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PubMed2004

Clonality and diversity of the fish pathogen Lactococcus garvieae in Mediterranean countries.

Infection with Lactococcus garvieae is considered the most important risk factor for the European trout industry, and the losses are approximately 50% of the total production. To improve our understanding of the genetic links among strains originating from different countries, we examined the population structure of L. garvieae by comparing 81 strains isolated from different sources and ecosystems (41 farms in six countries) in which the bacterium is commonly found. Genetic similarities (as assessed with molecular tools, including restriction fragment length polymorphism ribotyping with two endonucleases) were compared with serological data. The combined results reveal that in endemic sites the bacterial population displays a clonal structure, whereas bacterial diversity characterizes sites where the infection is sporadic.

Animals↗

PubMed2026

Bacterial stress responses lower mRNA-protein level correlations.

Diverse bacterial pathogens have evolved complex regulatory mechanisms to adapt to various environmental stresses during infection. The uncertainty in mRNA-protein levels in response to environmental stressors complicates our understanding of bacterial physiology and their adaptation to stressful environments. To examine this issue, we have integrated transcriptomics and proteomics data on three human bacterial pathogens: Salmonella enterica Typhimurium, Yersinia pseudotuberculosis, and Staphylococcus aureus under 10 infection-relevant stress conditions. We observed positive correlations between mRNA and protein levels, which were decreased under different stress conditions. Essential genes exhibited higher expression levels with lower variation across the conditions and stronger mRNA-protein correlations compared to nonessential genes, highlighting their critical role in bacterial adaptability and survival. Moreover, we identified a substantial number of genes with stress-induced noncorrelating mRNA-protein levels, particularly under conditions triggering strong stress responses. Particularly this level was dramatically lowered for osmotic stress-specific genes affected by impaired translational activity under osmotic stress. Our findings highlight the prevalence of noncorrelating mRNA-protein levels and the potential role of posttranslational modifications in modulating protein levels in response to environmental stressors during infection. This study provides a comprehensive framework for integrating transcriptomics and proteomics data and identifies potential gene products that might significantly impact the ability of diverse bacterial pathogens to adapt to hostile infection environments.

RNA, Messenger↗

PubMed1999

Home intravenous antibiotic therapy for patients with infective endocarditis.

Although home intravenous antibiotic therapy (HIAT) is increasingly being used for various infectious diseases, outpatient treatment of infective endocarditis (IE) is still uncommon. Recently, the American Heart Association recommended outpatient treatment of endocarditis only for infections with streptococci that are highly susceptible to penicillin. Herein, the experience with HIAT in patients with IE due to a diversity of pathogens is presented. During a 3-year period, 37 patients with IE who were in a stable condition and were cooperative were enrolled in a service for HIAT after completion of diagnostic procedures. Of the 37 patients, 21 were male; mean age was 64.3 years (range 20-87 years); in most cases (26/37), IE involved a native valve. Causative organisms were Streptococcus spp. (20), Staphylococcus spp. (10), Enterococcus spp. (2), Enterobacter spp. (1), and Erysipelothrix rhusiopathiae (1), while three were unknown. The most common antibiotics used were ceftriaxone and vancomycin. Almost three-quarters of the intravenous lines were peripheral. The mean duration of HIAT was 26.2 +/- 8.5 days, with 92% of the patients cured by it. Most complications were minor. Six patients were rehospitalised and two of them required valve replacement. In half of the rehospitalised patients, the complication was unrelated to HIAT. Surprisingly, almost all of the complications necessitating rehospitalisation occurred in patients with streptococcal IE and most involved native valves. HIAT may be suitable for IE due to a diversity of pathogens and involving prosthetic as well as native heart valves, provided there are proper patient and antibiotic selections, good follow-up, and vigilant monitoring of complications.

Adult↗

PubMed1987

Conservation of plasmids among plant-pathogenic Pseudomonas syringae isolates of diverse origins.

Thirty isolates of Pseudomonas syringae pv. tabaci, pv. angulata (pathogens on tobacco), pv. coronafaciens, and pv. striafaciens (pathogens on oats) were examined for plasmid DNAs. The strains were obtained from plants throughout the world, some over 50 years ago. Of the 22 tobacco pathogens, 16 contain predominantly one type of plasmid, the pJP27.00 type. The remaining six tobacco-specific strains do not harbor detectable plasmids. The oat pathogens contain one, two, or three plasmids. DNA homology studies indicate that the plasmid DNAs are highly conserved. More importantly, the plasmids harbored by strains isolated from one host plant are conserved most stringently; e.g., the plasmids from the tobacco pathogens are, with one exception, indistinguishable by restriction endonuclease digestion and Southern hybridization. There is also extensive homology among plasmids indigenous to the oat-specific P. syringae pv. coronafaciens and pv. striafaciens strains.

