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M Simonet

Publications and source records attributed to M Simonet.

At least 19 recordsLinked to original sources
PubMed2005

Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics.

MOTIVATION: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics. RESULTS: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.

Chromosome Mapping↗
PubMed2004

Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.

Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here, we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons with available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that, together with the two Y. pestis-specific plasmids, to our knowledge, represent the only new genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis. In contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive insertion sequence-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of preexisting gene expression pathways, appear to be more important than acquisition of genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.

Bacteriophages↗
PubMed2004

The pmrF polymyxin-resistance operon of Yersinia pseudotuberculosis is upregulated by the PhoP-PhoQ two-component system but not by PmrA-PmrB, and is not required for virulence.

The Yersinia pseudotuberculosis chromosome contains a seven-gene polycistronic unit (the pmrF operon) whose products share extensive homologies with their pmrF counterparts in Salmonella enterica serovar Typhimurium (S. typhimurium), another Gram-negative bacterial enteropathogen. This gene cluster is essential for addition of 4-aminoarabinose to the lipid moiety of LPS, as demonstrated by MALDI-TOF mass spectrometry of lipid A from both wild-type and pmrF-mutated strains. As in S. typhimurium, 4-aminoarabinose substitution of lipid A contributes to in vitro resistance of Y. pseudotuberculosis to the antimicrobial peptide polymyxin B. Whereas pmrF expression in S. typhimurium is mediated by both the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems, it appears to be PmrA-PmrB-independent in Y. pseudotuberculosis, with the response regulator PhoP interacting directly with the pmrF operon promoter region. This result reveals that the ubiquitous PmrA-PmrB regulatory system controls different regulons in distinct bacterial species. In addition, pmrF inactivation in Y. pseudotuberculosis has no effect on bacterial virulence in the mouse, again in contrast to the situation in S. typhimurium. The marked differences in pmrF operon regulation in these two phylogenetically close bacterial species may be related to their dissimilar lifestyles.

Animals↗
PubMed2001

Superantigen bacterial toxins: state of the art.

Superantigens (SAgs) are viral and bacterial proteins exhibiting a highly potent polyclonal lymphocyte-proliferating activity for CD4(+), CD8(+) and sometimes gammadelta(+) T cells of human and (or) various animal species. Unlike conventional antigens, SAgs bind as unprocessed proteins to invariant regions of major histocompatibility complex (MHC) class II molecules on the surface of antigen-presenting cells (APCs) and to particular motifs of the variable region of the beta chain (Vbeta) of T-cell receptor (TcR) outside the antigen-binding groove. As a consequence, SAgs stimulate at nano-to picogram concentrations up to 10 to 30% of host T-cell repertoire while only one in 10(5)-10(6) T cells (0.01-0.0001%) are activated upon conventional antigenic peptide binding to TcR. SAg activation of an unusually high percentage of T lymphocytes initiates massive release of pro-inflammatory and other cytokines which play a pivotal role in the pathogenesis of the diseases provoked by SAg-producing microorganisms. We briefly describe in this review the molecular and biological properties of the bacterial superantigen toxins and mitogens identified in the past decade.

Animals↗
PubMed2001

Silencing and reactivation of urease in Yersinia pestis is determined by one G residue at a specific position in the ureD gene.

Yersinia pestis, the plague agent, is a naturally nonureolytic microorganism, while all other Yersinia species display a potent urease activity. In this report we demonstrate that Y. pestis harbors a complete urease locus composed of three structural (ureABC) and four accessory (ureEFGD) genes. Absence of ureolytic activity is due to the presence of one additional G residue in a poly(G) stretch, which introduces a premature stop codon in ureD. The presence of the same additional G in eight other Y. pestis isolates indicates that this mutation is species specific. Spontaneous excision of the extra G occurs at a frequency of 10(-4) to 10(-5) and restores a ureolytic phenotype to Y. pestis. The virulence of two independent ureolytic clones of Y. pestis injected either intravenously, subcutaneously, or intragastrically did not differ from that of the parental strain in the mouse infection model. Coinfection experiments with an equal number of ureolytic and nonureolytic bacteria did not evidence any difference in the ability of the two variants to multiply in vivo and to cause a lethal infection. Altogether our results demonstrate that variation of one extra G residue in ureD determines the ureolytic activity of Y. pestis but does not affect its virulence for mice or its ability to multiply and disseminate.

Amino Acid Sequence↗
PubMed2000

The superantigenic toxin of Yersinia pseudotuberculosis: a novel virulence factor?

