Publications by authors named "Amir Arastehfar"

47 Publications

Pervasive but Neglected: A Perspective on COVID-19-Associated Pulmonary Mold Infections Among Mechanically Ventilated COVID-19 Patients.

Front Med (Lausanne) 2021 14;8:649675. Epub 2021 Jun 14.

Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran.

Recent studies from multiple countries have shown a high prevalence of coronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) among severely ill patients. Despite providing valuable insight into the clinical management of CAPA, large-scale prospective studies are limited. Here, we report on one of the largest multicenter epidemiological studies to explore the clinical features and prevalence of COVID-19-associated pulmonary mold infections (CAPMIs) among mechanically ventilated patients. Bronchoalveolar lavage (BAL) and serum samples were collected for culture, galactomannan (GM), and β-D-glucan (BDG) testing. Patients were classified as probable CAPMI based on the presence of host factors, radiological findings, and mycological criteria. During the study period, 302 COVID-19 patients were admitted to intensive care units (ICUs), among whom 105 were mechanically ventilated for ≥4 days. Probable CAPMI was observed among 38% of patients (40/105), among whom BAL culture of 29 patients turned positive for molds, while galactomannan testing on BAL (GM index ≥1) and serum (GM index >0.5) samples were positive for 60% (24/40) and 37.5% (15/39) of patients, respectively. (22/29; 75.8%) and (6/29; 20.6%) constituted 96.5% of the molds isolated. was isolated from a COVID-19 patient. None of the patients who presented with CAPMI were treated with antifungal drugs. Despite being prevalent, the absence of appropriate antifungal treatment highlights that CAPMI is a neglected complication among mechanically ventilated COVID-19 patients admitted to ICUs. CAPMI can be caused by species other than .
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http://dx.doi.org/10.3389/fmed.2021.649675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8236642PMC
June 2021

Multidrug-resistant species: underestimated fungal pathogens posing imminent threats in clinical settings.

Crit Rev Microbiol 2021 Jun 11:1-20. Epub 2021 Jun 11.

Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.

Species of and related genera are widely used in biotechnology and, hence, many species have their genome sequenced. Importantly, yeasts of the genus have been increasingly identified as a cause of life-threatening invasive trichosporonosis (IT) in humans and are associated with an exceptionally high mortality rate. spp. are intrinsically resistant to frontline antifungal agents, which accounts for numerous reports of therapeutic failure when echinocandins are used to treat IT. Moreover, these fungi have low sensitivity to polyenes and azoles and, therefore, are potentially regarded as multidrug-resistant pathogens. However, despite the clinical importance of spp., our understanding of their antifungal resistance mechanisms is quite limited. Furthermore, antifungal susceptibility testing is not standardized, and there is a lack of interpretive epidemiological cut-off values for minimal inhibitory concentrations to distinguish non-wild type isolates. The route of infection remains obscure and detailed clinical and environmental studies are required to determine whether the infections are endogenous or exogenous in nature. Although our knowledge on effective IT treatments is rather limited and future randomized clinical trials are required to identify the best antifungal agent, the current paradigm advocates the use of voriconazole, removal of central venous catheters and recovery from neutropenia.
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http://dx.doi.org/10.1080/1040841X.2021.1921695DOI Listing
June 2021

A High Rate of Recurrent Vulvovaginal Candidiasis and Therapeutic Failure of Azole Derivatives Among Iranian Women.

Front Microbiol 2021 28;12:655069. Epub 2021 Apr 28.

Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.

Recurrent vulvovaginal candidiasis (RVVC) is one of the most prevalent fungal infections in humans, especially in developing countries; however, it is underestimated and regarded as an easy-to-treat condition. RVVC may be caused by dysbiosis of the microbiome and other host-, pathogen-, and antifungal drug-related factors. Although multiple studies on host-related factors affecting the outcome have been conducted, such studies on -derived factors and their association with RVVC are lacking. Thus, fluconazole-tolerant (FLZT) isolates may cause fluconazole therapeutic failure (FTF), but this concept has not been assessed in the context of -associated vaginitis. Iran is among the countries with the highest burden of RVVC; however, comprehensive studies detailing the clinical and microbiological features of this complication are scarce. Therefore, we conducted a 1-year prospective study with the aim to determine the RVVC burden among women referred to a gynecology hospital in Tehran, the association of the previous exposure to clotrimazole and fluconazole with the emergence of FLZT and fluconazole-resistant (FLZR) isolates, and the relevance of these phenotypes to FTF. The results indicated that about 53% of the patients (43/81) experienced RVVC. and . constituted approximately 90% of the yeast isolates (72 patients). Except for one FLZT . isolate, FLZR and FLZT phenotypes were detected exclusively in patients with RVVC; among them, 27.9% (12/43) harbored FLZR strains. constituted 81.2% of FLZR (13/16) and 100% of the FLZT (13/13) isolates, respectively, and both phenotypes were likely responsible for FTF, which was also observed among patients with RVVC infected with fluconazole-susceptible isolates. Thus, FTF could be due to host-, drug-, and pathogen-related characteristics. Our study indicates that FLZT and FLZR isolates may arise following the exposure to over-the-counter (OTC) topical azole (clotrimazole) and that both phenotypes can cause FTF. Therefore, the widespread use of OTC azoles can influence fluconazole therapeutic success, highlighting the necessity of controlling the use of weak topical antifungals among Iranian women.
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http://dx.doi.org/10.3389/fmicb.2021.655069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113757PMC
April 2021

Clonal Candidemia Outbreak by Carrying Y132F in Turkey: Evolution of a Persisting Challenge.

Front Cell Infect Microbiol 2021 22;11:676177. Epub 2021 Apr 22.

Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.

