Simple and rapid multiplex PCR for identification of the main human diarrheagenic Escherichia coli

PCR diagnostics are insufficient for the detection of Diarrhoeagenic Escherichia coli in Ibadan, Nigeria

Understanding the contribution of different diarrhoeagenic Escherichia coli pathotypes to disease burden is critical to mapping risk and informing vaccine development. Targeting select virulence genes by PCR is the diagnostic approach of choice in high-burden, least-resourced African settings. We compared the performance of a commonly-used multiplex protocol to whole genome sequencing (WGS). PCR was applied to 3,815 E. coli isolates from 120 children with diarrhoea and 357 healthy controls. Three or more isolates per specimen were also Illumina-sequenced. Following quality assurance, ARIBA and Virulencefinder database were used to identify virulence targets. Root cause analysis of deviant PCR results was performed by examining target sensitivity using BLAST, Sanger sequencing false-positive amplicons, and identifying lineages prone to false-positivity using in-silico multilocus sequence typing and a Single Nucleotide Polymorphism phylogeny constructed using IQTree. The sensitivity and positive predictive value of PCR compared to WGS ranged from 0-77.8% while specificity ranged from 74.5-94.7% for different pathotypes. WGS identified more enteroaggregative E. coli (EAEC), fewer enterotoxigenic E. coli (ETEC) and none of the Shiga toxin-producing E. coli detected by PCR, painting a considerably different epidemiological picture. Use of the CVD432 target resulted in EAEC under-detection, and enteropathogenic E. coli eae primers mismatched more recently described intimin alleles common in our setting. False positive ETEC were over-represented among West Africa-predominant ST8746 complex strains. PCR precision varies with pathogen genome so primers optimized for use in one part of the world may have noticeably lower sensitivity and specificity in settings where different pathogen lineages predominate.

Are non-lactose-fermenting Escherichia coli important diarrhoeal pathogens in children and adults?

Introduction

Diarrhoeagenic Escherichia coli (DEC) remains one of the major causes of acute diarrhoea episodes in developing countries. The percentage of acute diarrhoea cases caused by DEC is 30-40 % in these countries. Approximately 10% of E. coli isolates obtained from stool specimens have been reported to be non-lactose-fermenting (NLF). The available literature is sparse regarding the pathogenicity of NLF E. coli causing infectious diarrhoea.

Aim

We aimed to elucidate the importance of NLF E. coli in causing diarrhoea in both adults and children by detecting various DEC pathotypes among NLF E. coli in stool samples taken from gastroenteritis cases.

Material and Methods

A total of 376 NLF E. coli isolates from 3110 stool samples from diarrhoea/gastroenteritis patients were included in the study. Up to three NLF colonies that were not confirmed as Vibrio cholerae , Aeromonas spp., Salmonella spp. or Shigella spp., but were identified as E. coli using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), were carefully picked up from each MacConkey agar plate and then meticulously streaked onto freshly prepared, sterilized nutrient agar plates, and biochemical reactions were conducted. Multiplex PCR was conducted for the EAEC, EPEC, ETEC and EHEC pathotypes and PCR for the ipaH gene was conducted for EIEC. The disc diffusion method was used for antibiotic sensitivity testing.

Results

Using multiplex PCR and ipaH PCR, a total of 63 pathotypes of DEC were obtained, with EAEC being the most predominant (n=31) followed by EIEC (n=22), EPEC (n=8) and ETEC (n=2). To further differentiate EIEC from Shigella , additional biochemical tests were performed, including acetate utilization, mucate and salicin fermentation, and aesculin hydrolysis. Antimicrobial susceptibility testing (AST) showed that maximum resistance was seen against ciprofloxacin (82.5 %) followed by ampicillin (77.8 %) and cotrimoxazole (68.2 %), and minimum resistance was seen against ertapenem (4.8 %).

Conclusion

In our study two pathotypes (EAEC, EIEC) were predominant among NLF E. coli and these were not only important aetiological agents in children, but also in adults. Our study also sheds light on the epidemiology of EIEC, which is one of the most neglected DEC pathotypes, as hardly any microbiological laboratories process NLF E. coli for EIEC.

Risk Factors and Associated Outcomes of Virulence Genes eae, entB, and pipD Carriage in Escherichia coli, Klebsiella pneumoniae, and Salmonella spp. From HIV-1 and HIV-Negative Gastroenteritis Patients in the Dschang Regional Hospital Annex

Background Enterobacteriaceae is one of the main families of gram-negative bacilli responsible for serious infections in humans. The severity of infection by these bacteria is a product of many factors, including virulence properties and antimicrobial resistance. This severity may be further intensified if there is an association between these factors and a depressed immune system, such as in HIV patients. This study aimed to determine the distribution of representative virulence genes among key Enterobacteriaceae isolates from HIV-1 and non-HIV gastroenteritis patients and the relationship between carrying these virulence genes and antimicrobial susceptibility, seropositive status, and severity of symptoms associated with Enterobacteriaceae infections in Dschang Regional Hospital Annex. Methodology A total of 200 gastroenteritis patients (100 HIV-1 and 100 non-HIV patients) were selected and evaluated for symptoms associated with gastroenteritis. Stool samples were obtained and cultured, from which Escherichia coli, Klebsiella pneumoniae, and Salmonella spp. isolates were obtained. Antibiotic susceptibility tests were performed on the isolates by agar disc diffusion using commonly used antibiotics. These isolates were tested for the possession of virulence genes by polymerase chain reaction (PCR); eae for E. coli, entB for K. pneumoniae, and pipD for Salmonella spp. Correlation tests and risk assessments were performed between the presence of virulence genes, antibiotic resistance, and specific symptoms. Results The isolates obtained from HIV-positive and HIV-negative patients were, respectively, 61 against 62 for E. coli, 10 against 21 for K. pneumoniae, and 11 against 15 for Salmonella spp.These organisms showed the highest resistance to amoxicillin and clavulanic acid, while the least resistance was observed against ofloxacin, gentamicin, and amikacin in both groups of patients. The virulence genes showed a generally higher occurrence in isolates from HIV-negative patients than HIV-positive patients, with the eae gene 5/61 (8.20%) against 12/62 (19.35%), the entB gene 4/10 (40.00%) against 14/21 (66.66%), and the pipD gene 5/11 (45.45%) against 7/15 (46.46%) in HIV-positive and negative patients, respectively. There was a significant correlation between eae gene carriage and resistance against imipenem (p = 0.047), gentamycin (p = 0.047), and doxycycline (p = 0.029); entB gene carriage and resistance toward levofloxacin (p = 0.017) in K. pneumoniae; and pipD gene carriage and resistance against levofloxacin (p = 0.039), imipenem (p = 0.041), and doxycycline (p = 0.042). The carriage of the virulence genes was seen to be a stronger risk only for the resistance of K. pneumoniae to ceftriaxone (odds ratio (OR) = 2.286) and gentamycin (OR = 3.000), and Salmonella spp. against imipenem (OR = 2.750) and doxycycline (OR = 2.118). The development of severe symptoms correlated significantly with virulence gene carriage in isolates, mainly in HIV-positive patients with eae (p = 0.017) and pipD (p = 0.025), with a strong risk association with the pipD gene (OR = 2.665). Conclusions Antibiotic resistance was associated with virulence gene carriage, indicating that virulence and antibiotic resistance can associate their effects and contribute to poor outcomes in the treatment of bacterial diseases in HIV patients. The possession of virulence genes increased the severity of symptoms associated with gastroenteritis in HIV-positive patients.