Recently, a superantigenic toxin designated YPM (Yersinia pseudotuberculosis-derived mitogen) was characterized in the supernatant of Y. pseudotuberculosis, a Gram-negative bacterium involved in human enteric infection. To assess the role of YPM in pathophysiology of Y. pseudotuberculosis, a superantigen-deficient mutant was constructed and its virulence was tested in a murine model of infection and compared with the virulence of the wild-type strain (wt). Determination of the survival rate after intravenous inoculation of mice clearly demonstrated a higher survival rate when animals were infected with the superantigen-deficient strain. This decreased virulence of the mutant strain could not be explained by a lower bacterial growth rate in spleen, liver or lung of infected animals. Therefore, production of IFNgamma, TNFalpha, IL-2, IL-6 and IL-10 was followed during the course of infection by cytokine assay in the blood and mRNA detection in the spleen. IL-6 and IFNgamma were the two major cytokines detected whereas TNFalpha production was never observed.

Animals↗
PubMed2000

Superantigen YPMa exacerbates the virulence of Yersinia pseudotuberculosis in mice.

Yersinia pseudotuberculosis, a gram-negative bacterium responsible for enteric and systemic infection in humans, produces a superantigenic toxin designated YPMa (Y. pseudotuberculosis-derived mitogen). To assess the role of YPMa in the pathogenesis of Y. pseudotuberculosis, we constructed a superantigen-deficient mutant and compared its virulence in a mouse model of infection to the virulence of the wild-type strain. Determination of the survival rate after intravenous (i.v.) bacterial inoculation of OF1 mice clearly showed that inactivation of ypmA, encoding YPMa, reduced the virulence of Y. pseudotuberculosis. Mice infected i.v. with 10(4) and 10(5) wild-type bacteria died within 9 days, whereas mice infected with the ypmA mutant survived 12 and 3 days longer, respectively. This decreased virulence of the ypmA mutant strain was not due to an impaired colonization of the spleen, liver, or lungs. In contrast to i.v. challenge, bacterial inoculation by the intragastric (i.g.) route did not reveal any difference in virulence between wild-type Y. pseudotuberculosis and the ypmA mutant since the 50% lethal doses were identical for both strains. Moreover, inactivation of ypmA gene did not affect the bacterial growth of Y. pseudotuberculosis in Peyer's patches, mesenteric lymph nodes (MLNs), and spleen after oral infection. Histological studies of spleen, liver, lungs, heart, Peyer's patches, and MLNs after i.v. or i.g. challenge with the wild type or the ypmA mutant did not reveal any feature that can be specifically related to YPMa. Our data show that the superantigenic toxin YPMa contributes to the virulence of Y. pseudotuberculosis in systemic infection in mice.

Animals↗
PubMed1999

Characterization of IS1541-like elements in Yersinia enterocolitica and Yersinia pseudotuberculosis.

We characterized Yersinia enterocolitica and Yersinia pseudotuberculosis insertion sequences related to insertion sequence 1541, recently identified in Yersinia pestis. For each of the two species, two insertion sequence copies were cloned and sequenced. Genetic elements from Y. pseudotuberculosis were almost identical to insertion sequence 1541, whereas these from Y. enterocolitica were less related. Phylogenetic analysis of the putative transposases encoded by insertion sequences from the three pathogenic members of the genus Yersinia showed that they clustered with those encoded by Escherichia coli and Salmonella enterica elements belonging to the insertion sequence 200/insertion sequence 605 group. Insertion sequences originating from Y. pestis and Y. pseudotuberculosis constitute a monophyletic lineage distinct from that of Y. enterocolitica.

Base Sequence↗
PubMed1999

Coordinate involvement of invasin and Yop proteins in a Yersinia pseudotuberculosis-specific class I-restricted cytotoxic T cell-mediated response.

