Parasite immune escape: new views into host-parasite interactions

Patterns in parasite diversity and interactions with anurans from the Atlantic Forest

Knowledge of parasite-host interactions is essential for understanding factors associated with the ecology and evolution of both groups. Some aspects, such as host size and phylogeny, as well as parasite specificity, are significant predictors that help unveil the parasite-host relationship. Thus, the goals of this study were: (1) to describe parasite diversity in regions of the Atlantic Forest; (2) to analyze which host characteristics can influence parasite richness of anuran's parasite component community; and (3) to investigate if the prevalence of parasite infection is related to specificity metrics (ecological and phylogenetic), number of infected hosts and parasite's abundance. We identified 49 parasite taxa, classified into three phyla: Nematoda, Acanthocephala, and Platyhelminthes. Supporting the existing literature, our findings corroborate the positive relationship between host size and parasite richness, further emphasizing the significance of this predictor. Parasite prevalence in the host community is related to the number of infected host species and parasite abundance, but not to phylogenetic and ecological specificity indices. This shows that parasite prevalence is strongly associated with infection opportunity, host sampling effort, and high parasite abundance.

A pilot study of microRNAs expression profile in plasma of patients with hydatid disease: potential immunomodulation of hydatid disease

Echinococcosis is a zoonotic disease, which seriously endangers human health. The immune game between parasite and host is not fully understood. Exosomes are thought to be one of the ways of information communication between parasite and host. In this study, we attempted to explore the communication between Echinococcus granulosus and its host through the medium of exosomes. We collected plasma from E. granulosus patients (CE-EXO) and healthy donors (HD-EXO) and extracted exosomes from the plasma. The expression profile of miRNA in plasma was determined by second generation sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to annotate the function of target genes of differential miRNAs. Meanwhile, we co-cultured plasma exosomes from healthy donors and plasma exosomes from E. granulosus patients with Jurkat T cells with or without phytohaemagglutinin (PHA) stimulation. The expression of CD69 on Jurkat T cells was detected by flow cytometry. The results showed that the miRNA of exosomes between healthy donors and E. granulosus patients was significantly different. GO and KEGG were used to annotate the function of target genes of differential miRNAs. The results indicate that many important pathways are involved in inflammation, metabolism, and immune response after parasite infection, such as p53 signaling pathway, PI3K-Akt signaling pathway, and glycolysis/gluconeogenesis. Flow cytometry showed that CE-EXO reduced the expression of CD69 + on Jurkat T cells. Our present results suggest that these differentially expressed miRNAs may be important regulators of parasite-host interactions. Meanwhile, functional prediction of its target genes provides valuable information for understanding the mechanism of host-parasite interactions. These results provide clues for future studies on E. granulosus escape from host immune attack, which could help control E. granulosus infection.

Cytomegalovirus vectors expressing Plasmodium knowlesi antigens induce immune responses that delay parasitemia upon sporozoite challenge

The development of a sterilizing vaccine against malaria remains one of the highest priorities for global health research. While sporozoite vaccines targeting the pre-erythrocytic stage show great promise, it has not been possible to maintain efficacy long-term, likely due to an inability of these vaccines to maintain effector memory T cell responses in the liver. Vaccines based on human cytomegalovirus (HCMV) might overcome this limitation since vectors based on rhesus CMV (RhCMV), the homologous virus in rhesus macaques (RM), elicit and indefinitely maintain high frequency, non-exhausted effector memory T cells in extralymphoid tissues, including the liver. Moreover, RhCMV strain 68-1 elicits CD8+ T cells broadly recognizing unconventional epitopes exclusively restricted by MHC-II and MHC-E. To evaluate the potential of these unique immune responses to protect against malaria, we expressed four Plasmodium knowlesi (Pk) antigens (CSP, AMA1, SSP2/TRAP, MSP1c) in RhCMV 68-1 or in Rh189-deleted 68-1, which additionally elicits canonical MHC-Ia-restricted CD8+ T cells. Upon inoculation of RM with either of these Pk Ag expressing RhCMV vaccines, we obtained T cell responses to each of the four Pk antigens. Upon challenge with Pk sporozoites we observed a delayed appearance of blood stage parasites in vaccinated RM consistent with a 75-80% reduction of parasite release from the liver. Moreover, the Rh189-deleted RhCMV/Pk vectors elicited sterile protection in one RM. Once in the blood, parasite growth was not affected. In contrast to T cell responses induced by Pk infection, RhCMV vectors maintained sustained T cell responses to all four malaria antigens in the liver post-challenge. The delayed appearance of blood stage parasites is thus likely due to a T cell-mediated inhibition of liver stage parasite development. As such, this vaccine approach can be used to efficiently test new T cell antigens, improve current vaccines targeting the liver stage and complement vaccines targeting erythrocytic antigens.