Base Sequence↗

PubMed1999

Species and genotypic diversities and similarities of pathogenic yeasts colonizing women.

We examined the patterns of strain relatedness among pathogenic yeasts from within and among groups of women to determine whether there were significant associations between genotype and host condition or body site. A total of 80 yeast strains were isolated, identified, and genotyped from 49 female volunteers, who were placed in three groups: (i) 19 women with AIDS, (ii) 11 pregnant women without human immunodeficiency virus (HIV) infection, and (iii) 19 women who were neither pregnant nor infected with HIV. Seven yeast species were recovered, including 59 isolates of Candida albicans, 9 isolates of Candida parapsilosis, 5 isolates of Candida krusei, 3 isolates of Candida glabrata, 2 isolates of Saccharomyces cerevisiae, and 1 isolate each of Candida tropicalis and Candida lusitaniae. Seventy unique genotypes were identified by PCR fingerprinting with the M13 core sequence and by random amplified polymorphic DNA analysis. Of the nine shared genotypes, isolates from three different hosts were of one genotype and pairs of strains from different body sites of the same host shared each of the other eight genotypes. Genetic similarities among groups of strains were calculated and compared. We found no significant difference in the patterns of relatedness of strains from the three body sites (oral cavity, vagina, and rectum), regardless of host conditions. The yeast microflora of all three host groups had similar species and genotypic diversities. Furthermore, a single host can be colonized with multiple species or multiple genotypes of the same species at the same or different body sites, indicating dynamic processes of yeast colonization on women.

AIDS-Related Opportunistic Infections↗

PubMed2005

Integrative genomic, transcriptional, and proteomic diversity in natural isolates of the human pathogen Burkholderia pseudomallei.

Natural isolates of pathogenic bacteria can exhibit a broad range of phenotypic traits. To investigate the molecular mechanisms contributing to such phenotypic variability, we compared the genomes, transcriptomes, and proteomes of two natural isolates of the gram-negative bacterium Burkholderia pseudomallei, the causative agent of the human disease melioidosis. Significant intrinsic genomic, transcriptional, and proteomic variations were observed between the two strains involving genes of diverse functions. We identified 16 strain-specific regions in the B. pseudomallei K96243 reference genome, and for eight regions their differential presence could be ascribed to either DNA acquisition or loss. A remarkable 43% of the transcriptional differences between the strains could be attributed to genes that were differentially present between K96243 and Bp15682, demonstrating the importance of lateral gene transfer or gene loss events in contributing to pathogen diversity at the gene expression level. Proteins expressed in a strain-specific manner were similarly correlated at the gene expression level, but up to 38% of the global proteomic variation between strains comprised proteins expressed in both strains but associated with strain-specific protein isoforms. Collectively, >65 hypothetical genes were transcriptionally or proteomically expressed, supporting their bona fide biological presence. Our results provide, for the first time, an integrated framework for classifying the repertoire of natural variations existing at distinct molecular levels for an important human pathogen.

Bacterial Proteins↗

PubMed2006

Integrating life history and cross-immunity into the evolutionary dynamics of pathogens.

Models for the diversity and evolution of pathogens have branched into two main directions: the adaptive dynamics of quantitative life-history traits (notably virulence) and the maintenance and invasion of multiple, antigenically diverse strains that interact with the host's immune memory. In a first attempt to reconcile these two approaches, we developed a simple modelling framework where two strains of pathogens, defined by a pair of life-history traits (infectious period and infectivity), interfere through a given level of cross-immunity. We used whooping cough as a potential example, but the framework proposed here could be applied to other acute infectious diseases. Specifically, we analysed the effects of these parameters on the invasion dynamics of one strain into a population, where the second strain is endemic. Whereas the deterministic version of the model converges towards stable coexistence of the two strains in most cases, stochastic simulations showed that transient epidemic dynamics can cause the extinction of either strain. Thus ecological dynamics, modulated by the immune parameters, eventually determine the adaptive value of different pathogen genotypes. We advocate an integrative view of pathogen dynamics at the crossroads of immunology, epidemiology and evolution, as a way towards efficient control of infectious diseases.

Antigenic Variation↗

PubMed1999

Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences.

