Pathotypic and Phylogenetic Study of Diarrheagenic Escherichia coli and Uropathogenic E. coli Using Multiplex Polymerase Chain Reaction

Developing the PIP-eco: An integrated genomic pipeline for identification and characterization of Escherichia coli pathotypes encompassing hybrid forms

Pathogenic Escherichia coli (E. coli) strains are distinguished by their diverse virulence factors, which contribute to a wide spectrum of diseases. These pathogens evolve through the horizontal transfer of virulence factors, resulting in the emergence of hybrid pathotypes with complex and heterogeneous characteristics. Recognizing their profound impact on public health, this study introduces the PIP-eco pipeline, a comprehensive analytical tool designed for the precise identification and characterization of E. coli pathotypes. This PIP-eco pipeline advances beyond traditional molecular techniques by facilitating detailed analysis of both single and hybrid pathotypes. It integrates targeted marker gene analysis, virulence factor-based phylogenetic analysis, and pathogenicity islands (PAIs) profiling to elucidate the genetic diversity of E. coli pathotypes and support their accurate classification. This integrative approach enables PIP-eco to uncover connections among various E. coli pathotypes, highlight shared virulence factors, and provide insights into their evolutionary trajectories. By utilizing experimentally validated marker genes, the pipeline ensures robust identification of pathotypes, particularly those of hybrid pathotypes. Additionally, PAI analysis offers comprehensive genetic investigations, revealing strain-specific variations and potential virulence mechanisms. As a result, the PIP-eco pipeline emerges as a useful tool for dissecting the evolutionary dynamics of E. coli and characterizing complex pathotypes, addressing the critical need for accurate detection and understanding of hybrid pathotypes.

Development of a newly designed biosensor using multi-walled carbon nanotubes (MWCNTs) with gold nanoparticles (AuNPs) in the presence of acetaminophen for detection of Escherichia coli

Escherichia coli is one of the main indicators in the quality control of water, pharmaceuticals, and other samples. Compared with the time-consuming and high prices of the classical methods, with their high risks in the case of insensitive, contamination and offline detections, biosensors have long been a fast and accurate approach for identifying different bacteria. The present study reports the development of a newly electrochemical biosensor using a glassy carbon electrode (GCE) modified by multi-walled carbon nanotubes/AuNPs/E. coli polyclonal antibody/Bovine Serum Albumin in 0.1 M phosphate-buffered saline ( pH 7) in the presence of acetaminophen, for the detection of E. coli in pharmaceuticals and some real samples. Acetaminophen was added as an indicator for the detection of E. coli by changes in conductivity and current. To identify E. coli, square-wave voltammetry (SWV), differential pulse voltammetry (DPV), and cyclic voltammetry (CV) techniques were used. According to the obtained results of square-wave voltammetry, a limit of 3.02 CFU/ml E. coli detection in 3 min with desirable sensitivity, repeatability, and reproducibility was found with the designed biosensor. This biosensor could be a powerful tool for the detection of indicator bacteria in the food industry, drug safety, quality control, clinical diagnostics, and environmental monitoring.

Phylogenetic Group Distribution of Uropathogenic Escherichia coli and Related Antimicrobial Resistance Pattern: A Meta-Analysis and Systematic Review

The phylogenetic classification of Escherichia coli isolates is of great importance not only for understanding the populations of E. coli but also for clarifying the relationship between strains and diseases. The present study aimed to evaluate the prevalence of phylogenetic groups, antibiotic susceptibility pattern, and virulence genes among uropathogenic E. coli (UPEC) isolated from different parts of Iran through a systematic review and meta-analysis. Several international electronic sources, including Web of Science, PubMed, Scopus, and Embase, were searched (2000–2020) in order to identify the studies compatible with our inclusion criteria. The meta-analysis was performed using the metaprop program in the STATA (version 11) software. Based on our comprehensive search, 28 studies meeting the eligibility criteria were included in the meta-analysis. The pooled prevalence of phylogroups B₂, D, B₁, and A was 39%, 26%, 18%, and 8%, respectively. In addition, there was a significant heterogeneity among different phylogroups. However, according to the results of Begg’s and Egger’s tests, there were no significant publication bias in phylogroups B₂, D, B₁, and A. This research provided the first comprehensive study on phylogroups of UPEC isolated in Iran. Our findings indicated that phylogroup B₂ and group D were the most predominant phylogenetic groups among UPEC isolates in various regions of Iran. In addition, we observed that certain phylogenetic groups are more antibiotic resistant than the others. It was also observed that the dissemination of virulent phylogroup B₂ and D should be controlled via comprehensive infection control measures. Additionally, certain strategies should be developed for monitoring the antibiotic therapy.