The dynamics of vector-borne relapsing diseases

In this paper, we describe the dynamics of a vector-borne relapsing disease, such as tick-borne relapsing fever, using the methods of compartmental models. After some motivation and model description we provide a proof of a conjectured general form of the reproductive ratio R₀, which is the average number of new infections produced by a single infected individual. A disease free equilibrium undergoes a bifurcation at R₀=1 and we show that for an arbitrary number of relapses it is a transcritical bifurcation with a single branch of endemic equilibria that is locally asymptotically stable for R₀ sufficiently close to 1. Furthermore, we show there is no backwards bifurcation. We then show that these results can be extended to variants of the model with an example that allows for variation in the number of relapses before recovery. Finally, we discuss implications of our results and directions for future research.

Microsporidia infection impacts the host cell's cycle and reduces host cell apoptosis

Intracellular parasites can alter the cellular machinery of host cells to create a safe haven for their survival. In this regard, microsporidia are obligate intracellular fungal parasites with extremely reduced genomes and hence, they are strongly dependent on their host for energy and resources. To date, there are few studies into host cell manipulation by microsporidia, most of which have focused on morphological aspects. The microsporidia Nosema apis and Nosema ceranae are worldwide parasites of honey bees, infecting their ventricular epithelial cells. In this work, quantitative gene expression and histology were studied to investigate how these two parasites manipulate their host’s cells at the molecular level. Both these microsporidia provoke infection-induced regulation of genes involved in apoptosis and the cell cycle. The up-regulation of buffy (which encodes a pro-survival protein) and BIRC5 (belonging to the Inhibitor Apoptosis protein family) was observed after infection, shedding light on the pathways that these pathogens use to inhibit host cell apoptosis. Curiously, different routes related to cell cycle were modified after infection by each microsporidia. In the case of N. apis, cyclin B1, dacapo and E2F2 were up-regulated, whereas only cyclin E was up-regulated by N. ceranae, in both cases promoting the G1/S phase transition. This is the first report describing molecular pathways related to parasite-host interactions that are probably intended to ensure the parasite’s survival within the cell.

Increased hepatic Th2 and Treg subsets are associated with biliary fibrosis in different strains of mice caused by Clonorchis sinensis

Previous studies showed that CD4⁺T cells responses might be involved in the process of biliary fibrosis. However, the underlying mechanism resulting in biliary fibrosis caused by Clonorchis sinensis remains not yet fully elucidated. The objectives of the present study were to investigate the different profiles of hepatic CD4⁺T cell subsets (Th1, Th2, Th17 and Treg cells) and their possible roles in the biliary fibrosis of different strains of mice (C57BL/6, BALB/c and FVB mice) induced by C. sinensis infection. C57BL/6, BALB/c and FVB mice were orally gavaged with 45 metacercariae. All mice were sacrificed on 28 days post infection in deep anesthesia conditions. The leukocytes in the liver were separated to examine CD4⁺T cell subsets by flow cytometry and the left lobe of liver was used to observe pathological changes, collagen depositions and the concentrations of hydroxyproline. The most serious cystic and fibrotic changes appeared in FVB infected mice indicated by gross observation, Masson’s trichrome staining and hydroxyproline content detection. In contrast to C57BL/6 infected mice, diffuse nodules and more intensive fibrosis were observed in the BALB/c infected mice. No differences of the hepatic Th1 subset and Th17 subset were found among the three strains, but the hepatic Th2 and Treg cells and their relative cytokines were dramatically increased in the BALB/c and FVB infected groups compared with the C57BL/6 infected group (P<0.01). Importantly, increased Th2 subset and Treg subset all positively correlated with hydroxyproline contents (P<0.01). This result for the first time implied that the increased hepatic Th2 and Treg cell subsets were likely to play potential roles in the formation of biliary fibrosis in C. sinensis-infected mice.

