Molecular characterization of diarrheagenic Escherichia coli pathotypes: Association of virulent genes, serogroups, and antibiotic resistance among moderate-to-severe diarrhea patients

Pathovars, occurrence, and characterization of plasmid-mediated quinolone resistance in diarrheal Escherichia coli isolated from farmers and farmed chickens in Tunisia and Nigeria

The poultry industry is a very important agricultural and industrial sector in Tunisia and Nigeria, with little information about occurrence of diarrheagenic Escherichia coli in the farmers and chickens. This study aimed to detect the prevalence of diarrheal E. coli in humans and poultry and to investigate plasmid-mediated quinolone resistance (PMQR) genes in both countries. Seventy-four isolates of E. coli were studied; nine different virulence genes were screened by PCR. Serotyping was performed only for pathotypes as well as the determining of antibiotic resistance profiles against 21 antibiotics. PMQR genes were investigated by PCR. EAEC was the most abundant pathotype (37/74; 50%) in human and chicken isolates, whereas single EHEC and EPEC (1/74, 1.35%) pathotypes were detected in Tunisia and Nigeria, respectively. About 17 (45.95%) quinolones/fluoroquinolones-resistant isolates were detected, from which the following PMQR genes were detected: aac(6')-Ib-cr (8/17, 47.05%), qepA (6/17, 35.29%), qnrA + qnrB (2/17, 11.76%), and qnrS gene (1/17, 5.88%). Our findings highlight high occurrence of EAEC pathotype in Tunisia and Nigeria, more frequent than EPEC and EHEC. Additionally, all E. coli pathotypes isolated from different sources (humans, poultry) showed resistance to several antibiotics, which are in use as therapeutic choices in Tunisia and Nigeria.

Sequence-subtype association of multi-drug-resistant diarrheagenic Escherichia coli

Background and Objectives

Multi-drug-resistant pathogens pose a significant threat as they can rapidly spread, leading to severe healthcare-associated invasive infections. In developing countries, diarrheagenic Escherichia coli (DEC) is a major bacterial pathogen responsible for causing diarrhea. However, the outbreak of resistant strains has made the treatment of DEC infections much more challenging. This study aimed to investigate the relationship between antibiotic resistance genes and other virulence categories in E. coli strains that cause diarrhea, particularly DEC.

Materials and Methods

The phylogenetic grouping was defined using PCR and multi-locus sequence type (MLST) methods.

Results

Among the isolates analyzed, 14 were identified as resistant and were classified into eight distinct sequence types: ST3, ST53, ST77, ST483, ST512, ST636, ST833, and ST774, indicating genetic diversity among the resistant strains. Certain sequence types, notably ST512 and ST636, were found to be associated with multiple antibiotic resistance in DEC. Regarding antibiotic susceptibility, strains showed the highest resistance to amoxicillin, suggesting that this antibiotic may not be effective in treating DEC infections. On the other hand, the isolates demonstrated susceptibility to amikacin and chloramphenicol, implying that these antibiotics could be more suitable treatment options for DEC infections.

Conclusion

The findings underscore the importance of promptly identifying antibiotic resistance patterns and their correlation with specific pathogenic virulence categories, as this knowledge can aid in selecting the most appropriate antibiotics for treating DEC infections. Considering the antibiotic resistance profiles and associated resistance genes is crucial in managing and containing diarrheal outbreaks and in selecting effective antibiotic therapies for DEC infections.

Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya

Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.

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.

Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family

Many plants and animals have symbiotic relationships with microorganisms, including bacteria. The interactions between bacteria and their hosts result in different outcomes for the host organism. The outcome can be neutral, harmful or have beneficial effects for participants. Remarkably, these relationships are not static, as they change throughout an organism's lifetime and on an evolutionary scale. One of the structures responsible for relationships in bacteria is O-antigen. Depending on the characteristics of its components, the bacteria can avoid the host's immune response or establish a mutualistic relationship with it. O-antigen is a key component in Gram-negative bacteria's outer membrane. This component facilitates interaction between the bacteria and host immune system or phages. The variability of the physical structure is caused by the genomic variability of genes encoding O-antigen synthesis components. The genes and pathways of O-polysaccharide (OPS) synthesis were intensively investigated mostly for Enterobacteriaceae species. Considering high genetic and molecular diversity of this structure even between strains, these findings may not have caught the entire variety possibly presented in non-model species. The current study presents a comparative analysis of genes associated with O-antigen synthesis in bacteria of the Oxalobacteraceae family. In contrast to existing studies based on PCR methods, we use a bioinformatics approach and compare O- antigens at the level of clusters rather than individual genes. We found that the O-antigen genes of these bacteria are represented by several clusters located at a distance from each other. The greatest similarity of the clusters is observed within individual bacterial genera, which is explained by the high variability of O-antigens. The study describes similarities of OPS genes inherent to the family as a whole and also considers individual unique cases of O-antigen genetic variability inherent to individual bacteria.

Real-time multiplex PCR assay reveals the increased prevalence of Campylobacter spp and diarrhoeagenic Escherichia coli in humans from Vellore, South India

Introduction. Bacterial dysentery is one of the greatest causes of morbidity and mortality worldwide. Campylobacter spp. and diarrhoeagenic Escherichia coli (DEC) are recognised as the most common causes of bacterial enteritis in developing countries including India.Hypothesis/Gap statement. Rapid and accurate identification of dysentery causing organisms using molecular methods is essential for better disease management, epidemiology and outbreak investigations.Aim. In view of the limited information available on the dysentery causing agents like Campylobacter spp., enterohemorrhagic E. coli (EHEC)/enteropathogenic E. coli (EPEC) and enteroinvasive E. coli (EIEC)/Shigella in India, this study was undertaken to investigate the presence of these pathogens in human and poultry stool samples by molecular methods.Methodology. In total, 400 human stool samples and 128 poultry samples were studied. Microaerophilic culture along with real-time multiplex PCR with the targets specific to the genus Campylobacter, Campylobacter jejuni, Campylobacter coli, EHEC, EPEC and EIEC/Shigella was performed. Further species confirmation was done using MALDI-TOF MS.Results. On microaerophilic culture, C. coli was isolated in one human sample and two C. jejuni and one C. fetus in poultry samples. On PCR analysis, among human stool samples, typical EPEC (42%) was predominantly seen followed by Campylobacter spp. (19%) and EIEC/Shigella (10%). In contrast, Campylobacter spp. (41%) was predominant in poultry samples, followed by typical EPEC (26%) and EIEC/Shigella (9%). Poly-infections with Campylobacter spp. and DEC were also observed among both sources.Conclusion. The present study documented the increased prevalence of Campylobacter spp. in humans compared with the results of previous studies from India. Typical EPEC was found to be predominant in children less than 5 years of age in this study. The high prevalence of coinfections in the current study indicates that a multiple aetiology of diarrhoea is common in our settings.

Detection of Two Copies of a blaNDM-1-Encoding Plasmid in Escherichia coli Isolates from a Pediatric Patient with Diarrhea

Purpose

To elucidate the contribution of a transferable plasmid harboring the bla_NDM-1 gene in an Escherichia coli clinical isolate to the spread of resistance determinants.

Methods

Nine extended-spectrum β-lactamase-producing E. coli were collected from diarrhea samples from a pediatric patient and genetic linkage was investigated through enterobacteriaceae repetitive intragenic consensus polymerase chain reaction (PCR). Bacterial species were identified by 16s rRNA sequencing, susceptibility testing with the use of a BD Phoenix^TM-100 Automated Microbiology System, and assessment of virulence genes by PCR. The transferability of bla_NDM-1 in E. coli strain TCM3e1 was confirmed by conjugation experiments. Complete sequencing of E. coli strain TCM3e1 was determined with the PacBio and Illumina NovaSeq platforms and the characteristics were analyzed with bioinformatics software.

