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PubMed2005

Comparative genomic hybridizations of Entamoeba strains reveal unique genetic fingerprints that correlate with virulence.

Variable phenotypes have been identified for Entamoeba species. Entamoeba histolytica is invasive and causes colitis and liver abscesses but only in approximately 10% of infected individuals; 90% remain asymptomatically colonized. Entamoeba dispar, a closely related species, is avirulent. To determine the extent of genetic diversity among Entamoeba isolates and potential genotype-phenotype correlations, we have developed an E. histolytica genomic DNA microarray and used it to genotype strains of E. histolytica and E. dispar. On the basis of the identification of divergent genetic loci, all strains had unique genetic fingerprints. Comparison of divergent genetic regions allowed us to distinguish between E. histolytica and E. dispar, identify novel genetic regions usable for strain and species typing, and identify a number of genes restricted to virulent strains. Among the four E. histolytica strains, a strain with attenuated virulence was the most divergent and phylogenetically distinct strain, raising the intriguing possibility that genetic subtypes of E. histolytica may be partially responsible for the observed variability in clinical outcomes. This microarray-based genotyping assay can readily be applied to the study of E. histolytica clinical isolates to determine genetic diversity and potential genotypic-phenotypic associations.

Algorithms↗
PubMed2006

The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression.

Helicobacter pylori produces acute superficial gastritis in nearly all of its human hosts. However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition characterized in part by diminished numbers of acid-producing parietal cells and increased risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic mouse model with an engineered ablation of parietal cells to show that loss of parietal cells provides an opportunity for a H. pylori isolate from a patient with ChAG (HPAG1) to bind to, enter, and persist within gastric stem cells. This finding raises the question of how ChAG influences H. pylori genome evolution, physiology, and tumorigenesis. Here we describe the 1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its predicted ORFs, were used for whole-genome genotyping of additional H. pylori ChAG isolates obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome transcriptional profiling of HPAG1's response to acid during in vitro growth indicates that genes encoding components of metal uptake and utilization pathways, outer membrane proteins, and virulence factors are among those associated with H. pylori's adaptation to ChAG.

Adenocarcinoma↗
PubMed2006

Species- and strain-specific control of a complex, flexible regulon by Bordetella BvgAS.

The Bordetella master virulence regulatory system, BvgAS, controls a spectrum of gene expression states, including the virulent Bvg(+) phase, the avirulent Bvg(-) phase, and at least one Bvg-intermediate (Bvg(i)) phase. We set out to define the species- and strain-specific features of this regulon based on global gene expression profiling. Rather than functioning as a switch, Bvg controls a remarkable continuum of gene expression states, with hundreds of genes maximally expressed in intermediate phases between the Bvg(+) and Bvg(-) poles. Comparative analysis of Bvg regulation in B. pertussis and B. bronchiseptica revealed a relatively conserved Bvg(+) phase transcriptional program and identified previously uncharacterized candidate virulence factors. In contrast, control of Bvg(-)- and Bvg(i)-phase genes diverged substantially between species; regulation of metabolic, transporter, and motility loci indicated an increased capacity in B. bronchiseptica, compared to B. pertussis, for ex vivo adaptation. Strain comparisons also demonstrated variation in gene expression patterns within species. Among the genes with the greatest variability in patterns of expression, predicted promoter sequences were nearly identical. Our data suggest that the complement of transcriptional regulators is largely responsible for transcriptional diversity. In support of this hypothesis, many putative transcriptional regulators that were Bvg regulated in B. bronchiseptica were deleted, inactivated, or unregulated by BvgAS in B. pertussis. We propose the concept of a "flexible regulon." This flexible regulon may prove to be important for pathogen evolution and the diversification of host range specificity.

Bacterial Proteins↗
PubMed2001

Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome.

Yersinia pestis, the infamous plague-causing pathogen, appears to have emerged in relatively recent history. Evidence of this fact comes from several studies that document a lack of nucleotide diversity in the Y. pestis genome. In contrast, we report that variable-number tandem repeat (VNTR) sequences are common in the Y. pestis genome and occur frequently in gene coding regions. Larger tandem repeat arrays, most useful for phylogenetic analysis, are present at an average of 2.18 arrays per 10 kbp and are distributed evenly throughout the genome and the two virulence plasmids, pCD1 and pMT1. We examined allelic diversity at 42 chromosomal VNTR loci in 24 selected isolates (12 globally distributed and 12 from Siskiyou County, Calif.). Vast differences in diversity were observed among the 42 VNTR loci, ranging from 2 to 11 alleles. We found that the maximum copy number of repeats in an array was highly correlated with diversity (R = 0.86). VNTR-based phylogenetic analysis of the 24 strains successfully grouped isolates from biovar orientalis and most of the antiqua and mediaevalis strains. Hence, multiple-locus VNTR analysis (MLVA) appears capable of both distinguishing closely related strains and successfully classifying more distant relationships. Harnessing the power of MLVA to establish standardized databases will enable researchers to better understand plague ecology and evolution around the world.

