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PubMed2002

Inferences from whole-genome sequences of bacterial pathogens.

Genomic sequencing of bacterial pathogens has recently moved from the study of distantly related organisms to within-species comparisons of multiple strains. Strains often differ in their ability to cause disease, and comparative genomics is uncovering novel virulence determinants, hidden aspects of pathogenesis, and new targets for vaccine development. DNA microarrays and other gene-survey techniques are being used to quantify variability in gene content within bacterial populations, and to reveal the strain-specific basis for diversity and severity of pathology.

Bacteria↗
PubMed2001

Molecular diversity in the biosynthesis of GI tract glycoconjugates. A blood-group-related chart of microorganism receptors.

This paper examines the potential of carbohydrate blood-group antigens present on mucosal surfaces in acting as receptors for microorganisms. Mucosal surfaces express significant amounts of carbohydrate blood-group antigens under the control of the Secretor, Lewis and ABO systems. The exact glycoconjugate profile an individual presents to the lumen is complex, and can only be correctly determined by a combination of serology and genotyping. We have isolated and structurally resolved the glycolipids expressed in the small intestine of group O individuals having various common or rare phenotypes. Using this information, we have been able to construct a biosynthetic pathway and propose that the type, size and glycotopes expressed, are controlled to a major extent by blood-group-related glycosyltransferases. Many of these glycotopes are potential receptors for microorganisms; some resemble tumour antigens, while others resemble the lipopolysaccharides of some pathogens. Although the origins of the blood-group glycosyltransferases remain uncertain, it is evident that they significantly diversify the mucosal glycotopes exposed to microbes; and therein may be found a potential explanation for their existence.

ABO Blood-Group System↗
PubMed2006

Invasiveness is a variable and heterogeneous phenotype in Listeria monocytogenes serotype strains.

The ability of Listeria monocytogenes to breach mucosal and endothelial barriers of the host during infection is a hallmark property mediated by the internalins (Inl) A and B. We examined the invasive property of several L. monocytogenes strains representing 13 serotypes. We found that invasiveness is a heterogeneous phenotype amongst L. monocytogenes serotype strains. Despite this, many of the poorly invasive and non-invasive strains of L. monocytogenes express internalins at levels comparable to those of invasive isolates. Introduction of the inlAB locus from EGD-e into several poorly invasive strains had no effect on their invasive properties. A strain from serotype 4b that exhibits highly invasive properties was further examined. Deletion of the inlAB locus abrogated invasion of this strain while reintroduction of the inlAB locus into this strain restored invasiveness. An analysis of regions flanking the inlAB locus revealed considerable differences in the strains studied. Our results suggest that efficacious entry of L. monocytogenes into eukaryotic cells is complex and requires additional factors apart from internalins. Data presented here also suggest that the inlAB locus was introduced into L. monocytogenes by horizontal gene transfer with subsequent deletion and rearrangements occurring during evolution of this species.

Bacterial Proteins↗
PubMed2005

Emetic toxin formation of Bacillus cereus is restricted to a single evolutionary lineage of closely related strains.

An in-depth polyphasic approach was applied to study the population structure of the human pathogen Bacillus cereus. To assess the intraspecific biodiversity of this species, which is the causative agent of gastrointestinal diseases, a total of 90 isolates from diverse geographical origin were studied by genetic [M13-PCR, random amplification of polymorphic DNA (RAPD), multilocus sequence typing (MLST)] and phenetic [Fourier transform Infrared (FTIR), protein profiling, biochemical assays] methods. The strain set included clinical strains, isolates from food remnants connected to outbreaks, as well as isolates from diverse food environments with a well documented strain history. The phenotypic and genotypic analysis of the compiled panel of strains illustrated a considerable diversity among B. cereus connected to diarrhoeal syndrome and other non-emetic food strains, but a very low diversity among emetic isolates. Using all typing methods, cluster analysis revealed a single, distinct cluster of emetic B. cereus strains. The isolates belonging to this cluster were neither able to degrade starch nor could they ferment salicin; they did not possess the genes encoding haemolysin BL (Hbl) and showed only weak or no haemolysis. In contrast, haemolytic-enterotoxin-producing B. cereus strains showed a high degree of heterogeneity and were scattered over different clusters when different typing methods were applied. These data provide evidence for a clonal population structure of cereulide-producing emetic B. cereus and indicate that emetic strains represent a highly clonal complex within a potentially panmictic or weakly clonal background population structure of the species. It may have originated only recently through acquisition of specific virulence factors such as the cereulide synthetase gene.