As the second leading etiological agent of candidemia in Turkey and the cause of severe fluconazole-non-susceptible (FNS) clonal outbreaks, emerged as a major health threat at Ege University Hospital (EUH). Evaluation of microbiological and pertinent clinical profiles of candidemia patients due to . in EUH in 2019-2020. isolates were collected from blood samples and identified by sequencing internal transcribed spacer ribosomal DNA. Antifungal susceptibility testing was performed in accordance with CLSI M60 protocol and and HS1/HS2- were sequenced to explore the fluconazole and echinocandin resistance, respectively. Isolates were typed using a multilocus microsatellite typing assay. Relevant clinical data were obtained for patients recruited in the current study. FNS . isolates were recovered from 53% of the patients admitted to EUH in 2019-2020. Y132F was the most frequent mutation in Erg11. All patients infected with . isolates carrying Y132F, who received fluconazole showed therapeutic failure and significantly had a higher mortality than those infected with other FNS and susceptible isolates (50% . 16.1%). All isolates carrying Y132F grouped into one major cluster and mainly recovered from patients admitted to chest diseases and pediatric surgery wards. The unprecedented increase in the number of Y132F . , which corresponded with increased rates of fluconazole therapeutic failure and mortality, is worrisome and highlights the urgency for strict infection control strategies, antifungal stewardship, and environmental screening in EUH.
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http://dx.doi.org/10.3389/fcimb.2021.676177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8101544PMC
July 2021

Candidemia among Iranian Patients with Severe COVID-19 Admitted to ICUs.

J Fungi (Basel) 2021 Apr 8;7(4). Epub 2021 Apr 8.

Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.

As a novel risk factor, COVID-19 has led to an increase in the incidence of candidemia and an elevated mortality rate. Despite being of clinical importance, there is a lack of data regarding COVID-19-associated candidemia (CAC) among Iranian patients. Therefore, in this retrospective study, we assessed CAC epidemiology in the intensive care units (ICUs) of two COVID-19 centers in Mashhad, Iran, from early November 2020 to late January 2021. Yeast isolates from patients' blood were identified by 21-plex polymerase chain reaction (PCR) and sequencing, then subjected to antifungal susceptibility testing according to the CLSI M27-A3 protocol. Among 1988 patients with COVID-19 admitted to ICUs, seven had fungemia (7/1988; 0.03%), among whom six had CAC. The mortality of the limited CAC cases was high and greatly exceeded that of patients with COVID-19 but without candidemia (100% (6/6) vs. 22.7% (452/1988)). In total, nine yeast isolates were collected from patients with fungemia: five , three , and one . Half of the patients infected with (2/4) were refractory to both azoles and echinocandins. The high mortality of patients with CAC, despite antifungal therapy, reflects the severity of the disease in these patients and underscores the importance of rapid diagnosis and timely initiation of antifungal treatment.
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http://dx.doi.org/10.3390/jof7040280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068363PMC
April 2021

Dual drug delivery of vancomycin and imipenem/cilastatin by coaxial nanofibers for treatment of diabetic foot ulcer infections.

Mater Sci Eng C Mater Biol Appl 2021 Apr 15;123:111975. Epub 2021 Feb 15.

Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran. Electronic address:

Diabetic foot ulcer infections are the main causes of hospitalization in diabetics. The present study aimed to develop vancomycin and imipenem/cilastatin loaded core-shell nanofibers to facilitate the treatment of diabetic foot ulcers. Therefore, novel core-shell nanofibers composed of polyethylene oxide, chitosan, and vancomycin in shell and polyvinylpyrrolidone, gelatin, and imipenem/cilastatin in core compartments were prepared using the electrospinning technique. The nanofibers were characterized using scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, tensile test, and drug release. The antibacterial activity of drug-loaded nanofibers in different drugs concentrations was evaluated against Methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli, and Pseudomonas aeruginosa by disk diffusion method. Furthermore, the cytotoxicity of fibers was investigated by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide assay. The obtained results showed that the prepared nanofibers were smooth having a core-shell structure with almost no cytotoxicity. The nanofibrous mats exhibited significant antibacterial activity against S. aureus and MRSA with the inhibition zones of 2.9 and 2.5 cm and gram-negative bacteria species of E. coli and P. aeruginosa with the inhibition zones of 1.9 and 2.8 cm, respectively. With respect to the significant antibacterial activities of these nanofibrous mats, they might be used as suitable drug delivery devices not only for diabetic foot ulcer infections but also for other chronic wounds.
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http://dx.doi.org/10.1016/j.msec.2021.111975DOI Listing
April 2021

Environmental Clonal Spread of Azole-Resistant with Erg11-Y132F Mutation Causing a Large Candidemia Outbreak in a Brazilian Cancer Referral Center.

J Fungi (Basel) 2021 Mar 30;7(4). Epub 2021 Mar 30.

Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil.

Clonal outbreaks due to azole-resistant (ARCP) isolates have been reported in numerous studies, but the environmental niche of such isolates has yet to be defined. Herein, we aimed to identify the environmental niche of ARCP isolates causing unremitting clonal outbreaks in an adult ICU from a Brazilian cancer referral center. sensu stricto isolates recovered from blood cultures, pericatheter skins, healthcare workers (HCW), and nosocomial surfaces were genotyped by multilocus microsatellite typing (MLMT). Antifungal susceptibility testing was performed by the EUCAST (European Committee for Antimicrobial Susceptibility Testing) broth microdilution reference method and was sequenced to determine the azole resistance mechanism. Approximately 68% of isolates were fluconazole-resistant (76/112), including pericatheter skins (3/3, 100%), blood cultures (63/70, 90%), nosocomial surfaces (6/11, 54.5%), and HCW's hands (4/28, 14.2%). MLMT revealed five clusters: the major cluster contained 88.2% of ARCP isolates (67/76) collected from blood (57/70), bed (2/2), pericatheter skin (2/3), from carts (3/7), and HCW's hands (3/27). ARCP isolates were associated with a higher 30 day crude mortality rate (63.8%) than non-ARCP ones (20%, = 0.008), and resisted two environmental decontamination attempts using quaternary ammonium. This study for the first time identified ARCP isolates harboring the Erg11-Y132F mutation from nosocomial surfaces and HCW's hands, which were genetically identical to ARCP blood isolates. Therefore, it is likely that persisting clonal outbreak due to ARCP isolates was fueled by environmental sources. The resistance of Y132F ARCP isolates to disinfectants, and their potential association with a high mortality rate, warrant vigilant source control using effective environmental decontamination.
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http://dx.doi.org/10.3390/jof7040259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8066986PMC
March 2021

The clinical profiles and outcomes of HIV-negative cryptococcal meningitis patients in type II diabetes mellitus.