Antimalarial Drug Therapy: The Role of Parasite Biology and Drug Resistance

Malaria continues to affect public health and economic growth in many regions of the world. The number of infections continues to rise and is associated with increased mortality, despite basic science and public health efforts. Drug therapy remains the mainstay of treatment and prevention of this disease. Plasmodium has a complex life cycle involving an arthropod vector and distinct stages within the human host. Each parasite stage plays a unique role in transmission, disease, and latency. These different stages may vary in their response to the various antimalarial compounds. This article will review antimalarial therapies and drug resistance in the context of the parasites' biology.

Effects of a recombinant schistosomal-derived anti-inflammatory molecular (rSj16) on the lipopolysaccharide (LPS)-induced activated RAW264.7

Macrophages as a principal component of immune system play an important role in the initiation, modulation, and final activation of immune response against pathogens including schistosomes. Classical (M1) or alternative (M2) activation states of macrophage have different functions during infections. Previously, we report that the schistosomal-derived anti-inflammatory molecule coding gene (named Sj16) was isolated and the recombinant Sj16 (rSj16) was expressed in Escherichia coli. rSj16 has been demonstrated to have definite anti-inflammatory effect in vivo and in vitro on rodent model. To study the molecular basis on anti-inflammatory of rSj16, in the present paper, we investigate the effects of rSj16 on the lipopolysaccharide (LPS)-induced activated RAW264.7, a murine macrophage cell line. We found that rSj16 inhibited LPS-induced activation of RAW264.7, as evidenced by impacting the proliferation, phagocytosis, and migration of the RAW264.7. After pretreated with rSj16, it showed the most potent inhibitory effects of rSj16 on the nitric oxide production in RAW264.7 cells. Furthermore, rSj16 also significantly decreased the levels of proinflammatory cytokines such as PGE2, IL-1β, IL-6, IL-12, IL-23, and TNF-α, whereas it increased the levels of immunosuppressive cytokine IL-10. rSj16 can also inhibit the LPS-induced activation of NF-κβ. These results further imply that Sj16 contributes to the immune evasion of Schistosoma japonicum through alternatively activated macrophage (M2), and rSj16 is expected to serve as a potential drug source for the medication of inflammatory disorders.

Human cerebral malaria and Plasmodium falciparum genotypes in Malawi

BACKGROUND

Cerebral malaria, a severe form of Plasmodium falciparum infection, is an important cause of mortality in sub-Saharan African children. A Taqman 24 Single Nucleotide Polymorphisms (SNP) molecular barcode assay was developed for use in laboratory parasites which estimates genotype number and identifies the predominant genotype.

METHODS

The 24 SNP assay was used to determine predominant genotypes in blood and tissues from autopsy and clinical patients with cerebral malaria.

RESULTS

Single genotypes were shared between the peripheral blood, the brain, and other tissues of cerebral malaria patients, while malaria-infected patients who died of non-malarial causes had mixed genetic signatures in tissues examined. Children with retinopathy-positive cerebral malaria had significantly less complex infections than those without retinopathy (OR = 3.7, 95% CI [1.51-9.10]).The complexity of infections significantly decreased over the malaria season in retinopathy-positive patients compared to retinopathy-negative patients.

CONCLUSIONS

Cerebral malaria patients harbour a single or small set of predominant parasites; patients with incidental parasitaemia sustain infections involving diverse genotypes. Limited diversity in the peripheral blood of cerebral malaria patients and correlation with tissues supports peripheral blood samples as appropriate for genome-wide association studies of parasite determinants of pathogenicity.