Yersinia pseudotuberculosis is a pathogenic enteric bacteria that evades host cellular immune response and resides extracellularly in vivo. Nevertheless, an important contribution of T cells to defense against Yersinia has been previously established. In this study we demonstrate that Lewis rats infected with virulent strains of Y. pseudotuberculosis, mount a Yersinia-specific, RT1-A-restricted, CD8+ T cell-mediated, cytotoxic response. Sensitization of lymphoblast target cells for cytolysis by Yersinia-specific CTLs required their incubation with live Yersinia and was independent of endocytosis. Although fully virulent Yersinia did not invade those cells, they attached to their surface. In contrast, invasin-deficient strain failed to bind to blast targets or to sensitize them for cytolysis. Furthermore, an intact virulence plasmid was an absolute requirement for Yersinia to sensitize blast targets for cytolysis. Using a series of Y. pseudotuberculosis mutants selectively deficient in virulence plasmid-encoded proteins, we found no evidence for a specific role played by YadA, YopH, YpkA, or YopJ in the sensitization process of blast targets. In contrast, mutations suppressing YopB, YopD, or YopE expression abolished the capacity of Yersinia to sensitize blast targets. These results are consistent with a model in which extracellular Yersinia bound to lymphoblast targets via invasin translocate inside eukaryotic cytosol YopE, which is presented in a class I-restricted fashion to CD8+ cytotoxic T cells. This system could represent a more general mechanism by which bacteria harboring a host cell contact-dependent or type III secretion apparatus trigger a class I-restricted CD8+ T cell response.

Adhesins, Bacterial↗
PubMed1999

PCR detection of aminoglycoside resistance genes: a rapid molecular typing method for Acinetobacter baumannii.

Aminoglycoside resistance is common among strains of Acinetobacter baumannii responsible for nosocomial infections, and inactivation of these antibiotics by enzymatic modification is the main mechanism. Different types of aminoglycoside acetyltransferases (AAC), nucleotidyltransferases (ANT), and phosphotransferases (APH) are synthesized by clinical isolates, and several enzymes can be produced by a single strain. Using a multiplex PCR procedure carried out on bacterial thermolysates, we analyzed the aminoglycoside resistance gene content of strains belonging to eight clusters identified by pulsed-field gel electrophoresis. In a single reaction were combined three primer pairs in order to amplify the genes coding for AAC(6')-Ih, AAC(3)-I, and AAC(3)-II, three primer pairs for the genes coding for ANT(2'')-I, APH(3')-VI, and rRNA 16S as internal control, and finally two primer pairs for the genes coding for AAC(6')-Ib and APH(3')-I. According to the aminoglycoside resistance gene patterns, the strains of the eight clusters were distributed into seven classes. This simple and rapid (< 8 h) fingerprinting technique could be a useful tool for the epidemiological investigation of A. baumannii nosocomial infections.

Acetyltransferases↗
PubMed1999

Molecular epidemiology of tuberculosis in the Nord Department of France during 1995.

In order to determine the current situation and to evaluate the human to human transmission of Mycobacterium tuberculosis in Northern France, the genetic polymorphism of strains was studied by using IS6110 fingerprint. One hundred and fifty-eight cases of bacteriologically confirmed tuberculosis were analyzed. One hundred and twenty-six patients (82%) were infected with genetically different isolates and 28 isolates (18%) were grouped into 14 clusters. No risk factors for recent Mycobacterium tuberculosis infections such as age, HIV status, immigrants, living in big cities were identified. This study shows that there was no major epidemic situation of tuberculosis in Northern France in 1995. Tuberculosis was characterized by a low proportion of HIV positive patients and a high proportion of elderly patients.

AIDS-Related Opportunistic Infections↗
PubMed1999

Cytotoxic T-cell-mediated response against Yersinia pseudotuberculosis in HLA-B27 transgenic rat.

Yersinia-induced reactive arthritis is highly associated with HLA-B27, the role of which in defense against the triggering bacteria remains unclear. The aim of this study was to examine the capacity of rats transgenic for HLA-B27 to mount a cytotoxic T-lymphocyte (CTL) response against Y. pseudotuberculosis and to determine the influence of the HLA-B27 transgene on this response. Rats transgenic for HLA-B*2705 and human beta(2)-microglobulin of the 21-4L line, which do not spontaneously develop disease, and nontransgenic syngeneic Lewis (LEW) rats were infected with Y. pseudotuberculosis. Lymph node cells were restimulated in vitro, and the presence of for Y. pseudotuberculosis-specific CTLs against infected targets was determined. Infection of 21-4L rats triggered a CD8(+) T cell-mediated cytotoxic response specific for Y. pseudotuberculosis. Analysis of this response demonstrated restriction by an endogenous major histocompatibility complex molecule. However, no restriction by HLA-B27 was detected. In addition, kinetics studies revealed a weaker anti-Yersinia CTL response in 21-4L rats than in nontransgenic LEW rats, and the level of cytotoxicity against 21-4L lymphoblast targets sensitized with Y. pseudotuberculosis was lower than that against nontransgenic LEW targets. We conclude that HLA-B27 transgenic rats mount a CTL response against Y. pseudotuberculosis that is not restricted by HLA-B27. Yet, HLA-B27 exerts a negative effect on the level of this response, which could contribute to impaired defense against Yersinia.

