Multilocus Sequence Analysis for Leishmania braziliensis Outbreak Investigation
Publication Date
February 13, 2014
Journal
PLOS Neglected Tropical Diseases
Authors
Mariel A. Marlow, Mariana C. Boité, Gabriel Eduardo M. Ferreira, Mario Steindel, et al
Volume
8
Issue
2
Pages
e2695
DOI
https://dx.plos.org/10.1371/journal.pntd.0002695
Publisher URL
http://journals.plos.org/plosntds/article?id=10.1371%2Fjournal.pntd.0002695
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24551258
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923721
Europe PMC
http://europepmc.org/abstract/MED/24551258
Web of Science
000332017500026
Scopus
84895742674
Mendeley
http://www.mendeley.com/research/multilocus-sequence-analysis-leishmania-braziliensis-outbreak-investigation-2
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1386040"], "description"=>"<p>Blue nodes represent mucocutaneous cases and purple nodes represent disseminated cases. Non-highlighted or black nodes signify cutaneous cases.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "concatenated", "sequences", "fragments", "86", "strains"], "article_id"=>934720, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.g005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_network_based_on_concatenated_sequences_of_six_gene_fragments_for_86_strains_of_L_V_braziliensis_from_Brazil_with_clinical_form_of_the_case_designated_/934720", "title"=>"Median-joining network based on concatenated sequences of six gene fragments for 86 strains of <i>L.</i> (<i>V.</i>) <i>braziliensis</i> from Brazil, with clinical form of the case designated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386038"], "description"=>"<p>Colors represent genetic clusters (POP) as follows: green, POP1; yellow, POP2; blue, POP3. The size of the individual pie charts was weighted according to number of strains from the state included in the analysis. A chart representing three samples is provided as a reference. State names are the same as described in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002695#pntd.0002695.s001\" target=\"_blank\">Supporting Information S1</a>.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "clusters", "brazilian", "strains", "designated"], "article_id"=>934718, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.g003", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographical_distribution_of_genetic_clusters_of_Brazilian_L_V_braziliensis_strains_as_designated_by_STRUCTURE_by_state_K_3_n_86_/934718", "title"=>"Geographical distribution of genetic clusters of Brazilian <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains as designated by STRUCTURE by state (<i>K</i> = 3, n = 86).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386047", "https://ndownloader.figshare.com/files/1386048"], "description"=>"<div><p>With the emergence of leishmaniasis in new regions around the world, molecular epidemiological methods with adequate discriminatory power, reproducibility, high throughput and inter-laboratory comparability are needed for outbreak investigation of this complex parasitic disease. As multilocus sequence analysis (MLSA) has been projected as the future gold standard technique for <i>Leishmania</i> species characterization, we propose a MLSA panel of six housekeeping gene loci (6<i>pgd</i>, <i>mpi</i>, <i>icd</i>, <i>hsp</i>70, <i>mdh</i>mt, <i>mdh</i>nc) for investigating intraspecific genetic variation of <i>L.</i> (<i>Viannia</i>) <i>braziliensis</i> strains and compare the resulting genetic clusters with several epidemiological factors relevant to outbreak investigation. The recent outbreak of cutaneous leishmaniasis caused by <i>L.</i> (<i>V.</i>) <i>braziliensis</i> in the southern Brazilian state of Santa Catarina is used to demonstrate the applicability of this technique. Sequenced fragments from six genetic markers from 86 <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains from twelve Brazilian states, including 33 strains from Santa Catarina, were used to determine clonal complexes, genetic structure, and phylogenic networks. Associations between genetic clusters and networks with epidemiological characteristics of patients were investigated. MLSA revealed epidemiological patterns among <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains, even identifying strains from imported cases among the Santa Catarina strains that presented extensive homogeneity. Evidence presented here has demonstrated MLSA possesses adequate discriminatory power for outbreak investigation, as well as other potential uses in the molecular epidemiology of leishmaniasis.</p></div>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "multilocus", "outbreak"], "article_id"=>934727, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0002695.s001", "https://dx.doi.org/10.1371/journal.pntd.0002695.s002"], "stats"=>{"downloads"=>8, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Multilocus_Sequence_Analysis_for_Leishmania_braziliensis_Outbreak_Investigation/934727", "title"=>"Multilocus Sequence Analysis for <i>Leishmania braziliensis</i> Outbreak Investigation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386046"], "description"=>"<p>F<i><sub>ST</sub></i> values can be found in the upper right triangle and p values with Bonferroni correction are reported in the lower left triangle of the matrix.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "corresponding", "clusters", "86", "brazilian"], "article_id"=>934726, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.t003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Matrix_of_F_ST_values_and_corresponding_p_values_for_the_three_clusters_identified_in_STRUCTURE_of_86_Brazilian_L_V_braziliensis_strains_/934726", "title"=>"Matrix of F<i><sub>ST</sub></i> values and corresponding p values for the three clusters identified in STRUCTURE of 86 Brazilian <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386043"], "description"=>"<p>Comparison of the results of the BURST and STRUCTURE analyses of the 86 <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains from Brazil.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "86", "strains"], "article_id"=>934723, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.t005", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_results_of_the_BURST_and_STRUCTURE_analyses_of_the_86_L_V_braziliensis_strains_from_Brazil_/934723", "title"=>"Comparison of the results of the BURST and STRUCTURE analyses of the 86 <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains from Brazil.