resistant Uropathogenic Escherichia coli (UPEC) Strains from Malaysian Patients

The rapid emergence of multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC) strains pose a critical challenge in urinary tract infection (UTI) treatments. However, little work elucidated the resistance mechanisms of the MDR UPEC clinical strains in Malaysia. Therefore, this study aimed to determine the antimicrobial susceptibility profiles and the prevalence of antimicrobial resistance genes among the UPEC strains. Polymerase chain reactions were conducted to detect the presence of 6 antimicrobial resistance genes among 60 UPEC strains. Meanwhile, the antimicrobial resistance profiles against 9 antimicrobials were examined through the Kirby-Bauer disk diffusion method. In this study, the MDR isolates accounted for 40.0% (24/60), with the highest prevalence of resistance towards ampicillin (43/60; 71.7%), followed by tetracycline (31/60; 51.7%), nalidixic acid (30/60; 50.0%), co-trimoxazole (20/60, 33.3%), ciprofloxacin (19/60, 31.7%), levofloxacin (16/60, 21.6%) and chloramphenicol (10/60, 16.7%). In contrast, low resistance rates were observed among minocycline (1/60; 1.7%) and imipenem (0/60; 0.0%). bla TEM was the most prevalent gene (36/60; 60.0%), followed by tetA (27/60; 45.0%), sul2 (25/60; 41.7%), sul1 (13/60; 21.7%) and tetB (8/60; 13.3%). Surprisingly, bla SHV was not detected among the UPEC isolates. The MDR, ampicillin and tetracycline-resistant isolates were significantly associated with a higher prevalence of tetA, sul1, sul2 and bla TEM. In contrast, tetB displayed no significant relationship with any of the antimicrobials tested. The patient's age and gender were not the risk factors for the carriage of the resistance genes. Our findings identified the common resistance genes carried by the antimicrobial resistant UPEC isolates and provide valuable insights into developing the best antibiotic prescription regime to treat UTIs in our local scene.

Molecular characterization of ESBL-producing uropathogenic Escherichia coli isolates among kidney transplant patients: Emergence and spread of B2-ST131 clone type

This study was conducted to identify the distribution of virulence determinants in uropathogenic Escherichia coli (UPEC) isolates obtained from kidney transplant (KTP) and non-transplant patients (non-KTP) with urinary tract infections (UTI). Additionally, the (GTG)5 fingerprinting technique was used to investigate the genetic diversity of Extended-Spectrum B-Lactamase (ESBL)-positive isolates. In this case-control study, 111 urine isolates were obtained from non-KTPs and KTPs, respectively. The presence of genetic markers encoding adhesion proteins, toxins and major E. coli phylogroups was assessed through PCR amplification. Molecular typing of ESBL-positive UPEC strains was performed using (GTG)5 fingerprinting and Multilocus sequence typing (MLST) techniques. Overall, 65 and 46 UPEC isolates were obtained from non-KTPs and KTPs, respectively. Among the studied isolates, traT (85.6%) gene was the most frequently observed virulence gene, followed by kpsMT (49.5%). Using the 80% cut-off point, all the 35 UPEC isolates were classified into four major clusters, namely A, B, C, and D. The majority of the Sequence Type (ST) 131 isolates belonged to cluster A. Additionally, three ST1193 isolates belonged to cluster A and phylogroup B2. Moreover, ST38, ST131 and ST10 were in different cluster. In general, we observed significant differences in the papA, ompT, sat, and vat genes between KTPs and non-KTPs. Furthermore, since all the isolates carried one or more virulence factors (VFs), these findings are concerning in the context of managing UTIs caused by the UPEC strain. Additionally, the distribution of ST and Clonal Complex (CC) among isolates in the main clusters revealed significant differences between MLST and (GTG)5 fingerprinting analysis.

Synergistic Antimicrobial Activity of Eugenol in Combination with Fosfomycin to Combat Escherichia coli and Potential Effect on Plasmid-Mediated Fosfomycin Resistance Genes

The presence of multidrug-resistant pathogenic microorganisms makes it challenging to cure bacterial illnesses. Syzygium aromaticum has been used for medicinal purposes since ancient times. The objective of this study was to investigate the potential synergistic effect of the combination of Eugenol and Fosfomycin against clinically Uropathogenic Escherichia coli (UPEC) and their possible co-treatment as well as their contribution to plasmid-mediated Fosfomycin resistance (fosA3 and fosA4) genes using molecular assays. Eugenol was extracted from clove (Syzygium aromaticum) plants using steam distillation by Clevenger and analyzed by high-performance liquid chromatography (HPLC). UPEC accounted for 63.6 % of all isolates. Specifically, 99.3 % of the UPEC isolates exhibited resistance to multiple types of antibiotics [multidrug-resistant (MDR)]. The MIC for Eugenol was 1.25-5 μg/mL, and Fosfomycin was 512-1024 μg/mL, while the MBC for Eugenol was 5-10 μg/mL and Fosfomycin was 2048 μg/mL. The synergistic effects were considerable, with 1/4 MIC of Eugenol resulting in 1/8 MIC Fosfomycin. Eugenol inhibited most of the UPEC isolates at 4-8 hours, Fosfomycin at 8-12 hours, and co-treatment at 4-8 hours. The fosA3 and fosA4 genes were detected in 5.7 % and 2.9 % of the isolates, respectively. The results showed variable gene expression changes in response to the different treatments.

