scholarly journals Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence typing

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0243688
Author(s):  
Rebeca Huebner ◽  
Robert Mugabi ◽  
Gabriella Hetesy ◽  
Lawrence Fox ◽  
Sarne De Vliegher ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Bovine Mastitis ◽  
The United States ◽  
Genetic Lineage ◽  
Single Nucleotide Variants ◽  
Discrimination Power ◽  
Core Group ◽  
Mlst Scheme

Staphylococcus chromogenes is a common skin commensal in cattle and has been identified as a frequent cause of bovine mastitis and intramammary infections. We have developed a seven locus Multilocus Sequence Typing (MLST) scheme for typing S. chromogenes. Sequence-based typing systems, such as MLST, have application in studies of genetic diversity, population structure, and epidemiology, including studies of strain variation as a factor in pathogenicity or host adaptation. The S. chromogenes scheme was tested on 120 isolates collected from three geographic locations, Vermont and Washington State in the United States and Belgium. A total of 46 sequence types (STs) were identified with most of the STs being location specific. The utility of the typing scheme is indicated by a discrimination power of 95.6% for all isolates and greater than 90% for isolates from each of the three locations. Phylogenetic analysis placed 39 of the 46 STs into single core group consistent with a common genetic lineage; the STs in this group differ by less than 0.5% at the nucleotide sequence level. Most of the diversification in this lineage group can be attributed to mutation; recombination plays a limited role. This lineage group includes two clusters of single nucleotide variants in starburst configurations indicative of recent clonal expansion; nearly 50% of the isolates sampled in this study are in these two clusters. The remaining seven STs were set apart from the core group by having alleles with highly variable sequences at one or more loci. Recombination had a higher impact than mutation in the diversification of these outlier STs. Alleles with hypervariable sequences were detected at five of the seven loci used in the MLST scheme; the average sequence distances between the hypervariable alleles and the common core alleles ranged from 12 to 34 nucleotides. The extent of these sequence differences suggests the hypervariable alleles may be remnants of an ancestral genotype.

scholarly journals Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence typing

2020 ◽  
Author(s):  
Rebeca Huebner ◽  
Robert Mugabi ◽  
Gabriella Hetesy ◽  
Lawrence Fox ◽  
Sarne De Vliegher ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Bovine Mastitis ◽  
The United States ◽  
Genetic Lineage ◽  
Single Nucleotide Variants ◽  
Discrimination Power ◽  
Core Group ◽  
Intramammary Infections ◽  
Mlst Scheme ◽  
Nucleotide Sequence Level

AbstractStaphylococcus chromogenes is a common skin commensal in cattle and has been identified as a frequent cause of bovine mastitis and intramammary infections. To better understand the extent of strain diversity within this species and to facilitate study of strain variation as a factor in pathogenicity, we have developed a seven locus Multilocus Sequence Typing (MLST) scheme. The scheme was tested on 120 isolates collected from three geographic locations, Vermont and Washington State in the United States and Belgium. A total of 46 sequence types (STs) were identified with most of the STs being location specific. The utility of the typing scheme is indicated by a discrimination power of 95.6% for all isolates and greater than 90% for isolates from each of the three locations. Phylogenetic analysis placed 39 of the 46 STs into single core group consistent with a common genetic lineage; the STs in this group differ by less than 0.5% at the nucleotide sequence level. Most of the diversification in this lineage group can be attributed to mutation; recombination plays a limited role. This lineage group includes two clusters of single nucleotide variants in starburst configurations indicative of recent clonal expansion; nearly 50% of the isolates sampled in this study are in these two clusters. The remaining seven STs were set apart from the core group by having alleles with highly variable sequences at one or more loci. Recombination had a higher impact than mutation in the diversification of these outlier STs. Alleles with hypervariable sequences were detected at five of the seven loci used in the MLST scheme; the average sequence distances between the hypervariable alleles and the common core alleles ranged from 12 to 34 nucleotides. The extent of these sequence differences suggests the hypervariable alleles may be remnants of an ancestral genotype.

scholarly journals Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing

2008 ◽  
Vol 190 (8) ◽  
pp. 2831-2840 ◽  
Author(s):  
Narjol González-Escalona ◽  
Jaime Martinez-Urtaza ◽  
Jaime Romero ◽  
Romilio T. Espejo ◽  
Lee-Ann Jaykus ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Vibrio Parahaemolyticus ◽  
Molecular Phylogenetics ◽  
Clonal Complex ◽  
Housekeeping Genes ◽  
The United States ◽  
Health Concern ◽  
Mlst Scheme

