Implication of efflux pumps and ERG11 genes in resistance of clinical Trichosporon asahii isolates to fluconazole

Introduction. Trichosporon asahii has been recognized as an opportunistic agent having a limited sensitivity to antifungal treatment.Hypothesis/Gap Statement. Molecular mechanisms of azole resistance have been rarely reported for Trichosproron asahii. Similar to other fungi, we hypothesized that both ERG11 gene mutation and efflux pumps genes hyper-expression were implicated.Aim. The current work aimed to study the sensitivity of clinical T. asahii isolates to different antifungal agents and to explore their resistance mechanisms by molecular methods including real-time PCR and gene sequencing.Methods. The sensitivity of T. asahii isolates to fluconazole, amphotericin B and voriconazole was estimated by the Etest method. Real-time PCR was used to measure the relative expression of Pdr11, Mdr and ERG11 genes via the ACT1 housekeeping gene. Three pairs of primers were also chosen to sequence the ERG11 gene. This exploration was followed by statistical study including the receiver operating characteristic (ROC) curve analysis to identify a relationship between gene mean expression and the sensitivity of isolates.Results. In 31 clinical isolates, the resistance frequencies were 87, 16.1 and 3.2 %, respectively, for amphotericin B, fluconazole and voriconazole. Quantitative real-time PCR demonstrated that only Mdr over-expression was significantly associated with FCZ resistance confirmed by univariate statistical study and the ROC curve analysis (P <0.05). The ERG11 sequencing revealed two mutations H380G and S381A in TN325U11 (MIC FCZ=8 µg ml^-1) and H437R in TN114U09 (MIC FCZ=256 µg ml^-1) in highly conserved regions (close to the haem-binding domain) but their involvement in the resistance mechanism has not yet been assigned.Conclusion. T. asahii FCZ resistance mechanisms are proven to be much more complex and gene alteration sequence and/or expression can be involved. Only Mdr gene over-expression was significantly associated with FCZ resistance and no good correlation was observed between FCZ and VCZ MIC values and relative gene expression. ERG11 sequence alteration seems to play a major role in T. asahii FCZ resistance mechanism but their involvement needs further confirmation.

Unusual case of otomycosis caused by Saksenaea vasiformis

Saksenaea vasiformis is a species of the order Mucorales rarely reported as a cause of human mucormycosis. We report an unusual case of S. vasiformis otitis occurring in a diabetic woman after penetration of an insect in the right ear. Direct microscopic examination of the clinical sample showed hyaline and non septate hyphae belonging to the order Mucorales. Fungal identification was performed by sequencing the ITS region of the rDNA. To our knowledge, this is the first report of S. vasiformis infection in Tunisia.

Microsatellite analysis of the population structure in Rhizopus arrhizus

OBJECTIVES

Rhizopus arrhizus is recognized as an emergent agent of superficial and invasive mucormycosis. Despite an increasing number of these infections, the molecular epidemiology of Rhizopus species has not been well studied.

MATERIALS AND METHODS

In this study, 43 R. arrhizus strains (25 environmental and 18 clinical isolates) were genotyped using six novel panels of microsatellite markers.

RESULTS

Upon the analysis of 43 isolates, 4-8 distinct alleles were detected for each marker. The discriminatory power for the individual markers ranged from 0·522 to 0·830. The combination of all six markers yielded 33 different haplotypes with a high degree of discrimination (0·989 D value). A four-marker combination were selected as the most parsimonious panel achieving D > 0·95. One clinical isolate and one environmental isolate shared the same genotype suggesting the possible nosocomial outbreak of mucormycosis in hospitalized patients. We have noted that the strains isolated from cutaneous mucormycosis were different from the strains isolated from rhino-orbito-cerebral mucormycosis. Then, the hypothesis of particular tropism of infectious strains for a given site is not excluded. The standardized indices of association IA and rBarD were significantly different from zero (P < 0·01), suggesting a prevailing clonal reproduction. The environmental population was significantly differentiated from clinical populations (Fst = 0·2249).

CONCLUSIONS

Microsatellite typing method described in our study showed an excellent degree of discriminatory power. It is a promising tool for illuminating the molecular epidemiology of R. arrhizus species, including strain relatedness and transmission pathways.

