Biology subjects

Marie Touchon

Publications and source records attributed to Marie Touchon.

3 recordsLinked to original sources

bioRxiv2016

Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

Elizabethkingia anophelis is an emerging pathogen. Genomic analysis of strains from clinical, environmental or mosquito sources is needed to understand the epidemiological emergence of E. anophelis and to uncover genetic elements implicated in antimicrobial resistance, pathogenesis, or niche adaptation. Here, the genomic sequences of two nosocomial isolates that caused neonatal meningitis in Bangui, Central African Republic, were determined and compared with Elizabethkingia isolates from other world regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent distinct genomic species and led to re-identification of several strains. Phylogenetic analysis of E. anophelis strains revealed several sublineages and demonstrated a single evolutionary origin of African clinical isolates, which carry unique antimicrobial resistance genes acquired by horizontal transfer. The Elizabethkingia genus and the species E. anophelis had pan-genomes comprising respectively 7,801 and 6,880 gene families, underlining their genomic heterogeneity. African isolates were capsulated and carried a distinctive capsular polysaccharide synthesis cluster. A core-genome multilocus sequence typing scheme applicable to all Elizabethkingia isolates was developed, made publicly available (http://bigsdb.web.pasteur.fr/elizabethkingia), and shown to provide useful insights into E. anophelis epidemiology. Furthermore, a clustered regularly interspaced short palindromic repeats (CRISPR) locus was uncovered in E. meningoseptica, E. miricola and in a few E. anophelis strains. CRISPR spacer variation was observed between the African isolates, illustrating the value of CRISPR for strain subtyping. This work demonstrates the dynamic evolution of E. anophelis genomes and provides innovative tools for Elizabethkingia identification, population biology and epidemiology.\n\nIMPORTANCEElizabethkingia anophelis is a recently recognized bacterial species involved in human infections and outbreaks in distinct world regions. Using whole-genome sequencing, we showed that the species comprises several sublineages, which differ markedly in their genomic features associated with antibiotic resistance and host-pathogen interactions. Further, we have devised high-resolution strain subtyping strategies and provide an open genomic sequence analysis tool, facilitating the investigation of outbreaks and tracking of strains across time and space. We illustrate the power of these tools by showing that two African healthcare-associated meningitis cases observed 5 years apart were caused by the same strain, providing evidence that E. anophelis can persist in the hospital environment.

Microbiology↗

bioRxiv2015

Identification and analysis of integrons and cassette arrays in bacterial genomes

Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program - IntegronFinder - to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attl site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as -Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.

Bioinformatics↗

bioRxiv2015

Identification of protein secretion systems in bacterial genomes

Bacteria with two cell membranes (diderms) have evolved complex systems for protein secretion. These systems were extensively studied in some model bacteria, but the characterisation of their diversity has lagged behind due to lack of standard annotation tools. We built models for accurate identification of protein secretion systems and related appendages in bacteria with LPS-containing outer membranes. They can be used with MacSyFinder (standalone program) or online (http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::txsscan). They include protein profiles and information on the systems composition and genetic organisation. They can be used to search for T1SS-T6SS, T9SS, and accessorily for flagella, Type IV and Tad pili. We identified ~10,000 systems in bacterial genomes, where T1SS and T5SS were by far the most abundant and widespread. The recently described T6SSiii and T9SS were restricted to Bacteroidetes, and T6SSii to Francisella. T2SS, T3SS, and T4SS were frequently encoded in single-copy in one locus, whereas most T1SS were encoded in two loci. The secretion systems of diderm Firmicutes were similar to those found in other diderms. Novel systems may remain to be discovered, since some clades of environmental bacteria lacked all known protein secretion systems. Our models can be fully customized, which should facilitate the identification of novel systems.Introduction

Microbiology↗