Animals↗
PubMed1998

Molecular characterization of IS1541 insertions in the genome of Yersinia pestis.

The genome of Yersinia pestis, the causative agent of plague, contains at least 30 copies of an element, designated IS1541, which is structurally related to IS200 (85% identity). One such element is inserted within the chromosomal inv gene (M. Simonet, B. Riot, N. Fortineau, and P. Berche, Infect. Immun. 64:375-379, 1996). We characterized other IS1541 insertions by cloning 14 different Y. pestis 6/69M loci carrying a single copy of this insertion sequence (IS) into Escherichia coli and, for each element, sequencing 250 bp of both flanking regions. In no case was this IS element inserted into large open reading frames; however, in eight cases, it was detected downstream (17 to 139 bp) of genes thought to be transcribed monocistronically or which constituted the last gene of an operon, and in only one case was it detected upstream (37 bp) of the first gene of an operon. Sequence analysis revealed stem-loop structures (deltaG, < -10 kcal) resembling rho-independent transcription terminators in 8 of the 14 insertion sites. These motifs might constitute hot spots for insertion of this IS1541 element within the Y. pestis genome.

Amino Acid Sequence↗
PubMed1998

Nosocomial outbreak of Klebsiella pneumoniae producing SHV-5 extended-spectrum beta-lactamase, originating from a contaminated ultrasonography coupling gel.

Klebsiella pneumoniae resistant to ceftazidime was isolated from six adult women and two neonates hospitalized between July and November 1993 in the Department of Obstetrics and Gynecology of Boucicaut Hospital (Paris, France). The epidemiological investigation revealed a notably short delay (less than 48 h) between admission and contamination of the six adults and peripartum transmission to the neonates. The only environmental source of ceftazidime-resistant K. pneumoniae was the ultrasonography coupling gel used in the emergency room. Phenotypic (biotyping and antibiotyping) and genotypic (plasmid profile and pulsed-field gel electrophoresis) analysis of all the clinical isolates indicated the spread of a single strain. It produced SHV-5 and TEM-1 beta-lactamases, as demonstrated by isoelectric focusing and gene sequencing. The risk of cross-contamination in ultrasonography procedures is usually low and had not been associated so far with bacteria producing an extended-spectrum beta-lactamase (ESBL). Furthermore, this is the first time an epidemic of an SHV-5 ESBL-producing member of the family Enterobacteriaceae has been reported from a French hospital.

Adult↗
PubMed1997

Novel transferable beta-lactam resistance with cephalosporinase characteristics in Salmonella enteritidis.

An isolate of Salmonella enteritidis was found to produce a plasmid-encoded beta-lactamase (DHA-1) that conferred resistance to extended-spectrum cephalosporins and cephamycins. The substrate and inhibition profiles of this enzyme resemble a class C beta-lactamase. This is the first report of a plasmid-mediated cephalosporinase of this class in the Salmonella genus.

Anti-Bacterial Agents↗
PubMed1997

Urease is not involved in the virulence of Yersinia pseudotuberculosis in mice.

A chromosomal locus (ure) involved in the production of urease activity in the bacterial pathogen Yersinia pseudotuberculosis was characterized. The genetic organization of the Y. pseudotuberculosis ure locus closely resembles that of the related ureolytic Yersinia species Y. enterocolitica. This locus encompasses seven open reading frames encoding polypeptides with predicted molecular weights of 10,894 (UreA), 15,820 (UreB), 61,001 (UreC), 25,801 (UreE), 24,551 (UreF), 20,330 (UreG), and 31,308 (UreD). The polypeptides have 85 to 96% identity with the corresponding Ure polypeptides of Y. enterocolitica serotype 0:8. Restriction fragment length polymorphisms of the ure loci from 12 unrelated Y. pseudotuberculosis strains produced by HaeIII and MboI indicate a low level of genetic variability of this locus in this species. The role of urease in the pathogenicity of Y. pseudotuberculosis was studied by constructing an isogenic urease-negative mutant obtained by disruption of structural gene ureB by aphA-3', which encodes kanamycin resistance. Experimental infection of mice with this mutant demonstrates that urease is not essential for Y. pseudotuberculosis virulence. Urease might be required mostly during the saprophytic life of this pathogen.

Amino Acid Sequence↗