BMC Infect Dis 2021 Feb 27;21(1):224. Epub 2021 Feb 27.

Department of Neurology, Jiangxi Chest Hospital, Jiangxi, 330000, P. R. China.

Background: The clinical profiles and outcomes of cryptococcal meningitis have been shown to vary depending on the underlying condition. The aim of this study was to investigate clinical characteristics and outcomes in patients with and without type II diabetes mellitus.

Methods: A retrospective study was performed. Clinical data of HIV-negative cryptococcal meningitis patients with type II diabetes mellitus (n = 26) and without type II diabetes mellitus (n = 52) referring to the Jiangxi Chest Hospital between January 2012 to December 2018 were analyzed. The data were analyzed using chi square, none-parametric tests, and logistic regression. P-values < 0.05 were considered significant.

Results: In this study, cryptococcal meningitis patients suffering from type II diabetes mellitus had a higher mortality (23.08% vs. 7.69%; P = 0.055), and required longer hospitalization (59.58 vs. 42.88 days; P = 0.132). Moreover, cerebrospinal fluid examinations revealed that cryptococcal meningitis patients with type II diabetes mellitus had higher opening pressure (271.54 vs. 234.23 mmHO; P = 0.125).The results of multivariate regression analysis revealed that cryptococcal meningitis patients with type II diabetes were more often presented with visual disorders (28.54% vs. 11.54%; [95% CI 0.056-0.705]; p = 0.012), and had higher cerebrospinal fluid protein levels (1027.62 ± 594.16 vs. 705.72 ± 373.88 mg/l; [95% CI 1.000-1.002]; p = 0.016). Among patients with type II diabetes mellitus, nausea and vomiting was more frequent at the initial visit in those died (100% vs. 50%; p = 0.027), and 66% of died type II diabetes mellitus patients were poorly controlled blood glucose level, compared with 30% in survival type II diabetes mellitus patients.

Conclusion: This study suggests that cryptococcal meningitis patients with type II diabetes mellitus differ significantly from cryptococcal meningitis patients without type II diabetes mellitus with respect to clinical symptoms such as visual disorders and cerebrospinal fluid examination. The presence of nausea and vomiting among type II diabetes mellitus patients could have implication in mortality.
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http://dx.doi.org/10.1186/s12879-021-05867-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7913410PMC
February 2021

Efficacy of LAMB against Emerging Azole- and Multidrug-Resistant Isolates in the Model.

J Fungi (Basel) 2020 Dec 18;6(4). Epub 2020 Dec 18.

Institute of Hygiene and Medical Microbiology, Medical University Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria.

While being the third leading cause of candidemia worldwide, numerous studies have shown severe clonal outbreaks due to fluconazole-resistant (FLCR) isolates associated with fluconazole therapeutic failure (FTF) with enhanced mortality. More recently, multidrug resistant (MDR) blood isolates have also been identified that are resistant to both azole and echinocandin drugs. Amphotericin B (AMB) resistance is rarely reported among isolates and proper management of bloodstream infections due to FLZR and MDR isolates requires prompt action at the time of outbreak. Therefore, using a well-established model, we assessed whether (a) laboratory-based findings on azole or echinocandin (micafungin) resistance in lead to therapeutic failure, (b) LAMB could serve as an efficient salvage treatment option, and (c) distinct mutations in impact mortality. Our in vivo data confirm fluconazole inefficacy against FLCR isolates carrying Y132F, Y132F + K143R, Y132F + G307A, and G307A + G458S in Erg11p, while LAMB proved to be an efficacious accessible option against both FLCR and MDR isolates. Moreover, positive correlation of in vitro and in vivo data further highlights the utility of as a reliable model to investigate azole and polyene drug efficacy.
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http://dx.doi.org/10.3390/jof6040377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7767002PMC
December 2020

Clinical and microbiological features of candiduria in critically ill adult patients in Shiraz, Iran (2016-2018): deviations from international guidelines and fluconazole therapeutic failure.

Med Mycol 2020 Dec 10. Epub 2020 Dec 10.

Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.

Candiduria is common among patients admitted to intensive care units (ICUs); however, clinical and microbiological data are limited, which accounts for non-compliance with international guidelines, including over treatment of asymptomatic candiduria that promotes antifungal resistance. This prospective study included adult patients admitted to ICUs of five referral hospitals in Shiraz, Iran, during 2016-2018. Species were identified by MALDI-TOF MS, and antifungal susceptibility was assessed according to CLSI M27-A3/S4. Among 2086 patients, 162 and 293 developed candiduria and bacteriuria, respectively. In total, 174 yeast isolates were collected; 88.5% were Candida albicans (91/174; 52.2%), C. glabrata (38/174; 21.8%), and C. tropicalis (25/174; 14.3%). Antifungal resistance was rare; only two isolates (one C. tropicalis and one C. krusei) were fluconazole resistant. Symptomatic candiduria was noted in 31.4% of patients (51/162); only 37% (19/51) of them were treated and 36.82% (7/19) showed fluconazole therapeutic failure. Two symptomatic patients developed candidemia shortly after candiduria. Among asymptomatic patients, 31.5% (35/111) were overtreated with fluconazole. The mortality rate was 25.3% (41/162); it did not differ between symptomatic and asymptomatic patients. Our results indicate that deviation from standard-of-care treatment for candiduria is a matter of concern given the high rate of fluconazole therapeutic failure among patients with symptomatic candiduria.