Diarrheagenic Escherichia coli and Their Antibiotic Resistance Patterns in Dairy Farms and Their Microbial Ecosystems

Ruminants are the largest reservoir for all types of Escherichia coli, including the pathogenic ones, which can potentially be transmitted to humans via the food chain and environment. A longitudinal study was performed to estimate the prevalence and antibiotic-resistant pattern of pathogenic E. coli (pE.coli) strains in dairy farm environments. A total of 846 environmental samples (water, lagoon slurry, bedding, feed, feces, soil, and compost) were collected in summer over two years from five dairy farms in Maryland, USA. An additional 40 soil samples were collected in winter and summer seasons for evaluating microbiome composition. Collected environmental samples were screened for the presence of pE.coli, which was isolated using a selective culture medium, for later confirmation and virotyping using PCR with specific primers. The overall prevalence of pE.coli in dairy farms was 8.93% (71/846), with the most common virotype identified in isolates being ETEC, followed by STEC. The highest pE.coli prevalence were recorded in lagoon slurry (21.57%) while the lowest was in compost heap (2.99%). Among isolates, 95.87% of the virotypes were resistant to 9 classes of antibiotics whereas only 4.12% were sensitive. The highest proportion (68.04%) of resistance was found for quinolones (e.g., ciprofloxacin). The resulting metagenomic analysis at the phylum and genus levels of the grazing land soil suggests that climatic conditions actively influence the abundance of bacteria. Proteobacteria, which contains many Gram-negative foodborne pathogens (including pE.coli), was the most predominant phylum, accounting for 26.70% and 24.93% of soil bacteria in summer and winter, respectively. In addition to relative abundance, there was no significant difference in species diversity between seasons when calculated via Simpson (D) and Shannon (H) index. This study suggests that antibiotic-resistant E. coli virotypes are present in the dairy farm environment, and proper steps are warranted to control its transmission irrespective of seasonality.

Genome Assessment of Carbapenem- and Colistin-Resistant Escherichia coli from Patients in a Sentinel Hospital in China

Antimicrobial-resistant (AMR) pathogens are a significant threat to public health worldwide. However, the primary carrier of AMR genes, particularly against last-resort antibiotics, is still only partially studied in Chinese hospitals. In a sentinel hospital in China, we collected 157 E. coli strains from patients between January and July 2021. One bla_NDM-1-, nine bla_NDM-5-, and one mcr-1-positive E. coli recovered from inpatients were identified as resistant to meropenem and colistin. There are 37 virulence genes discovered in the 11 strains, including astA in strain EC21Z-147 (O128: H4), which belongs to the enteroaggregative E. coli (EAEC). The bla_NDM gene is distributed into distinct ST types, including ST48, ST616, ST410, ST711, and ST2003, while the mcr-1 gene was identified in ST117. The conjugative plasmids IncX3, IncI1-I, and IncI2 mediated the bla_NDM-5 and mcr-1 genes detected among inpatients. Notably, the youngest age at which mcr-1-positive E. coli has been reported was at one day old, in a child in which the strain is closely related to strains with animal origins. Hospitals are major environments for the spread and dissemination of critical virulence and AMR genes, which requires active monitoring systems at the genome level to surveil the spread of virulence and AMR.

Development and Effective Utilization of a Rapid Multiplex Real-Time PCR of Diarrheagenic Escherichia coli for Food Poisoning Cases

Diarrheagenic Escherichia coli (DEC) causes diarrheal symptoms in humans. The comprehensive detection of DEC from feces using SYBR Green real-time PCR assay requires multiple runs. Moreover, PCR screening can have discrepancies related to the conformance between the results from PCR screening and culturing. We aimed to develop a real-time PCR for the comprehensive testing of DEC for diagnostic support that can be used in any general laboratory and proposed its effective utilization. We tested specificity for the designed primer sets using 100 strains. Moreover, screening and isolation of DEC were performed using the proposed multiplex real-time PCR system for 308 fecal samples collected from 37 food poisoning incidences that occurred in Gifu Prefecture, Japan from 2017 to 2019. Furthermore, the factor of discrepant results between PCR screening and culturing was analyzed by quantifying the number of DEC cell and whole E. coli cell using real-time PCR for 47 PCR screening-positive fecal samples. The results obtained from the developed multiplex real-time PCR system were in 99% concordance with those from the conventional techniques. A total of 49 fecal samples were detected with virulence genes for the screening. Of the samples which were positive with virulence genes by PCR screening, 38.3% could not be detected from the strain for bacterial culture. We found that the culturing positive samples were significantly high in numbers for the DEC cells, but no significant difference was noted in the whole E. coli cells with culturing negative samples. The multiplex real-time PCR developed in this study was found to be rapid and practical for DEC testing. The PCR screening for DEC using this method can provide rapid information toward the diagnostic support of DEC infection.

Prevalence, Virulence Gene Profiling, and Characterization of Enteroaggregative Escherichia coli from Children with Acute Diarrhea, Asymptomatic Nourished, and Malnourished Children Younger Than 5 Years of Age in India

OBJECTIVE

To study the significance of enteroaggregative Escherichia coli (EAEC) as a pathogen causing acute diarrhea and a commensal in healthy nourished and malnourished children younger than five years of age in the Chandigarh region and to address possible traits of EAEC virulence genes, biofilm formation, phylogroups, and antibiotic resistance that would be correlated with diarrhea or carriage.

STUDY DESIGN

Stool samples were obtained from children with acute diarrhea (n = 548), as well as nourished (n = 550), and malnourished controls without diarrhea (n = 110). E coli isolates were confirmed as EAEC by pCVD432 polymerase chain reaction. Multiplex polymerase chain reactions were used to identify 22 virulence-related genes and phylogeny. Antibiotic susceptibility, adherence, and biofilm-forming potential also were studied.

