Spatio-temporal Genetic Structuring of Leishmania major in Tunisia by Microsatellite Analysis

In Tunisia, cases of zoonotic cutaneous leishmaniasis caused by Leishmania major are increasing and spreading from the south-west to new areas in the center. To improve the current knowledge on L. major evolution and population dynamics, we performed multi-locus microsatellite typing of human isolates from Tunisian governorates where the disease is endemic (Gafsa, Kairouan and Sidi Bouzid governorates) and collected during two periods: 1991–1992 and 2008–2012. Analysis (F-statistics and Bayesian model-based approach) of the genotyping results of isolates collected in Sidi Bouzid in 1991–1992 and 2008–2012 shows that, over two decades, in the same area, Leishmania parasites evolved by generating genetically differentiated populations. The genetic patterns of 2008–2012 isolates from the three governorates indicate that L. major populations did not spread gradually from the south to the center of Tunisia, according to a geographical gradient, suggesting that human activities might be the source of the disease expansion. The genotype analysis also suggests previous (Bayesian model-based approach) and current (F-statistics) flows of genotypes between governorates and districts. Human activities as well as reservoir dynamics and the effects of environmental changes could explain how the disease progresses. This study provides new insights into the evolution and spread of L. major in Tunisia that might improve our understanding of the parasite flow between geographically and temporally distinct populations.     

A Review Molecular Typing Methods for <Emphasis Type="Italic">Aspergillus flavus</Emphasis> Isolates

Aspergillus flavus is the second most important Aspergillus species causing human infections. The importance of this fungus increases in regions with a dry and hot climate. Small phylogenetic studies in Aspergillus flavus indicate that the morphological species contains several genetically isolated species. Different genotyping methods have been developed and employed in order to better understand the genetic and epidemiological relationships between environmental and clinical isolates. Understanding pathogen distribution and relatedness is essential for determining the epidemiology of nosocomial infections and aiding in the design of rational pathogen control methods. Typing techniques can also give us a deeper understanding of the colonization pattern in patients. Most of these studies focused on Aspergillus fumigatus because it is medically the most isolated species. To date, there has not been any publication exclusively reviewing the molecular typing techniques for Aspergillus flavus in the literature. This article reviews all these different available methods for this organism.     

TLR4 activation induces IL-1β release via an IPAF dependent but caspase 1/11/8 independent pathway in the lung

Background

The IL-1 family of cytokines is known to play an important role in inflammation therefore understanding the mechanism by which they are produced is paramount. Despite the recent plethora of publications dedicated to the study of these cytokines, the mechanism by which they are produced in the airway following endotoxin, Lipopolysaccharide (LPS), exposure is currently unclear. The aim was to determine the mechanism by which the IL-1 cytokines are produced after LPS inhaled challenge.

Methods

Mice were challenged with aerosolised LPS, and lung tissue and bronchiolar lavage fluid (BALF) collected. Targets were measured at the mRNA and protein level; caspase activity was determined using specific assays.

Results

BALF IL-1b/IL-18, but not IL-1a, was dependent on Ice Protease-Activating Factor (IPAF), and to a lesser extent Apoptosis-associated Speck-like protein containing a CARD (ASC). Interestingly, although we measured an increase in mRNA expression for caspase 1 and 11, we could not detect an increase in lung enzyme activity or a role for them in IL-1a/b production. Further investigations showed that whilst we could detect an increase in caspase 8 activity at later points in the time course (during resolution of inflammation), it appeared to play no role in the production of IL-1 cytokines in this model system.

Conclusions

TLR4 activation increases levels of BALF IL-1b/IL-18 via an IPAF dependent and caspase 1/11/8 independent pathway. Furthermore, it would appear that the presence of IL-1a in the BALF is independent of these pathways. This novel data sheds light on innate signalling pathways in the lung that control the production of these key inflammatory cytokines.     

Invasive Aspergillosis: Resistance to Antifungal Drugs

Although the arsenal of agents with anti-Aspergillus activity has expanded over the last decade, mortality due to invasive aspergillosis remains unacceptably high. Resistance of the Aspergillus spp. species to antifungal drugs increased in the last 20 years with the increase in antifungal drugs use and might partially account for treatment failures. Recent advances in our understanding of mechanisms of antifungal drug action in Aspergillus, along with the standardization of in vitro susceptibility testing methods, have brought resistance testing to the forefront of clinical mycology. Recent modifications in taxonomy and understanding of the acquired resistance mechanisms of Aspergilli to drugs should support a better management of Aspergillus infections. In this paper, we review the current knowledge on epidemiology and underlying mechanisms involved in antifungal resistance in Aspergillus.     

Simple and Highly Discriminatory VNTR-Based Multiplex PCR for Tracing Sources of Aspergillus flavus Isolates

Aspergillus flavus is second only to A. fumigatus in causing invasive aspergillosis and it is the major agent responsible for fungal sinusitis, keratitis and endophthalmitis in many countries in the Middle East, Africa and Southeast Asia. Despite the growing challenge due to A. flavus, data on the molecular epidemiology of this fungus remain scarce. The objective of the present study was to develop a new typing method based on the detection of VNTR (Variable number tandem repeat) markers. Eight VNTR markers located on 6 different chromosomes (1, 2, 3, 5, 7 and 8) of A. flavus were selected, combined by pairs for multiplex amplifications and tested on 30 unrelated isolates and six reference strains. The Simpson index for individual markers ranged from 0.398 to 0.818. A combined loci index calculated with all the markers yielded an index of 0.998. The MLVA (Multiple Locus VNTR Analysis) technique proved to be specific and reproducible. In a second time, a total of 55 isolates from Chinese avian farms and from a Tunisian hospital have been evaluated. One major cluster of genotypes could be defined by using the graphing algorithm termed Minimum Spanning Tree. This cluster comprised most of the isolates collected in an avian farm in southern China. The MLVA technique should be considered as an excellent and cost-effective typing method that could be used in many laboratories without the need for sophisticated equipment.     