Results

The results showed that all nine E. coli strains were the same clone. E. coli strain TCM3e1 was resistant to 12 antimicrobial agents and carried the virulence gene EAST-1. Conjugation transfer analysis showed that bla_NDM-1 was carried on a self-transmissible plasmid. Two copies of the bla_NDM-1 gene were present on an IncC plasmid and some resistance genes with two or three copies were located downstream of the bla_NDM-1 gene and formed a tandem repeat fragment (bla_DNM-1-bleo-sul1- aadA17- dfrA12).

Conclusion

A transmissible plasmid harboring two copies of the bla_NDM-1 gene, including clonal dispersions of the bla_NDM-1 gene, was identified in clinical isolates. These findings emphasized the necessity of surveillance of the plasmid-borne bla_NDM-1 to prevent dissemination.

Antibiotic potentiating action of α-PINENE and borneol against EPEC and ETEC sorotypes

Escherichia coli is considered the main cause of intestinal and extra-intestinal infections, they have virulence mechanisms in different pathotypes and the ability to receive or transmit antimicrobial resistance genes. The aim of this work was to investigate the antibacterial and antimicrobial modulating activity of α-pinene and borneol against E. coli and enteropathogenic (EPEC) and enterotoxigenic (ETEC) serotypes. The broth microdilution methodology with multidrug-resistant Escherichia coli, EPEC and ETEC was used to determine the Minimum Inhibitory Concentration (MIC) and evaluation of the modulating activity of antibiotics (ciprofloxacin, sulfamethoxazole-trimethoprim and metronidazole) of α-pinene and borneol. It was concluded that α-pinene and borneol showed a low antimicrobial action against multi-resistant E. coli, however, this action was not observed against the EPEC and ETEC serotypes. A synergistic action of borneol associated with ciprofloxacin against ETEC was noted.

Enteropathogenic Escherichia coli—A Summary of the Literature

Diarrheal disease is still a major public health concern, as it is still considered an important cause of death in children under five years of age. A few decades ago, the detection of enteropathogenic E. coli was made by detecting the O, H, and K antigens, mostly by agglutination. The recent protocols recommend the molecular methods for diagnosing EPEC, as they can distinguish between typical and atypical EPEC by identifying the presence/absence of specific virulence factors. EPEC are defined as diarrheagenic strains of E. coli that can produce attaching and effacing lesions on the intestinal epithelium while being incapable of producing Shiga toxins and heat-labile or heat-stable enterotoxins. The ability of these strains to produce attaching and effacing lesions enable them to cause localized lesions by attaching tightly to the surface of the intestinal epithelial cells, disrupting the surfaces of the cells, thus leading to the effacement of the microvilli. EPEC are classified on typical and atypical isolates, based on the presence or absence of E. coli adherence factor plasmids. All the EPEC strains are eae positive; typical EPEC strains are eae+, bfpA+, while atypical strains are eae+, bfpA−. No vaccines are currently available to prevent EPEC infections.

The first evaluation relationship of integron genes and the multidrug-resistance in class A ESBLs genes in enteropathogenic Escherichia coli strains isolated from children with diarrhea in Southwestern Iran

Enteropathogenic Escherichia coli (EPEC) is one of the most important diarrheagenic agents among infants under 5 years in developing countries. This study aimed to investigate the relationship of integron genes and class A extended-spectrum ESBLs genes in MDR E. coli strains isolated from children with diarrhea in Southwestern Iran. Totally, 321 fecal samples were collected from diarrheal children under 5 years admitted to teaching hospitals of Abadan and Khorramshahr, southwest Iran. Routine bacteriological tests were performed for the identification of E. coli isolates. Multiplex PCR was used for the presence of eae, bfp, stx1, and stx2 genes to detected EPEC strains. Serogrouping was performed for EPEC strains. The EPEC isolates' antibiotic resistance pattern was determined by the disk-diffusion technique. All EPEC isolates were screened for integron and class A β-lactamase genes. Of the 14 EPEC isolates, 12 (85.7%) were found to be ESBL-positive by double disk synergy test (DDST) and PCR. In addition, bla_CTX-M and bla_TEM genes were detected in 83.3% (n = 10) and 58.3% (n = 7) of EPEC isolates, respectively. None of the isolates had the bla_KPC gene. On the other hand, 64.2% (n = 9) and 7.1% (n = 1) were positive only for intlI and intlII genes, respectively. The results demonstrated that EPEC is one of the major causes of childhood diarrhea in our region and that the distribution of class 1 integrons and ESBLs in EPEC strains is highly prevalent. Moreover, the results revealed that continuous monitoring of the emergence and expansion of MDR in EPEC strains is necessary.