RESULTS

Overall, 16.6% of children were malnourished. EAEC detection was greater among children with acute diarrhea (16%) than nourished (6%) and malnourished nondiarrheal controls (2.7%). We found an association of EAEC infections with age <2 years (P = .0001) in the diarrheal group. Adhesive variants adhesion fimbriae IV and adhesion fimbriae II were significantly associated with diarrhea. The aggR and aar genes showed a positive and negative association with the severity of disease (P = .0004 and P = .0003). A high degree of multidrug resistance was found (73.8%) in the diarrheal group. Most EAEC strains from the diarrheal group belonged to B2 and D phylogroups, whereas strains from non-diarrheal groups, which belonged to phylogroup B1.

CONCLUSIONS

EAEC is a significant contributor to childhood diarrhea, its presence as a commensal, and the significance of the association of various virulence factors among the EAEC isolated from diarrheal and non-diarrheal stools. These data reinforce the importance of aggR and aar as positive and negative regulators and the contribution of AAF/II and AAF/IV fimbria for the pathobiology of EAEC.

Comparative analysis of virulence determinants, phylogroups, and antibiotic susceptibility patterns of typical versus atypical Enteroaggregative E. coli in India

Enteroaggregative Escherichia coli (EAEC) is an evolving enteric pathogen that causes acute and chronic diarrhea in developed and industrialized nations in children. EAEC epidemiology and the importance of atypical EAEC (aEAEC) isolation in childhood diarrhea are not well documented in the Indian setting. A comparative analysis was undertaken to evaluate virulence, phylogeny, and antibiotic sensitivity among typical tEAEC versus aEAEC. A total of 171 EAEC isolates were extracted from a broad surveillance sample of diarrheal (N = 1210) and healthy children (N = 550) across North India. Polymerase chain reaction (PCR) for the aggR gene (master regulator gene) was conducted to differentiate tEAEC and aEAEC. For 21 virulence genes, we used multiplex PCR to classify possible virulence factors among these strains. Phylogenetic classes were identified by a multiplex PCR for chuA, yjaA, and a cryptic DNA fragment, TspE4C2. Antibiotic susceptibility was conducted by the disc diffusion method as per CLSI guidelines. EAEC was associated with moderate to severe diarrhea in children. The prevalence of EAEC infection (11.4%) was higher than any other DEC group (p = 0.002). tEAEC occurrence in the diarrheal group was higher than in the control group (p = 0.0001). tEAEC strain harbored more virulence genes than aEAEC. astA, aap, and aggR genes were most frequently found in the EAEC from the diarrheal population. Within tEAEC, this gene combination was present in more than 50% of strains. Also, 75.8% of EAEC strains were multidrug-resistant (MDR). Phylogroup D (43.9%) and B1 (39.4%) were most prevalent in the diarrheal and control group, respectively. Genetic analysis revealed EAEC variability; the comparison of tEAEC and aEAEC allowed us to better understand the EAEC virulence repertoire. Further microbiological and epidemiological research is required to examine the pathogenicity of not only typical but also atypical EAEC.

Enteroaggregative E. coli (EAEC) are an increasingly important cause of diarrhea. E. coli belonging to this category cause watery diarrhea, which is often persistent and can be inflammatory. It is also associated with traveler’s diarrhea in children and adults in middle and high-income countries. EAEC are defined by their ability to adhere to epithelial cells in a characteristic stacked brick-like pattern. However, the identification of these pathogenic strains remains elusive because of its heterogeneous nature. Genes that could contribute to the pathogenicity of EAEC encode adhesions, toxins, and other factors. Due to the heterogeneity of EAEC strains and differing host immune responses, not all EAEC infections are symptomatic. A critical factor in both recognizing EAEC pathogenesis and defining typical EAEC (tEAEC) strains is AggR, a transcriptional control for many EAEC virulence genes. The central role of aggR in virulence confers a strong priority to understand its pathogenicity. To identify EAEC, the CVD432 probe has been used. The CVD432 is a DNA probe from pAA plasmid of EAEC, has been reported to be specific for the detection of EAEC. The lack of sensitivity comes from the genetic heterogeneity of the EAEC strains and the wide geographic dispersal of strains. In our study, we performed a large surveillance of EAEC from North India among the pediatric population. Samples were collected by the microbiology staff at the Postgraduate Institute of Medical Education and Research (PGIMER) and referral system labs in Chandigarh (Manimajra), Punjab (Ludhiana), Haryana (Panchkula and Ambala Cantt), Himachal Pradesh (Hamirpur, Shimla, and Tanda), and Uttarakhand (Rishikesh, Rudrapur, and Haridwar)]. PGIMER is the largest tertiary care hospital in North India and serves patients from across Punjab, Jammu and Kashmir, Himachal Pradesh and Haryana. EAEC infections were detected using molecular methods. In our finding, astA, aap, and aggR genes were most frequently found in the EAEC from the diarrheal population. Within tEAEC, this gene combination is present in more than 50% of strains and helps to differentiate tEAEC from aEAEC. Our collection of EAEC strains helps in finding an appropriate marker for the early detection of EAEC. Our signature sequence (astA, aap, and aggR) will be ideal as focus genes for EAEC identification, as well as tEAEC and aEAEC. The multidrug resistance (MDR) was observed in 75.8% of the EAEC strains. tEAEC exhibits resistance to a greater number of antibiotics with respect to aEAEC. The phylogenetic analysis revealed that EAEC phylogeny is diverse and dispersed in all the phylogroups.

Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.

Age related differences in phylogenetic diversity, prevalence of Shiga toxins, Intimin, Hemolysin genes and select serogroups of Escherichia. coli from pastured meat goats detected in a longitudinal cohort study

Background

Little is known on significance, diversity and characteristics of gut E. coli in goats despite their importance as food animals globally. We characterized the temporal dynamics in diversity of E. coli in fecal samples from a cohort of goat kids and adult meat goats on pasture over a one-year period. Isolates were characterized based on phylogenetic grouping, virulence genes; shiga toxins 1 and 2 (Stx1&Stx2) (STEC), intimin (eaeA), hemolysin (hly) and select important sero-groups (026, 045, 0103, 0126 and 0146) using molecular methods.

Results

A total of 516 E. coli isolates were screened. Prevalence of virulence genes and STEC was 65 and 56% respectively. Prevalence of virulence genes and STEC was significantly higher in goat kids less than six months (76% /66%) than adults (48% /28%). Isolates with virulence profiles of two or more genes were also higher in young goat kids (50%) than adults (20%). Entero-pathogenic E. coli (EPEC-eaeA gene only) were mostly from pre-weaned goat kids while hly gene only isolates were significantly higher in adults. The stx1, stx2 and hly genes peaked around weaning (60, 63 and 52%) respectively. Goats kids were mostly hosts to group D (59%) while adults older than one year had B1 (75%) isolates. Group D isolates were most abundant at weaning (64%) and diarrhea samples (74%). Group B2 isolates overall (6%) were mostly detected around weaning (63%) while A isolates were 4% overall. Twenty-four isolates belonged to sero-groups 026, 0103 and 0146 with 70% of the isolates detected around weaning. Nineteen of these isolates were STEC with most harboring the stx1/stx2/hly/eae (25%) profile. Most belonged to O26 sero-group (75%) and phylogroup D (75%).