Detection of virulence factors and antifungal susceptibility of human and avian Aspergillusflavus isolates

Aspergillusflavus is the second leading cause of invasive and non-invasive aspergillosis. Secretion of hydrolytic enzymes is considered as a virulence factor in this species. Our work aimed to study in vitro production of some virulence factors, to evaluate the biofilm production against human and avian A. flavus isolates and to investigate the antifungal susceptibility agents. Hydrolytic enzymes, biofilm production and molecular typing were studied for 62 human and 36 avian A. flavus isolates by specific solid media and six microsatellite markers. The susceptibility to antifungal agents was evaluated for 37 human isolates. All human and avian A. flavus isolates showed positive activities of extracellular hydrolase: phospholipase, protease and hemolysin. A positive elastase activity was seen in 64.51% of human A. flavus isolates and 86.1% of avian A. flavus isolates. All A. flavus in these two populations formed biofilms. Statistical significant difference was observed for the mean phospholipase activities (P=0.025) and biofilm quantification (P=0.0001) between human and avian A. flavus isolates. The in vitro susceptibility results showed a resistance in 83.7%, 81.08% and 16.21% of A. flavus isolates respectively to amphotericin B, itraconazole and posaconazole. No association was noted between all virulence factors and the genotypes of human and avian isolates. Our study allowed us to show that human strains have a higher production of extracellular hydrolases and biofilm then avian strains. These virulence factors appear to act synergistically to contribute to the virulence of A. flavus strains. Moreover, significant correlation between virulence patterns and antifungal susceptibility profiles was observed.

Contribution of the internal transcribed spacer regions to the detection and identification of human fungal pathogens

Fungi are morphologically and phylogenetically diverse. There identification is largely based on phenotypic methods. Thus, related species, phenotypic variants and rare species may be unidentified. So, molecular methods have been introduced for identification of pathogenic molds to overcome these problems. In this study, we report the contribution of molecular tools (PCR sequencing) to identify fungal pathogens in both clinical and environmental samples. A total of 82 mold isolates were used (50 clinical samples and 32 environmental samples). PCR and direct sequencing, targeting the internal transcribed spacer (ITS) regions, were performed. We employed comparative sequence analysis to identify molds by using the GenBank database. 89% of isolates were identified by phenotypic methods. PCR- sequencing allowed the fungal identification in all cases. The concordance between molecular and morphological identification was obtained for 33 cases (40.2%). In 36 cases (43.9%), the molecular study gave the exact species identification. PCR sequencing allowed as revising mycological identification for 13 fungi strains (15.9%). The concordance of identification at species level by phenotypic method and by sequence analysis was obtained for 28% of clinical samples and for 59% of environmental samples. The phylogenetic tree for the ITS sequences showed six different clusters that are composed of isolates belonging to the same genus or species. PCR sequencing has been shown to be useful for the detection of the presence of fungal DNA in both environmental and clinical samples. It is rapid and more sensitive for the identification of medically important fungi.

Prevalence of free living amoeba in the domestic waters reservoirs in Sfax, Tunisia

Free living amoebas (FLA) are opportunistic pathogen found in different water sources in the environment. The aim of this study was to investigate the prevalence of free living amoeba in different samples of domestic water reserves (DWR) in Sfax region from Tunisia. It was a prospective study dealing with 486 water samples collected from different DWR. After filtration through a cellulose acetate membrane samples were cultured on non-nutrient agar and the FLA were detected and strained with Giesma, Trichrome and red nuclear stain for morphological and morphotypic studies. FLA were found in 62% of samples. The Acanthopodial morphotype was detected in 43%, Polytactic (38%), Monotactic (28%), Fan-shaped (17%), Rugose (11%), Dactilopodial (10%) and Eruptive (9%). These results demonstrate that domestic water reserves are a significant source of the FLA and maintenance of DWR is recommended.

Environmental and molecular study of fungal flora in asthmatic patients

The aim of the present study was to investigate the epidemiological and fungal environmental profile in asthmatic patients. We conducted a prospective study involving 49 patients with allergic asthma. One hundred and forty-five clinical samples and 289 environmental samples were performed. Only 30 patients accepted to participate to the environmental study at their home. For specific IgE antibodies, ELISA assay was conducted for 21 patients. Molecular ITS sequencing was performed for 37 isolates. The frequency of attacks was significantly associated with the seasonality, which was closely related to climate (P=0.024), exposure to animals (cats, P=0.025), plants (olive, P=0.018), physical effort (P=0.04) and the number of permanent occupants in house (>6) (P=0.026). Fungal contaminants were detected from 78.6% of biological samples and 97.8% of environmental samples. Antibodies corresponding to the studied allergens were detected in 10 patients (10/21). PCR sequencing allowed as rectified morphological identification for 27.02% (10/37) strains of Aspergillus. The allergy in molds is an indisputable reality that is necessary to look for in front of any severe asthma. So, it is important to establish clearly a relationship between exposure to fungi and health disorders in order to set up specific and effective preventive measures.

