The Janus Face of NKT Cell Function in Autoimmunity and Infectious Diseases

Natural killer T cells (NKT) are a subset of T lymphocytes bridging innate and adaptive immunity. These cells recognize self and microbial glycolipids bound to non-polymorphic and highly conserved CD1d molecules. Three NKT cell subsets, type I, II, and NKT-like expressing different antigen receptors (TCR) were described and TCR activation promotes intracellular events leading to specific functional activities. NKT can exhibit different functions depending on the secretion of soluble molecules and the interaction with other cell types. NKT cells act as regulatory cells in the defense against infections but, on the other hand, their effector functions can be involved in the pathogenesis of several inflammatory disorders due to their exposure to different microbial or self-antigens, respectively. A deep understanding of the biology and functions of type I, II, and NKT-like cells as well as their interplay with cell types acting in innate (neuthrophils, innate lymphoid cells, machrophages, and dendritic cells) and adaptive immunity (CD4⁺,CD8⁺, and double negative T cells) should be important to design potential immunotherapies for infectious and autoimmune diseases.

Coupled, multi-strain epidemic models of mutating pathogens

We introduce and analyze coupled, multi-strain epidemic models designed to simulate the emergence and dissemination of mutant (e.g. drug-resistant) pathogen strains. In particular, we investigate the mathematical and biological properties of a general class of multi-strain epidemic models in which the infectious compartments of each strain are coupled together in a general manner. We derive explicit expressions for the basic reproduction number of each strain and highlight their importance in regulating the system dynamics (e.g. the potential for an epidemic outbreak) and the existence of nonnegative endemic solutions. Importantly, we find that the basic reproduction number of each strain is independent of the mutation rates between the strains - even under quite general assumptions for the form of the infectious compartment coupling. Moreover, we verify that the coupling term promotes strain coexistence (as an extension of the competitive exclusion principle) and demonstrate that the strain with the greatest reproductive capacity is not necessarily the most prevalent. Finally, we briefly discuss the implications of our results for public health policy and planning.

Potential of real-time PCR threshold cycle (CT) to predict presence of free toxin and clinically relevant C. difficile infection (CDI) in patients with cancer

OBJECTIVES

Clostridium difficile infection (CDI) is a toxin-mediated disease. Oncology patients are at increased risk for developing CDI. Diagnosis of CDI by PCR has led to misclassification of some C. difficile carriers as CDI cases. We determined if an optimized C. difficile PCR cycle threshold value (C_T) could reliably predict presence of free toxin, and in turn improve the utility of PCR in detecting clinically relevant CDI in oncology patients.

METHODS

183 consecutive patients positive for C. difficile by the Xpert C. difficile were additionally tested using the cell culture cytotoxicity neutralization assay (CYT) and enzyme immunoassays (EIA). C_T values at diagnosis and relevant clinical information were recorded. Receiver operating characteristic (ROC) curve was used to assess predictive validity and to find optimal C_T for CYT positive cases. Severity of CDI was assessed by blinded charts review.

RESULTS

Using CYT as the reference, ROC-derived Youden cut-off C_T of 28.0 predicted 77% cytotoxin positive cases, and 91% and 100% of severe and complicated CDI episodes respectively. The median C_T values for non-severe, severe, and complicated CDI episodes were 28.0, 24.5 and 22.5 respectively (p = 0.005).

CONCLUSIONS

Lower C_T value of the Xpert C. difficile PCR was associated with the presence of toxin and increased CDI severity. C_T values may be beneficial in interpreting positive C. difficile PCR results.

PBIT: Pipeline Builder for Identification of drug Targets for infectious diseases

Summary

PBIT (Pipeline Builder for Identification of drug Targets) is an online webserver that has been developed for screening of microbial proteomes for critical features of human drug targets such as being non-homologous to human proteome as well as the human gut microbiota, essential for the pathogen's survival, participation in pathogen-specific pathways etc. The tool has been validated by analyzing 57 putative targets of Candida albicans documented in literature. PBIT integrates various in silico approaches known for drug target identification and will facilitate high-throughput prediction of drug targets for infectious diseases, including multi-pathogenic infections.

Availability and Implementation

PBIT is freely accessible at http://www.pbit.bicnirrh.res.in/ .

Contact

thomass@nirrh.res.in.

