The bacterial pangenome as a new tool for analysing pathogenic bacteria.

The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position.

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

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.

Q fever and pregnancy: disease, prevention, and strain specificity.

The link between fetal morbidity and Q fever and the necessity of long-term antibiotics for Coxiella burnetii infection during pregnancy have been recently questioned in the Netherlands, where the clone responsible for the Q fever outbreak harbors the QpH1 plasmid. In this context, we assessed pregnancy outcomes according to antibiotic administration in a new series and compared the plasmid type between isolates associated with abortion and other clinical isolates to determine if there is a link between genotype and abortion in humans. All French patients who received a diagnosis of Q fever during pregnancy at the French National Referral Centre for Q Fever from 2006 through July 2011 were included. On the other hand, the plasmid types of 160 clinical isolates, including seven isolates from patients who experienced an abortion, were compared. The differences between the QpDV and QpH1 plasmid sequences were analyzed. Acute Q fever was a cause of fetal morbidity, and the absence of long-term cotrimoxazole therapy was associated with fetal death (p < 0.0001). Genotypic analysis showed that the QpDV plasmid was more frequent in isolates associated with abortion (p = 0.03). A comparison of the plasmid sequences revealed that four QpDV proteins had no direct counterparts in QpH1, with two whose functions were not present in QpH1. The different obstetrical morbidity of C. burnetii relative to different geographical areas could be related to strain specificity, possibly based on differences in plasmid sequences, or to a failure of public health authorities to detect early miscarriages.