Tinea manuum due to Trichophyton erinacei from Tunisia

Trichophyton erinacei is a zoonotic fungus affecting hedgehogs. Although several human infections with this organism have been documented in the literature, it has rarely been isolated as a human pathogen. This paper reports on an erythematous lesion spotted on the hand of a 10-year-old girl. Based on the culture of the patient's skin scrapings, the pathogen was mycologically identified as T. erinacei, which was further confirmed by sequencing the internal transcribed spacers of the fungal nuclear ribosomal DNA using universal primer ITS1-ITS4. This is the first case of T. erinacei in a Tunisian patient. A survey was carried out on the environment of our patient, and the results revealed the presence of hedgehogs with suspect scaly lesions. The same fungus was isolated from the hair and scales of the hedgehog, which was confirmed by PCR sequencing. The frequency of T. erinacei has often been underestimated, which is attributed not only to the gaps of knowledge still existing in the current understanding of the dermatophyte but also to differential diagnosis problems. Molecular study offers a simple and rapid tool to identify the source of infection and, hence, avoid the risk of recurrence.

Epidemiological profile of fungal keratitis in Sfax (Tunisia)

Fungal keratitis is responsible for a significant burden of blinding disease in the developing world.

OBJECTIVE

The aim of this study was to determine the etiological agents, predisposing factors and therapy of keratomycosis in our region.

METHODS

Retrospective study of 60 patients with clinically and cultured confirmed fungi keratitis, who were attended at department of mycology in Sfax (1995 to 2012).

RESULTS

The mean age of patients was 47.2 years (sex ratio: 1.58). At least, one presumed predisposing factor was identified in 83.3% of cases. Corneal traumatism was established as the most common predisposing factor (61.6%) with vegetative matter (42.4%). Patients had corneal ulcer in 40% or abscess in 47.6%. All cases were positive on direct microscopy and 93% of cultures were positive. Filamentous fungi form the major etiologic agents (83%): Fusarium species (49% with F. solani [66%]), Aspergillus sp. (22%), Alternaria (5%), Scedosporium sp. (2%); and non-identified mold in (5%). Yeast were identified in 17% of cases. Topical agents were used in 97% of cases: ketoconazole 2%, amphotericin B (0.5%). Fluconazole per os was administrated for 11% of cases, itraconazole (2 cases) and voriconazole (one case). Keratoplasty was indicated for 27% of cases. The outcome was favorable in 16% of patients. Among the patients, 71% had persistent corneal deposit sequelae. Four patients lost the eyeball.

CONCLUSION

Corneal traumatism was the principal risk factor for fungal keratitis in young and middle-aged farmers. Fusarium solani is the predominant cause in Sfax. Early diagnosis, coupled with appropriate treatment, is crucial for increasing the chance of complete recovery.

[Pneumocystis: epidemiology and molecular approaches]

Pneumocystosis is a common opportunistic infection in immunocompromised patients, especially in AIDS patients. The diagnosis of this pneumonia has presented several difficulties due to the low sensitivity of conventional staining methods and the absence of culture system for Pneumocystis. The molecular biology techniques, especially the PCR, have improved the detection of DNA of this fungus in invasive and noninvasive samples, and in the environment which highlighted human transmission and the existence of environmental source of Pneumocystis. In addition, various molecular biology techniques were used for typing of Pneumocystis strains, especially P. jirovecii, which is characterized by a significant genetic biodiversity. Finally, the widespread use of cotrimoxazole for the treatment and prophylaxis of pneumocystosis has raised questions about possible resistance to sulfa drugs in P. jirovecii.