An innovative chemometric method for processing direct introduction high resolution mass spectrometry metabolomic data: independent component–discriminant analysis (IC–DA)

Introduction

To perform large scale metabolomic analyses, high throughput approaches are required. The direct introduction mass spectrometry (DIMS) approach appears to be very attractive to achieve this goal. However, processing DIMS data is still very challenging due to the large number of samples and the intrinsic complexity of the mass spectra.

Objectives

The objective of this study is to develop a computational procedure, based on an innovative chemometric method, i.e. Independent component–discriminant analysis (IC–DA), for processing DIMS data.

Method

Metabolomic fingerprints were obtained by direct introduction high resolution mass spectrometry (DI-HRMS) analysis of urine samples of subjects that had been professionally exposed to pesticides. Spectral data were processed using the developed IC–DA procedure. Results obtained from this method were compared to those obtained by the conventional Partial least squares–discriminant analysis (PLS–DA). For both the IC–DA and PLS–DA methods, a validation was performed based on a permutation test.

Result

IC–DA results enabled a good detection of discriminant variables and a clear discrimination of control samples and exposure classes whereas a less striking discrimination was obtained with PLS–DA. Putative annotation of these variables was performed using metabolomic databases. Targeted correlation analysis was used for the detection of ions associated with the most discriminant variables, consolidating their identity assignment.

Conclusion

This study demonstrated the efficiency of IC–DA to discriminate the different exposure groups. As well the improvement of high throughput metabolomic studies was provided by combining DI–HRMS with this new chemometric tool.

     

Olive mill wastewater disposal in evaporation ponds in Sfax (Tunisia): moisture content effect on microbiological and physical chemical parameters

The study of the isotherms desorption of olive mill wastewater (OMW) was investigated to describe its water activity under different saturated environments. The microbial biodegradation of OMW during its storage in 5 evaporation ponds located in Agareb (Sfax-Tunisia) was carried out during the oil-harvesting year held 105 days in 2004. Gravimetric static method using saturated salt solutions was used and OMW as placed at 30°C and under different water activities ranging from 0.11 to 0.90. Eight models were taken from the literature to describe experimental desorption isotherms. During storage, the evolution of physico-chemical parameters including pH, temperature, evaporation, humidity, total phosphorus, chemical oxygen demand (COD), biological oxygen demand (BOD) and phenols and three microbiological flora (aerobic mesophilic bacteria, yeasts and moulds) were considered. At 30°C, when relative humidity increased in the experimented ponds of 69, 84 and 90%, the evaporation speed decreased from 1.24 × 10⁻⁵ to 5 × 10⁻⁶ cm³ s⁻¹, from 6 × 10⁻⁵ to 7 × 10⁻⁶ cm³ s⁻¹ and from 5 × 10⁻⁶ to 1.1 × 10⁻⁷ cm³ s⁻¹ respectively. The desorption isotherm exhibited a sigmoidal curve corresponding to type II, typical of many organic material. The GAB and Peleg models gave the best fit for describing the relationship between the equilibrium moisture content and water activity in OMW (R ² = 0.998). During the storage period, the analysis showed an increase of all the physico-chemical parameters studied, except phenols and total phosphorus concentrations. The microbiological study showed the predominance of yeasts and moulds and the decrease of bacteria population after 75 days reflecting both effect of recalcitrant compounds and the water activity on microbial growth.     

Molecular Genotyping of <Emphasis Type="Italic">Candida parapsilosis</Emphasis> Species Complex

Background

The Candida parapsilosis complex species has emerged as an important cause of human disease. The molecular identification of C. parapsilosis isolates at the species level can be helpful for epidemiological studies and then for the establishment of appropriate therapies and prophylactic measures.

Methods

The present study was undertaken to analyze 13 short tandem repeat (STR) markers (7 minisatellites and 6 microsatellites) in a global set of 182 C. parapsilosis complex isolates from different origins including invasive and superficial clinical sites.

Results

Upon the analysis of 182 strains of C. parapsilosis complex species, 10–17 haplotypes were detected for each minisatellite marker. The combination of 7 minisatellite markers yielded 121 different genotypes with a 0.995 D value. Upon the analysis of 114 isolates (68 from invasive infections and 46 from superficial infections), 21–32 genotypes were detected for each microsatellite marker. The combination of all 13 markers yielded 96 different genotypes among 114 isolates with a high degree of discrimination (0.997 D value).The same multilocus genotype was shared by isolates recovered from some patients and from the hand of theirs correspondent healthcare worker. For another patient, the same multilocus genotype of C. metapsilosis was detected in blood and skin confirming that candidemia usually arises as an endogenous infection following prior colonization.

Conclusions

These STR markers are a valuable tool for the differentiation of C. parapsilosis complex strains, to support epidemiological investigations especially studies of strain relatedness and pathways of transmission.