Supplementary information

Supplementary data are available at Bioinformatics online.

Q&A: What are pathogens, and what have they done to and for us?

Microbes are found on us, within us and around us. They inhabit virtually every environment on the planet and the bacteria carried by an average human, mostly in their gut, outnumber human cells. The vast majority of microbes are harmless to us, and many play essential roles in plant, animal and human health. Others, however, are either obligate or facultative pathogens exerting a spectrum of deleterious effects on their hosts. Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines. From the dawn of humanity and throughout history, infectious diseases have shaped human evolution, demography, migrations and history.

Development of Protein-Protein Interaction Inhibitors for the Treatment of Infectious Diseases

Protein-protein interaction (PPI) inhibitors are a rapidly expanding class of therapeutics. Recent advances in our understanding of PPIs and success of early examples of PPI inhibitors demonstrate the feasibility of targeting PPIs. This review summarizes the techniques used for the discovery and optimization of a diverse set PPI inhibitors, focusing on the development of PPI inhibitors as new antibacterial and antiviral agents. We close with a summary of the advances responsible for making PPI inhibitors realistic targets for therapeutic intervention and brief outlook of the field.

Metal-Based Nanoparticles for the Treatment of Infectious Diseases

Infectious diseases can be transmitted and they cause a significant burden on public health globally. They are the greatest world killers and it is estimated that they are responsible for the demise of over 17 million people annually. The impact of these diseases is greater in the developing countries. People with compromised immune systems and children are the most affected. Infectious diseases may be caused by bacteria, viruses, and protozoa. The treatment of infectious diseases is hampered by simultaneous resistance to multiple drugs, indicating that there is a serious and pressing need to develop new therapeutics that can overcome drug resistance. This review will focus on the recent reports of metal-based nanoparticles that are potential therapeutics for the treatment of infectious diseases and their biological efficacy (in vitro and in vivo).

Preventive Effect of Cow's Milk Fermented with Lactobacillus paracasei CBA L74 on Common Infectious Diseases in Children: A Multicenter Randomized Controlled Trial

Background: Fermented foods have been proposed to prevent common infectious diseases (CIDs) in children attending day care or preschool.

OBJECTIVES

To investigate the efficacy of dietary supplementation with cow's skim milk fermented with the probiotic Lactobacillus paracasei CBA L74 in reducing CIDs in children attending day care or preschool. Methods: Multicenter, randomized, double-blind, placebo-controlled trial on healthy children (aged 12-48 months) consuming daily 7 grams of cow's skim milk fermented with L. paracasei CBA L74 (group A), or placebo (maltodextrins group B) attending day care or preschool during the winter season. The main outcome was the proportion of children who experienced ≥1 episode of CID during a 3-month follow-up. Fecal biomarkers of innate (α- and β-defensins, cathelicidin) and acquired immunity (secretory IgA) were also monitored. Results: A total of 126 children (71 males, 56%) with a mean (SD) age of 33 (9) months completed the study, 66 in group A and 60 in group B. At intention to treat analysis, the proportion of children presenting ≥1 CID was 60% in group A vs. 83% in group B, corresponding to an absolute risk difference (ARD) of -23% (95% CI: -37% to -9%, p < 0.01). At per-protocol-analysis (PPA), the proportion of children presenting ≥1 CID was 18% in group A vs. 40% in group B, corresponding to an absolute risk difference (ARD) of -22% (95% CI: -37% to -6%, p < 0.01). PPA showed that the proportion of children presenting ≥1 acute gastroenteritis (AGE) was significantly lower in group A (18% vs. 40%, p < 0.05). The ARD for the occurrence of ≥1 AGE was -22% (95% CI: -37% to -6%, p < 0.01) in group A. Similar findings were obtained at PPA regarding the proportion of children presenting ≥1 upper respiratory tract infection (URTI), which was significantly lower in group A (51% vs. 74%, p < 0.05), corresponding to an ARD of -23% (95% CI: -40% to -7%, p < 0.01). Significant changes in innate and acquired immunity biomarkers were observed only in subjects in group A. Conclusions: Dietary supplementation with cow's skim milk fermented with L. paracasei CBA L74 is an efficient strategy in preventing CIDs in children.