Animals↗
PubMed2003

[Contribution of cell and molecular biology and genetics to plant protection].

Plants resist to the majority of their potential aggressors by opposing physical and chemical barriers: cell walls, secondary metabolites.... Phenomena of specific recognition between a plant variety and a pathovar induce on the one hand, a local (hypersensitive) reaction that tends to limit pathogen growth and, on the other hand, a cascade of signals that allows the activation of a non-specific general (systemic) resistance. The contribution of genetics to the fight against pathogens depends on the natural variability that comes from the co-evolution between plants and their aggressors. Many plant varieties resistant to one or several pathogens have been obtained and are cultivated. The use of biotechnology will facilitate the rapid generation of new, resistant cultivars and cultivars with multiple resistances. New methods in order to increase the efficiency and the durability of resistance are envisaged.

Bacteria↗
PubMed1995

Molecular biology of bovine viral diarrhea virus and its interactions with the host.

The contributions of pestivirus molecular biology research to our understanding of Bovine Viral Diarrhea Virus (BVDV) biology and disease have been remarkable. Completion of nucleotide sequence information for genomes of NCP and CP-BVDV isolates was an important milestone. Subsequent work on the protein map of BVDV and polyprotein processing pathways paved the way for the interpretation of many other virologic and immunologic studies. Discovery of a correlation between genotype II and virulence (hemorrhagic syndrome) will help to clarify previously controversial data and to improve disease control. Description of multiple pathways of p80 expression in CP-BVDV offered insight into the pathogenesis of mucosal disease. Identification of gp53/ E2 as the target of neutralizing antibodies and source of antigenic hypervariability helped us to understand immunity to BVDV. Collectively, the advances described contribute to the implementation of improved diagnostic and control strategies to reduce losses inflicted by the bovine pestivirus.

Animals↗
PubMed1999

Molecular characterization of a Brucella species large DNA fragment deleted in Brucella abortus strains: evidence for a locus involved in the synthesis of a polysaccharide.

A Brucella melitensis 16M DNA fragment of 17,119 bp, which contains a large region deleted in B. abortus strains and DNA flanking one side of the deletion, has been characterized. In addition to the previously identified omp31 gene, 14 hypothetical genes have been identified in the B. melitensis fragment, most of them showing homology to genes involved in the synthesis of a polysaccharide. Considering that 10 of the 15 genes are missing in B. abortus and that all the polysaccharides described in the Brucella genus (lipopolysaccharide, native hapten, and polysaccharide B) have been detected in all the species, it seems likely that the genes described here might be part of a cluster for the synthesis of a novel Brucella polysaccharide. Several polysaccharides have been identified as important virulence factors, and the discovery of a novel polysaccharide in the brucellae which is probably not synthesized in B. abortus might be interesting for a better understanding of the pathogenicity and host preference differences observed between the Brucella species. However, the possibility that the genes described in this paper no longer encode the synthesis of a polysaccharide cannot be excluded. Brucellae belong to the alpha-2 subdivision of the class Proteobacteria, which includes other microorganisms living in association with eucaryotic cells, some of them synthesizing extracellular polysaccharides involved in the interaction with the host cell. The genes described in this paper might be a remnant of the common ancestor of the alpha-2 subdivision of the class Proteobacteria, and the brucellae might have lost such extracellular polysaccharide during evolution if it was not necessary for survival or for establishment of the infectious process. Nevertheless, further studies are necessary to identify the entire DNA fragment missing in B. abortus strains and to elucidate the mechanism responsible for such deletion, since only 9,948 bp of the deletion was present in the sequenced B. melitensis DNA fragment.

Amino Acid Sequence↗
PubMed1987

Epidemiology of heartwater in Guadeloupe and in the Caribbean.