Conclusion

To our knowledge this is the first study to highlight longitudinal age related differences in E. coli phylogenetic diversity, abundance of virulence genes and select important sero-groups in goats. Differences detected suggest a possible role of age and weaning stress in influencing E. coli diversity in the gut of goats. The findings are relevant to both animal and public health to advise on further studies on caprine E. coli isolates as animal and human pathogens.

Bovine Colostrum in the Treatment of Acute Diarrhea in Children: A Double-Blinded Randomized Controlled Trial

OBJECTIVES

To evaluate the effect of bovine colostrum (BC) on the treatment of children with acute diarrhea attending the outpatient clinic.

METHODS

This double-blind randomized controlled trial was conducted on 160 children with diarrhea; 80 cases were randomly treated with BC group and 80 cases randomly received placebo (placebo group). All cases were investigated for bacterial causes of diarrhea (Salmonella spp, Shigella spp, diarrheagenic E. coli (DEC), Campylobacter spp., and Vibrio cholerae) as well as for Rotavirus antigen in stool.

RESULTS

After 48 h, the BC group had a significantly lower frequency of vomiting, diarrhea and Vesikari scoring compared with the placebo group (p = 0.000, p = 0.000, p = 0.000, respectively), whether it was due to Rotavirus or E. coli infection.

CONCLUSIONS

BC is effective in the treatment of acute diarrhea and can be considered as adjuvant therapy in both viral and bacterial diarrhea to prevent diarrhea-related complications.

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

Introduction

The role of Escherichia coli in the pathogenesis of inflammatory bowel disease (IBD) is still controversial. The study aimed to investigate the pathotypes and the phylogenetic groups of E. coli in Egyptian patients with IBD in an attempt to find an association between any type or group with the severity of the disease.

Methods

Thirty ulcerative colitis (UC), 30 Crohn's disease (CD), and 20 control subjects with normal colonoscopy were included in a cross-sectional study. E. coli were isolated from stool samples by culture. Eight intestinal virulence genes coding for diarrheagenic E. coli were investigated using multiplex PCR. Phylogenetic grouping was performed by a triplex PCR. Antimicrobial susceptibility of all isolates was done using disc diffusion method.

Results

Enteroaggregative E. coli (EAEC) were identified in 25% (15/60) of IBD cases and in none of the controls (p=0.013). Out the 60 IBD cases, 30 (50%) were from phylogenetic group B2. No statistically significant differences in the distribution of E. coli phylogenetic groups were found between study groups. However, 80% of EAEC were assigned to group B2 and D. No statistically significant differences in calprotectin level or in disease severity scores were reported between the four phylogenetic groups. E. coli from both UC and CD patients showed a high rate of resistance to most antimicrobials when compared to the control group.

Conclusions

The identification of EAEC belonging mainly to group B2 and D in IBD cases may indicate the importance of this pathotype in the pathogenesis of IBD in Egyptian patients.

Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats using a Cohort Study

There is a scarcity of information on antibiotic resistance in goats. To understand shedding of resistant Escherichia coli in pastured goats, we collected fecal samples from a mixed age cohort over a one-year period. No antibiotic had been used on the study animals one year prior to and during the study period. Resistant isolates were detected in all age groups and prevalence in goat kids was significantly higher than adults; 43–48% vs. 8–25% respectively. The proportion of resistant isolates was higher when animals were congregated near handling facility than on pasture. Most isolates were resistant to tetracycline (51%) and streptomycin (30%), but also to antibiotics that had never been used on the farm; ampicillin (19%). TetB, bla_-TEM, (aadA and strpA/strpB) genes were detected in 70%, 43%, (44% and 24%) of tetracycline, ampicillin, and streptomycin resistant isolates respectively. Resistant isolates also harbored virulent genes and some belonged to D and B2 phylogenetic groups. Thus, pastured goats, despite minimal exposure to antibiotics, are reservoirs of resistant E. coli that may contaminate the environment and food chain and spread resistant genes to pathogenic bacteria and some that are potential animal and human pathogens. Environmental sources may play a role in acquisition of resistant bacteria in pastured goats.

Molecular and Phenotypic Characterization of Diarrheagenic Escherichia coli Strains Isolated from Bacteremic Children

Escherichia coli is an important cause of Gram-negative bacteremia. The aim of this study was to characterize at the molecular and phenotypic levels E. coli strains belonging to different diarrheagenic pathotypes [diarrheagenic E. coli (DEC)] isolated from bacteremia in children younger than 5 years of age. Seventy bacteremia E. coli strains were collected in a prospective study in 12 hospitals in Lima, Peru. The presence of virulence genes associated with DEC [enterotoxigenic (lt and st), enteropathogenic (eaeA), shiga toxin-producing (stx1and stx2), enteroinvasive (ipaH), enteroaggregative (aggR), and diffusely adherent (daaD)] was determined by multiplex real-time polymerase chain reaction (PCR). Those positive E. coli strains were further analyzed for 18 additional virulence factors encoding genes and others phenotypic features. Virulence genes associated with DEC were identified in seven bacteremic children (10%), including: one aggR-positive [enteroaggregative E. coli (EAEC)], one eaeA-positive [enteropathogenic E. coli (EPEC)], one st-positive [enterotoxigenic E. coli (ETEC)], one daaD-positive [diffusely adherent E. coli (DAEC)], and three strain positive for aggR and daaD (EAEC/DAEC) at the same time. All strains, except EPEC, had the Ag43 adhesin, and all, except ETEC had the siderophore gene fyuA. The phylogenetic profile of these strains was variable, two (B2), two (D), two (A), and one (B1) strain. These isolates were susceptible to all tested antibacterial agents except to ampicillin and gentamicin. The three EAEC/DAEC strains showed biofilm formation and aggregative adhesion and had the same repetitive extragenic palindromic-PCR patterns. These findings suggest that some DEC strains, especially agg-R and daa-D positive, might cause bacteremia in children.

Identification and quantification of virulence factors of enterotoxigenic Escherichia coli by high-resolution melting curve quantitative PCR

BACKGROUND

Diagnosis of enterotoxigenic E. coli (ETEC) associated diarrhea is complicated by the diversity of E.coli virulence factors. This study developed a multiplex quantitative PCR assay based on high-resolution melting curves analysis (HRM-qPCR) to identify and quantify genes encoding five ETEC fimbriae related to diarrhea in swine, i.e. K99, F41, F18, F6 and K88.

