scholarly journals MLST Reveals a Separate and Novel Clonal Group for Acidovorax avenae Strains Causing Red Stripe in Sugarcane from Argentina

2019 ◽  
Vol 109 (3) ◽  
pp. 358-365 ◽  
Author(s):  
Paola D. Fontana ◽  
Nicolás Tomasini ◽  
Cecilia A. Fontana ◽  
Valentina Di Pauli ◽  
Pier S. Cocconcelli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Clonal Complex ◽  
Random Amplified Polymorphic Dna ◽  
Economic Losses ◽  
Best Response ◽  
Wide Range ◽  
Dicotyledonous Plants ◽  
Sequence Types ◽  
Reference Strains

Acidovorax spp. cause a wide range of economically important diseases in monocotyledonous and dicotyledonous plants, including sugarcane, corn, rice, oat, millet, foxtail watermelon, and orchid. In Argentina, the red stripe disease of sugarcane caused by Acidovorax avenae affects 30% of the milling stems with important economic losses. To explore the genetic diversity of this bacterium associated with red stripe in Argentina, multilocus sequence typing (MLST) was applied. This study included 15 local strains isolated from four different sugarcane planting regions and selected after random amplified polymorphic DNA analysis and reference strains of A. citrulli, A. avenae, and A. oryzae to investigate their phylogenetic relationships. MLST analysis resulted in five sequence types among the sugarcane A. avenae strains which constitute a clonal complex, meaning a common and close origin. Sugarcane strains were related to A. avenae from other hosts and distant to A. citrulli. Signals of frequent recombination in several lineages of A. avenae was detected and we observed that A. oryzae is closely related to A. avenae strains. This study provides valuable data in the field of epidemiological and evolutionary investigations of novel clone of A. avenae strains causing sugarcane red stripe. The knowledge of the genetic diversity and strain-host specificity are important to select the genotypes with the best response to the red stripe disease.

scholarly journals High Genetic Diversity in Flavobacterium psychrophilum Isolates from Healthy Rainbow Trout (Oncorhynchus mykiss) Farmed in the Same Watershed, Revealed by Two Typing Methods

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Ségolène Calvez ◽  
Nora Navarro-Gonzalez ◽  
Charlène Siekoula-Nguedia ◽  
Catherine Fournel ◽  
Eric Duchaud
Keyword(s):  
Genetic Diversity ◽  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Clonal Complex ◽  
Economic Losses ◽  
High Genetic Diversity ◽  
Content Type ◽  
Flavobacterium Psychrophilum ◽  
Sequence Types ◽  
Apparently Healthy

ABSTRACT Flavobacterium psychrophilum affects salmonid health worldwide and causes economic losses. The genetic diversity of the pathogen must be considered to develop control methods. However, previous studies have reported both high and low levels of genetic diversity. The present longitudinal study aimed at assessing the genetic diversity of F. psychrophilum at a small temporal and geographic scale. Four farms located on the same watershed in France were studied. Rainbow trout (Oncorhynchus mykiss) batches were monitored, and apparently healthy individuals were sampled over 1 year. A total of 288 isolates were recovered from fish organs (gills and spleen) and eggs. Pulsed field gel electrophoresis revealed high genetic diversity. Multilocus sequence typing performed on a selection of 31 isolates provided congruent results, as follows: 18 sequence types (STs) were found, of which 13 were novel. The mean gene diversity (H = 0.8413) was much higher than that previously reported for this host species, although the sampling was restricted to a single watershed and 1 year. Seven isolates out of 31 were assigned to clonal complex ST10 (CC-ST10), which is the predominant clonal complex in the main salmonid production areas. A split decomposition tree reflected a panmictic population. This finding is important for aquaculture veterinarians in their diagnostic procedure, as the choice of adequate antibiotic treatment is conditioned by the correct identification of the causative agent. Furthermore, this study expands our knowledge on genetic diversity required for the development of an effective vaccine against F. psychrophilum. IMPORTANCE The bacterium Flavobacterium psychrophilum is a serious pathogen in many fish species, especially salmonids, that is responsible for considerable economic losses worldwide. In order to treat infections and to develop vaccines, the genetic diversity of this bacterium needs to be known. We assessed the genetic diversity of F. psychrophilum isolates from apparently healthy rainbow trout raised in several fish farms in the same watershed in France. Two different genotyping methods revealed high diversity. The majority of isolates were unrelated to clonal complex sequence type 10 (CC-ST10), the clonal complex that is predominant worldwide and associated with disease in rainbow trout. In addition, we found 13 novel sequence types. These results suggest that a diverse subpopulation of F. psychrophilum may be harbored by rainbow trout.