Lay Summary: Candiduria is an underestimated clinical presentation among critically ill patients and detailed data are scarce in this regard. Given the high rate of fluconazole therapeutic failure and development of candidemia in some cases, the mistreatment of candiduria should not be overlooked by clinicians.
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http://dx.doi.org/10.1093/mmy/myaa092DOI Listing
December 2020

Drug-Resistant Fungi: An Emerging Challenge Threatening Our Limited Antifungal Armamentarium.

Antibiotics (Basel) 2020 Dec 8;9(12). Epub 2020 Dec 8.

Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.

The high clinical mortality and economic burden posed by invasive fungal infections (IFIs), along with significant agricultural crop loss caused by various fungal species, has resulted in the widespread use of antifungal agents. Selective drug pressure, fungal attributes, and host- and drug-related factors have counteracted the efficacy of the limited systemic antifungal drugs and changed the epidemiological landscape of IFIs. Species belonging to , , , and are among the fungal pathogens showing notable rates of antifungal resistance. Drug-resistant fungi from the environment are increasingly identified in clinical settings. Furthermore, we have a limited understanding of drug class-specific resistance mechanisms in emerging species. The establishment of antifungal stewardship programs in both clinical and agricultural fields and the inclusion of species identification, antifungal susceptibility testing, and therapeutic drug monitoring practices in the clinic can minimize the emergence of drug-resistant fungi. New antifungal drugs featuring promising therapeutic profiles have great promise to treat drug-resistant fungi in the clinical setting. Mitigating antifungal tolerance, a prelude to the emergence of resistance, also requires the development of effective and fungal-specific adjuvants to be used in combination with systemic antifungals.
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http://dx.doi.org/10.3390/antibiotics9120877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764418PMC
December 2020

Molecular identification and antifungal susceptibility among clinical isolates of dermatophytes in Shiraz, Iran (2017-2019).

Mycoses 2021 Apr 20;64(4):385-393. Epub 2020 Dec 20.

Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.

Dermatophytosis is a common superficial mycotic infection affecting individual's quality of life worldwide. The present study aimed to perform species-level identification and evaluate the antifungal susceptibility patterns of dermatophytes isolated in Shiraz, Iran. This cross-sectional study was conducted on clinical samples collected during 2017-2019 from 307 patients suspected of having dermatophytosis. The isolates were identified by direct microscopy, culture and internal transcribed spacer ribosomal DNA sequencing, and their antifungal susceptibility patterns were determined by the microdilution method. Among 307 patients, dermatophytosis was diagnosed by microscopy in 190 (61.8%) subjects and confirmed in 130 (42.3%) cases by both microscopy and culture. It was found out tinea pedis was the most common clinical manifestation, and Trichophyton mentagrophytes was the most prevalent species (28.4%), followed by T tonsurans (23.8%), Microsporum canis (11.5%), T interdigitale (10%), T verrucosum (6.9%), T rubrum (6.9%), T benhamiae (4.6%), T violaceum (3%), T simii (3%), Epidermophyton floccosum (0.7%) and M ferrugineum (0.7%). Moreover, it was revealed that luliconazole with a geometric mean (GM) minimum inhibitory concentration (MIC) of 0.03 μg ml was the most effective agent against all tested isolates. Regardless of species, 30% of isolates responded to high MICs of griseofulvin (MIC  > 2 μg ml ). The increasing prevalence of nonindigenous species of T simii, T benhamiae and M ferrugineum in Shiraz, Iran, was a notable finding. In addition, infections due to zoophilic species showed an increasing trend. These epidemiological data, along with antifungal susceptibility patterns, may have implications for clinical decision-making and successful treatment.
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http://dx.doi.org/10.1111/myc.13226DOI Listing
April 2021

Genetically related micafungin-resistant Candida parapsilosis blood isolates harbouring novel mutation R658G in hotspot 1 of Fks1p: a new challenge?

J Antimicrob Chemother 2021 01;76(2):418-422

Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.

Background: Echinocandin resistance rarely occurs in clinical Candida parapsilosis isolates and the underlying mechanism is unknown.

Objectives: To determine the prevalence of echinocandin resistance and the underlying mechanism for a large collection of C. parapsilosis blood isolates and to determine whether the echinocandin-resistant isolates were clonally related.

Methods: C. parapsilosis blood isolates (n = 213) were subjected to antifungal susceptibility testing (CLSI M27), for micafungin, anidulafungin, amphotericin B and, if appropriate, caspofungin. Hotspot (HS) 1 and HS2 of FKS1 were sequenced for all isolates (n = 213) and microsatellite typing was performed for echinocandin-resistant isolates.

Results: All isolates were susceptible to amphotericin B and two isolates were intermediate to anidulafungin (MIC = 4 mg/L), while micafungin resistance was noted in four isolates (MIC >8 mg/L); three of which were also fluconazole resistant and therefore were MDR. Interestingly, micafungin-resistant isolates, but not those intermediate to anidulafungin, carried novel mutation R658G in HS1 of Fks1p; three of which also harboured Y132F+K143R in Erg11. The first isolate (MICR1) was recovered in November 2017 from a patient admitted to paediatric gastroenterology who showed therapeutic failure under caspofungin treatment. MICR2-MICR4 were collected during 2018-19 and were recovered from three echinocandin-naive paediatric-surgery patients; the isolates shared the same genotype.

Conclusions: Herein, for the first time (to the best of our knowledge), we identified micafungin-resistant C. parapsilosis blood isolates harbouring a novel mutation in HS1 of FKS1, which was likely attributable to in vitro micafungin resistance and in vivo caspofungin therapeutic failure. The acquisition of micafungin-resistant C. parapsilosis isolates in echinocandin-naive patients likely implicates clonal expansion, as supported by the close genetic relatedness of MICR2-MICR4.
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http://dx.doi.org/10.1093/jac/dkaa419DOI Listing
January 2021

Recent Increase in the Prevalence of Fluconazole-Non-susceptible Blood Isolates in Turkey: Clinical Implication of Azole-Non-susceptible and Fluconazole Tolerant Phenotypes and Genotyping.