METHODS

Five fimbriae expressed by ETEC were amplified in multiple HRM-qPCR reactions to allow simultaneous identification and quantification of five target genes. The assay was calibrated to allow quantification of the most abundant target gene, and validated by analysis of 30 samples obtained from piglets with diarrhea and healthy controls, and comparison to standard qPCR detection.

RESULTS

The five amplicons with melting temperatures (Tm) ranging from 74.7 ± 0.06 to 80.5 ± 0.15 °C were well-separated by HRM-qPCR. The area of amplicons under the melting peak correlated linearly to the proportion of the template in the calibration mixture if the proportion exceeded 4.8% (K88) or <1% (all other amplicons). The suitability of the method was evaluated using 30 samples from weaned pigs aged 6-7 weeks; 14 of these animals suffered from diarrhea in consequence of poor sanitary conditions. Genes encoding fimbriae and enterotoxins were quantified by HRM-qPCR and/or qPCR. The multiplex HRM-qPCR allowed accurate analysis when the total gene copy number of targets was more than 1 × 105 / g wet feces and the HRM curves were able to simultaneously distinguish fimbriae genes in the fecal samples. The relative quantification of the most abundant F18 based on melting peak area was highly correlated (P < 0.001; r2 = 0.956) with that of individual qPCR result but the correlation for less abundant fimbriae was much lower.

CONCLUSIONS

The multiplex HRM assay identifies ETEC virulence factors specifically and efficiently. It correctly indicated the predominant fimbriae type and additionally provides information of presence/ absence of other fimbriae types and it could find broad applications for pathogen diagnosis.

Viral and Bacterial Etiology of Acute Diarrhea among Children under 5 Years of Age in Wuhan, China

BACKGROUND

Acute diarrhea remains the serious problem in developing countries, especially among children under 5 years of age. Currently, only two or three common diarrhea pathogens were screened at most hospitals in China. The aim of this study was to provide a wide variety of diarrhea pathogens and their antimicrobial resistance patterns in children under 5 years of age.

METHODS

Totally 381 stool samples collected from Tongji Hospital between July 1, 2014 and June 30, 2015 were tested by culture and/or polymerase chain reaction for eight kinds of bacteria and five kinds of viruses. An antimicrobial sensitivity test was performed using dilution method recommended by the Clinical and Laboratory Standards Institute.

RESULTS

Viral infections were mainly identified in infants (0-11 months), whereas bacterial infections were more prevalent in the age of 24-59 months. About 69.8% of samples were positive for at least one pathogen, 51.7% of samples were virus positive, followed by bacteria positive cases (19.4%), and 12.6% of cases displayed co-infections with two viruses or a virus and a bacterium. Rotavirus was the most prevalent pathogen, followed closely by norovirus, while Salmonella was the most commonly isolated bacteria, followed by diarrheagenic Escherichia coli (DEC) and Campylobacter. More than 40% of Salmonella spp. and DEC isolates were resistant to first-line antibiotics (ampicillin, trimethoprim-sulfamethoxazole, and tetracycline). Around 10% of Salmonella spp. isolates were resistant to ceftriaxone and ciprofloxacin simultaneously. Campylobacter spp. displayed high resistance to ciprofloxacin but kept low resistance to azithromycin and doxycycline.

CONCLUSIONS

The etiology of acute diarrhea varies in children of different age groups. The high frequency of infection with viruses suggests the urgent demand for new viral vaccine development. Proper use of antibiotics in the treatment of acute diarrhea is crucial due to the high level of antibiotic resistance.

Multiplex PCR for simultaneous identification of E. coli O157:H7, Salmonella spp. and L. monocytogenes in food

The rapid detection of pathogens in food is becoming increasingly critical for ensuring the safety of consumers, since the majority of food-borne illnesses and deaths are caused by pathogenic bacteria. Hence, rapid, sensitive, inexpensive and convenient approaches to detect food-borne pathogenic bacteria is essential in controlling food safety. In this study, a multiplex PCR assay for the rapid and simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes was established. The invA, stx and hlyA genes specifically amplified DNA fragments of 284, 404 and 510 bp from Salmonella spp., L. monocytogenes and E. coli O157:H7, respectively. The 16S rRNA gene was targeted as an internal control gene in the presence of bacterial DNA. The specificity and sensitivity of the multiplex PCR were performed by testing different strains. The multiplex PCR assay was able to specifically simultaneously detect ten colony-forming unit/mL of each pathogen in artificially inoculated samples after enrichment for 12 h. The whole process took less than 24 h to complete, indicating that the assay is suitable for reliable and rapid identification of these three food-borne pathogens, which could be suitable in microbial epidemiology investigation.

Characteristics of bacterial pathogens associated with acute diarrhea in children under 5 years of age: a hospital-based cross-sectional study

Background

Acute diarrhea is a leading cause of morbidity and mortality in children, particularly in those under the age of 5 years. Rotavirus is recognized as the leading cause of acute diarrhea in children, however, the contribution of bacterial pathogens as causative agents varies throughout the world. Here we report a hospital-based prospective study to analyze the characteristics of bacterial pathogens associated with acute diarrhea in children under 5 years of age.

Methods

Stool samples were collected from 508 patients with acute diarrhea under 5 years of age who presented at our hospital. Nine pathogens were isolated and identified by culturing, serology or PCR, these included Salmonella spp., Shigella spp., Vibrio cholerae, diarrheagenic Escherichia coli (DEC), Aeromonas spp., Plesiomonas spp., Vibrio parahaemolyticus, Campylobacter spp. and Yersinia enterocolitica. Antimicrobial sensitivity tests of these pathogens were conducted. The most commonly detected pathogen, Salmonella spp., was further investigated by PCR and sequencing of antibiotic resistance-related genes.

Results

Pathogens were identified in 20.1 % of the 508 samples. The most commonly detected pathogens were Salmonella spp. (8.5 %), followed by DEC (4.7 %), Campylobacter jejuni (3.0 %) and Aeromonas spp. (2.0 %). The resistance rates to ampicillin and tetracycline in Salmonella spp. were >60 %, but were <30 % to cephalosporins and quinolones. More than 50 % of DEC strains displayed resistance to ampicillin, cefotaxime and tetracycline, and 60 % of C. jejuni strains were resistant to ciprofloxacin but highly sensitive to the other antibiotics. Among 12 cephalosporin-resistant Salmonella isolates, TEM-1 and CTX-M-14 determinants were present in two (16.7 %) isolates. PCR screening for plasmid-mediated quinolone resistance genes revealed gyrA mutations in one of three highly quinolone resistant isolates.