A total of 1000 expressed sequence tags (ESTs) corresponding to 760 unique sequence sets were identified using random sequencing of clones from a cDNA library constructed from mycelial RNA of Phytophthora infestans. A number of software programs, represented by a relational database and an analysis pipeline, were developed for the automated analysis and storage of the EST sequence data. A set of 419 nonredundant sequences, which correspond to a total of 632 ESTs (63.2%), were identified as showing significant matches to sequences deposited in public databases. A putative cellular identity and role was assigned to all 419 sequences. All major functional categories were represented by at least several ESTs. Four novel cDNAs containing sequences related to elicitins, a family of structurally related proteins that induce the hypersensitive response and condition avirulence of P. infestans on Nicotiana plants, were among the most notable genes identified. Two of these elicitin-like cDNAs were among the most abundant cDNAs examined. The set also contained several ESTs with high sequence similarity to unique plant genes.

Actins↗

PubMed2005

ISSR, ERIC and RAPD techniques to detect genetic diversity in the aphid pathogen Pandora neoaphidis.

The entomopathogenic fungus Pandora neoaphidis is an important natural enemy of aphids. ISSR, ERIC (Enterobacterial Repetitive Intergenic Consensus) and RAPD PCR-based DNA fingerprint analyses were undertaken to study intra-specific variation amongst 30 isolates of P. neoaphidis worldwide, together with six closely related species of Entomophthorales. All methods yielded scorable binary characters, and distance matrices were constructed from both individual and combined data sets. Neighbour-joining was used to construct consensus phylogenetic trees which showed that although P. neoaphidis isolates were highly polymorphic they separated into a monophyletic group compared with the other Entomophthorales tested. Three distinct subclades were found, with UK isolates occupying two of these. No specific correlation with aphid host species was established for any of the isolates apart from those in one cluster which contained isolates obtained from nettle aphid, Microlophium carnosum. ERIC, ISSR and RAPD analysis allowed the rapid genetic characterisation and differentiation of isolates with the generation of potential isolate- and cluster specific-diagnostic DNA markers.

Animals↗

PubMed2005

Subtractive hybridization reveals a high genetic diversity in the fish pathogen Photobacterium damselae subsp. piscicida: evidence of a SXT-like element.

Photobacterium damselae subsp. piscicida is the causative agent of fish pasteurellosis, a severe disease affecting cultured marine fish worldwide. In this study, suppression subtractive hybridization was used to identify DNA fragments present in the virulent strain PC554.2, but absent in the avirulent strain EPOY 8803-II. Twenty-one genomic regions of this type (that included twenty-six distinct putative ORFs) were analysed by DNA sequencing. Twenty ORFs encoded proteins with homology to proteins in other bacteria, including four homologues involved in siderophore biosynthesis, and four homologues related to mobile elements; three of these were putative transposases and one was a putative conjugative transposon related to the Vibrio cholerae SXT element. This sequence was shown to be integrated into a prfC gene homologue. Six ORFs showed no significant homology to known bacterial proteins. Among the 21 DNA fragments specific to strain PC554.2, 5 DNA fragments (representing 7 ORFs) were also absent in the avirulent strain ATCC 29690. The analysis of these differential regions, as well as the screening of their presence in a collection of strains, demonstrated the high genetic heterogeneity of this pathogen.

Animals↗

PubMed1993

Genetic similarity and phenotypic diversity of commensal and pathogenic strains of Candida albicans isolated from the oral cavity.

Colony phenotype and genetic similarity were assessed within and between groups of commensal and pathogenic strains of Candida albicans collected from the oral cavities of individuals in a single geographical locale. Thirty-eight percent of pathogenic isolates contained predominant or minor variant colony morphologies (other than smooth) when samples from the sites of infection were cultured on plates, while 16% of commensal isolates contained minor variant colony morphologies when samples from the sites of carriage were cultured. The genetic similarities of isolates within and between groups were assessed by DNA fingerprinting by using Southern blot hybridization with the fingerprinting probe Ca3 and analysis with the computer-assisted, automated Dendron system. Both the commensal and the pathogenic groups contained a major cluster of genetically similar C. albicans isolates representing 31 and 33% of the strains in the respective groups. When a combined dendrogram of both commensal and pathogenic isolates was generated, the major clusters of genetically similar isolates in each group mixed into one large cluster. Minor clusters in the individual dendrograms also mixed. These results suggest common clonal origins for commensal and pathogenic strains in the same geographical locale.

Adult↗

PubMed2000

Genetic diversity of the fish pathogen Aeromonas salmonicida demonstrated by random amplified polymorphic DNA and pulsed-field gel electrophoresis analyses.

