Hybrid Atypical Enteropathogenic and Extraintestinal Escherichia coli (aEPEC/ExPEC) BA1250 Strain: A Draft Genome

Diarrheagenic Escherichia coli is the major bacterial etiological agent of severe diarrhea and a major concern of public health. These pathogens have acquired genetic characteristics from other pathotypes, leading to unusual and singular genetic combinations, known as hybrid strains and may be more virulent due to a set of virulence factors from more than one pathotype. One of the possible combinations is with extraintestinal E. coli (ExPEC), a leading cause of urinary tract infection, often lethal after entering the bloodstream and atypical enteropathogenic E. coli (aEPEC), responsible for death of thousands of people every year, mainly children under five years old. Here we report the draft genome of a strain originally classified as aEPEC (BA1250) isolated from feces of a child with acute diarrhea. Phylogenetic analysis indicates that BA1250 genome content is genetically closer to E. coli strains that cause extraintestinal infections, other than intestinal infections. A deeper analysis showed that in fact this is a hybrid strain, due to the presence of a set of genes typically characteristic of ExPEC. These genomic findings expand our knowledge about aEPEC heterogeneity allowing further studies concerning E. coli pathogenicity and may be a source for future comparative studies, virulence characteristics, and evolutionary biology.

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Comparative analysis of genetic characterization of β-lactam-resistant Escherichia coli from bulk tank milk in Korea

Irish Veterinary Journal ◽

10.1186/s13620-021-00203-4 ◽

2021 ◽

Vol 74 (1) ◽

Author(s):

Hye-Ri Jung ◽

Koeun Kim ◽

Young Ju Lee

Keyword(s):

Escherichia Coli ◽

Clinical Mastitis ◽

Phylogenetic Groups ◽

Bulk Tank Milk ◽

Genetic Characteristics ◽

E Coli ◽

Intestinal Infections ◽

Antimicrobial Resistance Genes ◽

Bulk Tank ◽

Genotypic Characteristics

Abstract Background This study was conducted to analyze the genetic characteristics of 41 β-lactam-resistant Escherichia coli isolates, which are one of the common causes of environmental mastitis, isolated from the bulk tank milk of 290 dairy farms in five factories operated by three dairy companies in Korea. Results Analysis of the phenotypic and genotypic characteristics of β-lactam-resistant E. coli isolates revealed differences between factories even within the same company. Isolates from factory A1 and C1 showed high resistance to cephalothin (76.9 and 100%, respectively), which is a first-generation cephalosporins, whereas resistance to tetracycline was showed by only the isolates from factories B1 (60.0%), C2 (66.7%), and C3 (100%). Although all the 41 β-lactam-resistant E. coli isolates were positive for blaOXA-1, blaTEM-1 was highly prevalent in isolates from factories C2 (100%) and C3 (100%). Among 17 isolates resistant to both β-lactams and aminoglycosides, the most common multilocus sequence type was ST399 (13isolates, 76.5%). Furthermore, 2 (11.8%) and 12 (70.6%) isolates belonged to the phylogenetic groups B2 and D, respectively, which are invasive strains that cause intestinal infections, respectively. The predominant serogroup was O15 (70.6%), which is a globally distributed extraintestinal pathogen. Interestingly, one isolate from factory A1 belonged to O157 and carried six virulence genes, simultaneously. Conclusions Although E. coli isolates were isolated from bulk tank milk, and not the clinical mastitis samples, the presence of the phylogenetic groups B2 and D, and the serogroups O15 and O157, which harbor antimicrobial resistance genes and virulence factors, can pose a threat to public health.

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Draft Whole-Genome Sequences of Three Diarrheagenic Escherichia coli Strains Isolated from Farmed Deer in New Zealand

Genome Announcements ◽

10.1128/genomea.00300-18 ◽

2018 ◽

Vol 6 (16) ◽

pp. e00300-18

Author(s):

A. Springer Browne ◽

Patrick J. Biggs ◽

Alice Elliott ◽

Patricia Jaros ◽

Nigel P. French ◽

...

Keyword(s):

Escherichia Coli ◽

New Zealand ◽

Cervus Elaphus ◽

Red Deer ◽

Draft Genome ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

E Coli ◽

Diarrheagenic Escherichia Coli

ABSTRACT Escherichia coli bacteria commonly colonize the gastrointestinal tracts of farmed ruminants. Cattle are a well-recognized reservoir of zoonotic E. coli; we report here, however, the draft genome sequences of three diarrheagenic E. coli strains isolated from farmed red deer (Cervus elaphus) in the Manawatu region of New Zealand.

