Differentiation of faecal Escherichia coli from human and animal sources by random amplified polymorphic DNA-PCR (RAPD-PCR)

2004 ◽  
Vol 50 (1) ◽  
pp. 193-198 ◽  
Author(s):  
D. Venieri ◽  
A. Vantarakis ◽  
G. Komninou ◽  
M. Papapetropoulou
Keyword(s):  
Escherichia Coli ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Arbitrary Primers ◽  
E Coli ◽  
Rapd Pcr ◽  
Dna Pcr

In this study the assessment of randomly amplified polymorphic DNA (RAPD) analysis was established as a molecular epidemiological tool. RAPD analysis was performed to differentiate faecal Escherichia coli isolates from human and animal sources. E. coli strains (128) were isolated from human and animal faeces (from cattle and sheep). Genomic DNA was extracted and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting was performed. Seven arbitrary primers were tested with a view to discriminating between E. coli isolates from humans and E. coli isolates from animals. RAPD profiles were analysed with hierarchical cluster analysis using an unweighted pair group method. RAPD profiles obtained with three of the tested primers (1247, 1290 and 1254) established a distinct differentiation between E. coli isolates from humans and E. coli from animals. Low levels of misclassification and high levels of specificity make RAPD a sensitive, efficient and reliable means of distinguishing closely related strains.

scholarly journals Antibiotic Susceptibility and Genotype Patterns of Escherichia coli, Klebsiella pneumonia and Pseudomonas aeruginosa Isolated from Urinary Tract Infected Patients

2010 ◽  
Vol 59 (3) ◽  
pp. 207-212 ◽  
Author(s):  
M.I. ABOU-DOBARA ◽  
M.A. DEYAB ◽  
E.M. ELSAWY ◽  
H.H. MOHAMED
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Urinary Tract ◽  
Antibiotic Susceptibility ◽  
Susceptibility Testing ◽  
Random Amplified Polymorphic Dna ◽  
Test Methods ◽  
Klebsiella Pneumonia ◽  
E Coli ◽  
Rapd Pcr

Thirty nine isolates of Escherichia coli, twenty two isolates of Klebsiella pneumoniae and sixteen isolates of Pseudomonas aeruginosa isolated from urinary tract infected patients were analyzed by antimicrobial susceptibility typing and random amplified polymorphic DNA (RAPD)-PCR. Antibiotic susceptibility testing was carried out by microdilution and E Test methods. From the antibiotic susceptibility, ten patterns were recorded (four for E. coli, three for K. pneumoniae and three for P. aeruginosa respectively). Furthermore, genotyping showed seventeen RAPD patterns (seven for E. coli, five for K. pneumoniae and five for P. aeruginosa respectively). In this study, differentiation of strains of E. coli, K. pneumoniae and P. aeruginosa from nosocomial infection was possible with the use of RAPD.

scholarly journals Characterization of Alstroemeria Species using Random Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 482F-482 ◽  
Author(s):  
Deric D. Picton ◽  
Harrison G. Hughes
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Randomly Amplified Polymorphic Dna ◽  
Banding Patterns ◽  
Extraction Buffer ◽  
Rapd Pcr ◽  
High Degree ◽  
Species Hybrids ◽  
Color Variants

In this study, 11 species, hybrids, and color variants were characterized using randomly amplified polymorphic DNA (RAPD) analysis. Total genomic DNA was extracted using a 2% CTAB extraction buffer using fresh or frozen leaf material. The DNA was amplified using standard RAPD-PCR protocols utilizing 10-mer primers. All primers utilized exhibited a high degree of polymorphism in their banding patterns among the species and hybrids studied. The primers used produced ≈40 reproducible bands. It was possible to identify and uniquely distinguish all species and hybrids investigated using these bands.

scholarly journals Characterization of verocytotoxin-producingEscherichia coliO157 isolates from patients with haemolytic uraemic syndrome in Western Europe

