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Volume 26, Number 3—March 2020
Research

Stable and Local Reservoirs of Mycobacterium ulcerans Inferred from the Nonrandom Distribution of Bacterial Genotypes, Benin

Clément Coudereau, Alban Besnard, Marie Robbe-Saule, Céline Bris, Marie Kempf, Roch Christian Johnson, Télésphore Yao Brou, Ronald Gnimavo, Sara Eyangoh, Fida Khater, and Estelle MarionComments to Author 
Author affiliations: Université d’Angers, Angers, France (C. Coudereau, A. Besnard, M. Robbe-Saule, M. Kempf, F. Khater, E. Marion); INSERM, Angers (C. Coudereau, A. Besnard, M. Robbe-Saule, M. Kempf, F. Khater, E. Marion); Centre Hospitalo-Universitaire d’Angers, Angers (C. Bris, M. Kempf); Université d'Abomey Calavi, Abomey Calavi, Benin (R.C. Johnson); Fondation Raoul Follereau, Paris, France (R.C. Johnson); Maison de la Télédétection, Montpellier, France (T.Y. Brou); Centre de Diagnostic et Traitement de la Lèpre et de l’Ulcère de Buruli, Pobè, Bénin (R. Gnimavo); International Pasteur Institute Network, Yaoundé, Cameroon (S. Eyangoh)

Main Article

Figure 2

Graphical representations of the 8 Mycobacterium ulcerans genomes and their 940 single-nucleotide polymorphisms from Buruli ulcer patients in Benin and Nigeria. A) Principal component analysis (PCA) projection on the first 3 principal components with 8 groups of genomes clustering together, which we defined as genotypes. PCA was performed based on the Eigenstrat algorithm but applied to a haploid organism. Image on the left displays a PCA performed on all 174 genomes; image on the right displays

Figure 2. Graphical representations of the 8 Mycobacterium ulcerans genomes and their 940 single-nucleotide polymorphisms from Buruli ulcer patients in Benin and Nigeria. A) Principal component analysis (PCA) projection on the first 3 principal components with 8 groups of genomes clustering together, which we defined as genotypes. PCA was performed based on the Eigenstrat algorithm but applied to a haploid organism. Image on the left displays a PCA performed on all 174 genomes; image on the right displays a PCA performed after removing genomes from the first 3 genotypes (shown for better visualization of genome clustering). Axes x, y, and z represent the principal components 1, 2, and 3, respectively; inertia was 7% for component 1, 5% for component 2, and 4% for component 3. B) Graphical representation of the 940 single-nucleotide polymorphisms specific to the 8 genotypes, showing interdifferences and intradifferences of all genomes. Each line represents 1 genomic position, and each column represents 1 M. ulcerans genome. A color code has been chosen for each nucleotide (blue, adenine; green, guanine; red, cytosine; yellow, thymine). Each representation has been ordered and referenced against the genome 1232–13 belonging to genotype 1 (first column).

Main Article

Page created: February 20, 2020
Page updated: February 20, 2020
Page reviewed: February 20, 2020
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