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Usefulness of a Multiplex PCR for Detection of Diarrheagenic Escherichia coli in a Diagnostic Microbiology Laboratory Setting

Bangladesh Journal of Medical Microbiology ◽

10.3329/bjmm.v1i2.21506 ◽

2016 ◽

Vol 1 (2) ◽

pp. 38-42 ◽

Cited By ~ 4

Author(s):

Khairun Nessa ◽

Dilruba Ahmed ◽

Johirul Islam ◽

FM Lutful Kabir ◽

M Anowar Hossain

Keyword(s):

Escherichia Coli ◽

Multiplex Pcr ◽

Clinical Laboratory ◽

Proteinase K ◽

Microbiology Laboratory ◽

Pcr Assay ◽

E Coli ◽

Diarrheagenic Escherichia Coli ◽

Multiplex Pcr Assay ◽

Diagnostic Microbiology

A multiplex PCR assay was evaluated for diagnosis of diarrheagenic Escherichia coli in stool samples of patients with diarrhoea submitted to a diagnostic microbiology laboratory. Two procedures of DNA template preparationproteinase K buffer method and the boiling method were evaluated to examine isolates of E. coli from 150 selected diarrhoeal cases. By proteinase K buffer method, 119 strains (79.3%) of E. coli were characterized to various categories by their genes that included 55.5% enteroaggregative E. coli (EAEC), 18.5% enterotoxigenic E. coli (ETEC), 1.7% enteropathogenic E. coli (EPEC), and 0.8% Shiga toxin-producing E. coli (STEC). Although boiling method was less time consuming (<24 hrs) and less costly (<8.0 US $/ per test) but was less efficient in typing E. coli compared to proteinase K method (41.3% vs. 79.3% ; p<0.001). The sensitivity and specificity of boiling method compared to proteinase K method was 48.7% and 87.1% while the positive and negative predictive value was 93.5% and 30.7%, respectively. The majority of pathogenic E. coli were detected in children (78.0%) under five years age with 53.3% under one year, and 68.7% of the children were male. Children under 5 years age were frequently infected with EAEC (71.6%) compared to ETEC (24.3%), EPEC (2.7%) and STEC (1.4%). The multiplex PCR assay could be effectively used as a rapid diagnostic tool for characterization of diarrheagenic E. coli using a single reaction tube in the clinical laboratory setting.Bangladesh J Med Microbiol 2007; 01 (02): 38-42

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Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

Applied and Environmental Microbiology ◽

10.1128/aem.02635-12 ◽

2012 ◽

Vol 79 (1) ◽

pp. 411-414 ◽

Cited By ~ 21

Author(s):

Afonso G. Abreu ◽

Vanessa Bueris ◽

Tatiane M. Porangaba ◽

Marcelo P. Sircili ◽

Fernando Navarro-Garcia ◽

...

Keyword(s):

Escherichia Coli ◽

Content Type ◽

E Coli ◽

Diarrheagenic Escherichia Coli ◽

Virulence Markers ◽

Protein Encoding ◽

Encoding Genes ◽

Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

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The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France

10.1101/2021.06.24.449745 ◽

2021 ◽

Author(s):

Julie Marin ◽

Olivier Clermont ◽

Guilhem Royer ◽

Melanie Mercier-Darty ◽

Jean-Winoc Decousser ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

High Risk ◽

Virulence Genes ◽

Population Genomics ◽

E Coli ◽

O Antigen ◽

Similar Region ◽

Intestinal Infections ◽

Evolution Of Virulence

Escherichia coli is a commensal species of the lower intestine, but also a major pathogen causing intestinal and extra-intestinal infections. Most studies on genomic evolution of E. coli used isolates from infections, and/or focused on antibiotic resistance, but neglected the evolution of virulence. Here instead, we whole-genome sequenced a collection of 436 E. coli isolated from fecal samples of healthy adult volunteers in France between 1980 and 2010. These isolates were distributed among 159 sequence types (STs), the five most frequent being ST10 (15.6%), ST73 (5.5%) and ST95 (4.8%), ST69 (3.7%) and ST59 (3.7%), and 230 O:H serotypes. ST and serotype diversity increased over time. Comparison with 912 E. coli bacteremia isolates from similar region and time showed a greater diversity in commensal isolates. The O1, O2, O6 and O25-groups used in bioconjugate O-antigen vaccine were found in only 63% of the four main STs associated with a high risk of bacteremia (ST69, ST73, ST95 and ST131). In commensals, STs associated with a high risk of bacteremia increased in frequency. Both extra-intestinal virulence-associated genes and resistance to antibiotics increased in frequency. Evolution of virulence genes was driven by both clonal expansion of STs with more virulence genes, and increases in frequency within STs, whereas the evolution of resistance was dominated by increases in frequency within STs. This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over a 30-year period and suggests that the efficacy of O-antigen vaccines would be threatened by serotype replacement.

