Amplified Fragment Length Polymorphism, Serotyping, and Quinolone Resistance of Campylobacter jejuni and Campylobacter coli Strains from Chicken-Related Samples and Humans in Taiwan

2006 ◽  
Vol 69 (4) ◽  
pp. 775-783 ◽  
Author(s):  
SHAO W. FANG ◽  
CHING J. YANG ◽  
DANIEL Y. C. SHIH ◽  
CHENG C. CHOU ◽  
ROCH C. YU
Keyword(s):  
Campylobacter Jejuni ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Quinolone Resistance ◽  
Aflp Analysis ◽  
Campylobacter Coli

The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships between Campylobacter jejuni isolates from chicken-related samples (n = 32) and humans (n = 27) as well as between Campylobacter coli isolates from chicken-related samples (n = 27) and humans (n = 5). These isolates were collected between 1994 and 2003 in Taiwan. All C. jejuni and C. coli isolates showed highly heterogeneous fingerprints. C. jejuni isolates were separated in two distinct genetic clusters (A and B) at 40% genetic similarity and 42 different AFLP types at 90% similarity. However, three clusters at 40% genetic similarity and 33 different AFLP types at 90% similarity were observed in C. coli isolates. These results showed that AFLP analysis could be used to identify individual isolates of two Campylobacter species. Among C. jejuni isolates, the predominant AFLP type 1 was observed in five (7.9%) isolates, and types 5 and 12 in four (6.3%) isolates each. Cluster B consisted of 10 isolates, while the majority of isolates (n = 53) belonged to cluster A. In some AFLP types (1, 5, 12, 14 and 31), AFLP fingerprints of chicken-related isolates were closely related genetically to those of isolates from humans with gastroenteritis. The predominant serotypes in C. jejuni isolates were B:2 and Y:37. All isolates belonging to serotype O:19 grouped into one single AFLP type. Some chicken samples yielded multiple isolates of Campylobacter harboring simultaneously quinolone-resistant and quinolone-sensitive isolates attributed to the same species, or harboring C. jejuni and C. coli that have the characteristics of quinolone resistance.

scholarly journals Polymorphism and Genetic Relationships among Tea Genotypes from Turkey Revealed by Amplified Fragment Length Polymorphism Markers

2009 ◽  
Vol 134 (4) ◽  
pp. 428-434 ◽  
Author(s):  
Salih Kafkas ◽  
Sezai Ercişli ◽  
Yıldız Doğan ◽  
Yaşar Ertürk ◽  
Ayhan Haznedar ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Group Method ◽  
Aflp Analysis ◽  
Black Sea Region ◽  
Pair Group

Individuals in most countries around the world drink tea (Camellia sinensis). Tea drinking has attained ceremonial status in many places as a social and medicinal beverage. Although tea is of great importance in Turkey's economy, little is known about the pattern of genetic variation among the various tea genotypes grown in Turkey. A total of 32 tea genotypes found at the Ataturk Tea and Horticulture Research Institute in the eastern Black Sea region of Turkey were sampled. Fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis were applied for molecular characterization. The AFLP analysis with six primer combinations generated 835 fragments of which 567 were polymorphic, corresponding to 69.8% polymorphism. Resolving powers of the AFLP primers ranged from 62.6 to 81.9, yielding a total of 437.8; the polymorphic information content (PIC) ranged from 0.76 to 0.83, with an average of 0.79. Genetic similarity values ranged from 0.68 to 0.92, with an average of 0.76. The dendrogram derived by unweighted pair group method with arithmetic mean algorithm (UPGMA) and principal coordinate analysis (PCoA) revealed that all tea genotypes could be clearly divided into four distinct clusters. The results of this study will provide valuable information to the tea cultivar breeding program for the purpose of parental selection.

scholarly journals Identification of Rabbiteye Blueberry Cultivars (Vaccinium ashei Reade) and Analysis of Genetic Relationships Using Amplified Fragment Length Polymorphism (AFLP)

2004 ◽  
Vol 10 (4) ◽  
Author(s):  
E. Prokaj ◽  
H. Watanabe ◽  
Y. Suyama ◽  
M. Saigusa
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Crop Yields ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Vaccinium Ashei ◽  
Identification Technique

Proper cultivar identification is a requisite for commercial planting and breeding nurseries of cross-pollinated blueberry (Vaccinium ashei Reade) cultivars to insure high crop yields and optimize germplasm maintenance and utilization. Fourteen rabbiteye blueberry cultivars and three non-identified clones were screened with amplified fragment length polymorphism (AFLP) analysis with the aim of developing a fast and reliable identification technique. The selective primer pair applied (M-CTG/ E-ACC), which was previously tested, resulted in a large number of reproducible polymorphic fragments for cultivar identification. After comparison of the AFLP fingerprints, the Jaccard similarity indexes were calculated, and an UPGMA dendrogram was constructed. It was revealed that the three non-identified clones belong to the Tifblue' cultivar. Moreover, AFLP technique proved to be a fast, successful and reliable way in rabbiteye blueberry identification.

scholarly journals Amplified Fragment Length Polymorphism Analysis Provides Strategies for Improvement of Bitter Gourd (Momordica charantia L.)

