Claire Bertelli

EDGAR 2.0: an enhanced software platform for comparative gene content analyses

The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio.

Lausannevirus, a giant amoebal virus encoding histone doublets

Large viruses infecting algae or amoebae belong to the NucleoCytoplasmic Large DNA Viruses (NCLDV) and present genotypic and phenotypic characteristics that have raised major interest among microbiologists. Here, we describe a new large virus discovered in Acanthamoeba castellanii co-culture of an environmental sample. The virus, referred to as Lausannevirus, has a very limited host range, infecting Acanthamoeba spp. but being unable to infect other amoebae and mammalian cell lines tested. Within A. castellanii, this icosahedral virus of about 200 nm exhibits a development cycle similar to Mimivirus, with an eclipse phase 2 h post infection and a logarithmic growth leading to amoebal lysis in less than 24 h. The 346 kb Lausannevirus genome presents similarities with the recently described Marseillevirus, sharing 89% of genes, and thus belongs to the same family as confirmed by core gene phylogeny. Interestingly, Lausannevirus and Marseillevirus genomes both encode three proteins with predicted histone folds, including two histone doublets, that present similarities to eukaryotic and archaeal histones. The discovery of Lausannevirus and the analysis of its genome provide some insight in the evolution of these large amoebae-infecting viruses.

The Waddlia genome: a window into chlamydial biology

Growing evidence suggests that a novel member of the Chlamydiales order, Waddlia chondrophila, is a potential agent of miscarriage in humans and abortion in ruminants. Due to the lack of genetic tools to manipulate chlamydia, genomic analysis is proving to be the most incisive tool in stimulating investigations into the biology of these obligate intracellular bacteria. 454/Roche and Solexa/Illumina technologies were thus used to sequence and assemble de novo the full genome of the first representative of the Waddliaceae family, W. chondrophila. The bacteria possesses a 2′116′312bp chromosome and a 15′593 bp low-copy number plasmid that might integrate into the bacterial chromosome. The Waddlia genome displays numerous repeated sequences indicating different genome dynamics from classical chlamydia which almost completely lack repetitive elements. Moreover, W. chondrophila exhibits many virulence factors also present in classical chlamydia, including a functional type III secretion system, but also a large complement of specific factors for resistance to host or environmental stresses. Large families of outer membrane proteins were identified indicating that these highly immunogenic proteins are not Chlamydiaceae specific and might have been present in their last common ancestor. Enhanced metabolic capability for the synthesis of nucleotides, amino acids, lipids and other co-factors suggests that the common ancestor of the modern Chlamydiales may have been less dependent on their eukaryotic host. The fine-detailed analysis of biosynthetic pathways brings us closer to possibly developing a synthetic medium to grow W. chondrophila, a critical step in the development of genetic tools. As a whole, the availability of the W. chondrophila genome opens new possibilities in Chlamydiales research, providing new insights into the evolution of members of the order Chlamydiales and the biology of the Waddliaceae.

High Throughput Sequencing and Proteomics to Identify Immunogenic Proteins of a New Pathogen: The Dirty Genome Approach

Background With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. Methods/Principal Findings We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. Conclusions/Significance This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

Bifidobacterium longum Bacteremia in Preterm Infants Receiving Probiotics

Administration of probiotics to premature newborns has been shown to prevent necrotizing enterocolitis and reduce all-cause mortality. In our hospital, we documented 2 cases of Bifidobacterium longum subspecies infantis bacteremia in newborns receiving probiotics. By comparative genomics, we confirmed that the strains isolated from each patient originated from the probiotics.

Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms

Based on Darwins concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their hosts factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).

Low prevalence of Chlamydia trachomatis infection in asymptomatic young Swiss men

BackgroundPrevalence and risk factors for Chlamydia trachomatis infection among young men in Switzerland is still unknown. The objective of the present study was to assess prevalence and risk factors for C. trachomatis infection in young Swiss men.Methods517 young Swiss men were enrolled in this cross-sectional study during their compulsory military recruitment. Participants completed a questionnaire and gave urine samples which were screened for C. trachomatis DNA by PCR. Genotyping of positive samples was done by amplification and sequencing the ompA gene.ResultsThe prevalence of chlamydial infection among young Swiss male was 1.2% (95% confidence interval [95%CI], 0.4–2.5%). C. trachomatis infection was only identified among the 306 men having multiple sexual partner. Although frequent, neither unprotected sex (absence of condom use), nor alcohol and drug abuse were associated with chlamydial infection. Men living in cities were more frequently infected (2.9%, 95%CI 0.8–7.4%) than men living in rural areas (0.5%, 95%CI 0.1–1.9%, p = 0.046). Moreover, naturalised Swiss citizens were more often positive (4.9%, 95%CI 1.3–12.5%) than native-born Swiss men (0.5%, 95%CI 0.1–1.7%, p = 0.003).ConclusionIn comparison with other countries, the prevalence of chlamydial infection in men is extremely low in Switzerland, despite a significant prevalence of risky sexual behaviour. C. trachomatis infection was especially prevalent in men with multiple sexual partners. Further research is required (i) to define which subgroup of the general population should be routinely screened, and (ii) to test whether such a targeted screening strategy will be effective to reduce the prevalence of chlamydial infection among this population.