Childhood diarrhoeal diseases in developing countries

Diarrhoeal diseases collectively constitute a serious public health challenge globally, especially as the leading cause of death in children (after respiratory diseases). Childhood diarrhoea affecting children under the age of five accounts for approximately 63% of the global burden. Accurate and timely detection of the aetiology of these diseases is very crucial; but conventional methods, apart from being laborious and time-consuming, often fail to identify difficult-to-culture pathogens. The aetiological agent of an average of up to 40% of cases of diarrhoea cannot be identified. This review gives an overview of the recent trends in the epidemiology and treatment of diarrhoea and aims at highlighting the potentials of metagenomics technique as a diagnostic method for enteric infections.

Evolution of diarrheagenic Escherichia coli pathotypes in India

CONTEXT:

Diarrheagenic Escherichia coli (DEC) is the leading cause of infectious diarrhea in developing countries. On the basis of virulence and phenotypic characteristics, the DEC is categorized into multiple pathotypes. Each pathotype has different pathogenesis and geographical distribution. Thus, the proper management of disease relies on rapid and accurate identification of DEC pathotypes.

AIMS:

The aim of the study was to determine the prevalence of DEC pathotypes in India.

MATERIALS AND METHODS:

A cross-sectional study was carried out between January 2008 and December 2012 at Jawaharlal Nehru Medical College and KLES Dr. Prabhakar Kore Hospital and Medical Research Center, Belgaum (Karnataka), India. A total of 300 stool samples were collected from diarrhea patients with age >3 months. The DEC was identified by both conventional and molecular methods.

RESULTS:

Of 300 samples, E. coli were detected in 198 (66%) and 170 (56.6%) samples by culture and polymerase chain reaction, respectively. Among DEC (n = 198) isolates, eae gene (59.5%) was the most prevalent followed by stx (27.7%), east (27.2%), elt (12.6%), est (10.6%), ipaH (5.5%), and eagg (1.5%) genes. On the basis of virulence genes, enteropathogenic E. coli (33.8%) was the most common pathotype followed by Shiga toxin-producing E. coli (STEC, 23.2%), enterotoxigenic E. coli (ETEC, 13.6%), enteroinvasive E. coli (5.5%), enteroaggregative heat-stable enterotoxin 1-harboring E. coli (EAST1EC, 4.5%), STEC/ETEC (3.5%), STEC/enteroaggregative E. coli (STEC/EAEC, 1.0%), and EAEC (0.05%).

CONCLUSIONS:

The hybrid DEC is potentially more virulent than basic pathotypes. The pathotyping should be included in clinical settings for the proper management of DEC-associated diarrhea.

Guideline for the Antibiotic Use in Acute Gastroenteritis

Acute gastroenteritis is common infectious disease in community in adults. This work represents an update of 'Clinical guideline for the diagnosis and treatment of gastrointestinal infections' that was developed domestically in 2010. The recommendation of this guideline was developed regarding the following; epidemiological factors, test for diagnosis, the indications of empirical antibiotics, and modification of antibiotics after confirming pathogen. Ultimately, it is expected to decrease antibiotic misuse and prevent antibiotic resistance.

A study of virulence and antimicrobial resistance pattern in diarrhoeagenic Escherichia coli isolated from diarrhoeal stool specimens from children and adults in a tertiary hospital, Puducherry, India

BACKGROUND

Emergence of atypical enteropathogenic Escherichia coli (EPEC) and hybrid E. coli (harboring genes of more than one DEC pathotypes) strains have complicated the issue of growing antibiotic resistance in diarrhoeagenic Escherichia coli (DEC). This ongoing evolution occurs in nature predominantly via horizontal gene transfers involving the mobile genetic elements like integrons notably class 1 integron. This study was undertaken to determine the virulence pattern and antibiotic resistance among the circulating DEC strains in a tertiary care center in south of India.