Conclusions

Salmonella spp., DEC, Campylobacter spp. and Aeromonas spp. were the most commonly detected bacterial pathogens in children under the age of 5 years with acute diarrhea. Our findings indicate that ampicillin and tetracycline are not suitable as first line therapeutic drugs against Salmonella spp. Resistance to third generation cephalosporins and quinolones was also detected. TEM-1 and CTX-M-14 genetic determinants, and gyrA mutations, were the major mechanisms associated with high levels of cephalosporin and quinolone resistance, respectively, in Salmonella isolates.

FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny

Most Escherichia coli strains are nonpathogenic. However, for clinical diagnosis and food safety analysis, current identification methods for pathogenic E. coli either are time-consuming and/or provide limited information. Here, we utilized a custom DNA microarray with informative genetic features extracted from 368 sequence sets for rapid and high-throughput pathogen identification. The FDA Escherichia coli Identification (FDA-ECID) platform contains three sets of molecularly informative features that together stratify strain identification and relatedness. First, 53 known flagellin alleles, 103 alleles of wzx and wzy, and 5 alleles of wzm provide molecular serotyping utility. Second, 41,932 probe sets representing the pan-genome of E. coli provide strain-level gene content information. Third, approximately 125,000 single nucleotide polymorphisms (SNPs) of available whole-genome sequences (WGS) were distilled to 9,984 SNPs capable of recapitulating the E. coli phylogeny. We analyzed 103 diverse E. coli strains with available WGS data, including those associated with past foodborne illnesses, to determine robustness and accuracy. The array was able to accurately identify the molecular O and H serotypes, potentially correcting serological failures and providing better resolution for H-nontypeable/nonmotile phenotypes. In addition, molecular risk assessment was possible with key virulence marker identifications. Epidemiologically, each strain had a unique comparative genomic fingerprint that was extended to an additional 507 food and clinical isolates. Finally, a 99.7% phylogenetic concordance was established between microarray analysis and WGS using SNP-level data for advanced genome typing. Our study demonstrates FDA-ECID as a powerful tool for epidemiology and molecular risk assessment with the capacity to profile the global landscape and diversity of E. coli.

IMPORTANCE This study describes a robust, state-of-the-art platform developed from available whole-genome sequences of E. coli and Shigella spp. by distilling useful signatures for epidemiology and molecular risk assessment into one assay. The FDA-ECID microarray contains features that enable comprehensive molecular serotyping and virulence profiling along with genome-scale genotyping and SNP analysis. Hence, it is a molecular toolbox that stratifies strain identification and pathogenic potential in the contexts of epidemiology and phylogeny. We applied this tool to strains from food, environmental, and clinical sources, resulting in significantly greater phylogenetic and strain-specific resolution than previously reported for available typing methods.

Microbiological quality of water from the rivers of Curitiba, Paraná State, Brazil, and the susceptibility to antimicrobial drugs and pathogenicity of Escherichia coli

Water safety is determined by several markers, and Escherichia coli is one of the most important indicators of water quality. The objective of this study was to evaluate the microbiological parameters in environmental samples of fresh water from rivers of Curitiba and its metropolitan area in Paraná State, Brazil. In addition, we evaluated the pathogenicity and susceptibility to antimicrobial drugs in E. coli. These evaluations were performed by quantitative and qualitative methods employing selective media for isolating thermotolerant coliforms and biochemical tests for identifying E. coli. Pathogenic strains of E. coli were detected by PCR multiplex using specific primers. From the water samples, 494 thermotolerant coliforms were obtained, of which 96 (19.43%) isolates were characterized as E. coli. Three isolates were identified as enteroaggregative E. coli, one as enterotoxigenic E. coli, one as enteropathogenic E. coli, and two carried the Eae virulence gene. E. coli susceptibility to commonly employed antimicrobial drugs was analyzed by the disc diffusion method. The results showed 49 (51.04%) isolates resistant to all the drugs assayed, 16 (16.67%) with an intermediate resistance to all drugs, and 31 (32.29%) intermediately or fully resistant to one or more drugs tested. The highest rate of resistance was observed for tetracycline 30 μg, streptomycin 10 μg, and ceftazidime 30 μg. Detection of E. coli is associated with water contamination by fecal material from humans and warm-blooded animals. The occurrence of resistant strains can be the result of the indiscriminate use of antimicrobial drugs and poor sanitation in the areas assayed.

Prevalence and virulence characteristics of enteroaggregative Escherichia coli in a case-control study among patients from Iran

Enteroaggregative Escherichia coli (EAEC) is an important agent of diarrhoeal diseases worldwide. The role of EAEC virulence factors in the clinical outcome of infection is not completely defined. This case-control study investigated the prevalence of EAEC, its virulence genes and the antimicrobial resistance profile of adult patients with and without diarrhoea attending three different hospitals in Zanjan, Iran. A total of 550 individual stool specimens (350 from diarrhoeal patients and 200 from patients without diarrhoea) were collected. One hundred and forty-one EAEC isolates were identified by a HEp-2 cell assay and PCR. EAEC isolates were detected with slightly higher frequency in patients with (27.7%) than in patients without (22%) diarrhoea (P ≥ 0.05). The EAEC genes aggR, aap and pet were identified more frequently in case patients compared with controls (P ≤ 0.05). Many of the EAEC isolates from the diarrhoeal patients had two or more virulence genes compared with those without diarrhoea (P ≤ 0.05). EAEC isolates exhibited high-level resistance to amoxicillin (82.3%), co-amoxiclav (78%), aztreonam (73.8%), tetracycline (66.6%) and ceftazidime (63.8%). In addition, 53.2% of isolates were resistant to at least three different classes of antimicrobial agents and were considered to be multidrug resistant. These results indicate a high prevalence and heterogeneity of gene profiles of EAEC in diarrhoeal and control patients, and suggest that the presence of aggR, aap and pet, the number of genes present and the antimicrobial resistance profile may be markers for more-virulent EAEC isolates.

Xenomonitoring of different filarial nematodes using single and multiplex PCR in mosquitoes from Assiut Governorate, Egypt

Wuchereria bancrofti, Dirofilaria immitis, and Dirofilaria repens are filarial nematodes transmitted by mosquitoes belonging to Culex, Aedes, and Anopheles genera. Screening by vector dissection is a tiresome technique. We aimed to screen filarial parasites in their vectors by single and multiplex PCR and evaluate the usefulness of multiplex PCR as a rapid xenomonitoring and simultaneous differentiation tool, in area where 3 filarial parasites are coexisting. Female mosquitoes were collected from 7 localities in Assiut Governorate, were microscopically identified and divided into pools according to their species and collection site. Detection of W. bancrofti, D. immitis, and D. repens using single PCR was reached followed by multiplex PCR. Usefulness of multiplex PCR was evaluated by testing mosquito pools to know which genera and species are used by filarial parasites as a vector. An overall estimated rate of infection (ERI) in mosquitoes was 0.6%; the highest was Culex spp. (0.47%). W. bancrofti, D. immitis, and D. repens could be simultaneously and differentially detected in infected vectors by using multiplex PCR. Out of 100 mosquito pools, 8 were positive for W. bancrofti (ERI of 0.33%) and 3 pools each were positive for D. immitis and D. repens (ERI 0.12%). The technique showed 100% sensitivity and 98% specificity. El-Nikhila, El-Matiaa villages, and Sahel Seleem district in Assiut Governorate, Egypt are still endemic foci for filarial parasites. Multiplex PCR offers a reliable procedure for molecular xenomonitoring of filariasis within their respective vectors in endemic areas. Therefore, it is recommended for evaluation of mosquito infection after lymphatic filariasis eradication programs.