Bacillus cereus↗
PubMed1996

Evolutionary perspective on a composite Shigella flexneri 2a virulence plasmid-borne locus comprising three distinct genetic elements.

Nucleotide sequence analysis of a Shigella flexneri 2a virulence plasmid-borne locus revealed that it comprised three distinct genetic elements: a stretch of colicin 1a/1b-linked sequence, a truncated IS911 element, and a third element containing two ORFs that shared a high level of similarity to a Salmonella-specific chromosomal sequence. Examination of other known IS911-like sequences showed that these sequences also were frequently associated with other accessory elements and appeared to be prone to partial deletion events. Analysis of the data led to a model of the evolution of this unusual composite locus.

Amino Acid Sequence↗
PubMed1999

Genetic basis of encapsulation response in Anopheles gambiae.

The phenomenon of encapsulation of invading organisms is widespread in insects. Co-evolution has produced an intricate balance between the immune responses of the host and immune-suppressive (or immune-evading) properties of the parasite. Genome-wide genetic mapping revealed different loci in Anopheline mosquitoes were involved in melanotic encapsulation of different malaria parasites. Certain isolates of human malaria parasites can still suppress or avoid the immune response from refractory mosquitoes. Similar interactions with parasitoids were observed in Drosophila melanogaster. Species-specific encapsulation locus was identified for two parasitoids, respectively, and virulent strain of parasitoid can suppress the immune system of an otherwise resistant fruitfly. It is believed that the encapsulation loci in both mosquitoes and fruitfly may encode gene products that function at the early stages of parasite/parasitoid recognition or immediate signaling events. Future research on membrane receptor molecules and their roles in insect immunity will yield interesting insights into mosquito-parasite interactions.

Animals↗
PubMed1994

Agrobacterium vitis nopaline Ti plasmid pTiAB4: relationship to other Ti plasmids and T-DNA structure.

The Ti plasmid of the Agrobacterium vitis nopaline-type strain AB4 was subcloned and mapped. Several regions of the 157 kb Ti plasmid are similar or identical to parts of the A. vitis octopine/cucumopine (o/c)-type Ti plasmids, and other regions are homologous to the nopaline-type Ti plasmid pTiC58. The T-DNA of pTiAB4 is a chimaeric structure of recent origin: the left part is 99.2% homologous to the left part of the TA-DNA of the o/c-type Ti plasmids, while the right part is 97.1% homologous to the right part of an unusual nopaline T-DNA recently identified in strain 82.139, a biotype II strain from wild cherry. The 3' noncoding regions of the ipt genes from pTiAB4 and pTi82.139 are different from those of other ipt genes and contain a 62 bp fragment derived from the coding sequence of an ipt gene of unknown origin. A comparison of different ipt gene sequences indicates that the corresponding 62 bp sequence within the coding region of the AB4 ipt gene has been modified during the course of its evolution, apparently by sequence transfer from the 62 bp sequence in the 3' non-coding region. In pTi82.139 the original coding region of the ipt gene has remained largely unmodified. The pTiAB4 6b gene differs from its pTi82.139 counterpart by the lack of a 12 bp repeat in the 3' part of the coding sequence. This leads to the loss of four glutamic acid residues from a series of ten. In spite of these differences, the ipt and 6b genes of pTiAB4 are functional. Our results provide new insight into the evolution of Agrobacterium Ti plasmids and confirm the remarkable plasticity of these genetic elements. Possible implications for the study of bacterial phylogeny are discussed.

Amino Acid Sequence↗
PubMed1998

Role of plasma and extracellular matrix proteins in the physiopathology of foreign body infections.

Foreign body implants are highly susceptible to microorganism infection. The infectious agents may be of low pathogenicity (such as S. epidermidis) or involve more virulent strains (such as S. aureus). The common denominator for the three main elements that play a role in the physiopathology of such infections (bacteria, neutrophils, and different biomaterials) are host proteins deposited over the surface of the devices immediately after their implantation. These proteins modulate that host cells response but can also promote Staphylococcus adhesion to the biomaterial. Neutrophils and other cells such as fibroblasts adhere to several extracellular matrix proteins such as fibronectin, fibrinogen, collagen, vitronectin, via specific cell surface receptor. The evolution of the technology and the increasing numbers of long-term artificial implants require a better understanding of fundamental mechanisms of foreign body infections to reduce their incidence and optimize their treatment.

Bacterial Adhesion↗
PubMed2006

Understanding the genetics of regulation of aflatoxin production and Aspergillus flavus development.