Enteroaggregative Escherichia coli is associated with antibiotic resistance and urinary tract infection symptomatology

Background

Uropathogenic Escherichia coli (UPEC) is the causative agent of uncomplicated urinary tract infections (UTIs) in ambulatory patients. However, enteroaggregative E. coli (EAEC), an emergent bacterial pathogen that causes persistent diarrhoea, has recently been associated with UTIs. The aim of this study was to determine the frequency of EAEC virulence genes, antibiotic resistance, as well as biofilm production of UPEC isolates obtained from ambulatory patients with non-complicated UTIs that attended to the ISSSTE clinic in Chilpancingo, Guerrero, Mexico, and correlate these with the patients' urinary tract infection symptomatology.

Methods

One hundred clinical isolates were obtained. The identification of clinical isolates, antimicrobial susceptibility testing, and extended spectrum beta-lactamases (ESBLs) production were performed using the Vitek automated system. Assignment of E. coli phylogenetic groups was performed using the quadruplex phylo-group assignment PCR assay. UPEC virulence genes (hlyA, fimH, papC, iutA, and cnf1) and EAEC virulence genes (aap, aggR, and aatA) were detected by multiple PCR.

Results

We found that 22% of the isolates carried the aggR gene and were classified as UPEC/EAEC. The main phylogenetic group was B2 (44.1% were UPEC and 77.27% UPEC/EAEC isolates, respectively). Over half of the UPEC/EAEC isolates (63.64%) were obtained from symptomatic patients, however the aatA gene was the only one found to be associated with the risk of developing pyelonephritis (OR = 5.15, p = 0.038). A total of 77.71% of the UPEC/EAEC isolates were ESBL producers and 90.91% multidrug-resistant (MDR). In conclusion, UPEC/EAEC isolates are more frequent in symptomatic patients and the aatA gene was associated with a higher risk of developing pyelonephritis, along with UPEC genes hlyA and cfn1. UPEC/EAEC isolates obtained from UTI showed ESBL production and MDR.

Characterization and Antibiotic Susceptibility Profiles of Pathogenic Escherichia Coli Isolated from Diarrhea Samples within the Buffalo City Metropolitan Municipality, Eastern Cape, South Africa

Objectives:

Developing countries like South Africa are still faced with numerous challenges such as poor environmental sanitation, lack of clean drinking water and inadequate hygiene which have contributed largely to diarrheal infections and deaths in children. This study was aimed at investigating the prevalence of pathotypes, antimicrobial resistance and drug resistance determinants among Escherichia coli (E. coli) isolates from diarrhea stool samples within Buffalo City Municipality, Eastern Cape, South Africa.

Methods:

Fresh diarrheal stool samples were collected from 140 patients attending public health centres within the Municipality and presumptive E. coli isolates were obtained from the stool samples using E. coli chromogenic agar while PCR amplification methods were used to confirm the presumptive isolates as well as delineate them into pathotypes based on the presence of certain virulence genes. In addition, antimicrobial susceptibility and screening of some of the antimicrobial resistant determinants were performed on all the confirmed isolates.

Results:

A total of 394 presumptive E. coli isolates from 140 diarrhea stool samples were subjected to polymerase chain reaction amplification, of which 265 were confirmed positive as E. coli. Pathotypes delineation of the positive E. coli isolates validated the presence of ETEC 106 (40%), EAEC 48 (18%), DAEC 37 (14%), and EPEC 31 (11%) while no EIEC pathotype was detected. All E. coli isolates exhibited maximum susceptibility to gentamicin (95%), amikacin (91%), nitrofurantoin (91%), meropenem (90%), chloramphenicol (91%) norfloxacin (84%) and imipenem (83%). However, the isolates showed multidrug resistance to penicillin G, ampicillin, trimethoprim, tetracycline, doxycycline, and erythromycin, with over 71% of the isolates resistant to the drugs. The prevalence and distribution of the five resistance determinants assessed were as follow; sulphonamides; sulII (12%), beta lactams; [ampC (22%); blaTEM, (25%)], and tetracyclines (tetA (35%).

Conclusion:

The results from this study suggest the probable involvement of E. coli pathotypes as an etiologic agent of diarrhea in the study area and revealed high levels of multidrug resistance among the isolates, which could be a major health burden.