High incidence of fosfomycin-resistant uropathogenic E. coli among children

BACKGROUND

There are few epidemiological or molecular data on Escherichia coli (E. coli) strains resistant to fosfomycin. In this study, we described the occurrence and characterization of fosfomycin-resistant uropathogenic E. coli (UPEC) isolated from children.

MATERIALS AND METHODS

This study was carried out on 96 E. coli isolates obtained from children with urinary tract infections. Two methods were performed to detect fosfomycin resistance: The agar dilution method and the rapid fosfomycin test. The disc diffusion method was done to detect the antimicrobial susceptibility pattern of all isolates. The phylogenetic grouping of all isolates was done according to the modified Clermont method. Conventional PCR was performed to detect plasmid-mediated fosfomycin-resistant genes (fos genes) and the bla_CTX-M gene.

RESULTS

Analyses of data were performed by SPSS software. A high percentage of fosfomycin resistance (37/96; 38.5%) was reported among UPEC isolates. The fosfomycin-resistant strains showed a higher resistance rate than fosfomycin-susceptible isolates to different antibiotics. E group (62.2%) was the most predominant phylogenetic group among the fosfomycin-resistant UPEC isolates, followed by Group B2 (21.6%) and group D (13.5%). The fos genes were detected in 21 isolates with the fosA3 gene as the most frequent, which was detected in 11 isolates followed by fosA (8), fosC2 (4), fosA4(1), and fosA5(1) genes.

CONCLUSION

This is the first report of a high prevalence of plasmid-mediated fosfomycin-resistant UPEC in Egypt. All of these isolates were multidrug-resistant to the tested antibiotics. Close monitoring of such strains is mandatory to prevent widespread dissemination of the genes code for antibiotic resistance.

Phylogenetic groups, serogroups and virulence factors of uropathogenic Escherichia coli isolated from patients with urinary tract infection in Baghdad, Iraq

Background and Objectives

Uropathogenic Escherichia coli (UPEC) is divided into different phylogenetic groups that differ in their antibiotic resistance patterns, serogroups and pathogenicity. This study aimed to investigate the prevalence of phylogenetic groups of UPEC isolates and their relationship with serogroups and virulence factors in patients with UTIs.

Materials and Methods

Of the 412 urine samples tested a total of 150 UPEC were isolated and confirmed with PCR using 16S rRNA gene. Antibiotic resistance of the isolates was tested using disk diffusion method and the isolates were divided into phylogenetic groups by the quadruplex PCR method. The prevalence of serogroups and virulence genes were investigated using multiplex PCR.

Results

87 (58%) of the isolates belonged to phylogroup B2. Virulence genes fimH (95.3%), aer (49.3%) and serogroups O8 (22.3%), O25 (21.5%) showed the highest prevalence. The lowest drug resistance was observed against imipenem (4.6%) and meropenem (3.3%). The prevalence of multidrug-resistant and extended-spectrum beta-lactamases isolates were 60% and 61.3%, respectively. We also found a significant relationship between phylogenetic groups, serogroups and virulence factors among our isolates.

Conclusion

The high abundance of phylogenetic group B2, serogroups O8 and O25, and virulence genes fimH and aer indicate their importance in the pathogenesis of UPEC in this country.

Antibiotic resistance, phylogenetic typing, and virulence genes profile analysis of uropathogenic Escherichia coli isolated from patients in southern Iraq

Of the most common infectious diseases that occur mainly by uropathogenic Escherichia coli (UPEC) is urinary tract infections (UTIs). The purpose of this study was to investigate virulence factors, antibiotic resistance, and phylogenetic groups among UPEC strains isolated from patients with UTI in southern Iraq. A total of 100 UPEC isolates were collected from urine samples of UTI patients from various hospitals in southern Iraq, and confirmed by morphological and biochemical tests. Antimicrobial susceptibility testing on isolates was performed by disk diffusion method. Multiplex PCR techniques were used to evaluate the phylogenetic groups based on Clermont method and to detect the presence of six virulence factor genes. The majority of isolates belonged to the phylogenetic groups B2 (46%) and C (13%). The most prevalent virulence factors were fimH (96%), followed by aer (47%), papC (36%), cnf1 (17%), hly (15%), and afa (8%). Phenotypic testing showed that the isolates were most resistant to piperacillin, ticarcillin, amoxicillin/clavulanic acid (92%, 91%, and 88%, respectively) and most sensitive to amikacin and imipenem, respectively. The maximum antibiotic resistance and virulence factors were observed in the phylogenetic group B2. The results showed that the UPEC isolates had all six virulence factors with high frequency and the highest drug resistance. Besides, the results showed a direct relationship between virulence factors, gene diversity, phylogenetic background, and antimicrobial resistance in the UPEC isolates.