Aflatoxins are polyketide-derived, toxic, and carcinogenic secondary metabolites produced primarily by two fungal species, Aspergillus flavus and A. parasiticus, on crops such as corn, peanuts, cottonseed, and treenuts. Regulatory guidelines issued by the U.S. Food and Drug Administration (FDA) prevent sale of commodities if contamination by these toxins exceeds certain levels. The biosynthesis of these toxins has been extensively studied. About 15 stable precursors have been identified. The genes involved in encoding the proteins required for the oxidative and regulatory steps in the biosynthesis are clustered in a 70 kb portion of chromosome 3 in the A. flavus genome. With the characterization of the gene cluster, new insights into the cellular processes that govern the genes involved in aflatoxin biosynthesis have been revealed, but the signaling processes that turn on aflatoxin biosynthesis during fungal contamination of crops are still not well understood. New molecular technologies, such as gene microarray analyses, quantitative polymerase chain reaction (PCR), and chromatin immunoprecipitation are being used to understand how physiological stress, environmental and soil conditions, receptivity of the plant, and fungal virulence lead to episodic outbreaks of aflatoxin contamination in certain commercially important crops. With this fundamental understanding, we will be better able to design improved non-aflatoxigenic biocompetitive Aspergillus strains and develop inhibitors of aflatoxin production (native to affected crops or otherwise) amenable to agricultural application for enhancing host-resistance against fungal invasion or toxin production. Comparisons of aflatoxin-producing species with other fungal species that retain some of the genes required for aflatoxin formation is expected to provide insight into the evolution of the aflatoxin gene cluster, and its role in fungal physiology. Therefore, information on how and why the fungus makes the toxin will be valuable for developing an effective and lasting strategy for control of aflatoxin contamination.

Aflatoxins↗
PubMed2004

The LPG1 gene family of Leishmania major.

In Leishmania major, the core of the abundant surface lipophosphoglycan (LPG) is structurally related to that of the smaller glycosylinositolphospholipids (GIPLs) in containing galactosylfuranose (Gal(f)) residues in a Gal(f) (beta1, 3)Man motif. However, deletion of the putative Gal(f)-transferase (Gal(f)T) LPG1 affected Gal(f) incorporation in LPG but not GIPLs. We hypothesized that the presumptive GIPL Gal(f)-transferases could be homologous to LPG1, and identified three related genes in the L. major genome. These were termed LPG1L, LPG1R, and LPG1G, the latter of which was found in three identical copies located at the telomeres of chromosomes 5, 19, and 32 based on Leishmania genome project data. Neither LPG1 nor its homologues LPG1L and LPG1R were involved in the biosynthesis of GIPLs, as an lpg1(-)/lpg1l(-)/lpg1r(-) triple knockout (the first such in Leishmania) grew normally and made wild-type levels of Gal(f) -containing GIPLs. In contrast, overexpression of these three led to elevated galactose incorporation in glycoproteins. Gal(f)-containing glycoproteins had not been described in Leishmania but occur at high levels in other closely related trypanosomatids including Trypanosoma cruzi, Crithidia, Leptomonas, and Endotrypanum, and LPG1L and LPG1R homologs were detected in these species. These data suggest that the glyco-synthetic capabilities of Leishmania and perhaps other trypanosomatids may be larger than previously thought, with some activities being 'cryptic' in different lineages and potentially serving as reservoirs for glycoconjugate variation during evolution. Future tests will address whether the LPG1G family encodes the hypothesized GIPL-specific Gal(f)T.

Amino Acid Sequence↗
PubMed2002

Production of antibodies against glycolipids from the Mycobacterium tuberculosis cell wall in aerosol murine models of tuberculosis.

Evolution of antibodies against glycolipids from the Mycobacterium tuberculosis cell wall has been studied for the first time in experimental murine models of tuberculosis induced by aerosol, in which infection, reinfection, reactivation, prophylaxis and treatment with antibiotics have been assayed. Results show a significant humoral response against these antigens, where diacyltrehaloses (DAT) and sulpholipid I (SL-I) elicited higher antibody levels than protein antigens like antigen 85 protein complex (Ag85), culture filtrate proteins (CFP) and purified protein derivative (PPD). Only immunoglobulin M (IgM) antibodies have been detected against DAT and SL-I. Their evolution has a positive correlation with bacillary concentration in tissues.

Acyltransferases↗
PubMed1994

Autocrine enhancement of leukotriene synthesis by endogenous leukotriene B4 and platelet-activating factor in human neutrophils.