ABSTRACT Vibrio parahaemolyticus is an important human pathogen whose transmission is associated with the consumption of contaminated seafood. There is a growing public health concern due to the emergence of a pandemic strain causing severe outbreaks worldwide. Many questions remain unanswered regarding the evolution and population structure of V. parahaemolyticus. In this work, we describe a multilocus sequence typing (MLST) scheme for V. parahaemolyticus based on the internal fragment sequences of seven housekeeping genes. This MLST scheme was applied to 100 V. parahaemolyticus strains isolated from geographically diverse clinical (n = 37) and environmental (n = 63) sources. The sequences obtained from this work were deposited and are available in a public database (http://pubmlst.org/vparahaemolyticus ). Sixty-two unique sequence types were identified, and most (50) were represented by a single isolate, suggesting a high level of genetic diversity. Three major clonal complexes were identified by eBURST analysis. Separate clonal complexes were observed for V. parahaemolyticus isolates originating from the Pacific and Gulf coasts of the United States, while a third clonal complex consisted of strains belonging to the pandemic clonal complex with worldwide distribution. The data reported in this study indicate that V. parahaemolyticus is genetically diverse with a semiclonal population structure and an epidemic structure similar to that of Vibrio cholerae. Genetic diversity in V. parahaemolyticus appears to be driven primarily by frequent recombination rather than mutation, with recombination ratios estimated at 2.5:1 and 8.8:1 by allele and site, respectively. Application of this MLST scheme to more V. parahaemolyticus strains and by different laboratories will facilitate production of a global picture of the epidemiology and evolution of this pathogen.

scholarly journals Evaluation of a Diverse, Worldwide Collection of Wild, Cultivated, and Landrace Pepper (Capsicum annuum) for Resistance to Phytophthora Fruit Rot, Genetic Diversity, and Population Structure

2015 ◽  
Vol 105 (1) ◽  
pp. 110-118 ◽  
Author(s):  
R. P. Naegele ◽  
A. J. Tomlinson ◽  
M. K. Hausbeck
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phytophthora Capsici ◽  
The United States ◽  
Fruit Rot ◽  
Sources Of Resistance ◽  
Plant Introductions ◽  
Genetic Clusters ◽  
Commercial Breeding ◽  
Moderately Resistant

Pepper is the third most important solanaceous crop in the United States and fourth most important worldwide. To identify sources of resistance for commercial breeding, 170 pepper genotypes from five continents and 45 countries were evaluated for Phytophthora fruit rot resistance using two isolates of Phytophthora capsici. Genetic diversity and population structure were assessed on a subset of 157 genotypes using 23 polymorphic simple sequence repeats. Partial resistance and isolate-specific interactions were identified in the population at both 3 and 5 days postinoculation (dpi). Plant introductions (PIs) 640833 and 566811 were the most resistant lines evaluated at 5 dpi to isolates 12889 and OP97, with mean lesion areas less than Criollo de Morelos. Genetic diversity was moderate (0.44) in the population. The program STRUCTURE inferred four genetic clusters with moderate to very great differentiation among clusters. Most lines evaluated were susceptible or moderately susceptible at 5 dpi, and no lines evaluated were completely resistant to Phytophthora fruit rot. Significant population structure was detected when pepper varieties were grouped by predefined categories of disease resistance, continent, and country of origin. Moderately resistant or resistant PIs to both isolates of P. capsici at 5 dpi were in genetic clusters one and two.

scholarly journals Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

2021 ◽  
Author(s):  
Kyle M Lewald ◽  
Antoine Abrieux ◽  
Derek A Wilson ◽  
Yoosook Lee ◽  
William R Conner ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Weather Conditions ◽  
The United States ◽  
Future Research ◽  
Drosophila Suzukii ◽  
Significant Damage ◽  
Wide Range ◽  
Multiple Invasions

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

scholarly journals Contrasting Patterns of Genetic Diversity and Population Structure of Armillaria mellea sensu stricto in the Eastern and Western United States

2010 ◽  
Vol 100 (7) ◽  
pp. 708-718 ◽  
Author(s):  
Kendra Baumgartner ◽  
Renaud Travadon ◽  
Johann Bruhn ◽  
Sarah E. Bergemann
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Los Angeles ◽  
The United States ◽  
Sensu Stricto ◽  
Western United States ◽  
Eastern United States ◽  
Armillaria Mellea ◽  
Genetic Pools

Armillaria mellea infects hundreds of plant species in natural and managed ecosystems throughout the Northern hemisphere. Previously reported nuclear genetic divergence between eastern and western U.S. isolates is consistent with the disjunct range of A. mellea in North America, which is restricted mainly to both coasts of the United States. We investigated patterns of population structure and genetic diversity of the eastern (northern and southern Appalachians, Ozarks, and western Great Lakes) and western (Berkeley, Los Angeles, St. Helena, and San Jose, CA) regions of the United States. In total, 156 diploid isolates were genotyped using 12 microsatellite loci. Absence of genetic differentiation within either eastern subpopulations (θST = –0.002, P = 0.5 ) or western subpopulations (θST = 0.004, P = 0.3 ) suggests that spore dispersal within each region is sufficient to prevent geographic differentiation. In contrast to the western United States, our finding of more than one genetic cluster of isolates within the eastern United States (K = 3), revealed by Bayesian assignment of multilocus genotypes in STRUCTURE and confirmed by genetic multivariate analyses, suggests that eastern subpopulations are derived from multiple founder sources. The existence of amplifiable and nonamplifiable loci and contrasting patterns of genetic diversity between the two regions demonstrate that there are two geographically isolated, divergent genetic pools of A. mellea in the United States.

