Infectome: A platform to trace infectious triggers of autoimmunity

The “exposome” is a term recently used to describe all environmental factors, both exogenous and endogenous, which we are exposed to in a lifetime. It represents an important tool in the study of autoimmunity, complementing classical immunological research tools and cutting-edge genome wide association studies (GWAS). Recently, environmental wide association studies (EWAS) investigated the effect of environment in the development of diseases. Environmental triggers are largely subdivided into infectious and non-infectious agents. In this review, we introduce the concept of the “infectome”, which is the part of the exposome referring to the collection of an individual's exposures to infectious agents. The infectome directly relates to geoepidemiological, serological and molecular evidence of the co-occurrence of several infectious agents associated with autoimmune diseases that may provide hints for the triggering factors responsible for the pathogenesis of autoimmunity. We discuss the implications that the investigation of the infectome may have for the understanding of microbial/host interactions in autoimmune diseases with long, pre-clinical phases. It may also contribute to the concept of the human body as a superorganism where the microbiome is part of the whole organism, as can be seen with mitochondria which existed as microbes prior to becoming organelles in eukaryotic cells of multicellular organisms over time. A similar argument can now be made in regard to normal intestinal flora, living in symbiosis within the host. We also provide practical examples as to how we can characterise and measure the totality of a disease-specific infectome, based on the experimental approaches employed from the “immunome” and “microbiome” projects.     

Tracing environmental markers of autoimmunity: introducing the infectome

We recently introduced the concept of the infectome as a means of studying all infectious factors which contribute to the development of autoimmune disease. It forms the infectious part of the exposome, which collates all environmental factors contributing to the development of disease and studies the sum total of burden which leads to the loss of adaptive mechanisms in the body. These studies complement genome-wide association studies, which establish the genetic predisposition to disease. The infectome is a component which spans the whole life and may begin at the earliest stages right up to the time when the first symptoms manifest, and may thus contribute to the understanding of the pathogenesis of autoimmunity at the prodromal/asymptomatic stages. We provide practical examples and research tools as to how we can investigate disease-specific infectomes, using laboratory approaches employed from projects studying the “immunome” and “microbiome”. It is envisioned that an understanding of the infectome and the environmental factors that affect it will allow for earlier patient-specific intervention by clinicians, through the possible treatment of infectious agents as well as other compounding factors, and hence slowing or preventing disease development.     

An economic model of 2-hour post-dose ciclosporin monitoring in renal transplantation

BACKGROUND: Monitoring of microemulsion ciclosporin (cyclosporine; Neoral) by 2-hour post-dose drug concentrations (C2) is an accurate measure of ciclosporin absorption efficiency and exposure, and appears superior to trough (C0) monitoring for prediction of rejection risk. A predictive decision model was used to determine if this approach also reduces total treatment costs in the first 12 months after renal transplantation. METHODS: Parameter estimates for key clinical events were derived from the literature and from prospective pharmacokinetic studies comprising 234 adult HLA-non-identical renal graft recipients at seven Canadian centres. Patients were treated with microemulsion ciclosporin (Neoral), corticosteroids and azathioprine or mycophenolate mofetil. Using the perspective of the Canadian healthcare provider, total treatment costs for the C2 versus the C0 strategy were modelled over 12 months, and then remodelled using conservative estimates to extend the timeframe to 5 years. Health resources were valued in 1999 Canadian dollars. RESULTS: The incidence of acute rejection was estimated to be 25% at 1 year in patients monitored by C0 and 18% in those monitored by C2. Patient survival was considered to be independent of monitoring strategy, and graft loss was predicted to be 1.4% lower in the C2 group. The studies suggested no important differences in comorbidity and the costs of C0 and C2 monitoring and ambulatory-based adverse events were held equivalent. Using these inputs, the average cost per patient for the first year post-transplant was Can dollars 46,857 for C0 monitoring and Can dollars 45,306 for C2 monitoring, rising to Can dollars 146,879 and Can dollars 142,569 after 5 years. The predicted cost for initial hospitalisation was Can dollars 11,280 for C0 and Can dollars 10,806 for C2 monitoring. The cost of maintenance immunosuppressive drug use, graft loss and dialysis was Can dollars 19,098 in the C0 group and Can dollars 18,612 in the C2 group, while acute rejection treatment costs were Can dollars 2169 and Can dollars 1577, respectively. An additional Can dollars 14,310 was consumed by other events, including repeat hospitalisation, for each group. Sensitivity analysis indicated that the most influential parameters affecting savings due to C2 monitoring were a reduction in the duration of initial and follow-up hospitalisations and reduced risks of acute rejection and subsequent graft loss. CONCLUSIONS: Compared with traditional trough concentration monitoring, ciclosporin monitoring at 2 hours post-dose produced a predicted saving of Can dollars 1551 during the first year after renal transplant. Although modelling assumptions become more restrictive over time, this projection allows a preliminary assessment of the long-term economic impact of the routine use of C2 monitoring.     