Transmission stages dominate trypanosome within-host dynamics during chronic infections

Sleeping sickness is characterized by waves of the extracellular parasite Trypanosoma brucei in host blood, with infections continuing for months or years until inevitable host death. These waves reflect the dynamic conflict between the outgrowth of a succession of parasite antigenic variants and their control by the host immune system. Although a contributor to these dynamics is the density-dependent differentiation from proliferative “slender forms” to transmissible “stumpy forms,” an absence of markers discriminating stumpy forms has prevented accurate parameterization of this component. Here, we exploit the stumpy-specific PAD1 marker, which functionally defines transmission competence, to quantitatively monitor stumpy formation during chronic infections. This allows reconstruction of the temporal events early in infection. Mathematical modeling of these data describes the parameters controlling trypanosome within-host dynamics and provides strong support for a quorum-sensing-like mechanism. Our data reveal the dominance of transmission stages throughout infection, a consequence being austere use of the parasite's antigen repertoire.

Expulsion of Trichuris muris is associated with increased expression of angiogenin 4 in the gut and increased acidity of mucins within the goblet cell

Background

Trichuris muris in the mouse is an invaluable model for infection of man with the gastrointestinal nematode Trichuris trichiura. Three T. muris isolates have been studied, the Edinburgh (E), the Japan (J) and the Sobreda (S) isolates. The S isolate survives to chronicity within the C57BL/6 host whereas E and J are expelled prior to reaching fecundity. How the S isolate survives so successfully in its host is unclear.

Results

Microarray analysis was used as a tool to identify genes whose expression could determine the differences in expulsion kinetics between the E and S T. muris isolates. Clear differences in gene expression profiles were evident as early as day 7 post-infection (p.i.). 43 probe sets associated with immune and defence responses were up-regulated in gut tissue from an E isolate-infected C57BL/6 mouse compared to tissue from an S isolate infection, including the message for the anti-microbial protein, angiogenin 4 (Ang4). This led to the identification of distinct differences in the goblet cell phenotype post-infection with the two isolates.

Conclusion

Differences in gene expression levels identified between the S and E-infected mice early during infection have furthered our knowledge of how the S isolate persists for longer than the E isolate in the C57BL/6 mouse. Potential new targets for manipulation in order to aid expulsion have been identified. Further we provide evidence for a potential new marker involving the acidity of the mucins within the goblet cell which may predict outcome of infection within days of parasite exposure.

Evolution in Candida albicans populations during a single passage through a mouse host

The mechanisms and rates by which genotypic and phenotypic variation is generated in opportunistic, eukaryotic pathogens during growth in hosts are not well understood. We evaluated genomewide genetic and phenotypic evolution in Candida albicans, an opportunistic fungal pathogen of humans, during passage through a mouse host (in vivo) and during propagation in liquid culture (in vitro). We found slower population growth and higher rates of chromosome-level genetic variation in populations passaged in vivo relative to those grown in vitro. Interestingly, the distribution of long-range loss of heterozygosity (LOH) and chromosome rearrangement events across the genome differed for the two growth environments, while rates of short-range LOH were comparable for in vivo and in vitro populations. Further, for the in vivo populations, there was a positive correlation of cells demonstrating genetic alterations and variation in colony growth and morphology. For in vitro populations, no variation in growth phenotypes was detected. Together, our results demonstrate that passage through a living host leads to slower growth and higher rates of genomic and phenotypic variation compared to in vitro populations. Results suggest that the dynamics of population growth and genomewide rearrangement contribute to the maintenance of a commensal and opportunistic life history of C. albicans.

Antigenic variation in Plasmodium falciparum

The persistence of the human malaria parasite Plasmodium falciparum during blood stage proliferation in its host depends on the successive expression of variant molecules at the surface of infected erythrocytes. This variation is mediated by the differential control of a family of surface molecules termed PfEMP1 encoded by approximately 60 var genes. Each individual parasite expresses a single var gene at a time, maintaining all other members of the family in a transcriptionally silent state. PfEMP1/var enables parasitized erythrocytes to adhere within the microvasculature, resulting in severe disease. This review highlights key regulatory mechanisms thought to be critical for monoallelic expression of var genes. Antigenic variation is orchestrated by epigenetic factors including monoallelic var transcription at separate spatial domains at the nuclear periphery, differential histone marks on otherwise identical var genes, and var silencing mediated by telomeric heterochromatin. In addition, controversies surrounding var genetic elements in antigenic variation are discussed.