Involvement of main diarrheagenic Escherichia coli, with emphasis on enteroaggregative E. coli, in severe non-epidemic pediatric diarrhea in a high-income country

Background

Bacterial and viral enteric pathogens are the leading cause of diarrhea in infants and children. We aimed to identify and characterize the main human diarrheagenic E. coli (DEC) in stool samples obtained from children less than 5 years of age, hospitalized for acute gastroenteritis in Israel, and to examine the hypothesis that co-infection with DEC and other enteropathogens is associated with the severity of symptoms.

Methods

Stool specimens obtained from 307 patients were tested by multiplex PCR (mPCR) to identify enteroaggregative E. coli (EAEC), enterohemorrhagic (EHEC), enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC). Specimens were also examined for the presence of rotavirus by immunochromatography, and of Shigella, Salmonella and Campylobacter by stool culture; clinical information was also obtained.

Results

Fifty nine (19%) children tested positive for DEC; EAEC and atypical EPEC were most common, each detected in 27 (46%), followed by ETEC (n = 3; 5%), EHEC and typical EPEC (each in 1 child; 1.5%). Most EAEC isolates were resistant to cephalexin, cefixime, cephalothin and ampicillin, and genotypic characterization of EAEC isolates by O-typing and pulsed-field gel electrophoresis showed possible clonal relatedness among some. The likelihood of having > 10 loose/watery stools on the most severe day of illness was significantly increased among patients with EAEC and rotavirus co-infection compared to children who tested negative for both pathogens: adjusted odds ratio 7.0 (95% CI 1.45-33.71, P = 0.015).

Conclusion

DEC was common in this pediatric population, in a high-income country, and mixed EAEC and rotavirus infection was characterized by especially severe diarrhea.

Co-detection of virulent Escherichia coli genes in surface water sources

McNemar’s test and the Pearson Chi-square were used to assess the co-detection and observed frequency, respectively, for potentially virulent E. coli genes in river water. Conventional multiplex Polymerase Chain Reaction (PCR) assays confirmed the presence of the aggR gene (69%), ipaH gene (23%) and the stx gene (15%) carried by Enteroaggregative E. coli (EAEC), Enteroinvasive E. coli (EIEC) and Enterohermorrhagic E. coli (EHEC), respectively, in river water samples collected from the Berg River (Paarl, South Africa). Only the aggR gene was present in 23% of samples collected from the Plankenburg River system (Stellenbosch, South Africa). In a comparative study, real-time multiplex PCR assays confirmed the presence of aggR (EAEC) in 69%, stx (EHEC) in 15%, ipaH (EIEC) in 31% and eae (EPEC) in 8% of the river water samples collected from the Berg River. In the Plankenburg River, aggR (EAEC) was detected in 46% of the samples, while eae (EPEC) was present in 15% of the water samples analyzed using real-time multiplex PCR in the Plankenburg River. Pearson Chi-square showed that there was no statistical difference (p > 0.05) between the conventional and real-time multiplex PCRs for the detection of virulent E. coli genes in water samples. However, the McNemar’s test showed some variation in the co-detection of virulent E. coli genes, for example, there was no statistical difference in the misclassification of the discordant results for stx versus ipaH, which implies that the ipaH gene was frequently detected with the stx gene. This study thus highlights the presence of virulent E. coli genes in river water and while early detection is crucial, quantitative microbial risk analysis has to be performed to identify and estimate the risk to human health.

Distribution of Integrons and Gene Cassettes Among Uropathogenic and Diarrheagenic Escherichia coli Isolates in Iran

Integrons are considered to play a significant role in the evolution and spread of antimicrobial resistance genes. A total of 200 uropathogenic (UPEC) and diarrheagenic Escherichia coli (DEC) isolates from outpatients were investigated for antimicrobial susceptibility and the presence of class 1, 2, and 3 integron-associated integrase (intI) genes and gene cassettes. Conjugal transfer and Southern hybridization were performed to determine the genetic localization of class 1 integrons. One hundred ninety-two (96%) isolates were resistant to one or more antimicrobial agents. Antimicrobial resistance among DEC isolates was higher compared with the UPEC. Integrons were highly prevalent in both pathotypes (92.5%). Comparison of integrons among UPEC and DEC showed that DEC isolates harbored integrases (94% for intI1, 8% for intI2) with a slightly higher frequency than in UPEC isolates (87% for intI1, 7% for intI2) (p>0.05). Dihydrofolate reductase (dfrA) and aminoglycoside adenyl transferase (aad) gene cassettes were found most frequently in intI1-positive isolates. All isolates carried their class 1 integrons on conjugative plasmids. These results indicate that class 1 integrons are widespread among E. coli isolates. Therefore, appropriate surveillance and control measures are essential to prevent the further spread of integron-producing isolates.

Detection of major diarrheagenic bacterial pathogens by multiplex PCR panels

Diarrheal diseases remain a major threat to the youngest population in low- and middle-income countries. The main bacterial pathogens causing diarrhea are diarrheagenic Escherichia coli (DEC) that consists of enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enterohemorrhagic EHEC and enteroinvasive E. coli (EIEC), Salmonella, Shigella spp. (S. dysenteria, S. sonnei, S. flexneri) Campylobacter (C. coli, C. jejuni), Vibrio (V. vulnificus, V. parahaemolyticusm, V. cholerae), Yersinia enterocolitica and Aeromonas hydrophila. The aim of this study was to set up rapid multiplex PCR (mPCR) panels to identify these diarrheagenic pathogens based on their specific virulence genes. Primers against specific target genes were combined into three mPCR panels: one for diarrheal E. coli, one for pathogens causing mainly bloody diarrhea, and the third for the remaining pathogens. The panels were tested against a set of stool samples from Swedish children with diarrhea and controls and the analysis identified bacterial pathogens in 14/54 (26%) of the samples. These results show that our three developed mPCR panels can detect main bacterial diarrheagenic pathogens in clinical samples.