1995 ◽  
Vol 115 (1) ◽  
pp. 1-3 ◽  
Author(s):  
A. E. Heuvelink ◽  
N. C. A. J. van de Kar ◽  
J. F. G. M. Meis ◽  
L. A. H. Monnens ◽  
W. J. G. Melchers
Keyword(s):  
Haemolytic Uraemic Syndrome ◽  
Western Europe ◽  
Random Amplified Polymorphic Dna ◽  
E Coli ◽  
Pcr Fingerprinting ◽  
Phage Types ◽  
Rapd Pcr ◽  
Typing Methods ◽  
Dna Pcr

SummaryFifty verocytotoxin (VT)-producingEscherichia coli(VTEC) strains of serogroup O157 were characterized by phage typing, polymerase chain reaction (PCR) for VT genes and theE. coliattaching and effacing (eae) gene, and random amplified polymorphic DNA–PCR (RAPD–PCR) fingerprinting. The collection represented isolates obtained from patients with diarrhoea-associated haemolytic-uraemic syndrome (D+ HUS) and their family contacts, isolated in the Netherlands, Belgium and Germany between 1989 and 1993. Based on isolates from separate families (n= 27) seven different phage types were identified, types 2 (44%) and 4 (33%) were predominant. Eighty-five percent of the strains contained only VT2 gene sequences and 15% both VT1 and VT2. All strains of the dominant phage types 2 and 4 carried the VT2 gene. Strains that belonged to the minor phage types 8, 14, 32 carried both VT1 and VT2 genes, with the exception of two isolates identified as phage types 49 and 54 which contained only VT2 genes. All O157 VTEC strains possessed the chromosomally-locatedeaegene, which indicates its usefulness as virulence marker. RAPD–PCR fingerprinting identified four distinct banding patterns, with one profile found among 79% of the strains. Based on the combined results of all typing methods used in this study, the collection of 50 O157 VTEC strains could be divided into nine distinct groups. Strains isolated from different persons within one family could not be distinguished by any of these methods. The data suggest that O157 VTEC strains are members of one clone that has become widely distributed.

scholarly journals Characterization of typical and atypical enteropathogenic Escherichia coli (EPEC) strains of the classical O55 serogroup by RAPD analysis

1999 ◽  
Vol 30 (4) ◽  
pp. 365-368 ◽  
Author(s):  
Dennys M. Girão ◽  
Sílvia Y. Bando ◽  
Valéria Brígido de C. Girão ◽  
Carlos A. Moreira-Filho ◽  
Sérgio Eduardo L. Fracalanzza ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Epidemiological Studies ◽  
Enteropathogenic Escherichia Coli ◽  
E Coli ◽  
Typical Epec ◽  
Rapd Method ◽  
Atypical Strains

The genetic diversity of 41 typical and atypical enteropathogenic Escherichia coli (EPEC) strains of the serogroup O55 was analyzed by using the random amplified polymorphic DNA (RAPD) method. All typical EPEC O55 strains were grouped in two clusters (A and C) and belonged to the serotype O55:H6, while cluster B included all atypical strains, which were of the serotype O55:H7. The three groups also included non-motile strains. RAPD may be a useful method for epidemiological studies on E. coli O55 infection.

scholarly journals Prevalence of Escherichia coli O157 in Saskatchewan Cattle: Characterization of Isolates by Using Random Amplified Polymorphic DNA PCR, Antibiotic Resistance Profiles, and Pathogenicity Determinants

2006 ◽  
Vol 72 (6) ◽  
pp. 4347-4355 ◽  
Author(s):  
Sinisa Vidovic ◽  
Darren R. Korber
Keyword(s):  
Escherichia Coli ◽  
Random Amplified Polymorphic Dna ◽  
Multidrug Resistant ◽  
Feedlot Cattle ◽  
Point Prevalence ◽  
Pcr Analysis ◽  
Point Prevalence Study ◽  
E Coli ◽  
Dna Pcr