Unpacking β: Within-Host Dynamics and the Evolutionary Ecology of Pathogen Transmission

Rather than being fixed, pathogen transmission varies and is thus an object of natural selection. I examine how opportunities for selection on pathogen transmission depend on (a) pathogen fitness, (b) genetic variability, and (c) forces acting at within- and between-host levels. The transmission rate, β, influences processes such as epidemic spread, postepidemic fade-outs, and low-level persistence. Complexity of infection processes within hosts leads to different transmission rates among hosts and between types of pathogens (viruses, bacteria, eukaryotic Protozoa). Generality emerges, however, by “unpacking” β into within- and between-host opportunities for selection. This is illustrated by evolutionary biology of the bacterium Yersinia pestis, which causes plague in mammals, remains highly virulent and is transmitted by multiple routes, including fleas and direct contacts with infected hosts. The strength of within-host selection is manifested through infectivity, replication, pathogenicity, and dissemination from hosts. At the between-host level, responses to selection are less predictable because of environmental variation, whereas vector-borne transmission (usually by arthropods) provides additional opportunities for selection and trade-offs between vectors and hosts. In subdivided host populations, selection favors transmission before local pathogen extinction occurs, but key components (e.g. infectious periods of hosts) are determined by within-host dynamics. Pathogen transmission is often viewed in the context of transmission-virulence trade-offs, but within-host dynamics may cause host damage unrelated to transmission, and thus transmission-virulence trade-offs are not universal.

Relevance of the diversity among members of the Trypanosoma cruzi trans-sialidase family analyzed with camelids single-domain antibodies

The sialic acid present in the protective surface mucin coat of Trypanosoma cruzi is added by a membrane anchored trans-sialidase (TcTS), a modified sialidase that is expressed from a large gene family. In this work, we analyzed single domain camelid antibodies produced against trans-sialidase. Llamas were immunized with a recombinant trans-sialidase and inhibitory single-domain antibody fragments were obtained by phage display selection, taking advantage of a screening strategy using an inhibition test instead of the classic binding assay. Four single domain antibodies displaying strong trans-sialidase inhibition activity against the recombinant enzyme were identified. They share the same complementarity-determining region 3 length (17 residues) and have very similar sequences. This result indicates that they likely derived from a unique clone. Probably there is only one structural solution for tight binding inhibitory antibodies against the TcTS used for immunization. To our surprise, this single domain antibody that inhibits the recombinant TcTS, failed to inhibit the enzymatic activity present in parasite extracts. Analysis of individual recombinant trans-sialidases showed that enzymes expressed from different genes were inhibited to different extents (from 8 to 98%) by the llama antibodies. Amino acid changes at key positions are likely to be responsible for the differences in inhibition found among the recombinant enzymes. These results suggest that the presence of a large and diverse trans-sialidase family might be required to prevent the inhibitory response against this essential enzyme and might thus constitute a novel strategy of T. cruzi to evade the host immune system.

Stability and bifurcations in a model of antigenic variation in malaria

We examine the properties of a recently proposed model for antigenic variation in malaria which incorporates multiple epitopes and both long-lasting and transient immune responses. We show that in the case of a vanishing decay rate for the long-lasting immune response, the system exhibits the so-called "bifurcations without parameters" due to the existence of a hypersurface of equilibria in the phase space. When the decay rate of the long-lasting immune response is different from zero, the hypersurface of equilibria degenerates, and a multitude of other steady states are born, many of which are related by a permutation symmetry of the system. The robustness of the fully symmetric state of the system was investigated by means of numerical computation of transverse Lyapunov exponents. The results of this exercise indicate that for a vanishing decay of long-lasting immune response, the fully symmetric state is not robust in the substantial part of the parameter space, and instead all variants develop their own temporal dynamics contributing to the overall time evolution. At the same time, if the decay rate of the long-lasting immune response is increased, the fully symmetric state can become robust provided the growth rate of the long-lasting immune response is rapid.