At present, heartwater in the Caribbean is known with certainty only on Guadeloupe, Marie Galante and Antigua; the first 2 islands are widely infected. The most important factors responsible for particular aspects of heartwater in Guadeloupe are: Cowdria ruminantium of high virulence. A very resistant cattle population (Creole), not normally clinically affected. A fairly susceptible goat population (Creole) (22% goats born in endemic areas die after experimental inoculation) which, fortunately, includes breeding lines with inherited resistance characteristics. Amblyomma variegatum which is present all over the island and all through the year, but with a low infection rate (1-2% of adult ticks are infected) because of the short period of rickettsemia in infected animals. The low rate of tick infection results in a low endemicity of the disease. For goats, the epidemiologic situation can be regarded as unstable because the low rate of infection in ticks does not allow a natural immunization of the majority of young kids when they still have a non-specific resistance. The possible evolution of heartwater in the Caribbean and in the United States in considered.

Animals↗
PubMed2003

Lysogeny and bacteriophage host range within the Burkholderia cepacia complex.

The Burkholderia cepacia complex comprises a group of nine closely related species that have emerged as life-threatening pulmonary pathogens in immunocompromised patients, particularly individuals with cystic fibrosis or chronic granulomatous disease. Attempts to explain the genomic plasticity, adaptability and virulence of the complex have paid little attention to bacteriophages, particularly the potential contribution of lysogenic conversion and transduction. In this study, lysogeny was observed in 10 of 20 representative strains of the B. cepacia complex. Three temperate phages and five lytic phages isolated from soils, river sediments or the plant rhizosphere were chosen for further study. Six phages exhibited T-even morphology and two were lambda-like. The host range of individual phages, when tested against 66 strains of the B. cepacia complex and a representative panel of other pseudomonads, was not species-specific within the B. cepacia complex and, in some phages, included Burkholderia gladioli and Pseudomonas aeruginosa. These new data indicate a potential role for phages of the B. cepacia complex in the evolution of these soil bacteria as pathogens of plants, humans and animals, and as novel therapeutic agents.

Bacteriophages↗
PubMed2003

Position-based scanning for comparative genomics and identification of genetic islands in Haemophilus influenzae type b.

Bacteria exhibit extensive genetic heterogeneity within species. In many cases, these differences account for virulence properties unique to specific strains. Several such loci have been discovered in the genome of the type b serotype of Haemophilus influenzae, a human pathogen able to cause meningitis, pneumonia, and septicemia. Here we report application of a PCR-based scanning procedure to compare the genome of a virulent type b (Hib) strain with that of the laboratory-passaged Rd KW20 strain for which a complete genome sequence is available. We have identified seven DNA segments or H. influenzae genetic islands (HiGIs) present in the type b genome and absent from the Rd genome. These segments vary in size and content and show signs of horizontal gene transfer in that their percent G+C content differs from that of the rest of the H. influenzae genome, they contain genes similar to those found on phages or other mobile elements, or they are flanked by DNA repeats. Several of these loci represent potential pathogenicity islands, because they contain genes likely to mediate interactions with the host. These newly identified genetic islands provide areas of investigation into both the evolution and pathogenesis of H. influenzae. In addition, the genome scanning approach developed to identify these islands provides a rapid means to compare the genomes of phenotypically diverse bacterial strains once the genome sequence of one representative strain has been determined.

Amino Acid Sequence↗
PubMed2006

Impact of parasite sympatry on the geographic mosaic of coevolution.

Slave-making ants are specialized social parasites that steal the young from colonies of their host species to augment their slave supply. The degree of parasite-host specialization has been shown to shape the trajectory along which parasites and hosts coevolve and is a prime contributor to the geographic mosaic of coevolution. However, virtually nothing is known about extrinsic influences on parasite-host dynamics, although the simple addition of a competing slave-maker may significantly alter selection pressures. Here we report the effect of two sympatric slave-makers on a single host. We measured temporal and spatial changes in colonies of the primary host Temnothorax curvispinosus that had been placed in field enclosures along with a single colony of either one or both species of the North American slave-making ants Protomognathus americanus and Temnothorax duloticus. Each slave-maker species alone had a negative impact on its hosts, although one slave-maker species more frequently decimated its host assemblage and then went extinct. Nevertheless, the combined effect in mixed-parasite enclosures was, surprisingly, greatly attenuated. Virulent slave-maker growth and prudent slave-maker decay in these shared enclosures, together with field data showing an inverse proportional relationship between the two slave-makers in natural populations, suggest that their checkered distribution is a consequence of direct asymmetrical antagonism between parasites. Thus, our results imply a tripartite coevolutionary arms race, whereby intraguild interactions among social parasites strongly affect the realized selection pressures on hosts and contribute to the geographic mosaic of coevolution.

