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PubMed2001

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiological research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made.

Bacteria↗

PubMed2002

Host-pathogen interactions: the seduction of molecular cross talk.

Bacterial pathogens have evolved two major strategies to colonise the intestinal epithelium. Adherent microorganisms bind to the apical pole of the intestinal epithelium, whereas invasive microorganisms disrupt and invade the epithelium. Recognition of the genetic bases of bacterial pathogenicity and analysis of the molecular cross talks established between pathogens and their mammalian target cells have illuminated this diversity of interactions. We have compared the strategies of enteroinvasive pathogens, with emphasis on bacterial species such as Shigella, Yersinia, and Salmonella, that represent paradigms of interaction. Cross talks leading to alteration of the epithelial cell actin cytoskeleton appear as a recurrent theme during entry and dissemination into epithelial cells. Other cross talks alter the trafficking of cellular vesicles and induce changes in the intracellular compartment in which they reside, thus creating niches favourable to bacterial survival and growth. Finally, a variety of strategies also exist to deal with other components of the epithelial barrier, such as macrophages. Pro-phagocytic, anti-phagocytic, and pro-apoptotic processes appear to be of particular importance.

Actins↗

PubMed2002

What information is needed to design effective vaccination against intracellular pathogens causing chronic disease?

An appreciation of global features of immune regulation may lead to vaccination strategies effective in a genetically diverse population against a number of intracellular pathogens that cause chronic disease. Such global strategies appear more straightforward than strategies requiring a detailed knowledge of the specificity of 'protective T-cells'. Global strategies may be effective against the virus, bacteria and protozoa that respectively cause AIDS, tuberculosis and the leishmaniases.

AIDS Vaccines↗

PubMed2026

The chemical landscape of plant surface metabolites: Acylsugars as models of ecological function and structural diversity.

Plants produce a multifunctional assortment of specialized metabolites that play important roles in defense, environmental adaptation, and ecological interactions. Among these compounds, acylsugars, nonvolatile metabolites produced primarily in glandular trichomes of Solanaceae species, have emerged as informative model systems for understanding plant surface chemistry. Differences in acyl chain length, branching pattern, saturation, and attachment position generate extensive chemical diversity that influences herbivore deterrence, pathogen resistance, and the physicochemical properties of leaf surfaces. Recent advances in analytical chemistry, particularly liquid chromatography-ion mobility-tandem mass spectrometry (LC-IM-MS/MS), have greatly improved the ability to separate structurally related acylsugar isomers and characterize metabolite complexity at high resolution. When integrated with genomics, transcriptomics, and emerging spatial metabolomics approaches, these analytical tools provide new insights into acylsugar biosynthesis, pathway regulation, evolutionary diversification, and ecological function across plant species. This review positions acylsugars, particularly those of Solanum species, as model systems for understanding how structural diversity, spatial localization, and specialized metabolism shape ecological and physiological function at plant surfaces. We examine acylsugar structural diversity, biosynthetic pathways, ecological and physiological functions, and interactions with environmental and atmospheric processes. Major challenges, including extensive isomeric complexity, incomplete pathway characterization, and difficulties linking chemical structure to biological function, are discussed alongside emerging opportunities in integrative omics, crop improvement, sustainable pest management, and environmental monitoring. Overall, acylsugars provide a powerful model for linking molecular structure, spatial localization, and ecological function, offering broader insight into how specialized metabolism shapes plant adaptation, defense, and environmental interactions.

Acylsugars↗

PubMed2005

The diversity of dolichol-linked precursors to Asn-linked glycans likely results from secondary loss of sets of glycosyltransferases.

The vast majority of eukaryotes (fungi, plants, animals, slime mold, and euglena) synthesize Asn-linked glycans (Alg) by means of a lipid-linked precursor dolichol-PP-GlcNAc2Man9Glc3. Knowledge of this pathway is important because defects in the glycosyltransferases (Alg1-Alg12 and others not yet identified), which make dolichol-PP-glycans, lead to numerous congenital disorders of glycosylation. Here we used bioinformatic and experimental methods to characterize Alg glycosyltransferases and dolichol-PP-glycans of diverse protists, including many human pathogens, with the following major conclusions. First, it is demonstrated that common ancestry is a useful method of predicting the Alg glycosyltransferase inventory of each eukaryote. Second, in the vast majority of cases, this inventory accurately predicts the dolichol-PP-glycans observed. Third, Alg glycosyltransferases are missing in sets from each organism (e.g., all of the glycosyltransferases that add glucose and mannose are absent from Giardia and Plasmodium). Fourth, dolichol-PP-GlcNAc2Man5 (present in Entamoeba and Trichomonas) and dolichol-PP- and N-linked GlcNAc2 (present in Giardia) have not been identified previously in wild-type organisms. Finally, the present diversity of protist and fungal dolichol-PP-linked glycans appears to result from secondary loss of glycosyltransferases from a common ancestor that contained the complete set of Alg glycosyltransferases.