Predicting biological system objectives de novo from internal state measurements

Background

Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells to optimally produce byproducts of commercial value, such as bioethanol, as well as molecular compounds for disease therapy. Flux balance analysis (FBA) is an optimization framework that aids in this interrogation by generating predictions of optimal flux distributions in cellular networks. Critical features of FBA are the definition of a biologically relevant objective function (e.g., maximizing the rate of synthesis of biomass, a unit of measurement of cellular growth) and the subsequent application of linear programming (LP) to identify fluxes through a reaction network. Despite the success of FBA, a central remaining challenge is the definition of a network objective with biological meaning.

Results

We present a novel method called Biological Objective Solution Search (BOSS) for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables. Specifically, BOSS identifies a system objective by defining a putative stoichiometric "objective reaction," adding this reaction to the existing set of stoichiometric constraints arising from known interactions within a network, and maximizing the putative objective reaction via LP, all the while minimizing the difference between the resultant in silico flux distribution and available experimental (e.g., isotopomer) flux data. This new approach allows for discovery of objectives with previously unknown stoichiometry, thus extending the biological relevance from earlier methods. We verify our approach on the well-characterized central metabolic network of Saccharomyces cerevisiae.

Conclusion

We illustrate how BOSS offers insight into the functional organization of biochemical networks, facilitating the interrogation of cellular design principles and development of cellular engineering applications. Furthermore, we describe how growth is the best-fit objective function for the yeast metabolic network given experimentally-measured fluxes.

Gene conversion is a convergent strategy for pathogen antigenic variation

Recent studies on three unrelated vector-borne pathogens, Anaplasma marginale, Borrelia hermsii and Trypanosoma brucei, illustrate the central importance of gene conversion as a mechanism for antigenic variation, which results in subsequent evasion of the immune response and persistence in the reservoir host. The combination of genome sequence data and in vivo studies tracking variant emergence not only provides insight into the genetic mechanisms for variant generation and hierarchy in variant expression but also highlights gaps in our knowledge regarding variant capacity and usage in vivo.

The use of Trichuris suis and other helminth therapies to treat Crohn’s disease

Infections with gastrointestinal (GI) nematodes are prevalent worldwide, despite the fact that anti-helminthic medications are regarded as safe, efficient, and widely available globally. In this review, we highlight the potential therapeutic benefits that may be realized through the clinical use of Trichuris suis and other helminths for Crohn's disease (CD). Long-lived helminthic parasites are remarkable in their ability to down-regulate host immunity, protecting themselves from elimination, and also minimize severe pathological host changes. This review summarizes what is known about the underlying mechanisms that may account for the observed patterns in humans treated with helminths for CD. The Th2 arm of the immune system is emphasized as a component of primary importance in the association between the host immune system and GI nematode infections. Although GI nematode infections in humans cause significant morbidity and mortality, the existence and nature of protective mechanisms these helminths may confer remain largely unclear.

Mapping the antigenicity of the parasites in Leishmania donovani infection by proteome serology

Background

Leishmaniasis defines a cluster of protozoal diseases with diverse clinical manifestations. The visceral form caused by Leishmania donovani is the most severe. So far, no vaccines exist for visceral leishmaniasis despite indications of naturally developing immunity, and sensitive immunodiagnostics are still at early stages of development.

Methodology/Principle Findings

Establishing a proteome-serological methodology, we mapped the antigenicity of the parasites and the specificities of the immune responses in human leishmaniasis. Using 2-dimensional Western blot analyses with sera and parasites isolated from patients in India, we detected immune responses with widely divergent specificities for up to 330 different leishmanial antigens. 68 antigens were assigned to proteins in silver- and fluorochrome-stained gels. The antigenicity of these proteins did not correlate with the expression levels of the proteins. Although some antigens are shared among different parasite isolates, there are extensive differences and no immunodominant antigens, but indications of antigenic drift in the parasites. Six antigens were identified by mass spectrometry.

Conclusions/Significance

Proteomics-based dissection of the serospecificities of leishmaniasis patients provides a comprehensive inventory of the complexity and interindividual heterogeneity of the host-responses to and variations in the antigenicity of the Leishmania parasites. This information can be instrumental in the development of vaccines and new immune monitoring and diagnostic devices.