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Molecular diversity survey on diarrheagenic Escherichia coli isolates among children with gastroenteritis in Fars, Iran

Future Microbiology ◽

10.2217/fmb-2020-0151 ◽

2021 ◽

Author(s):

Amir Emami ◽

Neda Pirbonyeh ◽

Fatemeh Javanmardi ◽

Abdollah Bazargani ◽

Afagh Moattari ◽

...

Keyword(s):

Escherichia Coli ◽

Molecular Diversity ◽

Pediatric Patients ◽

Watery Diarrhea ◽

E Coli ◽

Diarrheagenic Escherichia Coli ◽

Clinical Laboratories ◽

Health Burden ◽

Stool Specimens ◽

Encoding Genes

Aim: To differentiate Escherichia coli isolates from diarrheal pediatric patients in clinical laboratories. Materials & methods: Patients with watery diarrhea were selected for sampling and tested for Diarrheagenic E. coli (DEC) by API kit. DEC isolates were tested for phylotyping, pathotyping and presence of determined virulence-encoding genes by specific molecular methods. Results: About 50% of isolates were detected as DECs (>55 and >31% were categorized B2 and D phylotypes respectively). Enterotoxigenic E. coli was the most and Enteroinvasive E. coli was the lowest prevalent pathotypes. csg and fim genes were the most present virulence factors. Conclusion: Typing of E. coli isolates from stool specimens will help to determine the diversity of diarrheal pathogens and take proper decisions to reduce the health burden of diarrheal diseases.

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EPIDEMIC DIARRHEA AMONG INFANTS ASSOCIATED WITH THE ISOLATION OF A NEW SEROTYPE OF ESCHERICHIA COLI: E. COLI 0127:B8

PEDIATRICS ◽

10.1542/peds.16.2.215 ◽

1955 ◽

Vol 16 (2) ◽

pp. 215-227

Author(s):

Merlin L. Cooper ◽

Edward W. Walters ◽

Helen M. Keller ◽

James M. Sutherland ◽

Hollis J. Wiseman

Keyword(s):

Escherichia Coli ◽

Rectal Swab ◽

Specific Treatment ◽

First Year ◽

Average Dose ◽

Clinical Value ◽

E Coli ◽

Severe Diarrhea ◽

First Year Of Life

During an outbreak of epidemic diarrhea a new serotype of Escherichia coli: E. coli 0127:B8, was isolated from 44 of 145 infants and from 1 nurse among 82 adult personnel in attendance. Among the 44 infants whose rectal swab cultures were positive, 20 were in the first month of life, 16 were 2 to 6 months of age, and 6 were 7 to 12 months of age, a total of 42 being in the first year of life. Severe epidemic diarrhea associated with the presence of E. coli 0127:B8 was characterized by the sudden development of extreme abdominal distention among some of the infants; explosive onset of diarrhea and the presence of a pungent, musty, objectionable odor not noticed around other patients with diarrhea. E. coli 0127: B8 was isolated more frequently while the patients were having diarrhea. Neomycin® was used orally for the specific treatment of patients with diarrhea. The early dosage was small due to our caution in using a new antibiotic. Over the 4 months period of this study the dosage was gradually increased. The average dose was 40 mg./kg./day for the patients with positive cultures and 46 mg./kg./day for those with negative cultures. Of 22 patients with positive cultures, 12 who were treated with Neomycin® alone or in addition to other antibiotics continued to show the presence of E. coli 0127:B8 after Neomycin® therapy had been terminated; however, only 2 of these patients had recurrence of diarrhea, both having had negative cultures while receiving Neomycin®. The administration of Neomycin® to every infant on the 2 wards, regardless of clinical condition, was followed by a decreasing incidence of diarrhea and decreasing detection of E. coli 0127:B8. The dose of Neomycin® was 40 to 50 mg./kg./day. It is our feeling that Neomycin® administered orally was of definite clinical value therapeutically and prophylactically but in the dosage used was inadequate bacteriologically. Four deaths occurred among the 44 infants whose rectal swab cultures were positive for E. coli 0127:B8 and necropsy studies were made on each. A hemorrhagic enteritis was present in 3 infants and in the fourth infant the cause of death was a congenital heart condition. Death of 1 patient with negative rectal swab cultures may very likely be attributed to severe diarrhea. Sera from patients and personnel failed to show the presence of agglutinins for E. coli 0127:B8. in vitro sensitivity tests showed that the order of decreasing bactericidal effectiveness of 5 antibiotics for E. coli 027:B8 was polymyxin, Neomycin®, chloramphenicol, Achromycin®, and Terramycin®. All strains were resistant to dihydrostreptomycin and sodium sulfadiazine. Only the last strains isolated from 2 patients showed increased resistance to Neomycin®, four-and sixteenfold when compared with the first strains isolated from the same patients.