METHODS

Diarrhoeal stool specimens were obtained from 120 children (< 5 years) and 100 adults (> 18 years), subjected to culture and isolation of diarrhoeal pathogens. Conventional PCR was performed to detect 10 virulence and 27 antimicrobial resistance (AMR) genes among the E. coli isolated.

RESULTS

DEC infection was observed in 45 (37.5%) children and 18 (18%) adults, among which [18 (40%), 10 (10%)] atypical EPEC was most commonly detected followed by [6 (13.3%), 4 (4%)] ETEC, [5 (11.1%) 2 (2%)] EAEC, [(3 (6.6%), 0 (0%)] EIEC, [3 (6.6%), 0 (0%] typical EPEC, and [4 (8.8%), 1 (1%)] STEC, and no NTEC and CDEC was detected. DEC co-infection in 3 (6.6%) children, and 1(1%) adult and sole hybrid DEC infection in 3 (6.6%) children was detected. The distribution of sulphonamide resistance genes (sulI, sulII, and sulIII were 83.3 and 21%, 60.41 and 42.1%, and 12.5 and 26.3%, respectively) and class 1 integron (int1) genes (41.6 and 26.31%) was higher in DEC strains isolated from children and adults, respectively. Other AMR genes detected were qnrS, qnrB, aac(6')Ib-cr, dhfr1, aadB, aac(3)-IV, tetA, tetB, tetD, catI, blaCTX, blaSHV, and blaTEM. None harbored qnrA, qnrC, qepA, tetE, tetC, tetY, ermA, mcr1, int2, and int3 genes.

CONCLUSIONS

Atypical EPEC was a primary etiological agent of diarrhea in children and adults among the DEC pathotypes. Detection of high numbers of AMR genes and class 1 integron genes indicate the importance of mobile genetic elements in spreading of multidrug resistance genes among these strains.

Molecular characterization of diarrheagenic Escherichia coli pathotypes: Association of virulent genes, serogroups, and antibiotic resistance among moderate-to-severe diarrhea patients

BACKGROUND

Diarrheagenic Escherichia coli (DEC) signifies as an important etiological agent of moderate-to-severe diarrhea. This study was primarily focused on molecular identification of DEC pathotypes; their association with serogroups and estimates of resistance profiles against different antibiotics regime.

METHODS

Five hundred seventy-two stool specimens from diarrhea patients were investigated for DEC pathotypes. Molecular pathotypes were identified by amplification of virulence genes associated with distinct pathotypes followed by sequencing. Diarrhea is a self-limiting disease, however, severity and persistence of infection suggest antibiotic use. Therefore, AST and MIC were determined against common antibiotic regimen. Correlations between molecular pathotypes and serogroups were analyzed by somatic "O" antigen serotyping.

RESULTS

The present findings reveal incidence of DEC as an etiological agent up to a level of 21% among all diarrheal age groups. DEC infection rate was higher in children. Enteropathogenic E. coliEPEC, a molecular pathotype of DEC, was found as a predominant pathotype with highest frequency of 13.7%. Two other molecular pathotypes enterotoxigenic E. coli (ETEC) and enteroaggregative E. coli (EAEC) accounted for 5.7% and 1.3%, respectively for all diarrhea incidences. Serological analysis deciphered somatic antigens O26, O2, and O3 as major serogroups identified among EPEC, ETEC, and EAEC pathotypes, respectively. All DEC pathotypes exhibited high levels of antibiotic resistance except for cotrimoxazole and norfloxacin.

CONCLUSION

Comprehensive molecular characterization of DEC pathotypes, their incidence estimates, and antibiogram patterns will help in ascertaining better diagnostic and therapeutic measures in management of diarrheal diseases.