3D printing and milling a real-time PCR device for infectious disease diagnostics

Diagnosing infectious diseases using quantitative polymerase chain reaction (qPCR) offers a conclusive result in determining the infection, the strain or type of pathogen, and the level of infection. However, due to the high-cost instrumentation involved and the complexity in maintenance, it is rarely used in the field to make a quick turnaround diagnosis. In order to provide a higher level of accessibility than current qPCR devices, a set of 3D manufacturing methods is explored as a possible option to fabricate a low-cost and portable qPCR device. The key advantage of this approach is the ability to upload the digital format of the design files on the internet for wide distribution so that people at any location can simply download and feed into their 3D printers for quick manufacturing. The material and design are carefully selected to minimize the number of custom parts that depend on advanced manufacturing processes which lower accessibility. The presented 3D manufactured qPCR device is tested with 20-μL samples that contain various concentrations of lentivirus, the same type as HIV. A reverse-transcription step is a part of the device's operation, which takes place prior to the qPCR step to reverse transcribe the target RNA from the lentivirus into complementary DNA (cDNA). This is immediately followed by qPCR which quantifies the target sequence molecules in the sample during the PCR amplification process. The entire process of thermal control and time-coordinated fluorescence reading is automated by closed-loop feedback and a microcontroller. The resulting device is portable and battery-operated, with a size of 12 × 7 × 6 cm3 and mass of only 214 g. By uploading and sharing the design files online, the presented low-cost qPCR device may provide easier access to a robust diagnosis protocol for various infectious diseases, such as HIV and malaria.

An online course improves nurses' awareness of their role as antimicrobial stewards in nursing homes

BACKGROUND

To support the role of nurses as active proponents of antimicrobial stewardship in long-term care facilities, we developed an educational intervention consisting of a free online course comprised of 6 interactive modules. Here, we report the effect of the course on the knowledge, beliefs, and attitudes toward antimicrobial stewardship of nurses working in long-term care facilities.

METHODS

We used a paired pre- and postcourse survey instrument to assess nurses' knowledge regarding the care of long-term care facility residents with infections and attitudes and beliefs regarding antimicrobial stewardship.

RESULTS

There were 103 respondents, registered nurses or licensed practical nurses, who completed the pre- and postsurveys. Their mean knowledge scores improved from 75% (precourse) to 86% (postcourse, P <.001). After the course, nurses' agreement that their role influences whether residents receive antimicrobials increased significantly (P <.001).

CONCLUSIONS

The online course improves nurses' knowledge regarding the care of long-term care facility residents with infections and improves their confidence to engage in antimicrobial stewardship activities. Empowering nurses to be antimicrobial stewards may help reduce unnecessary antibiotic use among institutionalized older adults.

Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases: The predominant clonal evolution model of pathogenic microorganisms

The predominant clonal evolution (PCE) model seeks to formulate a common population genetics framework for all micropathogens (namely, parasitic protozoa, fungi and yeasts, bacteria, and viruses). It relies on a definition of clonality that is only based on population structure features (namely, strongly restrained genetic recombination). Its clear-cut properties make it of strong interest for applied and basic research, since it permits the definition of stable, clearly delimited units of analysis below the species level: clonal genotypes and discrete genetic subdivisions (“near-clades”). These units of analysis can be used for clinical and epidemiological studies, vaccine and drug design, species description, and evolutionary studies on natural and experimental populations.

In this review, the evolutionary and population genetics background of the model will be only briefly mentioned, while considerable emphasis will be given to its practical significance for the study and control of neglected tropical diseases. The goal of the paper is to make this practical usefulness accessible to a broad audience of readers, including scientists who are not evolution specialists, such as epidemiologists, field scientists, and clinicians. For extensive developments about the evolutionary background of the model, see our previous papers [1–9]. Citations of these former articles lead to the many references quoted in them, which cannot be listed again here.

Adrenergic-mediated loss of splenic marginal zone B cells contributes to infection susceptibility after stroke

Infection is a major complication of acute stroke and causes increased mortality and morbidity; however, current interventions do not prevent infection and improve clinical outcome in stroke patients. The mechanisms that underlie susceptibility to infection in these patients are unclear. Splenic marginal zone (MZ) B cells are innate-like lymphocytes that provide early defence against bacterial infection. Here we show experimental stroke in mice induces a marked loss of MZ B cells, deficiencies in capturing blood-borne antigen and suppression of circulating IgM. These deficits are accompanied by spontaneous bacterial lung infection. IgM levels are similarly suppressed in stroke patients. β-adrenergic receptor antagonism after experimental stroke prevents loss of splenic MZ B cells, preserves IgM levels, and reduces bacterial burden. These findings suggest that adrenergic-mediated loss of MZ B cells contributes to the infection-prone state after stroke and identify systemic B-cell disruption as a target for therapeutic manipulation.