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386042"], "description"=>"<p>n – Sample size; P – Proportion of polymorphic loci; A – Mean number of alleles per locus; H<sub>e</sub> - Expected heterozygosity; H<sub>o</sub> – Observed heterozygosity; F<i><sub>IS</sub></i> – Inbreeding coefficient.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "clusters", "strains"], "article_id"=>934722, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.t004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterization_of_the_three_clusters_found_in_the_STRUCTURE_analysis_of_L_V_braziliensis_strains_from_Brazil_/934722", "title"=>"Characterization of the three clusters found in the STRUCTURE analysis of <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains from Brazil.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386037"], "description"=>"<p>POP1 – Cluster 1; POP2 – Cluster 2; POP3 – Cluster 3; State (number of strains).</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "estimating", "strains", "brazilian", "states"], "article_id"=>934717, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_STRUCTURE_output_estimating_genetic_structure_of_the_L_V_braziliensis_strains_from_twelve_Brazilian_states_n_86_K_3_/934717", "title"=>"STRUCTURE output estimating genetic structure of the <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains from twelve Brazilian states (n = 86, <i>K</i> = 3).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386036"], "description"=>"<p>Colors represent clonal complex (CC) as follows: yellow, CC1; green, CC2; orange, CC3; blue, unique sequence types. The size of the individual pie charts was weighted according to number of strains from the state included in the analysis. A chart representing three samples is provided as a reference. State names are the same as described in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002695#pntd.0002695.s001\" target=\"_blank\">Supporting Information S1</a>.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "clonal", "complexes", "brazilian", "strains"], "article_id"=>934716, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.g001", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographical_distribution_of_clonal_complexes_by_state_among_Brazilian_strains_of_L_V_braziliensis_n_86_/934716", "title"=>"Geographical distribution of clonal complexes by state among Brazilian strains of <i>L.</i> (<i>V.</i>) <i>braziliensis</i> (n = 86).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386045"], "description"=>"<p>Leishmaniasis clinical form of patient by genetic cluster as attributed by STRUCTURE analysis of 86 <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains from Brazil.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "attributed", "86", "strains"], "article_id"=>934725, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.t002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Leishmaniasis_clinical_form_of_patient_by_genetic_cluster_as_attributed_by_STRUCTURE_analysis_of_86_L_V_braziliensis_strains_from_Brazil_/934725", "title"=>"Leishmaniasis clinical form of patient by genetic cluster as attributed by STRUCTURE analysis of 86 <i>L.</i> (<i>V.</i>) <i>braziliensis</i> strains from Brazil.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386044"], "description"=>"<p>Amplicon size, analyzed sequence fragment length and primer sequence of the target regions for the six loci studied.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "primer", "regions", "loci"], "article_id"=>934724, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.t001", "stats"=>{"downloads"=>7, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amplicon_size_analyzed_sequence_fragment_length_and_primer_sequence_of_the_target_regions_for_the_six_loci_studied_/934724", "title"=>"Amplicon size, analyzed sequence fragment length and primer sequence of the target regions for the six loci studied.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386041"], "description"=>"<p>Green nodes represent autochthonous cases and red nodes represent imported cases.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "median-joining", "concatenated", "sequences", "fragments", "33", "strains", "santa"], "article_id"=>934721, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.g006", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reduced_median_joining_network_based_on_concatenated_sequences_of_six_gene_fragments_for_33_strains_of_L_V_braziliensis_from_Santa_Catarina_Brazil_with_year_city_of_residence_and_origin_of_case_designated_/934721", "title"=>"Reduced median-joining network based on concatenated sequences of six gene fragments for 33 strains of <i>L.</i> (<i>V.</i>) <i>braziliensis</i> from Santa Catarina, Brazil, with year, city of residence, and origin of case designated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-13 03:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1386039"], "description"=>"<p>Green nodes represent autochthonous cases and red nodes represent imported cases.</p>", "links"=>[], "tags"=>["genetics", "Molecular genetics", "population genetics", "microbiology", "Parasitology", "epidemiology", "Infectious disease epidemiology", "Molecular epidemiology", "concatenated", "sequences", "fragments", "86", "strains", "designated", "santa"], "article_id"=>934719, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Mariel A. Marlow", "Mariana C. Boité", "Gabriel Eduardo M. Ferreira", "Mário Steindel", "Elisa Cupolillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0002695.g004", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_network_based_on_concatenated_sequences_of_six_gene_fragments_for_86_strains_of_L_V_braziliensis_from_Brazil_with_case_origin_designated_for_strains_from_Santa_Catarina_/934719", "title"=>"Median-joining network based on concatenated sequences of six gene fragments for 86 strains of <i>L.</i> (<i>V.</i>) <i>braziliensis</i> from Brazil, with case origin designated for strains from Santa Catarina.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-13 03:12:42"}

PMC Usage Stats | Further Information

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Relative Metric

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