In vitro antifungal susceptibility profile of Iranian Fusarium isolates: Emphasising on the potent inhibitory effect of efinaconazole compared to other drugs

BACKGROUND

Fusarium species are opportunistic human pathogens that remarkably cause fungal infections ranging from superficial to fatal invasive disseminated infections. Fusarium species are notoriously resistant to the majority of antifungal agents.

OBJECTIVES

Therefore, detailed studies regarding in vitro susceptibility are required and may lead to a better prognosis of severe infections.

METHODS

We evaluated 25 antifungal drugs in vitro against 282 clinical and environmental Fusarium isolates.

RESULTS

Fusarium species demonstrated high MICs/MECs values to the most commonly used antifungal drugs in clinical practice. The geometric mean (GM) MICs for luliconazole (0.004 μg/ml) and lanoconazole (0.012 μg/ml) were the lowest, followed by efinaconazole (0.98 μg/ml) and amphotericin B (1.04 μg/ml).

CONCLUSIONS

Efinaconazole, a novel triazole, may be a promising candidate for the treatment of superficial Fusarium infections. Furthermore, the development of systemic formulations of these drugs as well as further in vitro and in vivo investigations could aid in the treatment of systemic fusariosis.

Antifungal susceptibility, genotyping, resistance mechanism, and clinical profile of Candida tropicalis blood isolates

Candida tropicalis is one of the major candidaemia agents, associated with the highest mortality rates among Candida species, and developing resistance to azoles. Little is known about the molecular mechanisms of azole resistance, genotypic diversity, and the clinical background of C. tropicalis infections. Consequently, this study was designed to address those questions. Sixty-four C. tropicalis bloodstream isolates from 62 patients from three cities in Iran (2014–2019) were analyzed. Strain identification, antifungal susceptibility testing, and genotypic diversity analysis were performed by MALDI-TOF MS, CLSI-M27 A3/S4 protocol, and amplified fragment length polymorphism (AFLP) fingerprinting, respectively. Genes related to drug resistance (ERG11, MRR1, TAC1, UPC2, and FKS1 hotspot9s) were sequenced. The overall mortality rate was 59.6% (37/62). Strains were resistant to micafungin [minimum inhibitory concentration (MIC) ≥1 μg/ml, 2/64], itraconazole (MIC > 0.5 μg/ml, 2/64), fluconazole (FLZ; MIC ≥ 8 μg/ml, 4/64), and voriconazole (MIC ≥ 1 μg/ml, 7/64). Pan-azole and FLZ + VRZ resistance were observed in one and two isolates, respectively, while none of the patients were exposed to azoles. MRR1 (T255P, 647S), TAC1 (N164I, R47Q), and UPC2 (T241A, Q340H, T381S) mutations were exclusively identified in FLZ-resistant isolates. AFLP fingerprinting revealed five major and seven minor genotypes; genotype G4 was predominant in all centers. The increasing number of FLZ-R C. tropicalis blood isolates and acquiring FLZ-R in FLZ-naive patients limit the efficiency of FLZ, especially in developing countries. The high mortality rate warrants reaching a consensus regarding the nosocomial mode of C. tropicalis transmission.

Molecular Identification, Genotypic Diversity, Antifungal Susceptibility, and Clinical Outcomes of Infections Caused by Clinically Underrated Yeasts, Candida orthopsilosis, and Candida metapsilosis: An Iranian Multicenter Study (2014-2019)