[Non-febrile syndromes in the traveler returning from tropical regions admitted in a monographic unit]

OBJECTIVE

The aim was to analyse those syndromes without fever in travellers who return from tropical regions evaluated at our Department of Infectology and Tropical Medicine. Clarifying these conditions intends to reach earlier diagnoses and, perhaps, to avoid the emergence and spread of imported diseases, as well as to establish appropriate preventive measures.

METHODS

An observational descriptive transversal study was performed, selecting those patients who returned from tropical regions without fever (n = 281), amongst all travellers evaluated in our department between 1998 and 2013. We analysed demographic features, information related to the trip, as well as the presenting complaints and the diagnoses.

RESULTS

A total of 281 international travellers presenting without fever were analysed. Only 39% had received health counsel prior to travelling. The most visited regions were Lat-in America (38.8%), Africa (37.8%) and Asia (13.6%). 15% of patients were asymptomatic or suffered from non-infectious conditions. Among the rest, most had either gastrointestinal (46%) or cutaneous (34%) syndromes. The main gastrointestinal condition was diarrhoea, with a microbiological diagnosis reached in almost 50% of cases. Regarding cutaneous syndromes, arthropods bites (31%) and different bacterial lesions (20%) were most common.

CONCLUSIONS

Approximately 10% of patients in Travel Medicine are international travellers returning from tropical regions, half of them with no fever. Most are diagnosed with infectious diseases, mainly gastrointestinal or cutaneous syn-dromes. Eosinophilia is the third problem in frequency among this group of patients, and sexually transmitted infections are rare in our cohort. It is important to emphasize in preventive activities.

Symptom screening rules to identify active pulmonary tuberculosis: Findings from the Zambian South African Tuberculosis and HIV/AIDS Reduction (ZAMSTAR) trial prevalence surveys

BACKGROUND

High tuberculosis (TB) burden countries should consider systematic screening among adults in the general population. We identified symptom screening rules to be used in addition to cough ≥2 weeks, in a context where X-ray screening is not feasible, aiming to increase the sensitivity of screening while achieving a specificity of ≥85%.

METHODS

We used 2010 Zambia South Africa Tuberculosis and HIV/AIDS Reduction (ZAMSTAR) survey data: a South African (SA) training dataset, a SA testing dataset for internal validation and a Zambian dataset for external validation. Regression analyses investigated relationships between symptoms or combinations of symptoms and active disease. Sensitivity and specificity were calculated for candidate rules.

RESULTS

Among all participants, the sensitivity of using only cough ≥2 weeks as a screening rule was less than 25% in both SA and Zambia. The addition of any three of six TB symptoms (cough <2 weeks, night sweats, weight loss, fever, chest pain, shortness of breath), or 2 or more of cough <2 weeks, night sweats, and weight loss, increased the sensitivity to ~38%, while reducing specificity from ~95% to ~85% in SA and ~97% to ~92% in Zambia. Among HIV-negative adults, findings were similar in SA, whereas in Zambia the increase in sensitivity was relatively small (15% to 22%).

CONCLUSION

High TB burden countries should investigate cost-effective strategies for systematic screening: one such strategy could be to use our rule in addition to cough ≥2 weeks.

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome

Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity.

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.