Frequency and antimicrobial resistance of diarrhoeagenic Escherichia coli from young children in Iran

Diarrhoea continues to be one of the most common causes of morbidity and mortality among infants and children in developing countries. Diarrhoeagenic Escherichia coli (DEC) is an emerging agent among pathogens that cause diarrhoea. Between March 2011 and January 2012, a total of 600 stool specimens from children younger than 5 years of age (450 with and 150 without diarrhoea) were investigated for enteroaggregative E. coli (EAEC), enterohaemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) using PCR. Antimicrobial susceptibility testing was performed following Clinical and Laboratory Standards Institute guidelines. The prevalence of DEC pathotypes was 30.4 % (137 patients) and 12 % (18 patients) in the diarrhoea group and the control group, respectively. The most frequently isolated pathotype in diarrhoeal children was ETEC. This pathotype was detected significantly more often in children with diarrhoea (14.4 %) than in children without diarrhoea (5.3 %). EAEC and EPEC were detected with slightly higher frequencies in children with (8 and 4.2 %, respectively) than in children without (4.6 and 2 %, respectively) (P>0.05) diarrhoea. EHEC was only detected in children with diarrhoea (3.8 %). Of the children from the diarrhoea group, 10 % were colonized with more than one DEC pathotype. The DEC isolates exhibited high-level resistance to erythromycin (100 %), azteronam (80.7 %), amoxicillin (74.4 %) and tetracycline (69.3 %), and 86.4 % of isolates were multidrug resistant. In conclusion, ETEC continues to be an important agent associated with diarrhoea in children from Tabriz, Iran.

Multi-drug-resistant enterotoxigenic and enterohemorrhagic Escherichia coli isolated from children with diarrhea

Multi-drug-resistant (MDR) diarrheagenic Escherichia coli (DEC) has rapidly spread worldwide and represents the most serious threat to the management of diarrhea in developing countries. During the period from March 2011 to January 2012, a total of 450 stool samples of diarrheal children aged 0-60 months were studied. In order to detect enterotoxigenic E. coli (ETEC) and enterohemorrhagic E. coli (EHEC) simultaneously, a mixture of four primer pairs specific for eltB, estA, vt1, and vt2 genes was used in a multiplex PCR. Antimicrobial susceptibility testing was performed as the Clinical and Laboratory Standards Institute (CLSI) guidelines. A total of 140 (31·1%) DEC were isolated from 450 stool samples. Diarrheagenic E. coli exhibited high-level resistance to aztreonam (80·7%), amoxicillin (74·4%), and tetracycline (69·3%). Also, 86·4% of E. coli isolates were resistant to at least three different classes of antimicrobial agents and considered as MDR. The frequency of ETEC and EHEC pathotypes was 46·4 and 12·1%, respectively and all of these isolates were MDR. In conclusion, MDR ETEC continues to be an important agent associated with diarrhea in children from Tabriz, Iran.

Prevalence of virulence genes associated with pathogenic Escherichia coli strains isolated from domestically harvested rainwater during low- and high-rainfall periods

The possible health risks associated with the consumption of harvested rainwater remains one of the major obstacles hampering its large-scale implementation in water limited countries such as South Africa. Rainwater tank samples collected on eight occasions during the low- and high-rainfall periods (March to August 2012) in Kleinmond, South Africa, were monitored for the presence of virulence genes associated with Escherichia coli. The identity of presumptive E. coli isolates in rainwater samples collected from 10 domestic rainwater harvesting (DRWH) tanks throughout the sampling period was confirmed through universal 16S rRNA PCR with subsequent sequencing and phylogenetic analysis. Species-specific primers were also used to routinely screen for the virulent genes, aggR, stx, eae, and ipaH found in enteroaggregative E. coli (EAEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), and enteroinvasive E. coli, respectively, in the rainwater samples. Of the 92 E. coli strains isolated from the rainwater using culture based techniques, 6% were presumptively positively identified as E. coli O157:H7 using 16S rRNA. Furthermore, virulent pathogenic E. coli genes were detected in 3% (EPEC and EHEC) and 16% (EAEC) of the 80 rainwater samples collected during the sampling period from the 10 DRWH tanks. This study thus contributes valuable information to the limited data available regarding the ongoing prevalence of virulent pathotypes of E. coli in harvested rainwater during a longitudinal study in a high-population-density, periurban setting.

Development and accuracy of quantitative real-time polymerase chain reaction assays for detection and quantification of enterotoxigenic Escherichia coli (ETEC) heat labile and heat stable toxin genes in travelers' diarrhea samples

Enterotoxigenic Escherichia coli (ETEC), the leading bacterial pathogen of travelers' diarrhea, is routinely detected by an established DNA hybridization protocol that is neither sensitive nor quantitative. Quantitative real-time polymerase chain reaction (qPCR) assays that detect the ETEC toxin genes eltA, sta1, and sta2 in clinical stool samples were developed and tested using donor stool inoculated with known quantities of ETEC bacteria. The sensitivity of the qPCR assays is 89%, compared with 22% for the DNA hybridization assay, and the limits of detection are 10,000-fold lower than the DNA hybridization assays performed in parallel. Ninety-three clinical stool samples, previously characterized by DNA hybridization, were tested using the new ETEC qPCR assays. Discordant toxin profiles were observed for 22 samples, notably, four samples originally typed as ETEC negative were ETEC positive. The qPCR assays are unique in their sensitivity and ability to quantify the three toxin genes in clinical stool samples.

A PLGA-encapsulated chimeric protein protects against adherence and toxicity of enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) are the most common cause of diarrhea among children. Colonization factors and enterotoxins are the major ETEC candidate vaccines. Since protection against ETEC mostly occurs by induction of IgA antibodies, much effort is focused on the development of oral vaccines. In this study oral immunogenicity of a poly(lactic-co-glycolic acid) (PLGA) encapsulated chimeric protein containing CfaB, CstH, CotA and LTB (Heat-labile B subunit) was investigated. The protein was encapsulated in PLGA by double emulsion method and nanoparticles were characterized physicochemically. Immunogenicity was assessed by evaluating IgG1, IgG2 and IgA titers after BALB/c mice vaccination. Non aggregated nanoparticles had a spherical shape with an average particle size of 252.7±23 nm and 91.96±4.4% of encapsulation efficiency. Western blotting showed maintenance of the molecular weight and antigenicity of the released protein. Oral immunization of mice induced serum IgG and fecal IgA antibody responses. Immunization induced protection against ETEC binding to Caco-2 cells. The effect of LT toxin on fluid accumulation in ileal loops was neutralized by inhibition of enterotoxin binding to GM1-ganglosides. Delivery of the chimeric protein in PLGA elicited both systemic and mucosal immune responses. The findings could be exploited to development of oral multi-component ETEC prophylactic measures.