Pathotyping and Antibiotic Resistance Profiling of Escherichia coli Isolates from Children with Acute Diarrhea in Amatole District Municipality of Eastern Cape, South Africa

BACKGROUND

Diarrhea has been reported as the leading cause of childhood mortality and morbidity globally but with disproportionate impacts in developing nations. Among bacterial etiologic agents of diarrhea, diarrheagenic Escherichia coli is the main cause of the disease among children under the age of 5 years. This study is aimed at determining the prevalence and antibiogram pattern of diarrheagenic Escherichia coli (DEC) pathotypes associated with diarrhea cases in the study area.

METHODS

A total of 120 presumptive isolates of E. coli were obtained from diarrheal stool samples from male and female patients below 12 years of age using chromogenic agar. Confirmation of the isolates and screening for virulence genes were determined by polymerase chain reaction (PCR) while antimicrobial susceptibility testing was performed using the disk diffusion method. The presence of antibiotic resistance genes to chloramphenicol and tetracycline among the confirmed isolates was also profiled by PCR based on the observed phenotypic resistance pattern.

RESULTS

Of the 120 presumptive isolates, 88.3% (106/120) were confirmed as E. coli through PCR. The molecular pathotyping of the confirmed isolates showed their distribution as 41% (43/106) of diffusely adhering E. coli (DAEC), 17% (18/106) of enterohemorrhagic E. coli (EHEC), 17% (18/106) of enteropathogenic E. coli (EPEC), and 10% (11/106) of enteroinvasive E. coli (EIEC), while enteroaggregative E. coli (EAEC) and enterotoxigenic E. coli (ETEC) were not detected, and the remaining 15% did not belong to any pathotype. Notably, high resistance of the isolates to commonly used antimicrobials was observed as follows: ampicillin (98%), chloramphenicol (94%), trimethoprim-sulfamethoxazole (96%), and tetracycline (90.6%), while a relatively low number of the confirmed isolates were resistant to ciprofloxacin (45%) and imipenem (36%). In addition, 94% of the isolates that exhibited phenotypic resistance against chloramphenicol harbored the catA1 resistance gene while 89% that showed resistance to tetracycline had tetA genes.

CONCLUSIONS

These findings showed that DEC could be considered as the leading etiologic bacterial agent responsible for diarrhea in the study community, and the observable high degree of resistance of the isolates to antimicrobial agents is of huge significance, calling for stakeholders to adopt and consolidate the existing antimicrobial stewardship scheme of the government, in order to ensure an uncompromised public health.

Genetic and Virulence Characteristics of a Hybrid Atypical Enteropathogenic and Uropathogenic Escherichia coli (aEPEC/UPEC) Strain

Hybrid strains of Escherichia coli combine virulence traits of diarrheagenic (DEC) and extraintestinal pathogenic E. coli (ExPEC), but it is poorly understood whether these combined features improve the virulence potential of such strains. We have previously identified a uropathogenic E. coli (UPEC) strain (UPEC 252) harboring the eae gene that encodes the adhesin intimin and is located in the locus of enterocyte effacement (LEE) pathogenicity island. The LEE-encoded proteins allow enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) to form attaching and effacing (A/E) lesions in enterocytes. We sought to characterize UPEC 252 through whole-genome sequencing and phenotypic virulence assays. Genome analysis unveiled that this strain harbors a complete LEE region, with more than 97% of identity comparing to E2348/69 (EPEC) and O157:H7 Sakai (EHEC) prototype strains, which was functional, since UPEC 252 expressed the LEE-encoded proteins EspB and intimin and induced actin accumulation foci in HeLa cells. Phylogenetic analysis performed comparing 1,000 single-copy shared genes clustered UPEC 252 with atypical EPEC strains that belong to the sequence type 10, phylogroup A. Additionally, UPEC 252 was resistant to the bactericidal power of human serum and colonized cells of the urinary (T24 and HEK293-T) and intestinal (Caco-2 and LS174T) tracts. Our findings suggest that UPEC 252 is an atypical EPEC strain that emerges as a hybrid strain (aEPEC/UPEC), which could colonize new niches and potentially cause intestinal and extraintestinal infections.

