A systematic approach to classify and characterize genomic islands driven by conjugative mobility using protein signatures

GI classification based on mobility protein signatures

Genomic islands in bacteria aid in the spread of resistance, virulence, and antiviral mechanisms, but their small size and genetic diversity make classification challenging. Predicting the mobility of GIs is crucial, especially in the present crisis of multidrug resistance. In a new article published in Nucleic Acids Research, we propose a method for the comprehensive classification of GIs based on their mobility profile. We can then analyze their gene cargo using this approach. We based our classification decision scheme on a collection of mobility protein motif definitions available in publicly accessible databases. This research serves as a starting point for improving our understanding of mobile genetic elements in bacterial genomes and how they move.

MSc and Ph.D. positions available

We are seeking MSc and Ph.D. candidates to study the barriers that limit the conjugative transfer of multidrug-resistance conjugating plasmids of the IncC group. Details on the projects and how to apply are provided in the announcement links below:

Announcements in French and English

Renewed CIHR funding

I am thrilled to announce that our CIHR funding has just been renewed! More exciting science to explore, and groundbreaking discoveries to make in the fascinating world of bacterial mobile genetic elements and conjugation.

MSc, Ph.D., and postdoctoral opportunities are to be announced soon!

Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids

Hypothetical evolutionary pathway of SGI1 and related genomic islands targeting dusA and yicC

Freshly out of the oven, we published a new article in PLoS Genetics today. We identified integrative elements distantly related to Salmonella Genomic Island 1 (SGI1), a key vector of antibiotic resistance genes in Gammaproteobacteria. SGI1 and its variants usually reside at the 3’ end of trmE, share a large, highly conserved core of genes, and carry a complex integron that confers multidrug resistance phenotypes to their hosts. Unlike members of the SGI1 group, the novel genomic islands that we identified target the 5’ end dusA or the 3’ end of yicC, lack multidrug resistance genes, and seem much more diverse. We showed that, like SGI1, these elements are mobilized by conjugative plasmids of the IncC group. Based on comparative genomics and functional analyses, we propose a hypothetical model of the evolution of SGI1 and its siblings from the progenitor of IncA and IncC conjugative plasmids via an intermediate dusA-specific integrative element through gene losses and gain of alternative integration/excision modules. Congratulations to Romain and Florence!

Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids

The multiple variants of Salmonella Genomic Island 1 (SGI1) and IncC conjugative plasmids are two functionally interacting families of mobile genetic elements commonly associated with multidrug resistance in the Gammaproteobacteria. SGI1 and its siblings are specifically mobilised in trans by IncC conjugative plasmids. Conjugative transfer of IncC plasmids is activated by the plasmid-encoded master activator AcaCD. SGI1 carries five AcaCD-responsive promoters that drive the expression of genes involved in its excision, replication, and mobilisation. SGI1 encodes an AcaCD homologue, the transcriptional activator complex SgaCD (also known as FlhDC_SGI1) that seems to recognise and activate the same SGI1 promoters. In a new article published today in the NAR Breakthrough section of Nucleic Acids Research, we demonstrated the importance of SgaCD in SGI1′s lifecycle. Mating assays revealed the requirement for SgaCD and its IncC-encoded counterpart AcaCD in the mobilisation of SGI1. An integrative approach combining ChIP-exo, Cappable-seq, and RNA-seq confirmed that SgaCD activates each of the 18 AcaCD-responsive promoters driving the expression of the plasmid transfer functions. A comprehensive analysis of the activity of the complete set of AcaCD-responsive promoters of SGI1 and the helper IncC plasmid was performed through reporter assays. qPCR and flow cytometry assays revealed that SgaCD is essential to elicit the excision and replication of SGI1 and destabilise the helper IncC plasmid. The system biology approach used in this article provides a better and deeper understanding of the complex interactions that drive the formidable spread of SGI1-like elements.