A comparison of capillary electrophoresis and direct sequencing in upstream conserved sequence region analysis of Pneumocystis jirovecii strains

The major surface glycoprotein (MSG) of Pneumocystis jirovecii is the most abundant surface protein and appears to play a critical role in the pathogenesis of pneumocystosis. The expressed MSG gene is located immediately downstream of a region called the upstream conserved sequence (UCS). The UCS contains a region of tandem repeats that vary in number and sequence. In the present study, we have used capillary electrophoresis and direct sequencing to detect the variability in the repeat units of UCS. By direct sequencing the PCR products from samples of 13 patients, we have identified three types of repeat units which consisted of 10 nt and three different patterns in the UCS region with three and four repeats: 1, 2, 3 (84.6 %); 1, 2, 3, 3 (8.2 %); and a new genotype 2, 2, 3, 3 (8.2 %). The same samples were analysed by capillary electrophoresis. Three samples (23 %) contained a mixture of two or three different patterns of UCS repeats. In conclusion, quantifying the number of repeat units in the UCS by capillary electrophoresis provides a potential new method for the rapid typing of P. jirovecii and the detection of mixed infection.

Acanthamoeba T4 genotype associated with keratitis infections in Tunisia

Acanthamoeba keratitis (AK) is a sight-threatening infection. We report five cases of AK diagnosed from 2005 to 2009 in the Laboratory of Parasitology-Mycology at Habib Bourguiba Sfax Hospital, Tunisia. All were associated with improper care of contact lenses (rinsing of contact lenses with tap water and inappropriate cleaning) and lens storage. The patients displayed different clinical presentations: corneal inflammation, corneal ulceration, and corneal abscess. The diagnosis was made after direct examination, culture, and polymerase chain reaction amplification with specific primers. The genotype classification was based on the highly variable DF3 region in the 18S rRNA gene. This is the first study characterizing Acanthamoeba genotype in Tunisia and North Africa. All Acanthamoeba isolates were associated to the T4 genotype. Three different DF3 sequence types were related to AK infections T4/10, T4/15, and T4/16.

[Toxoplasmosis in Sfax, Tunisia]

Abstract The frequency of toxoplasmosis depends on life-style and environment. Our objective was to study different epidemiological, clinical and biological aspects of toxoplasmosis in the Sfax area (Tunisia). This retrospective study has been performed on seria of 40,566 pregnant women in the Parasitology-Mycology Laboratory of Habib-Bourguiba Sfax hospital-Tunisia for 13 years from 1994 to 2006; 1,691 patients presenting with lymphadenopathy; 191 immunocompromised patients (78 HIV infected patients and 113 transplanted patients) and 21 patients presenting clinical signs of ocular toxoplasmosis. In pregnant women, the seroprevalence was 39.3% (15,952/40,567). Among 24,089 seronegative women, only 6,890 (28.6%) had been followed up during their pregnancy. An active toxoplasmosis possibly acquired during pregnancy was detected in 1.3% of cases. Sixteen congenital toxoplasmosis were detected. Toxoplasmosis was confirmed in 13.7% of the 169 patients with lymphadenitis. For HIV positive patients, 11.7% had cerebral toxoplasmosis. It revealed the HIV infection in four cases. Among transplant recipients, one case of active toxoplasmosis was diagnosed in a renal transplant recipient who received transplant from a seronegative donor. Twenty-one patients presenting toxoplasmic retinochoroiditis were treated by subconjonctival injections of clindamycin and systemic corticotherapy at a dose of 1 mg/kg per day. This clinical toxoplasmosis diversity explains the need for bioclinical confrontation to establish diagnosis.

Candida glabrata strain relatedness by new microsatellite markers

We investigated six microsatellite markers to type 85 unrelated and 118 related isolates of Candida glabrata from 36 patients. Three new markers were selected from the complete sequence of CBS138 and three previously described markers, RPM2, MTI and ERG3 were used. We found a genetic diversity of 0.949 by combining four of them. By applying the new microsatellite markers GLM4, GLM5 and GLM6 we were able to discriminate 29 isolates, originally identified by the more established markers, RPM2, MTI and ERG3. When epidemiologically closely related isolates from 36 patients were typed, 25 patients (72%) exhibited identical or highly related multilocus genotypes. We noted a microvariation in 4 of the patients. This minor change of one locus could be explained by a single step mutation. Since one of these patients had not received antifungal treatment; thus, the relationship between genome variation and antifungal therapy remains controversial. We can conclude from our analysis of these new microsatellite markers that they are highly selective and therefore should be considered as a useful typing system for differentiating related and unrelated isolates of C. glabrata, as well as being able to detect microvariation.