Characterization of virulence determinants and phylogenetic background of multiple and extensively drug resistant Escherichia coli isolated from different clinical sources in Egypt

Abstract

Escherichia coli is a multifaceted microbe since some are commensals, normally inhabiting the gut of both humans and animals while others are pathogenic responsible for a wide range of intestinal and extra-intestinal infections. It is one of the leading causes of septicemia, neonatal meningitis, urinary tract infections (UTIs), cystitis, pyelonephritis, and traveler’s diarrhea. The present study aims to survey the distribution and unravel the association of phylotypes, virulence determinants, and antimicrobial resistance of E. coli isolated from different clinical sources in Mansoura hospitals, Egypt. One hundred and fifty E. coli isolates were collected from different clinical sources. Antimicrobial resistance profile, virulence determinants, and virulence encoding genes were detected. Moreover, phylogenetic and molecular typing using ERIC-PCR analysis was performed. Our results have revealed that phylogroup B2 (26.67%) with the greatest content in virulence traits was the most prevalent phylogenetic group. Different virulence profiles and varying incidence of virulence determinants were detected among tested isolates. High rates of resistance to different categories of antimicrobial agents, dramatic increase of MDR (92.67%), and emergence of XDR (4%) were detected. ERIC-PCR analysis revealed great diversity among tested isolates. There was no clustering of isolates according to resistance, virulence patterns, or phylotypes. Our research has demonstrated significant phylogenetic diversity of E. coli isolated from different clinical sources in Mansoura hospitals, Dakahlia governorate, Egypt. E. coli isolates are equipped with various virulence factors which contribute to their pathogenesis in human. The elevated rates of antimicrobial resistance and emergence of MDR and XDR mirror the trend detected globally in recent years.

Key points

• Clinical E. coli isolates exhibited substantial molecular and phylogenetic diversity.

• Elevated rates of antimicrobial resistance and emergence of XDR in pathogenic E. coli.

• B2 Phylogroup with the highest VS was the most prevalent among pathogenic E. coli.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11740-x.

Molecular characterization and antimicrobial resistance of potentially human-pathogenic Escherichia coli strains isolated from riding horses

Background

Transmission of antimicrobial resistant and virulent Escherichia coli (E. coli) from animal to human has been considered as a public health concern. This study aimed to determine the phylogenetic background and prevalence of diarrheagenic E. coli and antimicrobial resistance in healthy riding-horses in Iran. In this research, the genes related to six main pathotypes of E. coli were screened. Also, genotypic and phenotypic antimicrobial resistance against commonly used antibiotics were studied, then phylo-grouping was performed on all the isolates.

Results

Out of 65 analyzed isolates, 29.23 % (n = 19) were determined as STEC and 6.15 % (n = 4) as potential EPEC. The most prevalent antimicrobial resistance phenotypes were against amoxicillin/clavulanic acid (46.2 %) and ceftriaxone (38.5 %). bla_TEM was the most detected resistance gene (98.4 %) among the isolates and 26.15 % of the E. coli isolates were determined as multi-drug resistant (MDR). Three phylo-types including B1 (76.92 %), A (13.85 %) and D (3.08 %) were detected among the isolates.

Conclusions

Due to the close interaction of horses and humans, these findings would place emphasis on the pathogenic and zoonotic potential of the equine strains and may help to design antimicrobial resistance stewardship programs to control the dissemination of virulent and multi-drug resistant E. coli strains in the community.

Multidrug Resistance and Virulence Factors of Escherichia coli Harboring Plasmid-Mediated Colistin Resistance: mcr-1 and mcr-3 Genes in Contracted Pig Farms in Thailand

The presence of the plasmid-mediated colistin resistance encoding mcr gene family in the Enterobacteriaceae is one of the crucial global concerns. The use of colistin in livestock rearing is believed to be the cause of mcr gene spreading and is of impact to public health. The objective of this research was to detect the frequency and virulent genes of mcr-positive Escherichia coli (MCRPE) in fecal samples from healthy pigs in a contract farming system across Thailand. A total of 696 pooled samples were derived from 80 farms, located in 49 provinces across six regions of Thailand. The colistin-resistant E. coli were identified by MALDI-TOF mass spectrometry and antimicrobial susceptibility testing by broth microdilution. The antibiogram was determined using an automated susceptibility machine, and the genetic characteristics were investigated for mcr-1–5 genes, phylogenetic group, replicon types, and virulent genes. In total, 31 of 696 samples were positive, with E. coli containing mcr-1 or combination of mcr-1 and mcr-3 with incidence of 4.45 and 0.43%. Phylogenetic groups A and B1 and the IncF and IncFIB replicon types were predominantly found in the MCRPE located in the central area, with multidrug-resistant traits against 3–14 types of antimicrobials. Additionally, 19 of 31 isolates identified as enterotoxigenic E. coli were with the stap and stb (enterotoxin-encoding genes). In conclusion, a low carriage rate of mcr-positive E. coli was detected in the large-scale farming of healthy pigs. The association between multidrug-resistant MCRPE and their pathogenic potential should be of concern.