Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium

Abstract

Bacillus anthracis is the causative agent of anthrax and is classified as a ‘Category A’ biological weapon. Six complete genomes of B. anthracis (A0248, Ames, Ames Ancestor, CDC684, H0491, and Sterne) are currently available. In this report, we add three African strain genomes: Sen2Col2, Sen3 and Gmb1. To study the pan-genome of B. anthracis, we used bioinformatics tools, such as Cluster of Orthologous Groups, and performed phylogenetic analysis. We found that the three African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the plcR gene and the four known prophages. These strains are most similar to the CDC684 strain and belong to the A cluster. We estimated that the B. anthracis pan-genome has 2893 core genes (99% of the genome size) and 85 accessory genes. We validated the hypothesis that B. anthracis has a closed pan-genome and found that the three African strains carry the two plasmids associated with bacterial virulence. The pan-genome nature of B. anthracis confirms its lack of exchange (similar to Clostridium tetani) and supports its exclusively pathogenic role, despite its survival in the environment. Moreover, thanks to the study of the core content single nucleotide polymorphisms, we can see that our three African strains diverged very recently from the other B. anthracis strains.

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

“…[19,21,23,59]. Thus, the closely related P. parmentieri species adhered to the categories of non-specialized species or opportunistic pathogens that often exhibit open pangenomes [86,92] along with for instance Escherichia coli [93], Streptococcus agalactiae [94], Listeria monocytogenes [95], Legionella pneumophila [96] or Salmonella typhi [97]. Fig.…”

“…Such a feature is regarded as characteristic for taxa, whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination [85]. Therefore, D. solani joined the group of real specialized pathogens with closed pangenomes [86] including e.g.…”

Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia

“…This is in agreement with the report by Kenefic et al demonstrating an introduction of WNA in the USA from Canada, and a progressive evolution from north to south. The West Africa clade from Guinea and Côte d’Ivoire [41] is branching out from lineage L2 at the same position as the WNA and Senegal-Gambia [42] clade. Apart from two Argentinian strains belonging to the L3_Pasteur II vaccine sublineage and one strain from the USA defining a recent split with a long branch within lineage L4, all the other A.Br.011/009 strains are from Italy and France.…”

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

“…Such a feature is regarded as characteristic of the taxa, whose representatives either occupy isolated ecological niches or lack e cient mechanisms for gene exchange and recombination [85]. Therefore, D. solani joined the group of real specialized pathogens with closed pangenomes [86] including e.g. Bacillus anthracis [62], Mycobacterium tuberculosis [87], Clostridium di cile [88], Yersinia pestis [89] or Staphylococcus aureus [90].…”

“…The authors associated the overrepresentation of the dispensable pangenome part with high genomic plasticity of P. parmentieri [91], suggesting a less clonal population structure with respect to that of D. solani [19,21,23,59]. Thus, the closely related P. parmentieri species adhered to the categories of non-specialized species or opportunistic pathogens that often exhibit open pangenomes [86,92] along with, for instance, Escherichia coli [93], Streptococcus agalactiae [94], Listeria monocytogenes [95], Legionella pneumophila [96] or Salmonella typhi [97]. One should bear in mind that the closed/open pangenome status of a species might have been affected by the number and representativeness of the genomes selected for the analysis [92].…”