Nahid Kondori

Respiratory infections are the leading cause of mortality and morbidity among cystic fibrosis (CF) patients. Pathogenic bacteria and fungi such as Pseudomonas aeruginosa , Staphylococcus aureus , and various yeasts as well as filamentous fungi are commonly identified opportunistic microorganisms recovered in the sputa from CF patients. The clinical significance of yeasts, particularly Candida species, in patients with CF is not fully understood. Furthermore, the emergence of antifungal resistance in clinical settings is a global concern. This study aimed to determine the prevalence of Candida species with special focus on Candida dubliniensis and Candida albicans in sputum samples from patients with CF and evaluate their susceptibility to antifungal agents. A total of 968 culture-positive sputum samples were collected from 193 patients with CF over a period of 1 year. Fungal isolates were identified to the species level using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. The antifungal susceptibility of Candida isolates was determined using Sensititre YeastOne panels. The most commonly isolated yeast species in these sputum samples were C. dubliniensis (13%) and C. albicans (32%). Colonization with C. dubliniensis or C. albicans was not associated with a deteriorated lung function. Voriconazole had the lowest minimum inhibitory concentration (MIC) against C. dubliniensis and C. albicans . Itraconazole showed higher MIC values to Candida albicans . An increased understanding of the antifungal susceptibility profiles of Candida species isolated from CF patients may provide valuable knowledge about treatment of yeast infections in this patient group. IMPORTANCE: Our findings indicate that colonization with Candida dubliniensis and Candida albicans does not exert a significant impact on pulmonary function in individuals with cystic fibrosis. Furthermore, antifungal resistance among the isolated Candida species was generally low.

The black fungus Exophiala causes a wide range of infections from superficial to subcutaneous, but also invasive fungal infections in immunocompromised patients as well as healthy individuals. In addition, Exophiala, is a common colonizer of the air ways of patients with cystic fibrosis. However, the source of infection and mode of transmission is still unclear. The aim of this study was to investigate the presence of Exophiala in samples collected from Swedish indoor environments. We found that the Exophiala species were commonly found in dishwashers and that Exophiala dermatitidis was the most common Exophiala species, being identified in 70% (26 out of the 37) of samples. Almost all E. dermatitidis isolates had the ability to grow at 42 °C (P = 0.0002) and were catalase positive. Voriconazole and posaconazole exhibited the lowest MICs, while caspofungin and anidulafungin lack the antifungal activities in vitro. Future studies are needed to illuminate the transmission mode of the fungi.

Summary: The aim of this study was to estimate the annual burden of fungal infections in Sweden using data mainly from 2016. Data on specific populations were obtained from Swedish national data registries. Annual incidence and prevalence of fungal disease was calculated based on epidemiological studies. Data on infections due to Cryptococcus sp., Mucorales, Histoplasma capsulatum, Coccidioides immitis and Pneumocystis jirovecii were retrieved from Karolinska University Laboratory and covers only 25% of Swedish population. In 2016, the population of Sweden was 9 995 153 (49.8% female). The overall burden of fungal infections was 1 713 385 (17 142/100 000). Superficial fungal infections affect 1 429 307 people (1429/100 000) based on Global Burden of Disease 14.3% prevalence. Total serious fungal infection burden was 284 174 (2843/100 000) in 2016. Recurrent Candida vulvovaginitis is common; assuming a 6% prevalence in women. Prevalence of allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitisation were estimated to be 20 095 and 26 387, respectively. Similarly, chronic pulmonary aspergillosis was estimated to affect 490 patients after tuberculosis, sarcoidosis and other conditions. Candidemia incidence was estimated to be 500 in 2016 (4.7/100 000) and invasive aspergillosis 295 (3.0/100 000). In Stockholm area, Mucorales were reported in three patients in 2015, while Cryptococcus spp. were reported in two patients. In 2016, there were 297 patients PCR positive for P jirovecii. The present study shows that the overall burden of fungal infections in Sweden is high and affects 17% of the population. The morbidity, mortality and the healthcare‐related costs due to fungal infections warrant further studies.