Despite the increasing occurrence of Candida orthopsilosis and Candida metapsilosis in clinical settings, little is known about their microbiological and clinical properties. Herein, we conducted a national retrospective study (2014–2019) from multiple centers in Iran. Among the 1,770 Candida isolates collected, we identified 600 Candida parapsilosis species complex isolates. Isolate identification was performed by 9-plex PCR, matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS), and rDNA sequencing, and antifungal susceptibility testing (AFST) followed CLSI M27-A3/S4; genotyping was performed by amplified fragment length polymorphism (AFLP) analysis; and clinical information was mined. Thirty-one isolates of C. orthopsilosis from various clinical sources, one mixed sample (blood) concurrently containing C. orthopsilosis and C. parapsilosis and one isolate of C. metapsilosis from a nail sample were identified. Although both 9-plex PCR and MALDI-TOF successfully identified all isolates, only 9-plex PCR could identify the agents in a mixed sample. For the C. orthopsilosis isolates, resistance (non-wild type) was noted only for itraconazole (n = 4; 12.5%). Anidulafungin and fluconazole showed the highest and voriconazole had the lowest geometric mean values. AFLP analysis showed three main and four minor genotypes. Interestingly, 90% of nail isolates clustered with 80% of the blood isolates within two clusters, and four blood isolates recovered from four patients admitted to a hospital clustered into two genotypes and showed a high degree of similarity (>99.2%), which suggests that C. orthopsilosis disseminates horizontally. Supported by our data and published case studies, C. orthopsilosis and C. metapsilosis can be linked to challenging clinical failures, and successful outcomes are not always mirrored by in vitro susceptibility. Accordingly, conducting nationwide studies may provide more comprehensive data, which is required for a better prognosis and clinical management of patients.

Molecular characterization and antifungal susceptibility testing of Candida nivariensis from blood samples - an Iranian multicentre study and a review of the literature

PURPOSE

Identification of the emerging yeast species Candida nivariensis among presumptively identified Iranian Candida glabrata isolates.

METHODOLOGY

Clinical C. glabrata species complex isolates from blood (n=71; 33.3 %), urine (n=100; 46.9 %), vaginal swabs (n=20;9.4 %), BAL (n=10; 4.7 %), and sputum (n=12; 5.6 %) from Iran were investigated. Isolates were characterized by CHROMagar, multiplex PCRs, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), amplified fragment length polymorphism (AFLP) fingerprinting, internal transcribed spacer (ITS)/large subunit (LSU) rDNA and FKS1/FKS2 sequencing, and the European Committee on Antimicrobial Susceptibility Testing broth microdilution method. A comprehensive literature review was conducted and all the relevant clinical and microbiological data were collected.

RESULTS

Four C. nivariensis isolates were recovered from blood samples of three subjects and were all consistently identified by nine-plex PCR, Bruker MALDI-TOF MS, and LSU and ITS rDNA sequencing. AFLP genotyping clustered the isolates into two groups. Sequencing of the FKS1 and FKS2 hotspots showed no accountable amino acid substitutions. All isolates were susceptible to amphotericin B, fluconazole, itraconazole, posaconazole, voriconazole, anidulafungin and micafungin.

CONCLUSION

In total, 4 out of 213 clinical C. glabrata species complex candidemia isolates were C. nivariensis. Improvement of the BioMerieux Vitek MS database is required to accurately identify C. nivariensis and it is advised to alternatively use CHROMagar and/or PCR-based techniques. As other species within the Nakaseomyces clade may cause infection and showed high MIC values for antifungals, inclusion of their spectra into the MALDI-TOF MS database seems relevant. Due to developing resistance to fluconazole and insufficient efficacy of caspofungin, the combination of catheter removal plus treatment with caspofungin, or voriconazole, or micafungin might be effective for patients.

Identification of chromoblastomycosis agents by PCR based reverse line blot (PCR-RLB) hybridization assay

Chromoblastomycosis is one of the most prevalent implantation fungal infections caused by melanized fungi, affecting individuals with certain risk factors with high morbidity due to its recalcitrant nature. It is difficult to identify the etiological agents and thus a suitable reproductive molecular identification method applicable in developing countries has been investigated. We report the identification of four different fungal causative agents of chromoblastomycosis by reverse line blotting hybridization (RLB) based on biotin-labeled PCR products and amine labeled probes to hybridize. Sixty five reference strains, including type strains, i.e. Fonsecaea pedrosoi, F. monophora, F. nubica, and Phialophora verrucosa, obtained from the CBS-KNAW were included in this study. Internal transcribed spacer 1 (ITS1) regions of relevant species were aligned and adjusted using BIONUMERICS v. 4.61 in order to design four specific probes to identify informative nucleotide polymorphisms. The final identification of these species by RLB assay was concordant with ITS sequencing and showed 100% specificity with no cross hybridization, able to identify all tested strains. The time and cost were less compare to other routine identification methods such as sequencing. This assay allows sensitive and specific simultaneous detection and identification of a different fungal species.