Animals↗
PubMed2002

[Microbiology and cystic fibrosis].

The respiratory infections are the rule in sick persons of cystic fibrosis. After the colonization in one's early childhood by Staphylococcus aureus and Haemophilus influenzae, it is established the colonization produced by the mucous strains of Pseudomonas aeruginosa, the principal etiogenic of this illness, that can become to isolate in more than 95% of sick persons at three years old. That's why the etiogenic factors of this bacterium are studied, as they are toxins, pigments, enzymes, and principally the alginate, hydrocarbonated polymer responsible of the mucous substance that covers these characteristic strains of cystic fibrosis sick persons. All these components are regulated by a complex genome, the biggest until noe sequenced in bacterium, and that explains the importance of the microorganism and its natural resistance or acquired to environmental alterations and to antibiotics and disinfectants. In the evolution of the clinic chart, it can appear others gramnegative bacteriums (among it emphasizes Burkholderia cepacia and Stenotrophomonas maltophilia), mycobacterium and even fungus; all that would explain the chronification of lung charts and the difficulty of these sick persons treatment.

ADP Ribose Transferases↗
PubMed2006

The host acts as a genetic bottleneck during serial infections: an insect-fungal model system.

The genetic variation of a pathogen population is a pivotal component of pathogen evolution, having important implications for emerging diseases, nosocomial infections, and laboratory subculturing practices. Furthermore, it is undoubtedly altered during infection of a host. We address this issue using an insect-fungal model system to examine the influence of serial host passage on the genetic variation of a pathogen population. Using amplified fragment length polymorphism, a strain of the opportunistic fungus, Aspergillus flavus, showing initially 98% genetic similarity, was assessed for changes in genetic diversity during repeated passage through Galleria mellonella larvae and compared to that of a parallel population serially subcultured on artificial media. In two independent trials, the genetic diversity of the population passed through the insect dropped significantly, while the genetic variation of the population subcultured on media increased or remained unchanged. However, there were no changes in virulence or the production of protease or aflatoxin, indicating an apparent lack of selection. We suggest that the insect acted as a genetic bottleneck, reducing the genetic diversity of the A. flavus population. The ability of a host to produce a genetic bottleneck in a pathogen population impacts our understanding of emerging diseases, nosocomial infections, and laboratory subculturing practices.

Animals↗
PubMed1975

A case of pigmentary hair naevus (Becker).

A healthy 14-year-old Norwegian male developed a typical Becker's naevus on the left shoulder and upper scapular region, about six months after an intracutaneous BCG-vaccination in the homolateral junction of the shoulder and upper arm. The evolution of the lesion had been modified by exposure to sunlight during the following six years, with partial fading of the hyperpigmentation. Biopsies taken from the centre and from the edge of the lesion at the age of 19 years showed the usual histological picture seen in cases of Becker's naevus, but focal areas within the periphery showed a chronic granulomatous infiltrate of lupoid pattern in the dermis, mainly follicular and perifollicular in distribution. Acid-fast bacilli were not demonstrable in the sections, and in culture no tubercle bacilli were isolated from a central and histologically non-specific site. The implications of the histological findings are discussed, stressing the possibility that Becker's naevus may be a form of cutaneous tuberculosis caused by BCG or other mycobacteria of low virulence, precipitated by ultraviolet light and possibly modified by immunological factors.

Adolescent↗
PubMed1997

PECAM-1/CD31, an endothelial receptor for binding Plasmodium falciparum-infected erythrocytes.

Excessive binding of Plasmodium falciparum-infected red blood cells (pRBCs) to the vascular endothelium (cytoadherence) and to uninfected erythrocytes (rosetting) may lead to occlusion of the microvasculature and thereby contribute directly to the acute pathology of severe human malaria. A number of endothelial receptors have been identified as targets for the pRBCs, including CD36, intercellular adhesion molecule-1 (ICAM-1) and chondroitin-4-sulfate (CSA). In vitro, CD36 is the most frequent target of strains from patients with mild as well as severe P. falciparum malaria, but is expressed at low levels on the cerebral microvasculature and therefore seems unlikely to be involved in the evolution of cerebral disease. Strains of P. falciparum that form rosettes are associated both with the occurrence of cerebral malaria and severe anemia. Here we report that malaria-infected RBCs adhere to platelet/endothelial cell adhesion molecule-1 (PECAM-1/CD31) on the vascular endothelium. pRBCs bind to endothelial cells, to PECAM-1/CD31 transfected cells, and directly to recombinant PECAM-1/CD31 absorbed onto plastic. Soluble PECAM-1/CD31 and monoclonal antibodies specific for the amino-terminal segment of PECAM-1/CD31 (domains 1-4) blocked the binding. Interferon-gamma (IFN-gamma)-essential for the development of cerebral malaria in the mouse-was found to augment adhesion of human pRBCs to PECAM-1/CD31 on endothelial cell monolayers. Our results suggest that PECAM-1/CD31 is a virulence-associated endothelial receptor of P. falciparum-infected RBCs.

