Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by comparative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates. \ua9 2014 Macmillan Publishers Limited. All rights reserved

Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by com- parative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates

Host specificity in the diversity and transfer of lsa resistance genes in group B Streptococcus

International audienceIn group B Streptococcus (GBS), cross-resistance to lincosamides, streptogramin A and pleuromutilins (LSAP) is mediated by the acquisition of lsa genes. Here, we characterized the diversity, mobility and ecology of lsa genes in this species

New insights concerning the distribution of Salmonella virulence factor Rck

International audienceSalmonella are facultative intracellular bacteria able to infect a broad range of hosts using several virulence factors, including the Rck outer membrane protein. This protein is responsible for (i) resistance to complement, in particular through membrane attack complex formation inhibition, (ii) bacterial adhesion, through laminin binding, and (iii) host-cell invasion, through a Zipper-like mechanism following interaction with the EGF-R. The rck ORF belongs to the pefI-srgC operon, carried on the virulence plasmid of Salmonella. Currently, rck has only been characterized on the virulence plasmid of three serovars, i.e. Enteritidis, Typhimurium and Bovismorbificans. As the literature suggested a larger distribution, our aim was to study the prevalence of the rck ORF in the genus Salmonella taking advantage of the large online database Enterobase and of its experimental data associated (e.g. in silico serovars prediction, wgMLST sequence type). 188,233 genomes belonging to more than 471 Salmonella serovars were analyzed. Our results revealed the presence of the rck gene in 39 serovars and a predominance of some alleles for some serovars. They also suggest that the gene might not be exclusively carried on plasmids. Finally, despite a relatively high number of haplotypes, amino acid sequences comparison revealed a strong conservation of the protein sequences, as the majority of the identified variants showed only minor sequence variations with the three currently described Rck proteins. In conclusion, Rck is more widely distributed in Salmonella serovars than previously expected and consequently could play a role in the virulence of all these serovars

Fastgene : une identification rapide des agressions bioterroristes

Avec l'accroissement actuel des conflits asymétriques, une attaque bioterroriste à l'encontre des forces armées françaises ou sur le territoire national n'est malheureusement plus à exclure. Avec le soutien de la DGA, nous avons développé la technologie FASTGENE qui permet la détection sensible, spécifique et peu coûteuse, de la présence d'agents pathogènes dans un échantillon en moins de 8 minutes. Cette technologie duale peut s'appliquer de nombreuses autres applications en dehors du domaine de la défense et de la sécurité. Détecter et identifier rapidement les microorganismes: un besoin essentiel pour contrer les bioterroristes Le risque bioterroriste est particulièrement préoccupant puisqu'il se différencie des autres risques terroristes par des effets initialement masqués, puis amplifiés exponentiellement par le caractère contagieux d'un nombre croissant d'infections. La capacité de défense vis-à-vis de ce risque repose sur plusieurs piliers parmi lesquels la surveillance de l'environnement et la reconnaissance d'une agression jouent un rôle central. Une surveillance permanente et une reconnaissance rapide permettent en principe de limiter au maximum les conséquences d'une attaque. A la suite de l'attaque par lettres contenant des bacilles du charbon en 2001, les autorités des États-Unis ont décidé de déployer au niveau fédéral un système de surveillance de la qualité biologique de l'air, appelé Biowatch (1). Ce système est composé d'un grand nombre de capteurs d'aérosols déployés dans les 30 plus grandes agglomérations. Les aérosols ainsi collectés sont analysés périodiquement par un réseau de laboratoires. Bien que ce système unique n'ait heureusement jamais été confronté à une attaque bioterroriste, son exploitation permet de tirer plusieurs enseignements capitaux sur les caractéristiques que doivent réunir un tel système :With the current increase of asymmetric conflicts, a bioterrorist attack against the French armed forces or on the national territory is unfortunately no longer excluded. FASTGENE technology enables the sensitive, specific and inexpensive detection of the presence of pathogens in a sample in less than 8 minutes. This dual technology can be applied to many other applications outside the field of defense and securityDétection génétique en temps réel par thermalisation microfluidique ultra rapid

A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches

Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes listeriosis, a serious foodborne illness. In the nature-to-human transmission route, Lm can prosper in various ecological niches. Soil and decaying organic matter are its primary reservoirs. Certain clonal complexes (CCs) are over-represented in food production and represent a challenge to food safety. To gain new understanding of Lm adaptation mechanisms in food, the genetic background of strains found in animals and environment should be investigated in comparison to that of food strains. Twenty-one partners, including food, environment, veterinary and public health laboratories, constructed a dataset of 1484 genomes originating from Lm strains collected in 19 European countries. This dataset encompasses a large number of CCs occurring worldwide, covers many diverse habitats and is balanced between ecological compartments and geographic regions. The dataset presented here will contribute to improve our understanding of Lm ecology and should aid in the surveillance of Lm. This dataset provides a basis for the discovery of the genetic traits underlying Lm adaptation to different ecological niches