5' exonuclease assay for detection of serogroup Y Neisseria meningitidis

The incidence of serogroup Y meningococcal disease has increased recently in the United States. Here, we describe the development of a 5' exonuclease assay for the detection of serogroup Y Neisseria meningitidis and demonstrate the usefulness of this assay for resolving serogroup identification of strains that are resistant to conventional serogrouping and for the nonculture identification of serogroup Y meningococcal disease.     

Priming of the vascular endothelial growth factor signaling pathway by thrombospondin-1, CD36, and spleen tyrosine kinase

CD36 plays a critical role in the inhibition of angiogenesis through binding to the type 1 repeats of thrombospondin-1 (TSP-1) and activating Fyn tyrosine kinase and MAPK pathways. Here, we reveal a novel association of CD36 with VEGFR-2 and spleen tyrosine kinase (Syk). We also address the correlation between the expression of CD36 and Syk by demonstrating that overexpression of CD36 in HUVECs up-regulates endogenous Syk expression. We also define a new role for TSP-1 and CD36 in the activation of the VEGFR-2 signaling pathway that requires Syk. Our findings also identify a role for Syk as a stimulator of VEGF-A-induced angiogenesis by increasing phosphorylation of Y1175 in VEGFR-2, which is a major tyrosine for promoting VEGF-A-induced endothelial cell migration. Together, these studies introduce a new signaling pathway for TSP-1, CD36, and Syk, and address the role of these proteins in regulating the angiogenic switch.     

Skin prick test to egg white provides additional diagnostic utility to serum egg white-specific IgE antibody concentration in children

BACKGROUND: Levels of IgE antibody to egg white of greater than 7 kIU/L are highly predictive of clinical reactivity to egg, and lower levels often require evaluation with oral food challenge (OFC) to establish definitive diagnosis. OFCs have inherent risks, and diagnostic criteria indicating high likelihood of passing would be clinically useful. OBJECTIVE: We sought to determine whether the size of the skin prick test (SPT) to egg white adds diagnostic utility for children with low egg white-specific IgE antibody levels. METHODS: A retrospective analysis of clinical history, egg white-specific IgE antibody levels, SPT responses, and egg OFC outcomes was performed. RESULTS: Children who passed (n = 29) egg OFCs and those who failed (n = 45) did not differ significantly in age, clinical characteristics, or egg white-specific IgE levels. There were, however, significant differences between both egg white SPT wheal response size and egg/histamine SPT wheal index. Children who failed egg OFCs had a median wheal of 5.0 mm; those who passed had a median wheal of 3.0 mm (P = .003). Children who failed egg OFCs had a median egg/histamine index of 1.00; those who passed had a median index of 0.71 (P = .001). For egg white-specific IgE levels of less than 2.5 kIU/L, an SPT wheal of 3 mm or an egg/histamine index of 0.65 was associated with a 50% chance of passing. CONCLUSION: In children with low egg white-specific IgE levels, those with smaller SPT wheal responses to egg were more likely to pass an egg OFC than those with larger wheal responses. The size of the egg white SPT response might provide additional information to determine the timing of egg OFC. CLINICAL IMPLICATIONS: The size of the egg white SPT wheal response might provide the clinician with additional information to determine the timing of egg OFC in children with low egg white-specific IgE antibody levels.     