Candida albicans is the most frequently isolated fungal species in hospital settings worldwide. However, non-albicans Candida species with decreased susceptibility to antifungals have emerged as an important cause of fungemia. The aims of this study were to determine the species distribution of fungi isolated from the blood samples of patients at a Swedish University Hospital and to define the in vitro susceptibilities of these isolates to nine antifungal agents. In total, 233 yeast isolates from 143 patients were included in this study. Antifungal susceptibility testing was performed using broth dilution Sensititre YeastOne panels, which comprised amphotericin B, 5-flucytosine, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, micafungin, and caspofungin. The most common species in all age groups was C. albicans (n = 93, 65%), followed by C. glabrata (n = 27, 19%) and C. parapsilosis (n = 15, 10%). C. glabrata was mostly found in elderly individuals, while C. parapsilosis was found mainly in young children (p = 0.008). Antifungal resistance was low in the Candida species, except for reduced susceptibility to fluconazole among C. glabrata strains. C. albicans is the most frequent colonizer of Swedish patients. In general antifungal resistance is uncommon in Candida species. Nevertheless, reduced susceptibilities to fluconazole and echinocandins were found in C. glabrata and C. parapsilosis, respectively.

Conventional mycological identifications based on the recognition of morphological characteristics can be problematic. A relatively new methodology applicable for the identification of microorganisms is based on the exploitation of taxon- specific mass patterns recorded from abundant cell proteins directly from whole-cell preparations, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This study reports the application of MALDI-TOF MS for the differentiation and identifications of black yeasts, isolated from the respiratory tracts of patients with cystic fibrosis (CF). Initial phenotypic and DNA sequence-based analyses identified these isolates to be Exophiala dermatitidis. The type strains of E. dermatitidis (CBS 207.35^T) and other species of Exophiala were included in the MALDI-TOF MS analyses to establish the references for comparing the mass spectra of the clinical isolates of Exophiala. MALDI-TOF MS analyses exhibited extremely close relationships among the clinical isolates and with the spectra generated from the type strain of E. dermatitidis. The relationships observed between the E. dermatitidis strains from the MALDI-TOF MS profiling analyses were supported by DNA sequence-based analyses of the rRNA ITS1 and ITS2 regions. These data demonstrated the applicability of MALDI-TOF MS as a reliable, rapid and cost-effective method for the identification of isolates of E. dermatitidis and other clinically relevant fungi and yeasts that typically are difficult to identify by conventional methods.

The laboratory diagnosis of dermatophytosis is usually based on direct microscopic examination and culturing of clinical specimens. A commercial polymerase chain reaction kit (Dermatophyte PCR) has had favorable results when used for detection of dermatophytes and identification of Trichophyton rubrum in nail specimens. This study investigated the efficacy of the Dermatophyte PCR kit for detecting dermatophytosis in 191 hair or skin specimens from patients with suspected dermatophytosis. PCR was positive for 37 % of samples, whereas 31 and 39 % of the specimens were positive by culturing and direct microscopy, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value for PCR analysis were 83, 84, 71, and 91 %, respectively. The sensitivity of the PCR test was higher in specimens obtained from skin (88 %) than in those obtained from hair (58 %), while the specificity remained almost the same (84 and 86 % for skin and hair, respectively). Our results show that the Dermatophyte PCR kit is a promising diagnostic tool for detection of dermatophytosis in skin samples, providing clinicians with a rapid diagnosis.