Animals↗

PubMed2000

Distribution of open reading frames of plasticity region of strain J99 in Helicobacter pylori strains isolated from gastric carcinoma and gastritis patients in Costa Rica.

The plasticity region of Helicobacter pylori strain J99 is a large chromosomal segment containing 33 strain-specific open reading frames (ORFs) with characteristics of a pathogenicity island. To study the diversity of the plasticity region, 22 probes corresponding to 20 ORFs inside the plasticity region and two ORFs on its boundaries were hybridized to genomic DNA isolated from clinical strains of H. pylori from patients with gastritis or gastric adenocarcinoma. Highly variable hybridization patterns were observed. The majority of the clinical strains presented a hybridization profile similar to that of J99; thus, these ORFs are not J99 strain specific. No association was found between a particular hybridization pattern and the clinical origin of the strain. Nevertheless, two single ORFs (JHP940 and JHP947) were more likely to be found in gastric cancer strains. They may be new pathogenicity markers. An in vitro expression study of these ORFs was also performed for the J99 strain, under different conditions. Thirteen ORFs were consistently expressed, six were consistently shut off, and three were expressed differentially. Most of the constitutionally expressed genes were located on the 3' part of the plasticity region. Our results show that the plasticity region, rather than being considered a pathogenicity island per se, should be considered a genomic island, which represents a large fragment of foreign DNA integrated into the genome and not necessarily implicated in the pathogenic capacity of the strain.

Blotting, Southern↗

PubMed2007

Identification of A/H5N1 influenza viruses using a single gene diagnostic microarray.

In previous work, a simple diagnostic DNA microarray that targeted only the matrix gene segment of influenza A (MChip) was developed and evaluated with patient samples. In this work, the analytical utility of the MChip for detection and subtyping of an emerging virus was evaluated with a diverse set of A/H5N1 influenza viruses. A total of 43 different highly pathogenic A/H5N1 viral isolates that were collected from diverse geographic locations, including Vietnam, Nigeria, Indonesia, and Kazakhstan, representing human, feline, and a variety of avian infections spanning the time period 2003-2006 were used in this study. A probabilistic artificial neural network was developed for automated microarray image interpretation through pattern recognition. The microarray assay and subsequent subtype assignment by the artificial neural network resulted in correct identification of 24 "unknown" A/H5N1 positive samples with no false positives. Analysis of a data set composed of A/H5N1, A/H3N2, and A/H1N1 positive samples and negative controls resulted in a clinical sensitivity of 97% and a clinical specificity of 100%.

Animals↗

PubMed1997

Helicobacter pylori eradication and its implications for the future.

It has become evident that at least some strains of Helicobacter pylori are pathogenic for humans. However, H. pylori are highly diverse and at least part of this variation involves characteristics related to pathogenicity. A large amount of evidence suggests that H. pylori infection of humans is ancient, and in general, the interaction is not terribly destructive. However, we should try to understand better the risks associated with infection with particular H. pylori strains, and limit treatment to those situations in which the indications for eradicating H. pylori are clear-cut. It is entirely possible that some H. pylori strains are commensals, and that others are symbionts. Eradicating those infections could ultimately cause more harm than good. It is too early to reach firm conclusions about whether all H. pylori infections need to be eradicated.

Anti-Bacterial Agents↗

PubMed1978

Reovirus-like agent and enterotoxigenic Escherichia coli infections in pediatric diarrhea in the Philippines.

Of 82 children hospitalized with diarrhea in the Philippines during January-June 1976, 14 (17%) had infections due to a reovirus-like agent as determined by detection of viral particles in stools by electron microscopy (12 [15%] of 82) and/or by a rise in titer of antibody to the serologically related Nebraska calf diarrhea virus (eight [20%] of 39). Escherichia coli producing heat-labile enterotoxin were found in six (7%) of 82 ill children and two (4%) of 49 healthy control children, while E. coli producing heat-stable enterotoxin were isolated from three children with diarrhea and two without gastroenteritis. Thirty-eight percent of enterotoxigenic E. coli isolated from children with diarrhea, but only 6% of isolates from healthy control, were of serotypes similar to those of enterotoxigenic E. coli isolated in previous studies of these pathogens by other investigators in geographically diverse areas (serotypes O6:H16, O8:H9, and O78:H12) (P less than 0.05). Eight (10%) of the children had infections with multiple enteric pathogens.