Biochemical and Pathogenic Properties of Shewanella alga and Shewanella putrefaciens

We characterized 49 strains of Shewanella spp. from clinical (n = 31) and nonhuman (n = 18) sources. Most Shewanella alga organisms (Gilardi biovar 2; Centers for Disease Control and Prevention [CDC] biotype 2) originated from clinical material (92%), failed to produce acid from carbohydrates other than d-ribose, and were biochemically and enzymatically fairly homogeneous. In contrast, Shewanella putrefaciens organisms (Gilardi biovars 1 and 3; CDC biotype 1) were more often associated with nonhuman sources (70%), were able to utilize a number of sugars (sucrose, l-arabinose, and maltose), and were found to exhibit wider variations in biochemical characteristics; three biotypes within S. putrefaciens were detected. Notable differences between the two species in enzymatic activity, determined with the API-ZYM system (bioMérieux, Hazelwood, Mo.), and cellular fatty acid profiles, determined by the MIDI system (Microbial ID Inc., Newark, Del.), were also detected. Pathogenicity studies of mice indicate that S. alga appears to be the more virulent species, possibly due to the production of a hemolytic substance.The taxon Shewanella putrefaciens (“Pseudomonas putrefaciens”) comprises a group of gram-negative oxidative and nonoxidative bacilli whose chief phenotypic attribute is the production of hydrogen sulfide gas (H₂S) on TSI slants (22). Although S. putrefaciens has been implicated occasionally as a human pathogen, it is most frequently recovered from nonhuman sources, including aquatic reservoirs (marine, freshwater, and sewage), natural energy reserves (oil and gas), soil, and fish, poultry, dairy, and beef products (14, 18, 20, 21). Most human isolates of S. putrefaciens occur as part of a mixed bacterial flora, clouding their clinical significance. However, a number of monomicrobic illnesses due to S. putrefaciens have been documented and include bacteremia, soft tissue infections, and otitis media (1, 2, 4, 13).For over two decades, it has been known that S. putrefaciens is a genetically heterogeneous species. These conclusions are based upon the wide variation in G+C content (44 to 54 mol%), results of DNA-DNA reassociation studies, and numerical taxonomy investigations (14, 17, 18, 20, 21). As late as the 1980s, Gilardi (6) recognized three distinct biovars within S. putrefaciens, while the Centers for Disease Control and Prevention (CDC) (22) recognized two biotypes based upon carbohydrate oxidation patterns and growth on salmonella-shigella (SS) medium and nutrient agar containing high salt (∼6%) concentrations. In 1990, Simidu et al. (19) proposed the name Shewanella alga for a tetrodotoxin-producing isolate recovered from red algae. Subsequent to this publication, Nozue and colleagues (15) found that strains of S. putrefaciens with high G+C contents (52 to 54 mol%) were genetically related to S. alga and not to the type strain of S. putrefaciens (ATCC 8071). Furthermore, the latter study found that all S. alga strains produced a hemolytic reaction on sheep blood agar while S. putrefaciens isolates lacked this activity.Of 40 clinical isolates of S. putrefaciens reidentified by Nozue and others (15), 33 (83%) were found to be S. alga based upon DNA homology values and phenotypic criteria. Domínguez et al. (5) later reported the first two Danish cases of S. alga bacteremia, which had originally been mistakenly attributed to S. putrefaciens. A follow-up 1997 systematic investigation of 76 Shewanella strains found that 16 of 19 human isolates (84%) resided within the S. alga group, based upon various taxonomic criteria including 16S rRNA sequencing, ribotyping, and whole-cell protein profiles (21). These studies suggest that S. alga may be the predominant human pathogen within the genus.Presently, it is unclear how easy it is to distinguish S. putrefaciens from S. alga in the clinical laboratory and whether or not differences in host tropism do occur and correlate with pathogenic characteristics and overt virulence. In light of these questions, we have analyzed the biochemical and enzymatic capabilities of 49 Shewanella strains from diverse sources (human and nonhuman) to address these issues and have performed pathogenicity studies on representative strains from each group. These studies serve as the basis of this report.