A review of molecular techniques to type Candida glabrata isolates

Candida glabrata has emerged as a common cause of fungal infection causing mucosal and systemic infections. This yeast is of concern because of its reduced antifungal susceptibility to azole antifungals such as fluconazole. A clear understanding of the epidemiology of Candida infection and colonisation required a reliable typing system for the evaluation of strain relatedness. In this study, we discuss the different molecular approaches for typing C. glabrata isolates. Recent advances in the use of molecular biology-based techniques have enabled investigators to develop typing systems with greater sensitivities. Several molecular genotypic approaches have been developed for fast and accurate identification of C. glabrata in vitro. These techniques have been widely used to study diverse aspects such as nosocomial transmission. Molecular typing of C. glabrata could also provide information on strain variation, such as microvariation and microevolution.

[Human demodicidosis in Sfax area (Tunisia)]

Demodicidosis is an ectoparasitosis, common to humans and many mammals. It is caused by the proliferation of a mite Demodex sp in the pilosebaceous follicles. Its pathogenic role remains controversial. The aim of our study was to report epidemiological and clinical particularities of cases of demodicidosis diagnosed in our region. Over a period of nine years (January 2000 to December 2008), 427 cases of demodicidosis were diagnosed. 73.2% of cases were blepharitis and 26.8% of cases were facial dermatosis. The mean age was 44 years. Women were slightly more affected (56%) than men. Among 787 chronic blepharitis, 243 cases were due to Demodex sp (30.9%). They were treated with yellow oxide of mercury (Ophtergine® 1%). In the face, this mite has been isolated from erythematous and pruritic papulopustular lesions, and their distribution was as follows: cheeks (22.1%), forehead (13.4%), and nose (11.5%). The diagnosis was confirmed by parasitological examination of scales showing more than 5 Demodex sp/cm(2) and response to treatment with metronidazole (Flagyl®) for three months. Currently, there were a large number of arguments for the incrimination of Demodex sp in pathogenesis of dermatosis and blepharitis. Dermatologists and ophthalmologists must therefore think to this mite. The density of Demodex sp found by parasitological exam is a determining factor in establishing an anti-Demodex treatment whose effectiveness is a further argument for the diagnosis.

Microsatellite analysis and susceptibility to FCZ of Candida glabrata invasive isolates in Sfax Hospital, Tunisia

We have noted that, during the last few years, there has been a redistribution of the most common Candida species with an increase in non-C. albicans Candida species, particularly Candida glabrata. In many countries, the high frequency of Candida glabrata shows the highest resistance rates. The main objective of this investigation was to analyze the genotypic variability of invasive C. glabrata isolates recovered over a period of six years and assess their in vitro susceptibility to fluconazole to determine the possible existence of relationships between genotype and susceptibility. We collected 50 invasive C. glabrata isolates (21.4%) from January 2001 to December 2007. The in vitro susceptibility profiles as determined by the E-test method showed that 8.3% of the isolates were resistant to fluconazole. The typing with three microsatellite markers RPM2, MTI and ERG3 demonstrated 12 multilocus genotypes distributed irregularly with a predominance of G1 (38%). A cluster (G9) was found among isolates collected in the same ward, at the same time period, suggesting cross transmission. Eleven of 13 patients who had previously been colonized by C. glabrata, were infected by their colonizing strains. However, we noted after prolonged treatment with fluconazole that there was an increase of the MIC for an isolate from one patient and in another patient, the selection of a more resistant variant. In our study, we didn't find an association between genotype and susceptibility to fluconazole. In conclusion, the predominance of some genotypes could be explained by nosocomial transmission or a selective ecological advantage rather than an emergence of a resistant isolate.

First case of Trichophyton soudanense isolated in Tunisia

This is a first case of Trichophyton soudanense isolated from Ivoiran student in Tunisia. A 24-year-old man was addressed for extensive erythematous, scaling lesions. Examination disclosed tinea capitis, tinea corporis, tinea pedis, and onychomycosis of toenails and fingernails. Isolates were identified as Trichophyton soudanense on the basis of macroscopy and microscopy colony characteristics. The patient was treated with fluconazole, topical econazole, and ciclopiroxolamine varnish. Although T. soudanense was identified since the late 1950s outside the African continent especially in the North America, Brazil, Australia, and many European countries, this is the first case reported in Tunisia. Accessibility to our universities for African students makes possible the emergence of this dermatophyte.