HortScience ◽  
2008 ◽  
Vol 43 (1) ◽  
pp. 127-133 ◽  
Author(s):  
Ambika B. Gaikwad ◽  
Tusar Kanti Behera ◽  
Anand K. Singh ◽  
Devanshi Chandel ◽  
Jawahir L. Karihaloo ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Momordica Charantia ◽  
Bitter Gourd ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Diversity Assessment

Monoecious bitter gourd (Momordica charantia L. var. minima and maxima Williams & Ng), a cucurbit of major economic importance, is widely cultivated in India, China, Africa, and South America. Although the morphology (i.e., growth habit and fruit shape, size, color, and surface texture) of Indian bitter gourd is diverse and gynoecious sex forms exist, a comprehensive diversity assessment of ecotypes has not been performed. Therefore, the genetic relatedness of 38 Indian cultigens (commercial varieties and cultivated landraces originating from different agroecological zones) was determined by amplified fragment length polymorphism (AFLP) analysis. Six primer combinations yielded a total of 519 bands of which 404 (77.8%) were polymorphic among the cultigens examined. Unweighted pair group cluster analyses were performed using Jaccard's genetic similarities to define genetic relationships among cultigens. Genetic similarities among cultigens ranged between 0.44 and 0.88, indicating that the bitter gourd cultigens examined were genetically diverse. Moreover, putative AFLP loci defined genetic relationships that allowed for partitioning of cultigens into two distinct groups [Group 1 and Group II (node 1); bootstrap = 100%] after cluster analysis. With rare exception, cultigens were grouped with respect to geographical region, in which cultigens within a group and subgroups possessed high degrees of genetic similarity. The relatively high marker indices (6.2 to 19.4), polymorphic information content of the markers used (0.20 to 0.25), and multiplex ratios (28.9 to 77.4) collectively indicate that the AFLP markers used are discriminatory in bitter gourd and that the analysis of the broad-based cultigens described provides valuable baseline information for advancing initial breeding strategies for this crop species.

scholarly journals High-Resolution Genotyping ofCampylobacter Strains Isolated from Poultry and Humans with Amplified Fragment Length Polymorphism Fingerprinting

1999 ◽  
Vol 65 (6) ◽  
pp. 2369-2375 ◽  
Author(s):  
Birgitta Duim ◽  
Trudy M. Wassenaar ◽  
Alan Rigter ◽  
Jaap Wagenaar
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Pcr Primers ◽  
Epidemiological Studies ◽  
Aflp Analysis ◽  
Campylobacter Coli ◽  
Chromosomal Dna ◽  
Typing Methods

ABSTRACT For epidemiological studies of Campylobacterinfections, molecular typing methods that can differentiate campylobacters at the strain level are needed. In this study we used a recently developed genotyping method, amplified fragment length polymorphism (AFLP), which is based on selective amplification of restriction fragments of chromosomal DNA, for genetic typing ofCampylobacter jejuni and Campylobacter colistrains derived from humans and poultry. We developed an automated AFLP fingerprinting method in which restriction endonucleasesHindIII and HhaI were used in combination with one set of selective PCR primers. This method resulted in evenly distributed band patterns for amplified fragments ranging from 50 to 500 bp long. The discriminatory power of AFLP was assessed with aC. jejuni strain, an isogenic flagellin mutant, and distinct C. jejuni strains having known pulsed-field gel electrophoresis and fla PCR-restriction fragment length polymorphism genotypes. Unrelated C. jejuni strains produced heterogeneous patterns, whereas genetically related strains produced similar AFLP patterns. Twenty-five Campylobacterstrains obtained from poultry farms in The Netherlands grouped in threeC. jejuni clusters that were separate from a C. coli cluster. The band patterns of 10 C. jejunistrains isolated from humans were heterogeneous, and most of these strains grouped with poultry strains. Our results show that AFLP analysis can distinguish genetically unrelated strains from genetically related strains of Campylobacter species. However, desirable genetically related strains can be differentiated by using other genotyping methods. We concluded that automated AFLP analysis is an attractive tool which can be used as a primary method for subtyping large numbers of Campylobacter strains and is extremely useful for epidemiological investigations.

scholarly journals Analysis of Genetic Variability among Phalaenopsis Species and Hybrids Using Amplified Fragment Length Polymorphism

2009 ◽  
Vol 134 (1) ◽  
pp. 58-66 ◽  
Author(s):  
Yeun-Kyung Chang ◽  
Richard E. Veilleux ◽  
Muhammad Javed Iqbal
Keyword(s):  
Genetic Variability ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Fragment Length Polymorphism ◽  
Species Conservation ◽  
Amplified Fragment Length Polymorphism ◽  
The United States ◽  
Group Method ◽  
Aflp Analysis