Front Microbiol 2020 6;11:587278. Epub 2020 Oct 6.

Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.

is the fourth leading cause of candidemia in Turkey. Although isolates from 1997 to 2017 were characterized as fully susceptible to antifungals, the increasing global prevalence of azole-non-susceptible (ANS) and the association between high fluconazole tolerance (HFT) and fluconazole therapeutic failure (FTF) prompted us to re-evaluate azole susceptibility of in Turkey. In this study, 161 blood isolates from seven clinical centers were identified by ITS rDNA sequencing, genotyped by multilocus microsatellite typing, and tested for susceptibility to five azoles, two echinocandins, and amphotericin B (AMB); antifungal resistance mechanisms were assessed by sequencing of and genes. The results indicated that isolates, which belonged to 125 genotypes grouped into 11 clusters, were fully susceptible to echinocandins and AMB; however, 18.6% of them had the ANS phenotype but only two carried the ANS-conferring mutation (Y132F). HFT was recorded in 52 isolates, 10 of which were also ANS. Large proportions of patients infected with ANS and HFT isolates (89 and 40.7%, respectively) showed FTF. Patients infected with azole-susceptible or ANS isolates did not differ in mortality, which, however, was significantly lower for those infected with HFT isolates ( = 0.007). There were significant differences in mortality ( = 0.02), ANS ( = 0.012), and HFT ( = 0.007) among genotype clusters. The alarming increase in the prevalence of blood isolates with ANS and HFT in Turkey and the notable FTF rate should be a matter of public health concern.
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http://dx.doi.org/10.3389/fmicb.2020.587278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7573116PMC
October 2020

SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files.

Bioinformatics 2021 07;37(11):1610-1612

Biotechvana, Parc Científic Universitat de València, Valencia, Spain.

Motivation: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis.

Result: SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets.

Availabilityand Implementation: SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa903DOI Listing
July 2021

COVID-19-Associated Candidiasis (CAC): An Underestimated Complication in the Absence of Immunological Predispositions?

J Fungi (Basel) 2020 Oct 8;6(4). Epub 2020 Oct 8.

Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA 92093, USA.

The recent global pandemic of COVID-19 has predisposed a relatively high number of patients to acute respiratory distress syndrome (ARDS), which carries a risk of developing super-infections. species are major constituents of the human mycobiome and the main cause of invasive fungal infections, with a high mortality rate. Invasive yeast infections (IYIs) are increasingly recognized as s complication of severe COVID-19. Despite the marked immune dysregulation in COVID-19, no prominent defects have been reported in immune cells that are critically required for immunity to . This suggests that relevant clinical factors, including prolonged ICU stays, central venous catheters, and broad-spectrum antibiotic use, may be key factors causing COVID-19 patients to develop IYIs. Although data on the comparative performance of diagnostic tools are often lacking in COVID-19 patients, a combination of serological and molecular techniques may present a promising option for the identification of IYIs. Clinical awareness and screening are needed, as IYIs are difficult to diagnose, particularly in the setting of severe COVID-19. Echinocandins and azoles are the primary antifungal used to treat IYIs, yet the therapeutic failures exerted by multidrug-resistant spp. such as and call for the development of new antifungal drugs with novel mechanisms of action.
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http://dx.doi.org/10.3390/jof6040211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7712987PMC
October 2020

The Quiet and Underappreciated Rise of Drug-Resistant Invasive Fungal Pathogens.

J Fungi (Basel) 2020 Aug 18;6(3). Epub 2020 Aug 18.

Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.

Human fungal pathogens are attributable to a significant economic burden and mortality worldwide. Antifungal treatments, although limited in number, play a pivotal role in decreasing mortality and morbidities posed by invasive fungal infections (IFIs). However, the recent emergence of multidrug-resistant and and acquiring invasive infections due to azole-resistant , , and spp. in azole-naïve patients pose a serious health threat considering the limited number of systemic antifungals available to treat IFIs. Although advancing for major fungal pathogens, the understanding of fungal attributes contributing to antifungal resistance is just emerging for several clinically important MDR fungal pathogens. Further complicating the matter are the distinct differences in antifungal resistance mechanisms among various fungal species in which one or more mechanisms may contribute to the resistance phenotype. In this review, we attempt to summarize the burden of antifungal resistance for selected non- and clinically important species together with their phylogenetic placement on the tree of life. Moreover, we highlight the different molecular mechanisms between antifungal tolerance and resistance, and comprehensively discuss the molecular mechanisms of antifungal resistance in a species level.
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http://dx.doi.org/10.3390/jof6030138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7557958PMC
August 2020

Cryptococcal Meningitis: A Rare Complication in HIV-Negative Patients with Nephrotic Syndrome in A Chinese Teaching Hospital.

Mycopathologia 2020 Dec 13;185(6):959-969. Epub 2020 Aug 13.

Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.

Cryptococcal meningitis (CM) is a rare complication in HIV-negative patients with nephrotic syndrome (NS), and knowledge about the clinical profile of NS with CM is limited. We performed a retrospective study of all patients with CM-NS admitted to the Jiangxi Chest Hospital (JCH) between 2011 and 2019 and systematically reviewed cases of CM-NS reported in the Chinese language. Among a total of 226 CM patients referred to the JCH, seven had NS (3.1%); these patients were combined with 22 CM-NS cases reported in the Chinese language for analysis. Headache, fever, nausea, and meningeal irritation were the most common initial symptoms, and the median time from symptom onset to CM diagnostic confirmation was 30 days. One patient initially tested negative for CM but was later confirmed to be positive. Among the 29 analysed patients, 41.4% (12/29) were misdiagnosed with other complications, including four patients from the JCH (4/7, 57.1%) and eight patients from published reports (8/22, 36.3%). The overall mortality rate was 17.2% (5/29); among these patients, 60% (3/5) were misdiagnosed. Induction treatment with amphotericin B plus 5-fluorocytosine (9/29) or amphotericin B plus fluconazole (7/29) successfully cleared the infection. Fluconazole may be a suitable alternative if 5-fluorocytosine is not readily available or not tolerated, and repetitive testing is important to reach a conclusive diagnosis in NS patients suspected of having CM.
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http://dx.doi.org/10.1007/s11046-020-00482-5DOI Listing
December 2020

Epidemiology of candidemia in Shiraz, southern Iran: A prospective multicenter study (2016-2018).