1. Platelet-activating factor (PAF) and leukotriene B4 (LTB4), two potent lipid mediators synthesized by activated neutrophils, are known to stimulate several neutrophil functional responses. In this study, we have determined that endogenous LTB4 and PAF exert autocrine effects on LT synthesis, as well as the underlying mechanism involved. 2. Pretreatment of neutrophils with either pertussis toxin (PT), or with receptor antagonists for LTB4 and PAF, resulted in an inhibition of LT synthesis induced by calcium ionophore, A23187. This inhibition was most marked at submaximal (100-300 nM) A23187 concentrations, whilst it was least at ionophore concentrations which induce maximal LT synthesis (1-3 microM). Thus newly-synthesized PAF and LTB4 can enhance LT synthesis induced by A23187 under conditions where the LT-generating system is not fully activated. 3. In recombinant human (rh) granulocyte-macrophage colony-stimulating factor (GM-CSF)-primed neutrophils, LT synthesis in response to chemoattractants (fMet-Leu-Phe or rhC5a) was also significantly inhibited by the LTB4 receptor antagonist, and to a lesser extent by PAF receptor antagonists. 4. Further investigation revealed that LTB4 and/or PAF exert their effects on LT synthesis via an effect on arachidonic acid (AA) availability, as opposed to 5-lipoxygenase (5-LO) activation. Indeed, the receptor antagonists, as well as PT, inhibited LT synthesis and AA release to a similar extent, whereas 5-LO activation (assessed with an exogenous 5-LO substrate) was virtually unaffected under the same conditions. Accordingly, we showed that addition of exogenous LTB4 could enhance AA availability in response to chemoattractant challenge in rhGM-CSF-primed cells, without significantly affecting the 5-LO activation status. Our data show that newly-generated PAF and LTB4 have the ability to positively feedback on LT synthesis by acting at the level of the phospholipase A2/re-esterification component of the LT biosynthetic pathway in neutrophils. Such autocrine affects are likely to represent an important amplification step of LT synthesis, and may as such contribute to the rapid onset, as well as to the evolution, of inflammatory responses.

Amino Acid Sequence↗
PubMed1997

Modulation of immune cell populations and activation markers in the pathogenesis of African swine fever virus infection.

African swine fever (ASF) virus induces immune cell alterations that may be detected by changes in peripheral blood cells phenotypic antigens and activation markers which were examined by flow cytometry, analyzing both cell proportion and/or expression intensity of superficial antigens. These studies were conducted in pigs with experimental acute of chronic ASF infection to determine whether changes among important surface activation markers and phenotypic antigens, and their correlative lymph node status, reflected similar or disparate aspects of immune pathology. In acute infection produced by virulent viruses, macrophage and B lymphocyte populations decreased in peripheral blood after a short activation period at the beginning of the infection. A significative decrease of interleukin 2 receptor (IL 2R) expression was also observed in those pigs. These variations correlated with lymph node cell depletion due to an intense lymphoid cell death by apoptosis, affecting mainly the B lymphocyte subpopulation as determined by immunohistochemistry. Nevertheless, pigs infected with an attenuated isolate undergoing chronic persistent infection, presented a distinct pattern of modification, according with a different clinicopathological evolution. Changes consisted in systemic immune activation coincident with the highest viremia titer, with an augmentation in CD8+ T lymphocyte, macrophage, and B cell populations, and MHC (major histocompatibility complex) antigens. Percentage elevation of circulating immune subpopulations was accompanied by cell accumulation with lymphoid hyperplasia but a conserved distribution of B lymphocytes in lymphoid organs of chronically infected pigs.

Acute Disease↗
PubMed2026

Convergent evolution of immune evasion in ESKAPE pathogens: A cross-pathogen architecture of conserved host-defense checkpoints.

Antimicrobial resistance in ESKAPE pathogens is primarily attributed to resistance genes, yet persistent infections despite appropriate therapy implicate immune evasion as an independent driver of treatment failure. Although immune-evasion mechanisms have been extensively characterized in individual pathogens, their shared architecture across the ESKAPE group remains insufficiently integrated. This review synthesizes current evidence to show that phylogenetically diverse ESKAPE pathogens have convergently evolved conserved strategies to evade host immunity under comparable selective pressures. A cross-pathogen immune-evasion framework emerges, encompassing impaired pathogen recognition, complement inhibition, phagocyte dysfunction, immunometabolic reprogramming, biofilm-mediated protection, and persistence-promoting inflammation, together with pathogen-specific virulence mechanisms. These processes intersect with adaptive immune dysfunction and emerging concepts, including quorum-sensing-mediated immunomodulation, trained immunity, and the itaconate-succinate immunometabolic axis, forming an interconnected persistence network rather than isolated virulence traits. This systems-level perspective identifies conserved host-directed therapeutic targets that may complement conventional antimicrobial therapy across species. However, host-directed therapies, immunotherapeutics, and vaccines remain largely preclinical or have shown inconsistent clinical efficacy. Mechanistic evidence is strongest for Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae, whereas substantial knowledge gaps persist for Enterococcus faecium, Acinetobacter baumannii, and Enterobacter spp. Overcoming persistent ESKAPE infections will require targeting conserved host-pathogen interactions alongside pathogen-specific antimicrobial resistance mechanisms.