scholarly journals Characterization and Genetic Diversity of Listeria monocytogenes Isolated from Cattle Abortions in Latvia, 2013–2018

2021 ◽  
Vol 8 (9) ◽  
pp. 195
Author(s):  
Žanete Šteingolde ◽  
Irēna Meistere ◽  
Jeļena Avsejenko ◽  
Juris Ķibilds ◽  
Ieva Bergšpica ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Listeria Monocytogenes ◽  
Virulence Factors ◽  
Causative Agent ◽  
Animal Species ◽  
Clonal Complex ◽  
The Third ◽  
Wide Range ◽  
Sequence Types

Listeria monocytogenes can cause disease in humans and in a wide range of animal species, especially in farm ruminants. The aim of the study was to determine the prevalence and genetic diversity of L. monocytogenes related to 1185 cattle abortion cases in Latvia during 2013–2018. The prevalence of L. monocytogenes among cattle abortions was 16.1% (191/1185). The seasonality of L. monocytogenes abortions was observed with significantly higher occurrence (p < 0.01) in spring (March–May). In 61.0% of the cases, the affected cattle were under four years of age. L. monocytogenes abortions were observed during the third (64.6%) and second (33.3%) trimesters of gestation. Overall, 27 different sequence types (ST) were detected, and four of them, ST29 (clonal complex, CC29), ST37 (CC37), ST451 (CC11) and ST7 (CC7), covered more than half of the L. monocytogenes isolates. Key virulence factors like the prfA-dependent virulence cluster and inlA, inlB were observed in all the analyzed isolates, but lntA, inlF, inlJ, vip were associated with individual sequence types. Our results confirmed that L. monocytogenes is the most important causative agent of cattle abortions in Latvia and more than 20 different STs were observed in L. monocytogenes abortions in cattle.

scholarly journals Genetic Diversity of Campylobacter jejuni Isolates from Farm Animals and the Farm Environment

2003 ◽  
Vol 69 (12) ◽  
pp. 7409-7413 ◽  
Author(s):  
F. M. Colles ◽  
K. Jones ◽  
R. M. Harding ◽  
M. C. J. Maiden
Keyword(s):  
Genetic Diversity ◽  
Campylobacter Jejuni ◽  
Human Disease ◽  
Clonal Complex ◽  
Food Samples ◽  
Complex Model ◽  
Farm Animals ◽  
Significant Genetic Differentiation ◽  
Sequence Types ◽  
Retail Food

ABSTRACT The genetic diversity of Campylobacter jejuni isolates from farm animals and their environment was investigated by multilocus sequence typing (MLST). A total of 30 genotypes, defined by allelic profiles (assigned to sequence types [STs]), were found in 112 C. jejuni isolates originating in poultry, cattle, sheep, starlings, and slurry. All but two of these genotypes belonged to one of nine C. jejuni clonal complexes previously identified in isolates from human disease and retail food samples and one clonal complex previously associated with an environmental source. There was some evidence for the association of certain clonal complexes with particular farm animals: isolates belonging to the ST-45 complex predominated among poultry isolates but were absent among sheep isolates, while isolates belonging to the ST-61 and ST-42 complexes were predominant among sheep isolates but were absent from the poultry isolates. In contrast, ST-21 complex isolates were distributed among the different isolation sources. Comparison with MLST data from 91 human disease isolates showed small but significant genetic differentiation between the farm and human isolates; however, representatives of six clonal complexes were found in both samples. These data demonstrate that MLST and the clonal complex model can be used to identify and compare the genotypes of C. jejuni isolates from farm animals and the environment with those from retail food and human disease.

scholarly journals Clonal analysis of the serogroup B meningococci causing New Zealand's epidemic

2005 ◽  
Vol 134 (2) ◽  
pp. 377-383 ◽  
Author(s):  
K. H. DYET ◽  
D. R. MARTIN
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
16S Rrna ◽  
Meningococcal Disease ◽  
Common Ancestor ◽  
Clonal Complex ◽  
Clonal Analysis ◽  
The Other ◽  
Disease Rates ◽  
Sequence Types