ABSTRACT The prevalence of Escherichia coli O157 associated with feedlot cattle in Saskatchewan was determined in a 10-month longitudinal study (3 feedlots) and a point prevalence study (20 feedlots). The prevalence of E. coli O157 at the three different sites in the horizontal study varied from 2.5 to 45%. The point prevalence of E. coli O157 among Saskatchewan cattle from 20 different feedlots ranged from 0% to a high of 57%. A statistically significant (P = 0.003) positive correlation was determined to exist between the density of cattle and the E. coli O157 prevalence rate. A significant correlation (P = 0.006) was also found between the E. coli O157 percent prevalence and the number of cattle housed/capacity ratio. All 194 E. coli O157 isolates obtained were highly virulent, and random amplified polymorphic DNA PCR analysis revealed that the isolates grouped into 39 different E. coli O157 subtypes, most of which were indigenous to specific feedlots. Two of the most predominant subtypes were detected in 11 different feedlots and formed distinct clusters in two geographic regions in the province. Antimicrobial susceptibility testing of the E. coli O157 isolates revealed that 10 were multidrug resistant and that 73 and 5 were resistant to sulfisoxazole and tetracycline, respectively.

scholarly journals RAPD-PCR Fingerprinting and Southern Analysis of Xanthomonas axonopodis pv. dieffenbachiae Strains Isolated from Different Aroid Hosts and Locations

Plant Disease ◽  
2004 ◽  
Vol 88 (9) ◽  
pp. 980-988 ◽  
Author(s):  
M. H. R. Khoodoo ◽  
Y. Jaufeerally-Fakim
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Systemic Disease ◽  
Dna Probes ◽  
Southern Analysis ◽  
Group Method ◽  
Arbitrary Primers ◽  
Host Preferences ◽  
Xanthomonas Axonopodis ◽  
Arithmetic Average ◽  
Rapd Pcr

Anthurium blight, caused by Xanthomonas axonopodis pv. dieffenbachiae, is a systemic disease of Anthurium and other aroids. The aims of this work were to study the genetic diversity among X. axonopodis pv. dieffenbachiae strains and to identify, from the polymerase chain reaction (PCR) profiles, DNA probes that would be specific for the pathovar dieffenbachiae. Twenty-five X. axonopodis pv. dieffenbachiae strains, isolated from different hosts and geographical locations including Mauritius, were fingerprinted using the random amplified polymorphic DNA (RAPD)-PCR technique. The fingerprints were analyzed by the National Taxonomy System Software (NTSYS). The specificity of some of the RAPD fragments selected from PCR profiles was tested by Southern analyses of the PCR products. Ten arbitrary primers were chosen from an initial set of 111 decamers. Two hundred and nine RAPD markers were generated in eight individual DNA profiles. A correlation was found between the serotypes and the RAPD profiles for some groups of isolates. A possible link was also observed between the host range of the isolates tested and their RAPD profiles for strains isolated from Dieffenbachia and Philodendron. These results were confirmed by Southern analysis. Cluster analysis by the unweighted pair group method, arithmetic average (UPGMA) confirmed that the pathovar is genetically diverse with some strains that were clustered together showing similar host preferences. DNA probes with a potential use in molecular diagnostics of Anthurium blight were identified. This preliminary work could be used to develop PCR primers that will enable the sensitive detection of the pathogen in latently infected plants.

scholarly journals Molecular Characterization of Commensal Escherichia coli Adapted to Different Compartments of the Porcine Gastrointestinal Tract

2012 ◽  
Vol 78 (19) ◽  
pp. 6799-6803 ◽  
Author(s):  
Sam Abraham ◽  
David M. Gordon ◽  
James Chin ◽  
Huub J. M. Brouwers ◽  
Peter Njuguna ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gastrointestinal Tract ◽  
Random Amplified Polymorphic Dna ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Different Strains ◽  
Different Characteristics