Using spatio-temporal surveillance data to test the infectious environment of children before type 1 diabetes diagnosis

The "hygiene hypothesis" postulates that reduced exposure to infections favours the development of autoimmunity and childhood type 1 diabetes (T1D). But on the other side, viruses, notably enteroviruses, are suspected to trigger T1D. The assessment of the possible relationships between infections and T1D still defies the classical tools of epidemiology. We report the methods and results of a geographical approach that maps the addresses of patients to a communicable diseases surveillance database. We mapped the addresses of patients at birth, infancy and T1D diagnosis to the weekly estimates of the regional incidences of 5 frequent communicable diseases routinely collected since 1984 by the French Sentinel network. The pre-diagnostic infectious environment of 3548 patients with T1D diagnosed between 0.5 and 15 years was compared to those of 100 series of age-matched "virtual controls" drawn randomly on the map. Associations were classified as "suggestive" (summer diarrhea, SD, and varicella, V) when p< 0.05, or "significant" (influenza-like infections, ILI) when they passed the Bonferroni correction for FDR. Exposure to ILI and SD were associated with T1D risk, while V seemed protective. In the subset of 2521 patients for which we had genome wide data, we used a case-only approach to search for interactions between SNPs and the infectious environment as defined by the Sentinel database. Two SNPs, rs116624278 and rs77232854, showed significant interaction with exposure to V between 1 and 3 years of life. The infectious associations found should be taken as possible markers of patients' environment, not as direct causative factors of T1D. They require replication in other populations. The increasing public availability of geographical environmental databases will expand the present approach to map thousands of environmental factors to the lifeline of patients affected by various diseases.

Approaches to biofilm-associated infections: the need for standardized and relevant biofilm methods for clinical applications

The concept of biofilms in human health and disease is now widely accepted as cause of chronic infection. Typically, biofilms show remarkable tolerance to many forms of treatments and the host immune response. This has led to vast increase in research to identify new (and sometimes old) anti-biofilm strategies that demonstrate effectiveness against these tolerant phenotypes. Areas covered: Unfortunately, a standardized methodological approach of biofilm models has not been adopted leading to a large disparity between testing conditions. This has made it almost impossible to compare data across multiple laboratories, leaving large gaps in the evidence. Furthermore, many biofilm models testing anti-biofilm strategies aimed at the medical arena have not considered the matter of relevance to an intended application. This may explain why some in vitro models based on methodological designs that do not consider relevance to an intended application fail when applied in vivo at the clinical level. Expert commentary: This review will explore the issues that need to be considered in developing performance standards for anti-biofilm therapeutics and provide a rationale for the need to standardize models/methods that are clinically relevant. We also provide some rational as to why no standards currently exist.

Role of Gut Microbiota and Infectious Burden in the Development of Autoimmune and Allergic Diseases

No Abstract#.

Use of Intra-Articular Amphotericin B in the Treatment of Candida parasilosis and albicans in Prosthetic Joint Infections (PJI): A Novel Approach to this Difficult Problem

BACKGROUND

Use of intra-articular antibiotics for the treatment of arthroplasty infections has gained some interest over the last few years.

OBJECTIVE

Some data exists on its use with bacterial arthroplasty infections.

METHOD

We used intra-articular amphotericin B in an attempt to cure these joint infections and perform a one stage revision.

RESULTS

Two patients were treated with intra-articular amphotericin B for 6 weeks followed by suppressive fluconazole for 4 months. Intra-articular joint fluid was cultured during this process for re-growth of fungus.

CONCLUSION

Both patients were treated successfully with the method with follow up showing no evidence of recurrence. IA administration of amphotericin B may be an alternative treatment in these patients.

Stable isotope biomarker breath tests for human metabolic and infectious diseases: a review of recent patent literature

INTRODUCTION

Stable isotope breath tests can rapidly and quantitatively report metabolic phenotypes and disease in both humans and microbes in situ. The labelled compound is administered and acted upon by human or microbial metabolism, producing a labelled gas that is detected in exhaled breath. Areas covered: This review details the unique advantages (and disadvantages) of phenotypic stable isotope based breath tests. A review of recent US patent applications and prosecutions since 2010 is conducted. Finally, current clinical trials, product pipelines and approved products are discussed. Expert opinion: Stable isotope breath tests offer new approaches for rapid and minimally invasive detection and study of metabolic phenotypes, both human and microbial. The patent literature has developed considerably in the last 6 years, with over 30 patent applications made. Rates of issuance remain high, although rejections citing 35 U.S.C. §101(subject matter eligibility), §102 (novelty), §103 (obviousness) and §112 (description, enablement and best mode) have occurred. The prior art is significantly greater for human metabolism than microbial, and may drive differing rates of future issuance. These biomarker and diagnostic tools can enable optimization of drug doses, diagnosis of metabolic disease and its progression, and detection of infectious disease and optimize its treatment.