Correction to: Rapid Identification of Seven Waterborne Exophiala Species by RCA DNA Padlock Probes

The Editorial Office of Mycopathologia reports that several paragraphs of Najafzadeh et al. were transcribed with only minor edits from previously published material by Najafzadeh M.J.

Susceptibility pattern of Candida albicans isolated from Iranian patients to antifungal agents

Background and Purpose:

Candidiasis is a major fungal infection, and Candida albicans is the major cause of infections in humans. The Clinical and Laboratory Standards Institute (CLSI) developed new breakpoints for antifungal agents against C. albicans. In this multi-center study, we aimed to determine the drug susceptibility profile of C. albicans, isolated from Iranian population according to new species-specific CLSI.

Materials and Methods:

Clinical samples were cultured on Sabouraud dextrose agar and were incubated at room temperature for seven days. The isolates were transferred to Professor Alborzi Clinical Microbiology Research Center, Shiraz, Iran. C. albicans were identified by using API 20C AUX system. Broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) of amphotericin B, caspofungin, voriconazole, fluconazole, posaconazole, itraconazole, and ketoconazole, based on CLSI document M27-S4 and new breakpoints for some azoles and caspofungin.

Results:

Overall, 397 C. albicans were isolated from patients admitted to ten university hospitals in Iran. The MIC90 of the isolates to amphotericin B, caspofungin, voriconazole, fluconazole, posaconazole, itraconazole, and ketoconazole were 0.125, 0.125, 0.125, 1, 0.064, 0.5, and 0.125 µg/ml, and rates of resistance were 0.5%, 0.3%, 3.8%, 2.8%, and 2.5% for amphotericin B, caspofungin, voriconazole, fluconazole, and itraconazole, respectively.

Conclusion:

According to our data, fluconazole is the drug of choice for management of patients at risk for systemic candidiasis throughout the region, since it is cost-effective with low side effects.

Evaluation of two molecular techniques for rapid detection of the main dermatophytic agents of tinea capitis

BACKGROUND

Tinea capitis is very common in Western China, with the most widespread aetiological agent being Trichophyton violaceum, while Microsporum canis is prevalent in the remainder of China. Conventional diagnostics and internal transcribed spacer (ITS) sequencing analyses have proven relatively limited due to the close phylogenetic relationship of anthropophilic dermatophytes. Therefore, alternative molecular tools with sufficient specificity, reproducibility and sensitivity are necessary.

OBJECTIVES

To evaluate two molecular techniques [multiplex ligation-dependent probe amplification (MLPA) and rolling circle amplification (RCA)] for rapid detection of the aetiological agents of tinea capitis, T. violaceum and M. canis.

METHODS

Probes of RCA and MLPA were designed with target sequences in the rDNA ITS gene region. Strains tested consist of 31 T. violaceum, 22 M. canis and 24 reference strains of species that are taxonomically close to the target species.

RESULTS

The specificity and reproducibility of RCA and MLPA in detection of T. violaceum and M. canis were both 100% in both species. Sensitivity testing showed that RCA was positive at concentrations down to 1·68 × 10(6) copies of DNA in the TvioRCA probe, and 2·7 × 10(8) copies of DNA in McRCA. MLPA yielded positive results at concentrations of DNA down to 1·68 × 10(1) copies in the TvioMLPA probe and 2·7 × 10(2) in McMLPA.

CONCLUSIONS

The two techniques were sufficiently specific and sensitive for discriminating the target DNA of T. violaceum and M. canis from that of closely related dermatophytes. RCA and MLPA are advantageous in their reliability and ease of operation compared with standard polymerase chain reaction and conventional methods.

Molecular detection of Pneumocystis jirovecii using polymerase chain reaction in immunocompromised patients with pulmonary disorders in northeast of Iran

Background and Purpose:

Pneumocystis pneumonia, caused by Pneumocystis jirovecii, is a fatal disease threatening patients with AIDS or immunosuppression. Assessment of colonization in these patients is of great significance, since it can lead to severe pulmonary disorders. Considering the scarcity of published reports on Pneumocystis jirovecii isolates from patients in Mashhad, Iran, we aimed to evaluate pneumocystis colonization in individuals with different pulmonary disorders.