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Diarrheagenic Escherichia coli pathotypes isolated from a swine farm in a region of Morelos state, Mexico

Salud Pública de México ◽

10.21149/11268 ◽

2020 ◽

Author(s):

Elsa María Tamayo-Legorreta ◽

Alejandro García-Radilla ◽

Eduardo Moreno-Vázquez ◽

Fabián Téllez-Figueroa ◽

Celia M Alpuche-Aranda

Keyword(s):

Escherichia Coli ◽

Multiplex Pcr ◽

Potential Risk ◽

Virulence Gene ◽

Central Mexico ◽

Swine Farm ◽

Fecal Samples ◽

E Coli ◽

Diarrheagenic Escherichia Coli

Objective. Determine the frequency of diarrheagenic Escherichia coli pathotypes colonizing swine. Materials and Methods. E. coli strains isolated of fecal samples from 280 swine, produced for local consumption, in a semi-technical farm of Morelos state, (central Mexico) were tested to identify the diarrheagenic E. coli pathotypes by multiplex PCR. Results. Of the 521-diarrheagenic E. coli isolates examined, 50 (9.6%) were positive for at least one virulence gene in 42 different animals. Thus, 15% (42/280) of the swine in this farm were colonized with pathogenic E. coli. Among the E. coli isolates, the pathotype EPEC (6.5%) was the most frequently, followed by EHEC (2.3%), ETEC and EIEC (0.4%). Conclusions. In this study, four different E. coli pathotypes were found among swine colonized by E. coli in this farm. Thus, these swine are reservoirs for these virulent bacteria and there is potential risk of causing diarrhea in swine and in the population consuming the meat.

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The Complete Genome of the Atypical Enteropathogenic Escherichia coli Archetype Isolate E110019 Highlights a Role for Plasmids in Dissemination of the Type III Secreted Effector EspT

Infection and Immunity ◽

10.1128/iai.00412-19 ◽

2019 ◽

Vol 87 (10) ◽

Cited By ~ 1

Author(s):

Tracy H. Hazen ◽

David A. Rasko

Keyword(s):

Escherichia Coli ◽

Complete Genome ◽

Genomic Analysis ◽

Host Cells ◽

Comparative Genomic ◽

Content Type ◽

E Coli ◽

Type Iii ◽

Severe Diarrhea ◽

Typical Epec

ABSTRACT Enteropathogenic Escherichia coli (EPEC) is a leading cause of moderate to severe diarrhea among young children in developing countries, and EPEC isolates can be subdivided into two groups. Typical EPEC (tEPEC) bacteria are characterized by the presence of both the locus of enterocyte effacement (LEE) and the plasmid-encoded bundle-forming pilus (BFP), which are involved in adherence and translocation of type III effectors into the host cells. Atypical EPEC (aEPEC) bacteria also contain the LEE but lack the BFP. In the current report, we describe the complete genome of outbreak-associated aEPEC isolate E110019, which carries four plasmids. Comparative genomic analysis demonstrated that the type III secreted effector EspT gene, an autotransporter gene, a hemolysin gene, and putative fimbrial genes are all carried on plasmids. Further investigation of 65 espT-containing E. coli genomes demonstrated that different espT alleles are associated with multiple plasmids that differ in their overall gene content from the E110019 espT-containing plasmid. EspT has been previously described with respect to its role in the ability of E110019 to invade host cells. While other type III secreted effectors of E. coli have been identified on insertion elements and prophages of the chromosome, we demonstrated in the current study that the espT gene is located on multiple unique plasmids. These findings highlight a role of plasmids in dissemination of a unique E. coli type III secreted effector that is involved in host invasion and severe diarrheal illness.

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Evolution of diarrheagenic Escherichia coli pathotypes in India

Journal of Laboratory Physicians ◽

10.4103/jlp.jlp_58_19 ◽

2019 ◽

Vol 11 (04) ◽

pp. 346-351

Author(s):

Pankaj Singh ◽

Sharda C. Metgud ◽

Subarna Roy ◽

Shashank Purwar

Keyword(s):

Escherichia Coli ◽

Cross Sectional Study ◽

Clinical Settings ◽

Accurate Identification ◽

Cross Sectional ◽

E Coli ◽

Medical College ◽

Diarrheagenic Escherichia Coli ◽

Proper Management ◽

Heat Stable

Abstract 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.

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