Med Mycol 2021 May;59(5):422-430

Department of Anesthesia and Critical Care Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.

Systematic candidemia studies, especially in southern Iran, are scarce. In the current prospective study, we investigated candidemia in three major healthcare centers of Shiraz, the largest city in southern Iran. Yeast isolates from blood and other sterile body fluids were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method. Clinical data were retrieved from patients' medical records. In total, 113 yeast isolates were recovered from 109 patients, over 60% of whom received fluconazole. Antifungal drugs were prescribed without considering species identification or AFST. The all-cause mortality rate was 28%. Almost 30% of the patients were from intensive care units (ICUs). Candida albicans (56/113; 49.5%) was the most prevalent species followed by C. glabrata (26/113; 23%), C. parapsilosis (13/113; 11.5%), C. tropicalis (7/113; 6.2%), and C. dubliniensis (5/113; 4.4%). Only five isolates showed antifungal resistance or decreased susceptibility to fluconazole: one C. orthopsilosis isolate from an azole-naïve patient and two C. glabrata, one C. albicans, and one C. dubliniensis isolates from patients treated with azoles, who developed therapeutic failure against azoles later. Our results revealed a low level of antifungal resistance but a notable rate of azole therapeutic failure among patients with candidemia due to non-albicans Candida species, which threaten the efficacy of fluconazole, the most widely used antifungal in southern regions of Iran. Candidemia studies should not be confined to ICUs and treatment should be administered based on species identification and AFST results.
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http://dx.doi.org/10.1093/mmy/myaa059DOI Listing
May 2021

First Report of Candidemia Clonal Outbreak Caused by Emerging Fluconazole-Resistant Candida parapsilosis Isolates Harboring Y132F and/or Y132F+K143R in Turkey.

Antimicrob Agents Chemother 2020 09 21;64(10). Epub 2020 Sep 21.

Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.

Clonal outbreaks of fluconazole-resistant (FLZR) isolates have been reported in several countries. Despite its being the second leading cause of candidemia, the azole resistance mechanisms and the clonal expansion of FLZR blood isolates have not been reported in Turkey. In this study, we consecutively collected blood isolates (= 225) from the fifth largest hospital in Turkey (2007 to 2019), assessed their azole susceptibility pattern using CLSI M27-A3/S4, and sequenced for all and , , and for a selected number of isolates. The typing resolution of two widely used techniques, amplified fragment length polymorphism typing (AFLP) and microsatellite typing (MST), and the biofilm production of FLZR isolates with and without Y132F were compared. Approximately 27% of isolates were FLZR (60/225), among which 90% (54/60) harbored known mutations in Erg11, including Y132F (24/60) and Y132F+K143R (19/60). Several mutations specific to FLZR isolates were found in , , and AFLP grouped isolates into two clusters, while MST revealed several clusters. The majority of Y132F/Y132F+K143R isolates grouped in clonal clusters, which significantly expanded throughout 2007 to 2019 in neonatal wards. isolates carrying Y132F were associated with significantly higher mortality and less biofilm production than other FLZR isolates. Collectively, we documented the first outbreak of FLZR blood isolates in Turkey. The , , and mutations exclusively found in FLZR isolates establishes a basis for future studies, which will potentially broaden our knowledge of FLZR mechanisms in MST should be a preferred method for clonal analysis of isolates in outbreak scenarios.
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http://dx.doi.org/10.1128/AAC.01001-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508617PMC
September 2020

Glucantime-loaded electrospun core-shell nanofibers composed of poly(ethylene oxide)/gelatin-poly(vinyl alcohol)/chitosan as dressing for cutaneous leishmaniasis.

Int J Biol Macromol 2020 Nov 28;163:288-297. Epub 2020 Jun 28.

School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. Electronic address:

Leishmaniasis, one of the main concerns of the World Health Organization, is a parasitic disease caused by Leishmania species. The main objective of this study was to prepare a topical drug delivery system that can deliver glucantime to the site of cutaneous Leishmania wounds. Using the electrospinning method, a core-shell nanofibrous mat composed of macromolecules including polyethylene oxide, gelatin, poly (vinyl alcohol) and chitosan was prepared. The prepared nanofibers were characterized by scanning electron microscopy (SEM), transmission electron microscopy, Fourier transform infrared spectroscopy (FT-IR), tensile test and in vitro drug release test. The anti-Leishmania activities of drug-loaded nanofibers against Leishmania promastigotes and its cytotoxicity on fibroblasts were determined respectively by flow-cytometry and indirect MTT methods. Results of morphological studies showed that uniform nanofibers were prepared without any bead with average diameter of 404 nm. The TEM investigation confirmed the core-shell structure of the fibers. The in-vitro drug release assay was executed using Franz diffusion cell, which indicted 84% of glucantime was released during the first 9 h. The results indicated that 4 and 6 cm of nanofibers mat were significantly killed promatigotes up to 78%. Moreover, the MTT assay also showed that the fabricated nanofibers do not possess any cytotoxicity towards fibroblast cells.
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http://dx.doi.org/10.1016/j.ijbiomac.2020.06.240DOI Listing
November 2020

COVID-19 Associated Pulmonary Aspergillosis (CAPA)-From Immunology to Treatment.

J Fungi (Basel) 2020 Jun 24;6(2). Epub 2020 Jun 24.

Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA 92093, USA.

