scholarly journals Genotypic Analysis of Escherichia coli Strains from Poultry Carcasses and Their Susceptibilities to Antimicrobial Agents

2001 ◽  
Vol 67 (4) ◽  
pp. 1940-1944 ◽  
Author(s):  
Ifigenia Geornaras ◽  
John W. Hastings ◽  
Alexander von Holy
Keyword(s):  
Escherichia Coli ◽  
South African ◽  
Length Polymorphism ◽  
Antimicrobial Agents ◽  
Susceptibility Testing ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Genotypic Analysis ◽  
Plasmid Profiling

ABSTRACT Plasmid profiling and amplified fragment length polymorphism (AFLP) analysis were used to genotype 50 Escherichia coli strains from poultry carcasses. Thirty different plasmid profiles were evident, and clustering of the AFLP data showed that they were a distinctly heterogeneous group of strains. Susceptibility testing against five antimicrobial agents used in the South African poultry industry showed all strains to be susceptible to danofloxacin and colistin, while the majority (96%) were resistant to two tetracyclines.

Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses

2006 ◽  
Vol 96 (10) ◽  
pp. 1097-1107 ◽  
Author(s):  
Larry J. Heilmann ◽  
Nadav Nitzan ◽  
Dennis A. Johnson ◽  
Julie S. Pasche ◽  
Curt Doetkott ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Vegetative Compatibility ◽  
Colletotrichum Coccodes ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Bootstrap Analysis ◽  
Nit Mutants

Amplified fragment length polymorphism (AFLP) using three primer sets was used to characterize 211 Colletotrichum coccodes isolates from North America, 112 of which were assigned to six vegetative compatibility groups (VCGs) using nitrate nonutilizing (nit) mutants. These isolates clustered into five corresponding groups by unweighted pairgroup method with arithmetic means-based cluster analysis of AFLP banding patterns. Isolates of C. coccodes belonging to NA-VCG1 and NA-VCG3 were closely related, as were isolates belonging to NA-VCG2 and NA-VCG5. Based on bootstrap analysis of AFLP data, the two isolates originally assigned to NA-VCG4 clustered with isolates belonging to NA-VCG2 and NA-VCG5. C. coccodes isolates that clustered with two isolates belonging to NA-VCG6 were the most diverged from other groups, including seven isolates collected from hosts other than potato. As opposed to the bootstrap analysis, a quadratic discriminant analysis (QDA) of AFLP data correctly categorized the two isolates of NA-VCG4. Furthermore, in isolates where VCG determinations had been made, this model correctly classified isolates of all VCGs. QDA classifications were identical to those made by the bootstrap analysis, with the exception of VCG4. Overall, classifications made by the QDA model were strongly correlated (r = 0.970, P < 0.001) to the VCGs assigned by traditional methods. All 99 C. coccodes isolates evaluated only by AFLP also were subjected to QDA, leading to the assignment of a presumptive VCG for each isolate. No isolates of VCG4 or VCG6 were identified by QDA within this population. Symptoms of black dot developed in plants inoculated with isolates collected from both potato and non-potato hosts. However, total yield was not significantly reduced by infection with non-potato isolates. The lack of any additional groups identified by AFLP analysis may be an indicator of a limited level of genetic variation among North American C. coccodes isolates. AFLP is a much more efficient technique for subspecific characterization in C. coccodes than VCG analysis utilizing nit mutants and will provide an effective means by which the population biology of this pathogen can be further investigated worldwide.

scholarly journals Genetic Diversity of Rhubarb Cultivars

2008 ◽  
Vol 133 (4) ◽  
pp. 587-592 ◽  
Author(s):  
Joseph C. Kuhl ◽  
Veronica L. DeBoer
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Length Polymorphism ◽  
Genetic Relationship ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
18Th Century ◽  
Pedigree Information ◽  
Aflp Analysis ◽  
Fingerprint Analysis

The genus Rheum L., commonly known as rhubarb, is composed of ≈60 species, primarily distributed throughout northern and central Asia. Rhubarb species have been used for medicinal purposes for thousands of years; however, it was not until the 18th century that the culinary use of petioles was first reported. Although the origin(s) of culinary rhubarb is not clear, it is thought that they originated from hybridization of rhubarb species originally brought to Europe for medicinal purposes. Most rhubarb cultivars lack pedigree information, and the genetic relationship among cultivars is largely unknown. Amplified fragment length polymorphism (AFLP) markers were generated for fingerprint analysis of 37 cultivars and four putative Rheum species accessions. Ten EcoRI and MseI primer combinations were analyzed for a total of 1400 scored polymorphisms, with an average of 140 polymorphisms per primer combination. Results show at least two clusters of related cultivars, as well as distantly related accessions. This study provides an estimate of rhubarb cultivar genetic diversity using AFLP analysis.

scholarly journals Genomic Relatedness of ChlamydiaIsolates Determined by Amplified Fragment Length Polymorphism Analysis

1999 ◽  
Vol 181 (15) ◽  
pp. 4469-4475 ◽  
Author(s):  
Adam Meijer ◽  
Servaas A. Morré ◽  
Adriaan J. C. Van Den Brule ◽  
Paul H. M. Savelkoul ◽  
Jacobus M. Ossewaarde
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Chlamydia Psittaci ◽  
Rrna Genes ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Genomic Relatedness

ABSTRACT The genomic relatedness of 19 Chlamydia pneumoniaeisolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (± 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittacifingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.