Animals↗
PubMed2026

Effector loss and gain drives host range at a fitness cost.

Epidemic preparedness depends on tracking microbial evolution that drives shifts in ecological behaviors such as disease emergence. However, the genetic constraints mediating microbial emergence for generalist and specialist behaviors remain poorly described. Here, we addressed this question by combining comparative and functional genomics with phylogeny-based evolutionary analyses of the cereal pathogen Xanthomonas translucens. We show that a generalist X. translucens subgroup arose from a specialist ancestor, and the loss of a single effector gene, xopAL1, contributed to the generalist host expansion by promoting host jump from barley to wheat. Deleting barley-specialist X. translucens xopAL1 recapitulated the host jump to wheat and demonstrates risk across each globally distributed genetic lineage. However, this niche expansion via XopAL1 loss incurs a significant fitness cost to colonize barley. Moreover, the specialist lineage gained an additional effector gene, xopAJ, which enhanced virulence on barley while restricting oat infection, thereby reinforcing niche specialization. We further conducted transcriptomic analysis of wheat and determined that XopAL1 triggers a defense response that involves the reduction of photosynthetic processes. Our work provides an experimentally validated evolutionary framework to understand mechanisms of intergenera host jump. Overall, we demonstrate that single events of gene loss and gain shape ecological behaviors by creating a dynamic trade-off between niche breadth and specialization.

Triticum↗
PubMed1989

Modification of foot-and-mouth disease virus after serial passages in the presence of antiviral polyclonal sera.

Foot-and-mouth disease virus (FMDV) shows a remarkable antigenic variability. Like other RNA viruses, this virus has a high rate of mutation. It has been proposed that selection exerted by the host's antibodies could play a major role in the rapid evolution of FMDV. The present work reports the selection of FMDV antibody-resistant populations (Nr), after serial passages of cloned FMDV A24 Cruzeiro strain on secondary monolayers of bovine fetal kidney cells in the presence of subneutralizing antiviral polyclonal sera (APS). After a limited number of passages under selective pressure, the virus population showed the following characteristics: (1) increased resistance to neutralization by APS; (2) altered electrophoretic mobility of structural viral proteins (VP1); (3) remarkable plaque size reduction, (4) a pronounced thermosensitivity (ts); and (5) decreased pathogenicity for mice, in both uncloned and cloned small plaque size populations. This indicates that FMDV populations under antibody pressure in vitro, have acquired, in addition to expected characteristics of natural FMDV variants (resistance to neutralization and altered viral structural proteins), phenotypic markers which correspond to attenuated, less virulent variants.

Antibodies, Viral↗
PubMed1998

An RNA virus can adapt to the multiplicity of infection.

RNA viruses evolve as complex distributions of mutants termed viral quasispecies. For this reason it is relevant to explore those environmental parameters that favour the selective advantage of some viral subpopulations over others. In the present study we provide direct evidence that the relative fitness of two competing viral subpopulations may depend on the multiplicity of infection (m.o.i.). Two closely related subpopulations of foot-and-mouth disease virus (FMDV) of serotype C, which differed in their history of cytolytic passages in BHK-21 cells, were subjected to growth-competition experiments in BHK-21 cells. One of the populations, termed S, was found to have a selective advantage over the other population, termed L, only when the competition passages were carried out at low m.o.i. In contrast, both populations, L and S, coexisted during serial passages carried out at high m.o.i. No differences between S and L were detected in assays of inhibition of infectivity by synthetic peptides, in cell binding-competition experiments, or in virulence for BHK-21 cells. However, FMDV S displayed increased heparin binding compared with L, and L higher virulence for Chinese hamster ovary (CHO) cells than S. These results with FMDV suggest that small differences in the interaction of the virus with the host cell may contribute to an m.o.i.-dependent selective advantage of one viral subpopulation over a closely related subpopulation. Therefore, different viral mutants from quasispecies replicating in vivo may be selected depending on the number of variant viruses relative to the number of susceptible cells.

Adaptation, Biological↗