scholarly journals Analyses of the genetic diversity and population structures ofHistoplasma capsulatumclinical isolates from Mexico, Guatemala, Colombia and Argentina, using a randomly amplified polymorphic DNA-PCR assay

2019 ◽  
Vol 147 ◽  
Author(s):  
J. H. Sahaza ◽  
E. Duarte-Escalante ◽  
C. Canteros ◽  
G. Rodríguez-Arellanes ◽  
M. R. Reyes-Montes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Geographic Origin ◽  
The United States ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Pcr Assay ◽  
Cophenetic Correlation ◽  
Group I ◽  
Rapd Pcr

AbstractWe studied the genetic diversity and the population structure of human isolates ofHistoplasma capsulatum, the causative agent of histoplasmosis, using a randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) assay to identify associations with the geographic distribution of isolates from Mexico, Guatemala, Colombia and Argentina. The RAPD-PCR pattern analyses revealed the genetic diversity by estimating the percentage of polymorphic loci, effective number of alleles, Shannon's index and heterozygosity. Population structure was identified by the index of association (IA) test. Thirty-seven isolates were studied and clustered into three groups by the unweighted pair-group method with arithmetic mean (UPGMA). Group I contained five subgroups based on geographic origin. The consistency of the UPGMA dendrogram was estimated by the cophenetic correlation coefficient (CCCr= 0.94,P= 0.001). Isolates from Mexico and Colombia presented higher genetic diversity than isolates from Argentina. Isolates from Guatemala grouped together with the reference strains from the United States of America and Panama. TheIAvalues suggest the presence of a clonal population structure in the ArgentinianH. capsulatumisolates and also validate the presence of recombining populations in the Colombian and Mexican isolates. These data contribute to the knowledge on the molecular epidemiology of histoplasmosis in Latin America.

scholarly journals Genetic Diversity and Population Structure of Races of Fusarium oxysporum Causing Cotton Wilt

2020 ◽  
Vol 10 (9) ◽  
pp. 3261-3269
Author(s):  
Hannah C Halpern ◽  
Peng Qi ◽  
Robert C Kemerait ◽  
Marin T Brewer
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Fusarium Oxysporum ◽  
Principal Components ◽  
Phylogenetic Trees ◽  
Elongation Factor ◽  
Intergenic Spacer ◽  
Pathogenic Fungi ◽  
The United States ◽  
Intergenic Spacer Region

Abstract To better understand the evolution of virulence we are interested in identifying the genetic basis of this trait in pathogenic fungi and in developing tools for the rapid characterization of variation in virulence among populations associated with epidemics. Fusarium oxysporum f. sp. vasinfectum (FOV) is a haploid fungus that causes devastating outbreaks of Fusarium wilt of cotton wherever it is grown. In the United States, six nominal races and eleven genotypes of FOV have been characterized based on the translation elongation factor (EF-1α) gene and intergenic spacer region (IGS), but it is unclear how race or genotype based on these regions relates to population structure or virulence. We used genotyping-by-sequencing to identify SNPs and determine genetic diversity and population structure among 86 diverse FOV isolates. Six individuals of Fusarium oxysporum closely related to FOV were genotyped and included in some analyses. Between 193 and 354 SNPs were identified and included in the analyses depending on the pipeline and filtering criteria used. Phylogenetic trees, minimum spanning networks (MSNs), principal components analysis (PCA), and discriminant analysis of principal components (DAPC) demonstrated that races and genotypes of FOV are generally not structured by EF-1α genotype, nor are they monophyletic groups with the exception of race 4 isolates, which are distinct. Furthermore, DAPC identified between 11 and 14 genetically distinct clusters of FOV, whereas only eight EF-1α genotypes were represented among isolates; suggesting that FOV, especially isolates within the widely distributed and common race 1 genotype, is more genetically diverse than currently recognized.

scholarly journals Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes

2004 ◽  
Vol 70 (12) ◽  
pp. 7210-7219 ◽  
Author(s):  
Blanca de las Rivas ◽  
Ángela Marcobal ◽  
Rosario Muñoz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Rflp Analysis ◽  
The United States ◽  
Oenococcus Oeni ◽  
23S Rrna ◽  
Rrna Gene ◽  
Single Strain

ABSTRACT Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria.

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