Predictive Fluorescent Amplified-Fragment Length Polymorphism Analysis of Escherichia coli: High-Resolution Typing Method with Phylogenetic Significance

1999 ◽  
Vol 37 (5) ◽  
pp. 1274-1279 ◽  
Author(s):  
Catherine Arnold ◽  
Lou Metherell ◽  
Geraldine Willshaw ◽  
Anthony Maggs ◽  
John Stanley
Keyword(s):  
Escherichia Coli ◽  
High Resolution ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Enzyme Electrophoresis ◽  
Typing Method ◽  
E Coli

The fluorescent amplified-fragment length polymorphism (FAFLP) assay potentially amplifies a unique set of genome fragments from each bacterial clone. It uses stringently hybridizing primers which carry a fluorescent label. Precise fragment sizing is achieved by the inclusion of an internal size standard in every lane. Therefore, a unique genotype identifier(s) can be found in the form of fragments of precise size or sizes, and these can be generated reproducibly. In order to evaluate the potential of FAFLP as an epidemiological typing method with a valid phylogenetic basis, we applied it to 87 strains ofEscherichia coli. These comprised the EcoR collection, which has previously been classified by multilocus enzyme electrophoresis (MLEE) and which represents the genetic diversity of the species E. coli, plus 15 strains of the clinically important serogroup O157. FAFLP with an unlabelled nonselectiveEcoRI primer (Eco+0) and a labelled selectiveMseI primer (Mse+TA) gave strain-specific profiles. Fragments of identical sizes (in base pairs) were assumed to be identical, and the genetic distances between the strains were calculated. A phylogenetic tree derived from measure of distance correlated closely with the MLEE groupings of the EcoR collection and placed the verocytotoxin-producing O157 strains on an outlier branch. Our data indicate that FAFLP is suitable for epidemiological investigation of E. coli infection, providing well-defined and reproducible identifiers of genotype for each strain. Since FAFLP objectively samples the whole genome, each strain or isolate can be assigned a place within the broad context of the whole species and can also be subjected to a high-resolution comparison with closely related strains to investigate epidemiological clonality.

Comparative Fingerprinting Analysis ofCampylobacter jejuni subsp. jejuni Strains by Amplified-Fragment Length Polymorphism Genotyping

2000 ◽  
Vol 38 (9) ◽  
pp. 3379-3387 ◽  
Author(s):  
Bjørn-Arne Lindstedt ◽  
Even Heir ◽  
Traute Vardund ◽  
Kjetil K. Melby ◽  
Georg Kapperud
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Epidemiological Surveillance ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Ofcampylobacter Jejuni

Amplified-fragment length polymorphism (AFLP) analysis with the endonucleases BglII and MfeI was used to genotype 91 Campylobacter jejuni subsp. jejunistrains from outbreaks and sporadic cases. AFLP-generated fragments were labeled with fluorescent dye and separated by capillary electrophoresis. The software packages GeneScan and GelCompar II were used to calculate AFLP pattern similarities and to investigate phylogenetic relationships among the genotyped strains. The AFLP method was compared with two additional DNA-based typing methods, pulsed-field gel electrophoresis (PFGE) using SmaI and restriction fragment length polymorphism analysis on PCR products (PCR-RFLP) of theflaA and flaB genes. We found that AFLP analysis of C. jejuni strains is a rapid method that offers better discriminatory power than do both PFGE and PCR-RFLP. AFLP and, to a lesser extent, PCR-RFLP could differentiate strains within the same PFGE profiles, which also makes PCR-RFLP an alternative to PFGE. We were able to clearly distinguish 9 of 10 recognized outbreaks by AFLP and to identify similarities among outbreak and sporadic strains. Therefore, AFLP is suitable for epidemiological surveillance ofC. jejuni and will be an excellent tool for source identification in outbreak situations.

scholarly journals AFLP Analysis for Genetic Diversity in Capsicum Annuum and Related Species

2006 ◽  
Vol 1 (3) ◽  
pp. 1934578X0600100
Author(s):  
Sanjog T. Thul ◽  
Ajit K. Shasany ◽  
Mahendra P. Darokar ◽  
Suman P. S. Khanuja
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Great Degree ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Variation Analysis ◽  
Average Similarity ◽  
Geographical Locations

Intra- and inter-specific genetic variation analysis was conducted using amplified fragment length polymorphism (AFLP) profiling in Capsicum accessions in the germplasms collected from different geographical locations in India. A total of 24 accessions were investigated belonging to six species, namely C. annuum, C. baccatum, C. chinence, C. eximium, C. frutescens and C. luteum. Average similarity within the 15 accessions of C. annuum was highest (100%) between accessions CIMAP/CA45 and CIMAP/CA49 obtained from IISR, Kerala and 43% among the species CIMAP/CC1 and CIMAP/CB2. In this analysis, accessions were clustered more pronouncedly according to their geographical locations than to their taxonomic labels. A great degree of intermixing of present day domesticated chillies is evident from the present study.

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