Like severe influenza, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome (ARDS) has emerged as an important disease that predisposes patients to secondary pulmonary aspergillosis, with 35 cases of COVID-19 associated pulmonary aspergillosis (CAPA) published until June 2020. The release of danger-associated molecular patterns during severe COVID-19 results in both pulmonary epithelial damage and inflammatory disease, which are predisposing risk factors for pulmonary aspergillosis. Moreover, collateral effects of host recognition pathways required for the activation of antiviral immunity may, paradoxically, contribute to a highly permissive inflammatory environment that favors fungal pathogenesis. Diagnosis of CAPA remains challenging, mainly because bronchoalveolar lavage fluid galactomannan testing and culture, which represent the most sensitive diagnostic tests for aspergillosis in the ICU, are hindered by the fact that bronchoscopies are rarely performed in COVID-19 patients due to the risk of disease transmission. Similarly, autopsies are rarely performed, which may result in an underestimation of the prevalence of CAPA. Finally, the treatment of CAPA is complicated by drug-drug interactions associated with broad spectrum azoles, renal tropism and damage caused by SARS-CoV-2, which may challenge the use of liposomal amphotericin B, as well as the emergence of azole-resistance. This clinical reality creates an urgency for new antifungal drugs currently in advanced clinical development with more promising pharmacokinetic and pharmacodynamic profiles.
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http://dx.doi.org/10.3390/jof6020091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7346000PMC
June 2020

Evaluation of Molecular Epidemiology, Clinical Characteristics, Antifungal Susceptibility Profiles, and Molecular Mechanisms of Antifungal Resistance of Iranian Species Complex Blood Isolates.

Front Cell Infect Microbiol 2020 21;10:206. Epub 2020 May 21.

Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.

Clonal expansion of fluconazole resistant (FLZ-R) isolates is increasingly being identified in many countries, while there is no study exploring the antifungal susceptibility pattern, genetic diversity, and clinical information for Iranian blood isolates. species complex blood isolates ( = 98) were recovered from nine hospitals located in three major cities, identified by MALDI-TOF MS, and their genetic relatedness was examined by AFLP fingerprinting. Antifungal susceptibility testing followed CLSI-M27-A3 and and hotspots 1/2 (HS1/2) of were sequenced to assess the azole and echinocandin resistance mechanisms, respectively. Ninety-four and four isolates were identified from 90 patients. Only 43 patients received systemic antifungal drugs with fluconazole as the main antifungal used. The overall mortality rate was 46.6% (42/90) and death mostly occurred for those receiving systemic antifungals (25/43) relative to those not treated (17/47). Although, antifungal-resistance was rare, one isolate was multidrug-resistant (FLZ = 16 μg/ml and micafungin = 8 μg/ml) and the infected patient showed therapeutic failure to FLZ prophylaxis. Mutations causing azole and echinocandin resistance were not found in the genes studied. AFLP revealed five genotypes (G) and G1 was the main one (59/94; 62.7%). Clinical outcome was significantly associated with city ( = 0.02, α <0.05) and Mashhad was significantly associated with mortality ( = 0.03, α <0.05). Overall, we found a low level of antifungal resistance for Iranian blood isolates, but the noted MDR strain can potentially become the source of future infections and challenge the antifungal therapy in antifungal-naïve patients. AFLP typing results warrants confirmation using other resolutive typing methods.
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http://dx.doi.org/10.3389/fcimb.2020.00206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253641PMC
June 2021

Low level of antifungal resistance of Candida glabrata blood isolates in Turkey: Fluconazole minimum inhibitory concentration and FKS mutations can predict therapeutic failure.

Mycoses 2020 Sep 5;63(9):911-920. Epub 2020 Aug 5.

Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.

Background: Candida glabrata is the third leading cause of candidaemia in Turkey; however, the data regarding antifungal resistance mechanisms and genotypic diversity in association with their clinical implication are limited.

Objectives: To assess genotypic diversity, antifungal susceptibility and mechanisms of drug resistance of C glabrata blood isolates and their association with patients' outcome in a retrospective multicentre study.

Patients/methods: Isolates from 107 patients were identified by ITS sequencing and analysed by multilocus microsatellite typing, antifungal susceptibility testing, and sequencing of PDR1 and FKS1/2 hotspots (HSs).

Results: Candida glabrata prevalence in Ege University Hospital was twofold higher in 2014-2019 than in 2005-2014. Six of the analysed isolates had fluconazole MICs ≥ 32 µg/mL; of them, five harboured unique PDR1 mutations. Although echinocandin resistance was not detected, three isolates had mutations in HS1-Fks1 (S629T, n = 1) and HS1-Fks2 (S663P, n = 2); one of the latter was also fluconazole-resistant. All patients infected with isolates carrying HS-FKS mutations and/or demonstrating fluconazole MIC ≥ 32 µg/mL (except one without clinical data) showed therapeutic failure (TF) with echinocandin and fluconazole; seven such isolates were collected in Ege (n = 4) and Gulhane (n = 3) hospitals and six detected recently. Among 34 identified genotypes, none were associated with mortality or enriched for fluconazole-resistant isolates.

Conclusion: Antifungal susceptibility testing should be supplemented with HS-FKS sequencing to predict TF for echinocandins, whereas fluconazole MIC ≥ 32 µg/mL may predict TF. Recent emergence of C glabrata isolates associated with antifungal TF warrants future comprehensive prospective studies in Turkey.
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http://dx.doi.org/10.1111/myc.13104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497236PMC
September 2020

Epidemiology of yeast species causing bloodstream infection in Tehran, Iran (2015-2017); superiority of 21-plex PCR over the Vitek 2 system for yeast identification.

J Med Microbiol 2020 May 28;69(5):712-720. Epub 2020 Apr 28.

Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.