Risk factors for hospital-acquired non-catheter-associated urinary tract infection

BACKGROUND AND PURPOSE

Nosocomial urinary tract infection in patients with no Foley catheter [non-catheter-associated urinary tract infection (non-CAUTI)] has been a serious health issue that is associated with an increase in the cost of care, morbidity, and mortality. Identifying the risk factors of non-CAUTI would help determine patients at high risk and prevent complications. This study aims to identify the risk factors of non-CAUTI.

METHOD

This study was conducted in four hospitals in three Middle Eastern countries: Jordan, Qatar, and Saudi Arabia. A convenience sample of 189 participants was recruited, of which 83 had non-CAUTI. Case-control design was used. Patients who had non-CAUTI while hospitalized were compared with others who did not. A questionnaire was developed based on the non-CAUTI diagnostic criteria from the Centers for Disease Control and Prevention. The questionnaire contained two parts: part one included participants' characteristics and part two assessed the symptoms of non-CAUTI.

CONCLUSION

Comorbidity is associated with a higher risk of having nosocomial non-CAUTI among hospitalized patients. This study showed that the diagnosis and management of comorbidity is important in lowering the risk of non-CAUTI in hospitalized patients. Age and antibiotic administration were statistically significant; however, their effects were small and were unlikely to have any clinical significance.

IMPLICATION FOR PRACTICE

Identifying patients at high risk is imperative to prevent the development of non-CAUTI. Nurse practitioners may implement an early intervention for patients with comorbidity to counteract its effect on patients' health.

An overview of diarrheagenic Escherichia coli in Iran: A systematic review and meta-analysis

BACKGROUND

Diarrheagenic Escherichia coli (DEC) is a common enteric pathogen that causes a wide spectrum of gastrointestinal infections, particularly in developing countries. This is a systematic review and meta-analysis to determine the prevalence of DEC in various geographical regions in Iran.

MATERIALS AND METHODS

English (PubMed, Web of Science, Scopus, Embase, Cochrane Library, and Google Scholar) and Persian (IranMedex, SID, Magiran, and Iran Doc) databases were comprehensively searched from January 1990 to April 2017. Study selection and data extraction were performed by two independent reviewers. After assessing heterogeneity among studies, a random effects model was applied to estimate pooled prevalence. Data analyses were done with the Stata software (version 12.0). This meta-analysis was registered with PROSPERO, number CRD42017070411.

RESULTS

A total of 73 studies with 18068 isolates were eligible for inclusion within the meta-analysis. The results of random effects model showed that the most prevalent DEC pathotypes were enterotoxigenic E. coli (ETEC) (16%; 95% confidence interval [CI]: 11%-23%), enteroaggregative E. coli (11%; 95% CI: 8%-15%), atypical enteropathogenic E. coli (EPEC) (11%; 95% CI: 8%-14%), Shiga toxin-producing E. coli (9%; 95% CI: 6%-13%), diffuse adherent E. coli (6%; 95% CI: 6%-12%), enteroinvasive E. coli (4%; 95% CI: 2%-6%), and typical EPEC (3%; 95% CI: 1%-5%).

CONCLUSION

This study showed that DEC infections in the Iranian population have low frequency. Our data suggest that the ETEC pathotype can be regarded as one of the most important etiological agents of diarrhea in this country. However, the prevalence of DEC pathotypes is diverse in different regions of Iran.

Effectiveness of antibiotics versus ibuprofen in relieving symptoms of nosocomial urinary tract infection: A comparative study

BACKGROUND AND PURPOSE

Antibiotic therapy has been the mainstay of treatment in the management of hospitalized patients with nosocomial urinary tract infection (UTI); however, its use is associated with an increase in resistance and high cost. Ibuprofen showed effectiveness in relieving symptoms of UTI, but its superiority is questionable. The goal of this study was to compare the effectiveness of antibiotics against ibuprofen in relieving symptoms of UTI and to identify factors that affect symptom relief.

METHODS

This study was conducted in three public hospitals in Jordan. Patients with nosocomial UTI were assigned to either antibiotics or ibuprofen. Symptoms of UTI were assessed at the time of initiation of treatment and 5 days later.

CONCLUSIONS

Antibiotics were more effective in relieving symptoms of UTI than Ibuprofen. Comorbidity and length of hospitalization affected symptom relief during the treatment of UTI.

IMPLICATION FOR PRACTICE

Nurse practitioners in the clinical settings can take an active role in helping patients with UTI to achieve relief of symptoms by supporting the use of antibiotics over ibuprofen in symptom resolution.