An epidemic of meningococcal disease caused by serogroup B meningococci expressing the P1.7-2,4 PorA protein began in New Zealand in 1991. The PorA type has remained stable. Different porB have been found in association with the P1.7-2,4 PorA, although type 4 has been most common. The clonal origins of B:P1.7-2,4 meningococci isolated from cases during 1990 to the end of 2003 were analysed. In 1990, the year immediately preceding the recognized increase in disease rates, all three subclones (ST-41, ST-42, and ST-154) of the ST-41/44 clonal complex occurred among the five isolates of B:P1.7-2,4. The two sequence types, ST-42 and ST-154, continued to cause most disease throughout New Zealand. Isolates belonging to subclone ST-41 were mostly identified early in the epidemic and in the South Island. 16S rRNA typing indicated that isolates belonging to the subclones ST-41 and ST-154 share a common ancestor, with those typing as ST-42 more distantly related with some genetically ambiguous. It is possible that ST-41 and ST-154 may have evolved one from the other but evolution to ST-42 is more difficult to explain. It is possible that one or more of the ST types could have been introduced into New Zealand prior to the first detection of clinical cases in 1990. Genetic diversity may have occurred during carriage in the community.

scholarly journals Random Amplification of Polymorphic DNA Analysis for Genetic Characterization of Two Breeds of Dogs, German Shepherd and Japanese Spitz

2013 ◽  
Vol 13 (2) ◽  
pp. 73-78
Author(s):  
Jarina Joshsi ◽  
Lumanti Manandhar ◽  
Patima Shrestha ◽  
Rani Gupta ◽  
Rojlina Manadhar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Neighbor Joining ◽  
German Shepherd ◽  
Polymorphic Loci ◽  
Random Amplification

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity in dog samples belonging to populations of German Shepherd and Japanese Spitz. A total of twelve samples were typed using eight RAPD primers. Out of eight primers, three primers gave result in six individuals of dogs. The phylogenetic tree constructed by the neighbor joining method based on Nei. Original measures revealed highest genetic identity found in German Shepherd as 0.9444 and highest genetic distance as 1.2809. The analysis predicts the number of polymorphic loci as 15 and the percentage of polymorphic loci as 83.3. Nepal Journal of Science and Technology Vol. 13, No. 2 (2012) 73-78 DOI: http://dx.doi.org/10.3126/njst.v13i2.7717

Genetic diversity of potato determined by random amplified polymorphic DNA analysis

1996 ◽  
Vol 15 (9) ◽  
pp. 662-667 ◽  
Author(s):  
L.M. Kawchuk ◽  
G.C. Kozub ◽  
J.D. Armstrong ◽  
D. R. Lynch ◽  
T. Demeke
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna

Genetic diversity in sunflower (Helianthus annuus L.) as revealed by random amplified polymorphic DNA analysis

1994 ◽  
Vol 45 (7) ◽  
pp. 1319 ◽  
Author(s):  
WR Lawson ◽  
RJ Henry ◽  
JK Kochman ◽  
GA Kong
Keyword(s):  
Genetic Diversity ◽  
Ribosomal Rna ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Efficient Tool ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Sunflower Genome ◽  
Pair Wise Comparison ◽  
Selection Of

A cross-section of sunflower genotypes grown in Australia including commercial cultivars (Suncross 40R, Hysun 33, Hysun 45CQ, Advance, DK3873), breeding lines (Sunfola, S37- 388, PhRR3, HA-R2, MC29, MC69, S37-388RR), wild sunflower varieties (H. annuus, H. argophyllus), a distantly related species (Tithonia diversifolia), and a hexaploid/diploid cross (H. tuberosus L.x H. annuus L.) were assessed for genetic diversity using RAPD (Random Amplified Polymorphic DNA) analysis. A considerable amount of polymorphism was revealed. Of the total of 158 markers amplified, 133 were polymorphic for at least one pair-wise comparison within the 16 genotypes. Overall, 33% dissimilarity was detected, with an average of 27% dissimilarity revealed among the hybrids and breeding lines, which exhibited 38% dissimilarity to the wild varieties H. annuus and H. tuberosus, and 51% dissimilarity to Tithonia and H. tuberosus x H, annuus. PCR of the 5S ribosomal RNA gene spacer region did not reveal any polymorphisms among the cultivated and breeding lines, but did distinguish between H. tuberosus and the other wild species. This survey of a selection of sunflower genotypes indicates that the genetic base of domesticated sunflower may be quite wide. These results suggest that RAPD methodology will provide an efficient tool for the analysis of the sunflower genome, in particular in breeding programs.

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