Search

International audience

Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.

International audience

International audience

International audience

Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)—leading to the cis-mobilization of an IME carrying tet(O)—was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.

International audience

Figure S3. Calibration curve of the gel filtration column. A Sephadex S200 HiLoad 16/60 column (GE Healthcare) was used as a final step of purification of RelSt3 protein. This column was calibrated and allowed us to estimate the apparent molecular weight of RelSt3. See complete legend in Additional file 4. (PPTX 40 kb)

Supplementary material text. This text includes supplementary Materials and Methods, complete Additional file legends, and tables for bacterial strains, plasmids and oligonucleotides used in this study. (DOC 201 kb)

International audience; Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on integrative and mobilizable elements (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.

International audience

International audience

Présentation Poster; International audience; Streptococcus thermophilus is dairy bacterium specie, phylogenetically close to pathogenic streptococci. Previous studies of genomic sequences from S. thermophilus strains showed extreme adaptation to milk environment. This organism seems to have evolved through loss-of-function: pseudogenes occupy 10% of its genome and a proportion of its sequences were acquired from other lactic acid bacteria. In particular, the genome of S. thermophilus has lost its pathogenicity but carries genes for methionine biosynthesis, a rare amino acid in milk. This metabolic pathway likely originatedfrom Lactococcus bulgaricus. S. thermophilus is not supposedly able to incorporate foreign DNA into its genome. However, this food-processing bacterium seems to possess functional late competence genes, as pathogenic, competent streptococci do. A recent work shows that S. thermophilus is a major host for antibiotic resistance genes among cheese microbia. In order to evaluate the potential for antibiotic resistance gene transfer from S. thermophilus to commensal streptococci, it appears important to study how this bacterium acquired such genes. We investigated the presence andfunctionality of competence genes in S. thermophilus genome. Competent streptococci homology sequence studies allowed us to identify a series of genes homologous to late competence genes from S. pneumoniae, including all essential ones. These genes are responsible for intake DNA system and genome integration. Their expressions are induced by the alternative sigma factor ComX. This protein binds to a specific sequence, the com-box, in promoter regions of late competence genes. The com-box sequence from S. pneumoniae was degenerated in order to establish a S. thermophilus com-box consensus sequence. It was then used to scan the whole genome. It was found not only upstream known late competence genes, but also up-stream novel ones, that could specifically belong to S. thermophilus ComX regulon. We are proposing to control ComX expression in S. thermophilus and determine which part of its genome belongs to the ComX regulon. In this organism, cloning tools are lacking in the perspective of genetic studies. We elaborated efficient expression systems for S. thermophilus protein studies. One was induced by an unmetabolized carbon source and the other is an adaptation of the Lactococcus lactis Pzn system to S. thermophilus. As this organism had a constitutive lactose operon expression, a LMG18311 strain lacking endogenous lacZ was generated, allowing the use of B-galactosidase assays to address the functionality of our expression systems.On the basis these tools, we will drive expression of the comX gene and analyze by quantitative PCR its ability to induce transcription of late competence genes. Their functionality will be addressed by visualization of foreign DNA intake and by measurement of selection marker integration in S. thermophilus.

International audience