Phylogenetic and pathotype analysis of Escherichia coli stool isolates from Egyptian patients with inflammatory bowel disease

Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns

Genotypically, 16S rRNA gene sequence analysis clearly differentiates between species. However, species delineation between Escherichia fergusonii and Escherichia coli is much more difficult and cannot be distinguished by 16S rRNA gene sequences alone. Hence, in this study, we attempted to differentiate E. fergusonii and E. coli isolated from faecal samples of disease-associated Korean individuals with inflammatory bowel disease (IBD)/ischemic colitis (IC) and test the antimicrobial susceptibility patterns of isolated strains. Phylogenetic analysis was performed using the adenylate kinase (adk) housekeeping gene from the E. coli multi locus sequence typing (MLST) scheme. Antimicrobial susceptibility and minimum inhibitory concentration (MIC) of all disease-associated strains in addition to healthy control isolates to 14 antibiotics were determined by broth microdilution-based technique. Next, 83 isolates from 11 disease-associated faecal samples were identified as E. fergusonii using 16S rRNA gene sequence analysis. Phylogenetic analysis using the adk gene from E. coli MLST scheme revealed that most of the strains (94%) were E. coli. A total of 58 resistance patterns were obtained from 83 strains of disease-associated (IBD/IC) isolates. All isolates were resistant to at least one tested antimicrobial agent, with the highest resistance against erythromycin (88.0%), ampicillin (86.7%), ciprofloxacin (73.5%), cephalothin (72.3%), gentamicin (59%), trimethoprim-sulfamethoxazole (53%), cefotaxime (49.4%), and ceftriaxone (48.2%). A total of 90.7% of isolates were extended-spectrum beta-lactamase (ESBL)-producers among the resistant strains to third-generation cephalosporins (cefotaxime or ceftriaxone). ESBL-producing E. coli isolates from patients with Crohn's disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) were 92.3%, 82.4%, and 100%, respectively. In conclusion, adk-based phylogenetic analysis may be the most accurate method for distinguishing E. coli and E. fergusonii from Escherichia genus. We identified four loci in adk gene sequences which makes it easier to discriminate between E. coli and E. fergusonii. Additionally, we believe that gut colonization by multidrug-resistant ESBL-producing E. coli may play a significant role in IBD/IC pathogenesis.

Role of adherent invasive Escherichia coli in pathogenesis of inflammatory bowel disease

Gut microbiota imbalances play an important role in inflammatory bowel disease (IBD), but no single pathogenic microorganism critical to IBD that is specific to the IBD terminal ileum mucosa or can invade intestinal epithelial cells has been found. Invasive Escherichia coli (E. coli) adhesion to macrophages is considered to be closely related to the pathogenesis of inflammatory bowel disease. Further study of the specific biological characteristics of adherent invasive E. coli (AIEC) may contribute to a further understanding of IBD pathogenesis. This review explores the relationship between AIEC and the intestinal immune system, discusses the prevalence and relevance of AIEC in Crohn's disease and ulcerative colitis patients, and describes the relationship between AIEC and the disease site, activity, and postoperative recurrence. Finally, we highlight potential therapeutic strategies to attenuate AIEC colonization in the intestinal mucosa, including the use of phage therapy, antibiotics, and anti-adhesion molecules. These strategies may open up new avenues for the prevention and treatment of IBD in the future.

Phylogrouping and characterization of Escherichia coli isolated from colonic biopsies and fecal samples of patients with flare of inflammatory bowel disease in Iran

Background

Although the etiopathogenesis of inflammatory bowel disease (IBD) is still poorly understood, Escherichia coli has been described as a potential causative microorganism in IBD pathogenesis and also disease progression, offering a potential therapeutic target for disease management. Therefore, we conducted this study to investigate the pathotypes, phylogenetic groups, and antimicrobial resistance of E. coli isolates from patients with IBD in Iran.

Methods

Fecal and biopsy colonic samples were collected from IBD patients experiencing flare-up episodes referred to Taleghani hospital in Tehran, Iran, between August 2020 and January 2021. Identification of E. coli strains was performed based on biochemical and molecular methods. Antibiotic susceptibility testing was performed as recommended by the Clinical and Laboratory Standards Institute. Phylogrouping and pathotyping of each isolate were carried out using polymerase chain reaction (PCR) and multilocus sequence typing (MLST) assays.

Results

A total of 132 non-duplicate E. coli strains were isolated from 113 IBD patients, including 96 ulcerative colitis (UC), and 17 Crohn’s disease (CD) patients. In our study, 55% of CD-related E. coli and 70.5% of UC-related isolates were non-susceptible to at least three or more unique antimicrobial classes, and were considered as multidrug-resistant (MDR) strains. E. coli strains exhibited a high level of resistance to cefazolin, ampicillin, tetracycline, ceftazidime, ciprofloxacin, and cefotaxime. Enterotoxigenic E. coli (ETEC) and diffusely adherent E. coli (DAEC) were the most prevalent pathotypes, and groups B2 and D were the predominant phylogroups.

Conclusion

In the present study, we found that E. coli strains that colonize the gut of Iranian patients with IBD most frequently belonged to phylogenetic groups B2 and D. We also conclude that E. coli isolates from IBD patients have been revealed to be resistant to commonly used antibiotics, in which most of them harbored strains that would be categorized as MDR.

Antimicrobial resistance and gene regulation in Enteroaggregative Escherichia coli from Egyptian children with diarrhoea: Similarities and differences

Enteroaggregative Escherichia coli (EAEC) is a common diarrhoeagenic human pathogen, isolated from patients in both developing and industrialized countries, that is becoming increasingly resistant to many frontline antibiotics. In this study, we screened 50 E. coli strains from children presenting with diarrhea at the outpatients clinic of Assiut University Children’s Hospital, Egypt. We show that all of these isolates were resistant to multiple classes of antibiotics and identified two as being typical EAEC strains. Using whole genome sequencing, we determined that both isolates carried, amongst others, bla_CTX-M and bla_TEM antibiotic resistance genes, as well as many classical EAEC virulence determinants, including the transcriptional regulator, AggR. We demonstrate that the expression of these virulence determinants is dependent on AggR, including aar, which encodes for a repressor of AggR, Aar. Since biofilm formation is the hallmark of EAEC infection, we examined the effect of Aar overexpression on both biofilm formation and AggR-dependent gene expression. We show that whilst Aar has a minimal effect on AggR-dependent transcription it is able to completely disrupt biofilm formation, suggesting that Aar affects these two processes differently. Taken together, our results suggest a model for the induction of virulence gene expression in EAEC that may explain the ubiquity of EAEC in both sick and healthy individuals.