Convergent immune evasion↗
PubMed1999

Genetic analysis reveals ongoing HIV type 1 evolution in infected human placental trophoblast.

To provide a better understanding of the role of placenta in vertical human immunodeficiency virus (HIV) transmission, we have studied the infection of placental trophoblast in a group of 15 mother-neonate pairs. By nested PCR amplification of the C2V3 env gene region, HIV-1 has been found to infect the placenta in five cases (33%). Phylogenetic analysis of the cloned sequences showed that all recovered maternal variants were of the B subtype. Further investigation into the ancestral relationships at the nucleotide level revealed that the trophoblast sequences evolved into a quasispecies population clearly distant from that observed in the mother. As expected, the populations transmitted to the trophoblast were also found to be more homogeneous than those in the mothers when characterized on the basis of pairwise nucleotide sequence distances. With regard to the predicted biological properties, the primary amino acid structure of the V3 loop domain was consistent, with a macrophage-tropic, non-syncytium-inducing phenotype in all patients. We also attempted to determine if any of a number of selected maternal or viral factors was associated with trophoblast infection. However, none of the followed parameters, including maternal age, disease stage, antiretroviral therapy, CCR5delta32 deletion status of the infant, and viral genotype, could be associated with viral transmission. Moreover, in one pair with proven trophoblast infection, HIV was also detected in the cord blood. Taken together, our data suggest that the productive trophoblast infection by HIV-1 in vivo is a relatively frequent event that may bear direct implications for a further transplacental propagation of the virus.

Adult↗
PubMed2002

The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria.

The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and Lactobacillus casei phage A2, are reported. Comparative genomics reveals that both phages are members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage type in low-GC-content gram-positive bacteria. Graded relatedness, the hallmark of evolving biological systems, was observed when different Sfi21-like phages were compared. Across the structural module, the graded relatedness was represented by a high level of DNA sequence similarity or protein sequence similarity, or a shared gene map in the absence of sequence relatedness. This varying range of relatedness was found within Sfi21-like phages from a single species as demonstrated by the different prophages harbored by Lactococcus lactis strain IL1403. A systematic dot plot analysis with 11 complete L. lactis phage genome sequences revealed a clear separation of all temperate phages from two classes of virulent phages. The temperate lactococcal phages share DNA sequence homology in a patchwise fashion over the nonstructural gene cluster. With respect to structural genes, four DNA homology groups could be defined within temperate L. lactis phages. Closely related structural modules for all four DNA homology groups were detected in phages from Streptococcus or Listeria, suggesting that they represent distinct evolutionary lineages that have not uniquely evolved in L. lactis. It seems reasonable to base phage taxonomy on data from comparative genomics. However, the peculiar modular nature of phage evolution creates ambiguities in the definition of phage taxa by comparative genomics. For example, depending on the module on which the classification is based, temperate lactococcal phages can be classified as a single phage species, as four distinct phage species, or as two if not three different phage genera. We propose to base phage taxonomy on comparative genomics of a single structural gene module (head or tail genes). This partially phylogeny-based taxonomical system still mirrors some aspects of the current International Committee on Taxonomy in Virology classification system. In this system the currently sequenced lactococcal phages would be grouped into five genera: c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages.

Base Sequence↗
PubMed1996

The evolution of parasitic diseases.

Parasites are characterized by their fitness-reducing effect on their hosts. Studying the evolution of parasitic diseases is an attempt to understand these negative effects as an adaptation of the parasite, the host, both or neither. Dieter Ebert and E. Allen Herre here discuss how the underlying concepts are general and are applicable for all types of disease-producing organisms, broadly defined here as parasites. The evolutionary processes that lead to the maintenance of the harmful effects are believed to be characterized by genetic correlations with other fitness components of the parasite. Depending on the shape of these correlations, any level of virulence can evolve.

Journal Article↗