Pathogen escape from host immunity by a genome program for antigenic variation

The vector-borne bacterium Borrelia hermsii, a relapsing fever agent, switches gene expression of a surface protein between different antigenic variants, thereby causing sequential waves of immune escape within hosts and increasing the likelihood of transmission. Analogous programmed systems of antigenic variation occur in African trypanosomes and Plasmodium falciparum. In these examples, switch rates to individual variants differ over a wide range. We studied how B. hermsii determines switch rates in two experimental infections: one where variants were identified by specific antisera and one based on identification by DNA sequence. Unexpressed loci of variant antigens copy into a single expression site at rates determined by extragenic features of silent loci rather than similarity between coding sequences of variants at silent sites and the single expression site. Two elements, in particular, determine switch rates. One set of elements overlaps the 5' ends of the expressed gene and the silent loci; greater sequence identity between elements was associated with a higher switch rate. The second set of elements flanks the expression site on the 3' side and occurs at variable distances downstream from silent loci; the nearer an element to a silent locus, the greater the switch rate of that locus into the expression site. In combination, these two features of the genome provide a simple mechanism to modulate switch rate whereby silent loci form a hierarchy of switch rates into the expression site. Although the switching hierarchy causes changes in individual cells that are stochastic, ordering of variants within hosts is semipredictable.

The emergence of Beijing family genotypes of Mycobacterium tuberculosis and low-level protection by bacille Calmette-Guérin (BCG) vaccines: is there a link?

The world is confronted with major tuberculosis (TB) outbreaks at a time when the protection of bacillus Calmette-Guérin (BCG) vaccine has become inconsistent and controversial. Major TB outbreaks are caused by a group of genetically similar strains of Mycobacterium tuberculosis (Mtb) strains, including the Beijing family genotypes. The Beijing family genotypes exhibit important pathogenic features such high virulence, multi-drug resistance and exogenous reinfection. These family strains have developed mechanisms that modulate/suppress immune responses by the host, such as inhibition of apoptosis of infected macrophages, diminished production of interleukin (IL)-2, interferon (IFN)-gamma, tumour necrosis factor (TNF)-alpha and elevated levels of IL-10 and IL-18. They demonstrate distinct expression of proteins, such as several species of alpha-crystallin (a known Mtb virulence factor), but decreased expression of some antigens such as heat shock protein of 65 kDa, phosphate transport subunit S and a 47-kDa protein. In addition, the Beijing family strains specifically produce a highly bioactive lipid (a polyketide synthase)-derived phenolic glycolipid. This altered expression of proteins/glycolipids may be important factors underlying the success of the Beijing family strains. The Beijing family strains are speculated to have originated from South-east Asia, where BCG vaccination has been used for more than 60 years. The hypothesis that mass BCG vaccination may have been a selective factor that favoured genotypic and phenotypic characteristic acquired by the Beijing family strains is discussed.

Immune reconstitution disease associated with parasitic infections following antiretroviral treatment

HIV-associated immune reconstitution disease (IRD) is the clinical presentation or deterioration of opportunistic infections that results from enhancement of pathogen-specific immune responses among patients responding to antiretroviral treatment (ART). The vast majority of reported cases of IRD have been associated with mycobacterial, chronic viral and invasive fungal infections; such cases result from dysregulated augmentation of cell-mediated type 1 cytokine-secreting host immune responses. However, the spectrum of infections now recognized as associated with IRD is expanding and includes a number of parasitic infections, which may be mediated by different immunopathological mechanisms. These include leishmaniasis (visceral, cutaneous, mucosal and post kala azar dermal leishmaniasis), schistosomiasis and strongyloidiasis. Since the major burden of HIV lies in resource-limited countries where access to ART is now rapidly expanding, increased awareness and knowledge of these phenomena is important. Here we review the clinical spectrum and pathogenesis of IRD associated with parasitic infections.

Antigenic variation by protozoan parasites: insights from Babesia bovis

Antigenic variation of surface membrane proteins by protozoan parasites enables these pathogenic organisms to avoid host immune responses and thus perpetuate long-term infections. Babesia bovis, the causative agent of severe babesiosis in cattle, was previously shown to undergo antigenic variation through modifications to its primary surface antigen, a protein called VESA1. In this issue, Al-Khedery and Allred provide a detailed description of the genes that encode VESA1 and present convincing evidence for progressive, segmental gene conversion in the generation of variant forms of this surface antigen.