Materials and Methods:

We used nested polymerase chain reaction (PCR) method to amplify mitochondrial large subunit-ribosomal ribonucleic acid (mtLSU-rRNA) gene in 60 bronchoalveolar lavage (BAL) samples, obtained from patients, referring to the Department of Internal Medicine (Pulmonary Diseases Section) at Imam Reza Hospital, affiliated to Mashhad University of Medical Sciences, Mashhad, Iran.

Results:

DNA of Pneumocystis jirovecii was detected in 10 out of 60 BAL samples (16.66%) via nested PCR method.

Conclusion:

According to the present findings, the colonization rate of Pneumocystis jirovecii was similar to the rates reported in other similar studies in Iran.

Identification problems with sterile fungi, illustrated by a keratitis due to a non-sporulating Chaetomium-like species

A 39-year-old farm worker was injured in her right eye by a piece of wire, which resulted in a corneal ulcer unresponsive to antibiotic treatment. The clinical appearance was that of a corneal infiltrate with feathery borders resembling fungal keratitis. Corneal scrapings were collected and the patient was started on natamycin 5% eye drops, fluconazole 0.3% eye drops, and oral fluconazole. A non-sporulating fungus was isolated from the samples. Based upon macroscopic and microscopic morphologic features, it was provisionally identified as a Papulaspora species due to the fact that members of this genus generally do not form diagnostically useful conidia. However, it was found through the use of ITS sequencing that the isolate clustered within the ascomycete genus Chaetomium. The sequence did not fully match with any sequences of available ex-type strains of Chaetomium, Thielavia and Papulaspora and hence might belong to an undescribed specie. However, without diagnostic morphological features the taxon cannot be introduced as a novel member of the genus Chaetomium. Antifungal susceptibility testing was performed according to published standards. The corneal ulcer was successfully treated with six weeks of antifungal therapy.

Molecular identification of Penicillium marneffei using rolling circle amplification

Penicillium marneffei is the aetiological agent of a severe systemic disease in immunocompromised hosts in Southeast Asia. In the present study, we evaluated an identification method based on rolling circle amplification (RCA) enabling rapid and specific detection of single nucleotide differences. Three padlock probes were designed on the basis of the internal transcribed spacers 1 and 2 (ITS) of the rRNA operon. One of these (PmPL1) allowed specific amplification of P. marneffei DNA within one working day using a newly conceived protocol, while no cross-reactivity was observed with other fungi including related biverticillate penicillia. Amplification products can be detected by electrophoresis on agarose gel. The method provides a powerful tool for a rapid specific identification of P. marneffei in the clinical laboratory and has potential for ecological studies.

Environmental isolation of black yeast-like fungi involved in human infection

The present study focuses on potential agents of chromoblastomycosis and other endemic diseases in the state of Paraná, Southern Brazil. Using a highly selective protocol for chaetothyrialean black yeasts and relatives, environmental samples from the living area of symptomatic patients were analysed. Additional strains were isolated from creosote-treated wood and hydrocarbon-polluted environments, as such polluted sites have been supposed to enhance black yeast prevalence. Isolates showed morphologies compatible with the traditional etiological agents of chromoblastomycosis, e.g. Fonsecaea pedrosoi and Phialophora verrucosa, and of agents of subcutaneous or systemic infections like Cladophialophora bantiana and Exophiala jeanselmei. Some agents of mild disease were indeed encountered. However, molecular analysis proved that most environmental strains differed from known etiologic agents of pronounced disease syndromes: they belonged to the same order, but mostly were undescribed species. Agents of chromoblastomycosis and systemic disease thus far are prevalent on the human host. The hydrocarbon-polluted environments yielded yet another spectrum of chaetothyrialean fungi. These observations are of great relevance because they allow us to distinguish between categories of opportunists, indicating possible differences in pathogenicity and virulence.