Antibodies, Bacterial↗

PubMed2006

Myxozoan infections in Mediterranean mariculture.

Fish mariculture has dramatically expanded in recent years in Mediterranean countries. In this scenario, several pathological problems have logically arisen and parasitological etiologies are increasingly being reported, either as primary or secondary pathogens. Myxozoa is the most diverse and economically important group of fish parasites, and several species are known to cause or contribute to losses in mariculture. Species of the genus Enteromyxum currently constitute the most serious parasitological threat. Some unusual biological characters, such as wide host spectrum and direct fish-to-fish transmission, together with high virulence for some host species, combine a dangerous cocktail which is emerging in recent years. Closed-system (recirculation) and heated-water locations are especially sensitive to chronic infections by these parasites, which can cause serious mortality and even discourage culture of some fish species at certain locations (i.e, Diplodus puntazzo). The presentation presents an overview of recent advances in research of marine myxozoans, focusing mainly in the most pathogenic, Enteromyxum spp. The incidence of these and other emerging infections, and the design of potential strategies for control will be introduced.

Animals↗

PubMed2000

Tropical environments, human activities, and the transmission of infectious diseases.

Throughout recent history, the tropical regions of the world have been affected more severely by infectious diseases than the temperate world. Much of the success of infectious diseases in that region is due to both biological and environmental factors that encourage high levels of biodiversity in hosts, vectors, and pathogens, and social factors that compromise efforts to control diseases. Several of these factors are described. Discussion then shifts to specific types of host-pathogen relationships. The most important of these in the tropics is the relationship between humans, a pathogen, and a vector that carries the pathogen from one human to another. Mosquitoes are the vector responsible for the transmission of many vector-borne human diseases. Characteristics of mosquito-human interactions are described, including cultural behaviors humans have developed that both increase the chances of transmission and help to limit that transmission. The transmission of water-borne diseases, fecal-oral transmission, zoonotic diseases, respiratory illnesses, and sexually transmitted diseases are also discussed. Attention is paid to how diseases with these modes of transmission differ in characteristics and importance in tropical human populations compared to those in temperate regions. Following this general discussion, three case studies are presented in some detail. The diseases chosen for the case studies include cholera, lymphatic filariasis, and dracunculiasis (guinea worm). These three case studies taken together provide examples of the diversity of human host-pathogen interactions as well as ways that human activities have both promoted their spread and helped to control them. The transmission of all three diseases is related to the nature and quality of water sources. The transmission of cholera, a water-borne disease, is related to sanitation practices, physical characteristics of the environment such as temperature and humidity, and modern shipping practices. Lymphatic filariasis, a mosquito-borne disease, has increased in frequency in parts of Africa in recent decades as a consequence of large-scale agricultural development projects that have shifted the nature and quantity of water sources and potential mosquito breeding sites. Dracunculiasis is transmitted by a small crustacean that contaminates sources of drinking water. Because its transmission can be prevented by a simple change in human behavior, filtering all water with a small piece of cloth before using it, dracunculiasis has been the focus of a major eradication effort that is near success.

Agriculture↗

PubMed2006

Solution structure of monomeric BsaL, the type III secretion needle protein of Burkholderia pseudomallei.

Many gram-negative bacteria that are important human pathogens possess type III secretion systems as part of their required virulence factor repertoire. During the establishment of infection, these pathogens coordinately assemble greater than 20 different proteins into a macromolecular structure that spans the bacterial inner and outer membranes and, in many respects, resembles and functions like a syringe. This type III secretion apparatus (TTSA) is used to inject proteins into a host cell's membrane and cytoplasm to subvert normal cellular processes. The external portion of the TTSA is a needle that is composed of a single type of protein that is polymerized in a helical fashion to form an elongated tube with a central channel of 2-3 nm in diameter. TTSA needle proteins from a variety of bacterial pathogens share sequence conservation; however, no atomic structure for any TTSA needle protein is yet available. Here, we report the structure of a TTSA needle protein called BsaL from Burkholderia pseudomallei determined by nuclear magnetic resonance (NMR) spectroscopy. The central part of the protein assumes a helix-turn-helix core domain with two well-defined alpha-helices that are joined by an ordered, four-residue linker. This forms a two-helix bundle that is stabilized by interhelix hydrophobic contacts. Residues that flank this presumably exposed core region are not completely disordered, but adopt a partial helical conformation. The atomic structure of BsaL and its sequence homology with other TTSA needle proteins suggest potentially unique structural dynamics that could be linked with a universal mechanism for control of type III secretion in diverse gram-negative bacterial pathogens.