Phalaenopsis is the second most valuable potted plant in the United States. Information on the genetic diversity and relationships among species and hybrids is important for breeding purposes and species conservation. In this study, genetic variability of 16 Phalaenopsis species and hybrids was analyzed using amplified fragment length polymorphism (AFLP) markers. Ten AFLP primer combinations amplified 1353 DNA fragments ranging in size from 100 to 350 bp and 1285 (95%) of them were polymorphic. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by the unweighted pair group method with arithmetic mean analysis clustered the germplasm into two main groups. Bootstrap values for the groups supported 70% of the clustering. A significant linear relationship (r = 0.724, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results of this study demonstrate the usefulness of AFLP analysis in Phalaenopsis and its potential application in breeding and species conservation.

scholarly journals Investigating Parentage and Hybridity of Three Azaleodendrons Using Amplified Fragment Length Polymorphism Analysis

HortScience ◽  
2007 ◽  
Vol 42 (3) ◽  
pp. 740-743 ◽  
Author(s):  
Ryan N. Contreras ◽  
Thomas G. Ranney ◽  
Susana R. Milla-Lewis ◽  
G. Craig Yencho
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Morphological Analysis ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Single Clone ◽  
Similar Appearance

Morphological analysis historically has been used to determine parentage of unknown hybrids. This can be difficult when potential parents have similar appearance, as in the case of three azaleodendron cultivars, Rhododendron L. ‘Fragrans’, ‘Fragrans Affinity’, and ‘Fragrant Affinity’. These cultivars are similar in name and appearance, and all are purported hybrids of R. catawbiense Michx. or R. ponticum L. and R. viscosum (L.) Torr. Amplified fragment length polymorphism (AFLP) analysis was conducted to determine whether the cultivars are synonyms or distinct clones and to elucidate the parental species. The three cultivars, suspected to be hybrids between taxa in subgenera Hymenanthes (Blume) K.Koch (evergreen rhododendrons) and Pentanthera (G.Don) Pojarkova (deciduous azaleas), and related taxa from each subgenus were evaluated using 31 AFLP primer combinations. Genetic similarity, calculated using Jaccard's coefficient, among the hybrids ranged from 53% to 71%, indicating that they are distinct cultivars and not a single clone. Genetic similarity was highest between the hybrids and R. ponticum among the evergreen rhododendrons, and R. viscosum among the deciduous azaleas. A dendrogram generated using the genetic similarity matrix grouped taxa into their respective subgenera, with the three cultivars nested intermediately between subgenera but more closely with subgenus Hymenanthes and particularly R. ponticum, suggesting it is the evergreen rhododendron parent. Furthermore, principle components grouped R. ponticum more closely with the hybrids and there were 18 AFLP fragments unique to R. ponticum and the hybrids. However, no unique AFLP bands were shared exclusively among the hybrids and the purported deciduous azalea parent, R. viscosum, suggesting that the original azalea parents may have been hybrids.

scholarly journals Use of Amplified-Fragment Length Polymorphism To Study the Ecology of Campylobacter jejuni in Environmental Water and To Predict Multilocus Sequence Typing Clonal Complexes

2012 ◽  
Vol 78 (7) ◽  
pp. 2470-2473 ◽  
Author(s):  
Simon Lévesque ◽  
Karen St-Pierre ◽  
Eric Frost ◽  
Robert D. Arbeit ◽  
Sophie Michaud
Keyword(s):  
Campylobacter Jejuni ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Multilocus Sequence Typing ◽  
Population Genetic ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Environmental Water ◽  
Content Type

ABSTRACTWe determined the genetic variability among water isolates ofCampylobacter jejuniby using amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST). Across a highly diverse collection of isolates, AFLP clusters did not correlate with MLST clonal complexes, suggesting that AFLP is not reliable for deciphering population genetic relationships and may be problematic for larger epidemiologic analyses.

scholarly journals Amplified Fragment Length Polymorphism Analysis ofCampylobacter jejuni Strains Isolated from Chickens and from Patients with Gastroenteritis or Guillain-Barr� or Miller Fisher Syndrome

2000 ◽  
Vol 66 (9) ◽  
pp. 3917-3923 ◽  
Author(s):  
Birgitta Duim ◽  
C. Wim Ang ◽  
Alex van Belkum ◽  
Alan Rigter ◽  
Nan W. J. van Leeuwen ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Miller Fisher Syndrome ◽  
Group Method ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Fisher Syndrome

ABSTRACT The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships between Campylobacter jejuni strains infecting chickens (n = 54) and those causing gastroenteritis in humans (n = 53). In addition,C. jejuni strains associated with the development of Guillain-Barr� syndrome (GBS) (n = 14) and Miller Fisher syndrome (MFS) (n = 4), two related acute paralytic syndromes in human, were included. Strains were isolated between 1989 and 1998 in The Netherlands. The AFLP banding patterns were analyzed with correlation-based and band-based similarity coefficients and UPGMA (unweighted pair group method using average linkages) cluster analysis. All C. jejuni strains showed highly heterogeneous fingerprints, and no fingerprints exclusive for chicken strains or for human strains were obtained. All strains were separated in two distinct genetic groups. In group A the percentage of human strains was significantly higher and may be an indication that genotypes of this group are more frequently associated with human diseases. We conclude that C. jejuni from chickens cannot be distinguished from human strains and that GBS or MFS related strains do not belong to a distinct genetic group.

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