Background: In the past two decades, the incidence of fungal infections has significantly increased worldwide. Despite treatment with a broad range of antifungal agents, nosocomial candidemia is associated with high mortality rates and resistance to antifungal agents is becoming increasingly prevalent in Candida species. Therefore, detection and identification of pathogens at the species level and antifungal susceptibility testing are essential to select the appropriate antifungal therapy. The incidence of candidemia and the antifungal susceptibility patterns of the associated strains have not been extensively studied in Iran. Objectives: The current study aimed to assess the microbial epidemiology of candidemia and the antifungal susceptibility profiles of Candida isolates. Patients and Methods: Out of 5141 blood culture specimens analyzed in Iran, 48 specimens from 32 patients were yeast-positive. The isolates were precisely identified at the species level using the well-established phenotypic polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The yeasts were also tested for antifungal susceptibility to fluconazole, itraconazole, ketoconazole, voriconazole, and caspofungin using the broth microdilution method. Results: Candidaparapsilosis (C. parapsilosis) was the most common yeast pathogen isolated (34.4%), followed by Candidaglabrata (C. glabrata) (28.1%), Candidaalbicans (C. albicans) (25%), Candidatropicalis (C. tropicalis) (9.4%), and Candidakefyr (C. kefyr) (3.1%). Candidaglabrata was isolated more often in elderly patients (> 60 years old). Conclusions: The results of antifungal susceptibility tests demonstrated that voriconazole was the most active drug against Candida isolates. Candida albicans is the most common yeast isolated from human blood world-wide; the unexpectedly higher rate of C. parapsilosis isolated in this study necessitates more studies with larger sample sizes in Iran. Keywords: Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; Candida parapsilosis; Voriconazole; Fungemia

Summary: The use of anti‐fungal agents has increased dramatically in recent years and new drugs have been developed. Several methods are available for determinations of their specific biological activities, i.e. the standard method for minimum inhibitory concentration‐determination is described in M‐38 [Clinical and Laboratory Standards Institute document M‐38 (CLSI M‐38)]. However, alternative methods, such as the E‐test, are currently available in Mycology laboratories. The susceptibilities of clinical isolates of Aspergillus spp. (n = 29), Fusarium spp. (n = 5), zygomycetes (n = 21) and Schizophyllum (n = 1) were determined for itraconazole, voriconazole and posaconazole, using the CLSI M‐38‐A broth dilution method and also by the E‐test. A good overall agreement (83.7%) between the two methods for all drugs and organisms was observed. Analyses of voriconazole showed a better agreement (93%) between the methods than posaconazole and itraconazole (85% and 74% respectively). Aspergillus spp. were the most susceptible fungi to the anti‐fungal agents tested in this study. Posaconazole was the most active drug against filamentous fungi in vitro, followed by itraconazole and voriconazole. The latter (voriconazole) demonstrated no significant in vitro activity against zygomycetes.

The black-pigmented fungusExophiala dermatitidisis considered to be a harmless colonizer of the airways of cystic fibrosis (CF) patients. The aim of this study was to establish the recovery rate ofE. dermatitidisin respiratory specimens from CF patients, transplant recipients, and subjects with other respiratory disorders in Sweden. Second, we wished to determine if particular clinical traits were associated withE. dermatitidiscolonization of the airways and the antifungal susceptibility profiles ofExophialastrains. Sputum and bronchoalveolar lavage samples (n= 492) derived from 275 patients were investigated.E. dermatitidiswas isolated in respiratory specimens from 19% (18/97) of the CF patients but in none of the other patient categories. All isolates were recovered after 6 to 25 days of incubation on erythritol-chloramphenicol agar (ECA) medium. Morphological and genetic analyses confirmed species identity. Pancreatic insufficiency was positively associated with the presence ofE. dermatitidisin sputum samples (P= 0.0198). Antifungal susceptibility tests demonstrated that voriconazole and posaconazole had the lowest MICs againstE. dermatitidis. In conclusion,E. dermatitidisis a frequent colonizer of the respiratory tract in CF patients in Sweden and appears to be associated with more advanced disease. WhetherE. dermatitidisis pathogenic remains to be elucidated.