The current taxonomy of Aeromonas salmonicida includes 4 subspecies. A. salmonicida subsp. salmonicida is associated with salmonid furunculosis, and A. salmonicida subsp. achromogenes, A. salmonicida subsp. masoucida, and A. salmonicida subsp. smithia are strains that show variation in some biochemical properties. This classification does not readily encompass isolates from a wide range of fish hosts currently described as atypical A. salmonicida. This study examined 17 typical strains, 39 atypical strains and 3 type A. salmonicida subspecies strains for genetic similarity using the random amplified polymophic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) techniques. On the basis of RAPD- and PFGE-derived profiles, similarity matrices and dendrograms were constructed. The results showed that species A. salmonicida constituted a genetically heterogeneous group of strains, encompassing within an homogeneous or clonal lineage comprised solely of typical strains and the A. salmonicida subsp. salmonicida type strain.

Aeromonas↗

PubMed1999

Use of RAPD (random amplified polymorphic DNA) to analyse genetic diversity of dematiaceous fungal pathogens.

Thirteen strains of chromoblastomycosis and phaeohyphomycosis etiologic agent fungi were obtained from different geographical origins. These strains were genotypically compared by means of the RAPD (Random Amplified Polymorphic DNA) technique. The data generated showed a high degree of polymorphism between distinct species and a low polymorphism between strains of the same species. The results generated by these tests were subjected to a numerical taxonomy analysis, using the unweighted pair-group method. A phenogram was constructed for the set of strains studied. Based on its structure, we concluded that genotypical data provide enough information to us to use the unweighted pair-group method to cluster the strains in accordance to their respective species. The phenogram grouped in a single branch the strains of Fonsecaea pedrosoi and F. compacta species, indicating a great similarity between these fungi, and suggesting that the classification as distinct species may not be appropriate for these species of the genus Fonsecaea.

Chromoblastomycosis↗

PubMed2004

[Diversity of phytophagous and pathogens and their damage to mints (Mentha)].

UNLABELLED: The aim of this work was to estimate the phytopathologic condition of mints grown and self-growing in Kaunas Botanical Garden of Vytautas Magnus University and elsewhere in Lithuania; and to identify the specific constitution, the spread and damage of the main pests and disease agents. MATERIAL AND METHODS: Observations and examination were carried out with two local, four introduced mint species and with four hybrids in 1997-2003. We estimated the plant condition by identifying the intensity of the diseases and the abundance, spreading and damage of the pests. During the study we detected and identified the following pests--agents of diseases: Puccinia menthae, Erysiphe biocellata and Verticillium sp.; and phytophagous: Tetranychus urticae, Eupteryx atropunctata, Ovatus crataegarius, Polia persicariae, Agriotes lineatus, Chrysomela coerulans, Cassida viridis, Longitarsus lycopi. The most dangerous mint disease in Lithuania is rust; pests causing more harm are: Eupteryx atropunctata, Longitarsus lycopi. According to our data the least resistant species to most diseases and pests were Mentha arvensis and Mentha piperita, however separate samples of these species were exceptionally resistant. More resistant species was Mentha spicata and its hybrids.

Ecology↗

PubMed2005

Pathogen-driven selection and worldwide HLA class I diversity.

The human leukocyte antigen (HLA; known as MHC in other vertebrates) plays a central role in the recognition and presentation of antigens to the immune system and represents the most polymorphic gene cluster in the human genome [1]. Pathogen-driven balancing selection (PDBS) has been previously hypothesized to explain the remarkable polymorphism in the HLA complex, but there is, as yet, no direct support for this hypothesis [2 and 3]. A straightforward prediction coming out of the PDBS hypothesis is that populations from areas with high pathogen diversity should have increased HLA diversity in relation to their average genomic diversity. We tested this prediction by using HLA class I genetic diversity from 61 human populations. Our results show that human colonization history explains a substantial proportion of HLA genetic diversity worldwide. However, between-population variation at the HLA class I genes is also positively correlated with local pathogen richness (notably for the HLA B gene), thus providing support for the PDBS hypothesis. The proportion of variations explained by pathogen richness is higher for the HLA B gene than for the HLA A and HLA C genes. This is in good agreement with both previous immunological and genetic data suggesting that HLA B could be under a higher selective pressure from pathogens.

Communicable Diseases↗

PubMedDate not supplied

Anti-cardiolipin antibody from a patient with antiphospholipid syndrome (APS) recognizes only an epitope expressed by cardiolipin/beta 2-glycoprotein-I (beta 2GPI) complex and induces APS.