Amino Acid Sequence↗

PubMed2004

Heterozygote advantage fails to explain the high degree of polymorphism of the MHC.

Major histocompatibility (MHC) molecules are encoded by extremely polymorphic genes and play a crucial role in vertebrate immunity. Natural selection favors MHC heterozygous hosts because individuals heterozygous at the MHC can present a larger diversity of peptides from infectious pathogens than homozygous individuals. Whether or not heterozygote advantage is sufficient to account for a high degree of polymorphism is controversial, however. Using mathematical models we studied the degree of MHC polymorphism arising when heterozygote advantage is the only selection pressure. We argue that existing models are misleading in that the fitness of heterozygotes is not related to the MHC alleles they harbor. To correct for this, we have developed novel models in which the genotypic fitness of a host directly reflects the fitness contributions of its MHC alleles. The mathematical analysis suggests that a high degree of polymorphism can only be accounted for if the different MHC alleles confer unrealistically similar fitnesses. This conclusion was confirmed by stochastic simulations, including mutation, genetic drift, and a finite population size. Heterozygote advantage on its own is insufficient to explain the high population diversity of the MHC.

Animals↗

PubMed2025

Colorectal cancer-associated Streptococcus gallolyticus: a hidden diversity expose.

Streptococcus gallolyticus subsp. gallolyticus (SGG) is a bacterial pathogen implicated in bacteremia and endocarditis and is often associated with colon tumors in elderly individuals. The development of colorectal cancer (CRC) has been linked to intestinal dysbiosis, characterized by increased proportions of SGG and other intestinal microbes. In this study, we present the complete nucleotide sequence of five novel clinical isolates of SGG associated with colorectal cancer, revealing unexpected genetic diversity. Sequencing an additional 30 SGG clinical isolates provided a more comprehensive description of this genetic diversity. We did not identify a pathogenicity island specific to CRC-associated SGG isolates. Most of these human-derived SGG isolates exhibit resistance to multiple antibiotics. Our findings also offer additional insights into multilocus sequence typing (MLST), capsular loci, and pilus organization. Analysis of the repertoire of surface proteins reveals high potential for binding and foraging complex polysaccharides. Finally, comparative genomics with the phylogenetically closest non-pathogenic subspecies S. gallolyticus subsp. macedonicus confirmed that SGG pathogenicity-associated factors mostly rely on a large repertoire of surface proteins involved in host colonization, presence of C5a peptidase to avoid innate immunity, bile salt hydrolase to persist in the gut, and of specific bacteriocin and type VII-dependent effectors to colonize the host colon. Additionally, the presence of extracellular polysaccharides in SGG probably helps the bacterium survive in harsher conditions.IMPORTANCEStreptococcus gallolyticus subsp. gallolyticus (SGG) was the first intestinal bacterium associated with colorectal cancer. It is now widely accepted that colonic microbiota dysbiosis contributes to oncogenesis, with a higher relative abundance of several potentially pro-carcinogenic bacteria. For example, the oncogenic role of Escherichia coli pks+ and enterotoxinogenic Bacteroides fragilis in colorectal cancer has been well established, identifying the role of genetic loci encoding toxins. Through the sequencing and analysis of 11 clinical SGG isolates from CRC patients and comparisons with non-CRC isolates, we uncovered a significant diversity among CRC-associated strains. Our findings suggest that SGG association with CRC is complex and is not linked to a specific strain or pathogenicity island, thus highlighting the opportunistic and versatile nature of SGG.

Humans↗

PubMed2005

A Second Kazal-like protease inhibitor from Phytophthora infestans inhibits and interacts with the apoplastic pathogenesis-related protease P69B of tomato.

The plant apoplast forms a protease-rich environment in which proteases are integral components of the plant defense response. Plant pathogenic oomycetes, such as the potato (Solanum tuberosum) and tomato (Lycopersicon esculentum) pathogen Phytophthora infestans, secrete a diverse family of serine protease inhibitors of the Kazal family. Among these, the two-domain EPI1 protein was shown to inhibit and interact with the pathogenesis-related protein P69B subtilase of tomato and was implicated in counter-defense. Here, we describe and functionally characterize a second extracellular protease inhibitor, EPI10, from P. infestans. EPI10 contains three Kazal-like domains, one of which was predicted to be an efficient inhibitor of subtilisin A by an additivity-based sequence to reactivity algorithm (Laskowski algorithm). The epi10 gene was up-regulated during infection of tomato, suggesting a potential role during pathogenesis. Recombinant EPI10 specifically inhibited subtilisin A among the major serine proteases, and inhibited and interacted with P69B subtilase of tomato. The finding that P. infestans evolved two distinct and structurally divergent protease inhibitors to target the same plant protease suggests that inhibition of P69B could be an important infection mechanism for this pathogen.