Melanization of a meristematic mutant of Fonsecaea monophora increases tolerance to stress factors while no effects on antifungal susceptibility

Melanin is a complex polymer, which is widely distributed in nature, and is known as an important virulence factor in opportunistic and pathogenic fungi. In this study, three melanin mutants of Fonsecaea monophora from a case of chromoblastomycosis were generated from a parent strain that lacked hyphal morphology but was meristematic instead. Two albino mutants, one of which (CBS 125187) produced secreted melanin and another (CBS 125149) lacked melanin, grew faster than a mutant with cell-wall-associated and secreted melanin (CBS 125188) and than the meristematic parent strain (CBS 122845) (P < 0.05). The albino strains were also more sensitive to low pH, high UV radiation, and oxidative stress (P < 0.05). However, susceptibility testing against eight antifungal agents showed no statistical difference (P > 0.05). The discovery of three melanin mutants of a single meristematic mutant provided an alternative way to study the role of cell-wall-associated and secreted melanins in the pathogenesis of black fungi.

Rapid detection of pathogenic fungi using loop-mediated isothermal amplification, exemplified by Fonsecaea agents of chromoblastomycosis

Loop-mediated isothermal amplification (LAMP) was developed for rapid detection of pathogenic or allergenic fungal in the environment. Primers applied were derived from the rDNA Internal Transcribed Spacer and the 5.8S rRNA gene. The assay enabled amplification of target fungi at the level of genus or closely related species using pure cultures after 1h reaction at 65 degrees C in a water bath. No cross-reactivity to related species was observed. The DNA detection limit was 0.2fg. The method also proved to work well with fungi on non-sterile adhesive tape. Amplification products were detected by visual inspection using SYBR Green I as well as by electrophoresis on agarose gels. As a model organism we selected Fonsecaea, a fungal genus containing etiologic agents of chromoblastomycosis, a widely distributed tropical and subtropical skin disease in otherwise healthy patients and supposed to be acquired by environmental inoculation. It is suggested that LAMP can also be used for rapid clinical diagnosis, for environmental detection, and for retrospective studies in archived clinical samples.

Genetic diversity and species delimitation in the opportunistic genus Fonsecaea

Genetic diversity and species delimitation were investigated among 39 isolates recovered from clinical and environmental sources in Central and South America, Africa, East Asia and Europe. All had been morphologically identified as Fonsecaea spp. Molecular analyses were based on sequences of the ribosomal internal transcribed spacers (ITS), -tubulin (TUB1) and actin (ACT1) regions. A phylogenetic approach using haplotype networks was used to evaluate species delimitation and genetic diversity. The presence and the modes of reproductive isolation were tested by measuring the index of differentiation (ID) and the index of association (IA). Based on the sequence data, the 39 Fonsecaea strains were classified into three major entities: (i) a group representing Fonsecaea pedrosoi, (ii) a second composed of F. monophora, and (iii) a third group including mostly strains from South America. The two major, clinically relevant Fonsecaea species, F. monophora and F. pedrosoi, also differed in the pathological symptoms found in patients. Moreover, F. pedrosoi is mostly recovered in clinical settings, whereas F. monophora is commonly isolated from the environment. One environmental strain with Fonsecaea-like appearance was shown to belong to a different species, only distantly related to the core-group of Fonsecaea.

Biodiversity of the genus Cladophialophora

Cladophialophora is a genus of black yeast-like fungi comprising a number of clinically highly significant species in addition to environmental taxa. The genus has previously been characterized by branched chains of ellipsoidal to fusiform conidia. However, this character was shown to have evolved several times independently in the order Chaetothyriales. On the basis of a multigene phylogeny (nucLSU, nucSSU, RPB1), most of the species of Cladophialophora (including its generic type C. carrionii) belong to a monophyletic group comprising two main clades (carrionii- and bantiana-clades). The genus includes species causing chromoblastomycosis and other skin infections, as well as disseminated and cerebral infections, often in immunocompetent individuals. In the present study, multilocus phylogenetic analyses were combined to a morphological study to characterize phenetically similar Cladophialophora strains. Sequences of the ITS region, partial Translation Elongation Factor 1-alpha and beta-Tubulin genes were analysed for a set of 48 strains. Four novel species were discovered, originating from soft drinks, alkylbenzene-polluted soil, and infected patients. Membership of the both carrionii and bantiana clades might be indicative of potential virulence to humans.