Taxogenomics of the order Chlamydiales

Bacterial classification is a long-standing problem for taxonomists and species definition itself is constantly debated among specialists. The classification of strict intracellular bacteria such as members of the order Chlamydiales mainly relies on DNA- or protein-based phylogenetic reconstructions because these organisms exhibit few phenotypic differences and are difficult to culture. The availability of full genome sequences allows the comparison of the performance of conserved protein sequences to reconstruct Chlamydiales phylogeny. This approach permits the identification of markers that maximize the phylogenetic signal and the robustness of the inferred tree. In this study, a set of 424 core proteins was identified and concatenated to reconstruct a reference species tree. Although individual protein trees present variable topologies, we detected only few cases of incongruence with the reference species tree, which were due to horizontal gene transfers. Detailed analysis of the phylogenetic information of individual protein sequences (i) showed that phylogenies based on single randomly chosen core proteins are not reliable and (ii) led to the identification of twenty taxonomically highly reliable proteins, allowing the reconstruction of a robust tree close to the reference species tree. We recommend using these protein sequences to precisely classify newly discovered isolates at the family, genus and species levels.

Insight into cross-talk between intra-amoebal pathogens.

BackgroundAmoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to different bacterial phyla and often show a larger genome size than human-infecting pathogens. This characteristic is proposed to be the result of frequent gene exchanges with other bacteria that share a sympatric lifestyle and contrasts with the genome reduction observed among strict human pathogens.ResultsWe sequenced the genome of a new amoebal pathogen, Legionella drancourtii, and compared its gene content to that of a Chlamydia- related bacterium, Parachlamydia acanthamoebae. Phylogenetic reconstructions identified seven potential horizontal gene transfers (HGTs) between the two amoeba-resistant bacteria, including a complete operon of four genes that encodes an ABC-type transporter. These comparisons pinpointed potential cases of gene exchange between P. acanthamoebae and Legionella pneumophila, as well as gene exchanges between other members of the Legionellales and Chlamydiales orders. Moreover, nine cases represent possible HGTs between representatives from the Legionellales or Chlamydiales and members of the Rickettsiales order.ConclusionsThis study identifies numerous gene exchanges between intracellular Legionellales and Chlamydiales bacteria, which could preferentially occur within common inclusions in their amoebal hosts. Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle.

Lausannevirus Seroprevalence among Asymptomatic Young Adults

Objectives: The giant Lausannevirus was recently identified as a parasite of amoeba that replicates rapidly in these professional phagocytes. This study aimed at assessing Lausannevirus seroprevalence among asymptomatic young men in Switzerland and hopefully identifying possible sources of contact with this giant virus. Methods: The presence of anti-Lausannevirus antibodies was assessed in sera from 517 asymptomatic volunteers who filled a detailed questionnaire. The coreactivity between Lausannevirus and amoeba-resisting bacteria was assessed. Results: Lausannevirus prevalence ranged from 1.74 to 2.51%. Sporadic condom use or multiple sexual partners, although frequent (53.97 and 60.35%, respectively), were not associated with anti-Lausannevirus antibodies. On the contrary, frequent outdoor sport practice as well as milk consumption were significantly associated with positive Lausannevirus serologies (p = 0.0066 and 0.028, respectively). Coreactivity analyses revealed an association between Criblamydia sequanensis (an amoeba-resisting bacterium present in water environments) and Lausannevirus seropositivity (p = 0.001). Conclusions: Lausannevirus seroprevalence is low in asymptomatic Swiss men. However, the association between virus seropositivity and frequent sport practice suggests that this member of the Megavirales may be transmitted by aerosols and/or exposure to specific outdoor environments. Milk intake was also associated with seropositivity. Whether the coreactivity observed for C. sequanensis and Lausannevirus reflects a common mode of acquisition or some unexpected cross-reactivity remains to be determined.