Study on the presence of resistant diarrheagenic pathotypes in Escherichia coli isolated from patients with urinary tract infection

AIM

This article aimed to analyze the diarrheagenic potential of E. coli isolated from urinary tract infection (UTI) and to recognize the presence of antibiotic resistance genes.

BACKGROUND

The marked genome plasticity of Escherichia coli has allowed the emergence of resistant pathogenic strains displaying an unusual arrangement of genes.

METHODS

In this cross-sectional study, 110 E. coli were isolated from patients with the symptoms of UTI in Sanandaj, west of Iran between July and September - 2015. The isolates were examined by the disk diffusion method for antibiotic susceptibility test and by polymerase chain reaction for the presence of genes characteristic of diarrheagenic E. coli (DEC), Uropathogenic E. coli (UPEC) virulence genes, extended-spectrum β-lactamase bla _CTX-M and plasmid-mediated quinolone resistance determinants, qnrA, qnrB, and qnrS.

RESULTS

The most and the least effective antibiotics were nitrofurantoin and cefotaxime (96.4% and 27.3% sensitivity, respectively). Of the 110 UTI isolates, 57.3% carried diarrheagenic genes. The bundle-forming pilus bfpA was the most prevalent diarrheagenic gene (39.1%). The most commonly detected DEC pathotype was enterotoxigenic E. coli (-ETEC, 12.7%). All the pathotypes carried the bla _CTX-M and qnr. The -UPEC hly hemolysin and pap adhesin genes were mainly detected among ETEC isolates.

CONCLUSION

Our results indicated the presence of resistant diarrheagenic pathotypes in UTI-associated E. coli. Such isolates may have the capacity of causing both extraintestinal and intestinal infections. Based on our knowledge, this is the first report of the presence of qnr in ETEC from urine.

Identification of different Escherichia coli pathotypes in north and north-west provinces of Iran

BACKGROUND AND OBJECTIVES

Diarrhea is one of the most prevalent diseases in the world, specially in developing countries. One of the most important causative agents of bacterial diarrhea is diarrheagenic Escherichia coli (DEC) which causes gastroenteritis and this group involving enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enterohemoragic E. coli (EHEC), enteroinvasive E. coli (EIEC), diffusely adherence E. coli (DAEC). The aim of this study was to identify different E. coli pathotypes in north and north-west of Iran, among the clinical isolates.

MATERIALS AND METHODS

In this study for identification of E. coli, 170 fecal samples were cultured on MacConkey agar and identified by biochemical tests. Samples with E. coli characteristics were selected (145 samples) and their genomes were purified by phenol-chloroform method. After extraction of genomes, lt and sta genes identified by PCR for ETEC, eae gene for atypical and eae and bfp for typical EPEC, AA region for EAEC, stx₁ and stx₂ and eae genes for EHEC (stx₁ or stx₂ or both for STEC) and invE for EIEC.

RESULTS

Finally 10 samples identified as ETEC (%5.88), 18 (%10.58) EPEC, 6 (%3.52) EHEC and 12 (7.05%) samples were STEC. None of the samples were positive for EAEC and EIEC.

CONCLUSION

The results obtained in this study showed that ETEC, EPEC, EHEC and STEC are prevalent bacterial agents in north and north-west of Iran. Complementary studies to identify these pathotypes in other seasons can help to adopt necessary policies against outbreaks in Iran.

Clinical risk factors, bacterial aetiology, and outcome of urinary tract infection in children hospitalized with diarrhoea in Bangladesh

Urinary tract infection (UTI) is common in children aged <5 years with diarrhoea, but little is known about risk factors, aetiology and outcome of such children. We aimed to evaluate these knowledge gaps of UTI in children aged <5 years with diarrhoea. We enrolled all children aged <5 years with diarrhoea admitted to Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh, between May 2011 and April 2013, who had history of fever (⩾38 °C) and obtained a urine sample for culture. Diarrhoea with UTI (confirmed by culture) constituted cases (n = 26) and those without UTI constituted controls (n = 78). Threefold controls were randomly selected. The case-fatality rate was comparable in cases and controls (4% vs. 1%, P = 0·439). Escherichia coli (69%) and Klebsiella (15%) were the most commonly isolated pathogens. Persistent diarrhoea, pneumonia and prior antibiotics use were identified as risk factors for UTI in logistic regression analysis (P < 0·05 for all). Thus, children with diarrhoea presenting with persistent diarrhoea, pneumonia, and prior antibiotic use should be investigated for UTI for their prompt management that may reduce morbidity.