Given the limited number of candidaemia studies in Iran, the profile of yeast species causing bloodstream infections (BSIs), especially in adults, remains limited. Although biochemical assays are widely used in developing countries, they produce erroneous results, especially for rare yeast species. We aimed to assess the profile of yeast species causing BSIs and to compare the accuracy of the Vitek 2 system and 21-plex PCR. Yeast blood isolates were retrospectively collected from patients recruited from two tertiary care training hospitals in Tehran from 2015 to 2017. Relevant clinical data were mined. Identification was performed by automated Vitek 2, 21-plex PCR and sequencing of the internal transcribed spacer region (ITS1-5.8S-ITS2). In total, 137 yeast isolates were recovered from 107 patients. The overall all-cause 30-day mortality rate was 47.7 %. Fluconazole was the most widely used systemic antifungal. (58/137, 42.3 %), (30/137, 21.9 %), sensu stricto (23/137, 16.8 %), (10/137, 7.3 %) and () (4/137, 2.9 %) constituted almost 90 % of the isolates and 10 % of the species detected were rare yeast species (12/137; 8.7 %). The 21-plex PCR method correctly identified 97.1 % of the isolates, a higher percentage than the Vitek 2 showed (87.6 %). was the main cause of yeast-derived fungaemia in this study. Future prospective studies are warranted to closely monitor the epidemiological landscape of yeast species causing BSIs in Iran. The superiority of 21-plex PCR over automated Vitek 2 indicates its potential clinical utility as an alternative identification tool use in developing countries.
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http://dx.doi.org/10.1099/jmm.0.001189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7451039PMC
May 2020

Candida tropicalis is the most prevalent yeast species causing candidemia in Algeria: the urgent need for antifungal stewardship and infection control measures.

Antimicrob Resist Infect Control 2020 04 7;9(1):50. Epub 2020 Apr 7.

Parasitology and Mycology Department, Mustapha University Hospital, 16000, Algiers, Algeria.

Background: Despite being associated with a high mortality and economic burden, data regarding candidemia are scant in Algeria. The aim of this study was to unveil the epidemiology of candidemia in Algeria, evaluate the antifungal susceptibility pattern of causative agents and understand the molecular mechanisms of antifungal resistance where applicable. Furthermore, by performing environmental screening and microsatellite typing we sought to identify the source of infection.

Methods: We performed a retrospective epidemiological-based surveillance study and collected available blood yeast isolates recovered from the seven hospitals in Algiers. To identify the source of infection, we performed environmental screening from the hands of healthcare workers (HCWs) and high touch areas. Species identification was performed by API Auxa-Color and MALDI-TOF MS and ITS sequencing was performed for species not reliably identified by MALDI-TOF MS. Antifungal susceptibility testing followed CLSI M27-A3/S4 and included all blood and environmental yeast isolates. ERG11 sequencing was performed for azole-resistant Candida isolates. Microsatellite typing was performed for blood and environmental Candida species, where applicable.

Results: Candida tropicalis (19/66) was the main cause of candidemia in these seven hospitals, followed by Candida parapsilosis (18/66), Candida albicans (18/66), and Candida glabrata (7/66). The overall mortality rate was 68.6% (35/51) and was 81.2% for C. tropicalis-infected patients (13/16). Fluconazole was the main antifungal drug used (12/51); 41% of the patients (21/51) did not receive any systemic treatment. Candida parapsilosis was isolated mainly from the hands of HCWs (7/28), and various yeasts were collected from high-touch areas (11/47), including Naganishia albida, C. parapsilosis and C. glabrata. Typing data revealed interhospital transmission on two occasions for C. parapsilosis and C. glabrata, and the same clone of C. parapsilosis infected two patients within the same hospital. Resistance was only noted for C. tropicalis against azoles (6/19) and fluconazole-resistant C. tropicalis isolates (≥8 μg/ml) (6/19) contained a novel P56S (5/6) amino acid substitution and a previously reported one (V234F; 1/6) in Erg11p.

Conclusions: Collectively, our data suggest an urgent need for antifungal stewardship and infection control strategies to improve the clinical outcome of Algerian patients with candidemia. The high prevalence of C. tropicalis joined by fluconazole-resistance may hamper the therapeutic efficacy of fluconazole, the frontline antifungal drug used in Algeria.
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http://dx.doi.org/10.1186/s13756-020-00710-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140370PMC
April 2020

Madurella real-time PCR, a novel approach for eumycetoma diagnosis.

PLoS Negl Trop Dis 2020 01 15;14(1):e0007845. Epub 2020 Jan 15.

Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.

The genus Madurella comprising four species, M. fahalii, M. mycetomatis, M. pseudomycetomatis, and M. tropicana, represents the prevalent cause of eumycetoma worldwide. The four species are phenotypically similar and cause an invariable clinical picture, but differ markedly in their susceptibility to antifungal drugs, and epidemiological pattern. Therefore, specific identification is required for optimal management of Madurella infection and to reveal proper epidemiology of the species. In this study, a novel multiplex real-time PCR targeting the four Madurella species was developed and standardized. Evaluation of the assay using reference strains of the target and non-target species resulted in 100% specificity, high analytical reproducibility (R2 values >0.99) and a lowest detection limit of 3 pg target DNA. The accuracy of the real-time PCR was further assessed using biopsies from eumycetoma suspected patients. Unlike culture and DNA sequencing as gold standard diagnostic methods, the real-time PCR yielded accurate diagnosis with specific identification of the causative species in three hours compared to one or two weeks required for culture. The novel method reduces turnaround time as well as labor intensity and high costs associated with current reference methods.
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http://dx.doi.org/10.1371/journal.pntd.0007845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986762PMC
January 2020

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

Med Mycol 2020 Aug;58(6):766-773

Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.

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.
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http://dx.doi.org/10.1093/mmy/myz124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398758PMC
August 2020

Identification of Mycoses in Developing Countries.

J Fungi (Basel) 2019 Sep 29;5(4). Epub 2019 Sep 29.

Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.

Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of and and are highly relevant for developing countries. An galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.
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http://dx.doi.org/10.3390/jof5040090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6958481PMC
September 2019
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