Amino Acid Sequence↗

PubMed2006

Within-host competition in genetically diverse malaria infections: parasite virulence and competitive success.

Humans and animals often become coinfected with pathogen strains that differ in virulence. The ensuing interaction between these strains can, in theory, be a major determinant of the direction of selection on virulence genes in pathogen populations. Many mathematical analyses of this assume that virulent pathogen lineages have a competitive advantage within coinfected hosts and thus predict that pathogens will evolve to become more virulent where genetically diverse infections are common. Although the implications of these studies are relevant to both fundamental biology and medical science, direct empirical tests for relationships between virulence and competitive ability are lacking. Here we use newly developed strain-specific real-time quantitative polymerase chain reaction protocols to determine the pairwise competitiveness of genetically divergent Plasmodium chabaudi clones that represent a wide range of innate virulences in their rodent host. We found that even against their background of widely varying genotypic and antigenic properties, virulent clones had a competitive advantage in the acute phase of mixed infections. The more virulent a clone was relative to its competitor, the less it suffered from competition. This result confirms our earlier work with parasite lines derived from a single clonal lineage by serial passage and supports the virulence-competitive ability assumption of many theoretical models. To the extent that our rodent model captures the essence of the natural history of malaria parasites, public health interventions which reduce the incidence of mixed malaria infections should have beneficial consequences by reducing the selection for high virulence.

Animals↗

PubMed2000

A long terminal repeat retrotransposon Cgret from the phytopathogenic fungus Colletotrichum gloeosporioides on cranberry.

A repetitive DNA element cloned from the cranberry fruit rot pathogen Colletotrichum gloeosporioides has been characterized. Sequence data indicate that it is a long terminal repeat (LTR) retrotransposon of 7,916 base pairs. LTR of 544 base pairs occur at either end of an internal region of 6,828 base pairs. This element, designated Cgret (C. gloeosporioides retrotransposon), encodes two putative polypeptides which have high homology to the gag and pol genes of other fungal retrotransposons. The sequence and structure suggest that Cgret is a member of the gypsy group of LTR retrotransposons. The Cgret retrotransposon was present in all of the cranberry isolates of the fungus C. gloeosporioides from New Jersey and Massachusetts, but not in the cranberry isolates from Wisconsin or Chile. Polymorphisms were detected among field isolates of C. gloeosporioides from various hosts, using hybridization probes derived from the LTR and the reverse transcriptase domain of Cgret. The structural integrity of Cgret suggests that it is still a functional retrotransposon and may be used as a molecular marker to study the genetic diversity distribution of this fungal pathogen.

Chile↗

PubMed1992

Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro.

Nested-primer polymerase chain reaction (PCR) has been applied to the molecular cloning of 4.6-kb half-genome fragments of human immunodeficiency virus type 1 (HIV-1) taken directly from the peripheral blood mononuclear cells (PBMC) of an individual with neurological symptoms of HIV-1 infection. In a similar manner, gp120-coding portions of the envelope gene were cloned after PBMC from the same blood sample were cocultivated with uninfected PBMC for 28 days. The complete 1.6-kb nucleotide sequence of the gp120 gene was determined from each of 35 clones examined. Two of 13 (15%) PBMC-derived gp120 genes and 3 of 22 (14%) coculture-derived gp120 genes were defective as a result of frameshifts and an in-frame stop codon(s). Mean diversity between individual gp120-coding sequences in PBMC was fivefold greater (3.24%) than after coculture (0.65%). A predominant sequence of "strain" was found after coculture that was distinct from the diverse viral genotypes detected in vivo and therefore was selectively amplified during in vitro propagation. Multiple distinct third variable (V3) regions encoding the principal neutralizing domain of the envelope protein were detected in PBMC-derived genes, suggesting the presence of immunologic diversity of HIV env genes in vivo not reflected in the cocultured virus sample. The large size of the HIV fragments generated in this study will permit analysis of the diversity of immunologic reactivity, gene function, and pathogenicity of HIV genomes present within infected individuals, including the functional significance of the loss of diversity that occurs upon coculture.

Acquired Immunodeficiency Syndrome↗