OBJECTIVE: As the antiphospholipid syndrome (APS) is characterized by antibodies which bind negatively charged phospholipids either directly or mainly through different target epitopes located on the beta-2-glycoprotein-I (beta 2GPI) molecule, the aim of this study is to describe an additional target epitope for anti-cardiolipin binding. METHODS: The binding characteristics of affinity purified anti-cardiolipin antibodies from a patient with monoclonal gammopathy associated with clinically overt APS were studied; inhibition studies were also carried out. These antibodies were used for the active induction of experimental APS. RESULTS: The affinity purified anti-cardiolipin antibodies were found to bind a target epitope created by the complex of cardiolipin/beta 2GPI, while not reacting with a complex composed by another phospholipid (phosphatidylserine/beta 2GPI), as confirmed by direct binding and competition assays. Immunization of naive mice with this unique affinity purified anti-cardiolipin antibody resulted in the induction of experimental APS (thrombocytopenia, prolonged coagulation timed and fetal resorptions). The anti-cardiolipin/beta 2GPI injected mice developed high titers of mouse anti-cardiolipin/beta 2GPI antibodies with the same binding characteristics as the human antibody which was used for disease induction. CONCLUSION: APS is a unique syndrome that is characterized by a diversity of pathogenic anti-phospholipid antibodies which may explain the diversity of clinical manifestations reported in patients.

Aged↗

PubMed2006

Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host.

BACKGROUND: The ability of emerging pathogens to infect new species is likely related to the diversity of pathogen variants present in existing reservoirs and their degree of genomic plasticity, which determines their ability to adapt to new environments. Certain simian immunodeficiency viruses (SIVcpz, SIVsm) have demonstrated tremendous success in infecting new species, including humans, resulting in the HIV-1 and HIV-2 epidemics. Although SIV diversification has been studied on a population level, the essential substrates for cross-species transmission, namely SIV sequence diversity and the types and extent of viral diversification present in individual reservoir animals have not been elucidated. To characterize this intra-host SIV diversity, we performed sequence analyses of clonal viral envelope (env) V1V2 and gag p27 variants present in individual SIVsm-infected sooty mangabeys over time. RESULTS: SIVsm demonstrated extensive intra-animal V1V2 length variation and amino acid diversity (le38%), and continual variation in V1V2 N-linked glycosylation consensus sequence frequency and location. Positive selection was the predominant evolutionary force. Temporal sequence shifts suggested continual selection, likely due to evolving antibody responses. In contrast, gag p27 was predominantly under purifying selection. SIVsm V1V2 sequence diversification is at least as great as that in HIV-1 infected humans, indicating that extensive viral diversification in and of itself does not inevitably lead to AIDS. CONCLUSION: Positive diversifying selection in this natural reservoir host is the engine that has driven the evolution of the uniquely adaptable SIV/HIV envelope protein. These studies emphasize the importance of retroviral diversification within individual host reservoir animals as a critical substrate in facilitating cross-species transmission.

Animals↗

PubMed2026

Genetic architecture and evolution of stripe rust resistance uncovered using diverse panels of wheat lines and North American Puccinia striiformis f. sp. tritici isolates.

Screening global wheat germplasm with a diverse collection of pathogen races expands the catalog of novel Yr loci and identifies new sources of broad-spectrum resistance against evolving Pst populations. Newly emerging highly virulent races of Puccinia striiformis f. sp. tritici (Pst) often defeat deployed resistance genes (Yr), highlighting the need for novel sources of durable resistance. A global diversity panel of 377 spring wheat (Triticum aestivum L.) lines was screened for all-stage resistance (ASR) against a panel of diverse 20 Pst isolates at the seedling stage and for adult-plant-stage resistance (APR) against natural mix of field races. Genome-wide association mapping identified 77 unique Yr loci. Of these, 34 overlapped with the previously mapped 1150 Yr loci, confirming the robustness of our GWAS results, while 43 were likely novel. Comparison of the nine adult-plant-stage Yr loci mapped in our study with known APR genes identified only one overlap, with Yr29. Except for Yr29, APR genes Yr18 and Yr36 were detected at low frequencies, indicating that resistance in our panel may arise from less characterized or novel sources. Two wheat lines, lacking widely effective Yr5 and Yr15 alleles, exhibited resistance to all 20 Pst races at the seedling stage and natural field races at the adult stage, suggesting that they may carry novel, broad-spectrum ASR alleles. Wheat improvement had no effect on the frequency of ASR alleles but resulted in a threefold increase in the frequency of APR alleles, suggesting that the latter were subjected to more consistent breeding selection over time. Our findings underscore the value of combined screening of diverse germplasm with diverse pathogen races to identify novel sources of broad-spectrum resistance for breeding stripe rust resistant cultivars.

Triticum↗