ABSTRACTThe role ofEscherichia colias a pathogen has been the focus of considerable study, while much less is known about it as a commensal and how it adapts to and colonizes different environmental niches within the mammalian gut. In this study, we characterizeEscherichia coliorganisms (n= 146) isolated from different regions of the intestinal tracts of eight pigs (dueodenum, ileum, colon, and feces). The isolates were typed using the method of random amplified polymorphic DNA (RAPD) and screened for the presence of bacteriocin genes and plasmid replicon types. Molecular analysis of variance using the RAPD data showed thatE. coliisolates are nonrandomly distributed among different gut regions, and that gut region accounted for 25% (P< 0.001) of the observed variation among strains. Bacteriocin screening revealed that a bacteriocin gene was detected in 45% of the isolates, with 43% carrying colicin genes and 3% carrying microcin genes. Of the bacteriocins observed (H47, E3, E1, E2, E7, Ia/Ib, and B/M), the frequency with which they were detected varied with respect to gut region for the colicins E2, E7, Ia/Ib, and B/M. The plasmid replicon typing gave rise to 25 profiles from the 13 Inc types detected. Inc F types were detected most frequently, followed by Inc HI1 and N types. Of the Inc types detected, 7 were nonrandomly distributed among isolates from the different regions of the gut. The results of this study indicate that not only may the different regions of the gastrointestinal tract harbor different strains ofE. colibut also that strains from different regions have different characteristics.

scholarly journals A Comparative Study of the Adherent-Invasive Escherichia coli Population and Gut Microbiota of Healthy Vegans versus Omnivores

2020 ◽  
Vol 8 (8) ◽  
pp. 1165
Author(s):  
Rebecca Veca ◽  
Christian O’Dea ◽  
Jarred Burke ◽  
Eva Hatje ◽  
Anna Kuballa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gut Microbiota ◽  
Random Amplified Polymorphic Dna ◽  
Fecal Microbiota ◽  
Vegan Diet ◽  
Rrna Gene ◽  
E Coli ◽  
Abundance And Diversity ◽  
The Individual ◽  
Diversity Profiles

Adherent-invasive Escherichia coli (AIEC) strains carry virulence genes (VGs) which are rarely found in strains other than E. coli. These strains are abundantly found in gut mucosa of patients with inflammatory bowel disease (IBD); however, it is not clear whether their prevalence in the gut is affected by the diet of the individual. Therefore, in this study, we compared the population structure of E. coli and the prevalence of AIEC as well as the composition of gut microbiota in fecal samples of healthy participants (n = 61) on either a vegan (n = 34) or omnivore (n = 27) diet to determine whether diet is associated with the presence of AIEC. From each participant, 28 colonies of E. coli were typed using Random Amplified Polymorphic DNA (RAPD)–PCR. A representative of each common type within an individual was tested for the presence of six AIEC-associated VGs. Whole genomic DNA of the gut microbiota was also analyzed for its diversity profiles, utilizing the V5-V6 region of the16S rRNA gene sequence. There were no significant differences in the abundance and diversity of E. coli between the two diet groups. The occurrence of AIEC-associated VGs was also similar among the two groups. However, the diversity of fecal microbiota in vegans was generally higher than omnivores, with Prevotella and Bacteroides dominant in both groups. Whilst 88 microbial taxa were present in both diet groups, 28 taxa were unique to vegans, compared to seven unique taxa in the omnivores. Our results indicate that a vegan diet may not affect the number and diversity of E. coli populations and AIEC prevalence compared to omnivores. The dominance of Prevotella and Bacteroides among omnivores might be accounted for the effect of diet in these groups.

Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp.bulgaricus and L. delbrueckii subsp.lactis

1999 ◽  
Vol 65 (10) ◽  
pp. 4351-4356 ◽  
Author(s):  
Sandra Torriani ◽  
Giacomo Zapparoli ◽  
Franco Dellaglio
Keyword(s):  
Numerical Analysis ◽  
Dairy Products ◽  
Lactobacillus Delbrueckii ◽  
Randomly Amplified Polymorphic Dna ◽  
Specific Pcr ◽  
Single Colony ◽  
Rapd Pcr ◽  
Reliable Differentiation ◽  
Dna Pcr ◽  
Proline Iminopeptidase

ABSTRACT Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp.bulgaricus and L. delbrueckii subsp.lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene ofL. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp.delbrueckii LMG 6412T, which clustered withL. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains.

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