Antibiotic resistance in cholera: Mechanistic insights from IncC plasmid-mediated dissemination of a novel family of genomic islands

The increasing association of the etiological agent of cholera, Vibrio cholerae serogroup O1 and O139, with multiple antibiotic resistance threatens to deprive health practitioners of this effective tool. Drug resistance in cholera results mainly from acquisition of mobile genetic elements. Genomic islands conferring multidrug resistance and mobilizable by IncC conjugative plasmids were reported to circulate in non-O1/non-O139 V. cholerae clinical strains isolated from the 2010 Haitian cholera outbreak. As these genomic islands can be transmitted to pandemic V. cholerae serogroups, their mechanism of transmission needed to be investigated. Today, we published a new article in mSphere in which we reveal plasmid- and genomic island-encoded factors required for the resistance island’s excision, mobilization and integration, as well as regulation of these functions. We also present the discovery of related genomic islands carrying diverse phage resistance genes but lacking antibiotic resistance-conferring genes in a wide range of marine dwelling bacteria. This discovery suggest these elements are ancient and recently acquired drug resistance genes.

Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss

The Salmonella genomic island 1 (SGI1) and its variants propagate multidrug resistance in several species of human and animal pathogens with the help of IncA and IncC conjugative plasmids that are absolutely required for SGI1 dissemination. These helper plasmids are known to trigger the excision of SGI1 from the chromosome. In a new paper published today in PLOS Genetics, we showed that IncC plasmids also trigger the replication of the excised, circular form of SGI1 by enabling the expression of an SGI1-borne replication initiator gene. In return, high-copy replication of SGI1 interferes with the persistence of the IncC plasmid and prevents its cotransfer into a recipient cell, thereby allowing integration and stabilization of SGI1 into the chromosome of the new host. Transient SGI1 replication seems to be a key feature of the life cycle of this family of genomic islands. Sequence database analysis revealed that SGI1 variants encode either a replication initiator protein with a RepA_C domain, or an alternative replication protein with N-terminal replicase and primase C terminal 1 domains. This finding is important to better understand the complex interactions between SGI1-like elements and their helper plasmids that lead to widespread and highly efficient propagation of multidrug resistance genes to a broad range of human and animal pathogens.

IncC conjugative plasmids and SXT/R391 elements repair double-strand breaks caused by CRISPR–Cas during conjugation

Bacteria have evolved multiple defence mechanisms against bacteriophages. For instance, restriction-modification systems provide innate immunity by degrading invading DNAs that lack proper methylation. CRISPR–Cas systems provide adaptive immunity by sampling the genome of past invaders and cutting the DNA of closely related DNA molecules. These barriers also restrict horizontal gene transfer mediated by conjugative plasmids. We recently found that several families of conjugative plasmids are able to fight back. In a paper featured as a NAR Breakthrough article, we show that IncC conjugative plasmids are highly resilient to host defence systems during entry into a new host by conjugation. Using a TnSeq strategy, we uncovered a conserved operon of five genes that confer a novel host defence evasion (hde) phenotype. hde promotes both resistance against type I restriction-modification and CRISPR–Cas evasion by repairing double-strand DNA breaks via recombination between short sequence repeats. All or parts of hde are also found in lambdoid bacteriophages including Lambda, in IncA and untyped conjugative plasmids, and in the integrative and conjugative element R391, which is also resilient against CRISPR–Cas. Hence, the conserved hde operon considerably broadens the host range of large families of mobile elements that spread multidrug resistance. Congratulations to David, Kevin and Frédéric for this interesting contribution to our understanding of plasmid biology.

We are recruiting : MSc and PhD positions available.

We are currently looking for MSc or PhD candidates to work on various aspects of the interactions between IncC conjugative plasmids and the resistance island SGI1.

Due to Covid-19 restrictions, start date is expected to be January 2021. Applicants must have a strong background in microbiology, genetics and molecular biology, have had a past experience in a research laboratory and be perfectly fluent in written and spoken English and/or French. Only serious applications from excellent candidates with the specified background will be considered for these positions.

Before applying, applicants are strongly advised to refer to the Université de Sherbrooke website (here) regarding the specific costs related to tuition fees for international students in Québec.

Applicants must apply by e-mail and provide a complete CV, their complete transcripts and a copy of their last diploma, a letter of motivation, and three letters of recommendation from three different academic references. Documents must be provided in PDF format only. Incomplete application will not be considered.

Terry Beveridge Poster Award at CSM 2019

Nicolas Rivard received the Terry Beveridge Poster Award for his poster entitled “Antimicrobial resistance dissemination in Vibrio cholerae: mechanistic insights into the insidious role of IncC plasmids” that he presented in the Molecular Genetic & Cellular Microbiology section at CSM 2019.

Congratulations Nicolas!