The invasin and complement-resistance protein Rck of Salmonella is more widely distributed than previously expected

International audienceThe rck open reading frame (ORF) on the pefI-srgC operon encodes an outer membrane protein responsible for invasion of nonphagocytic cell lines and resistance to complement-mediated killing. Until now, the rck ORF was only detected on the virulence plasmids of three serovars of Salmonella subsp. enterica (i.e., Bovismorbificans, Enteritidis, and Typhimurium). The increasing number of Salmonella genome sequences allowed us to use a combination of reference sequences and whole-genome multilocus sequence typing (wgMLST) data analysis to probe the presence of the operon and of rck in a wide array of isolates belonging to all Salmonella species and subspecies. We established the presence of partial or complete operons in 61 subsp. enterica serovars as well as in 4 other subspecies with various syntenies and frequencies. The rck ORF itself was retrieved in 36 subsp. enterica serovars and in two subspecies with either chromosomal or plasmid-borne localization. It displays high conservation of its sequence within the genus, and we demonstrated that most of the allelic variations identified did not alter the virulence properties of the protein. However, we demonstrated the importance of the residue at position 38 (at the level of the first extracellular loop of the protein) in the invasin function of Rck. Altogether, our results highlight that rck is not restricted to the three formerly identified serovars and could therefore have a more important role in virulence than previously expected. Moreover, this work raises questions about the mechanisms involved in rck acquisition and about virulence plasmid distribution and evolution. IMPORTANCE The foodborne pathogen Salmonella is responsible for a wide variety of pathologies depending on the infected host, the infecting serovars, and its set of virulence factors. However, the implication of each of these virulence factors and their role in the specific host-pathogen interplay are not fully understood. The significance of our research is in determining the distribution of one of these factors, the virulence plasmid-encoded invasin and resistance to complement killing protein Rck. In addition to providing elements of reflection concerning the mechanisms of acquisition of specific virulence genes in certain serotypes, this work will help to understand the role of Rck in the pathogenesis of Salmonella

Streptococcal group B integrative and mobilizable element IMESag- rpsI encodes a functional relaxase involved in its transfer

International audienceStreptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3'-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A-J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1 Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag-rpsI and that this spread would explain the presence of the same IMESag-rpsI type in GBS strains belonging to different CCs

Listeria monocytogenes: Investigation of Fitness in Soil Does Not Support the Relevance of Ecotypes

International audienceListeria monocytogenes ( Lm ) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm , little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR < 2%), phenotype 2 “moderate survivors” (2% < SR < 5%) and phenotype 3 “good survivors” (SR > 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness

Parallel Evolution of Group B Streptococcus Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations

International audienceGroup B Streptococcus (GBS) is a commensal of the gastrointestinal and genitourinary tracts, while a prevailing cause of neonatal disease worldwide. Of the various clonal complexes (CCs), CC17 is overrepresented in GBS-infected newborns for reasons that are still largely unknown. Here, we report a comprehensive genomic analysis of 626 CC17 isolates collected worldwide, identifying the genetic traits behind their successful adaptation to humans and the underlying differences between carriage and clinical strains. Comparative analysis with 923 GBS genomes belonging to CC1, CC19, and CC23 revealed that the evolution of CC17 is distinct from that of other human-adapted lineages and recurrently targets functions related to nucleotide and amino acid metabolism, cell adhesion, regulation, and immune evasion. We show that the most distinctive features of disease-specific CC17 isolates were frequent mutations in the virulence-associated CovS and Stk1 kinases, underscoring the crucial role of the entire CovRS regulatory pathway in modulating the pathogenicity of GBS. Importantly, parallel and convergent evolution of major components of the bacterial cell envelope, such as the capsule biosynthesis operon, the pilus, and Rib, reflects adaptation to host immune pressures and should be taken into account in the ongoing development of a GBS vaccine. The presence of recurrent targets of evolution not previously implicated in virulence also opens the way for uncovering new functions involved in host colonization and GBS pathogenesis. IMPORTANCE The incidence of group B Streptococcus (GBS) neonatal disease continues to be a significant cause of concern worldwide. Strains belonging to clonal complex 17 (CC17) are the most frequently responsible for GBS infections in neonates, especially among late-onset disease cases. Therefore, we undertook the largest genomic study of GBS CC17 strains to date to decipher the genetic bases of their remarkable colonization and infection ability. We show that crucial functions involved in different steps of the colonization or infection process of GBS are distinctly mutated during the adaptation of CC17 to the human host. In particular, our results implicate the CovRS two-component regulator of virulence in the differentiation between carriage-and disease-associated isolates. Not only does this work raise important implications for the ongoing development of a vaccine against GBS but might also drive the discovery of key functions for GBS adaptation and pathogenesis that have been overlooked until now