An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

Background and Purpose: Opportunistic fungal infections have been on a growingtrend since the last two decades. Among the opportunistic fungal agents, Candidaspecies, Cryptococcus neoformans, and Aspergillus fumigatus account for most of thelife-threatening infections in immunocompromised individuals. Regarding this, thepresent study aimed to investigate the molecular identification and antifungalsusceptibility pattern of Candida species isolated from HIV-infected patients.Materials and Methods: This study was conducted on 80 clinical samples collectedfrom HIV-infected patients with suspected candidiasis referring to Tagore MedicalCollege and Hospital, Rathinamangalam and Government Hospital of ThoracicMedicine, in Chennai, India, for 18 months (i.e., May 2016-December 2017). Phenotypicand molecular identification was accomplished using internal transcribed spacer region 1(ITS1) and ITS4 primers. The antifungal susceptibility pattern of the isolates against fourantifungal agents was also determined by both disk diffusion and broth dilution methods.Results: In the present study, the prevalence of candidiasis was obtained as 75% (n=60).Candida tropicalis was the predominant identified species. All the emerging species(i.e., Kodamaea ohmeri, Hanseniaspora opuntiae, and C. orthopsilosis) were identifiedthrough molecular identification since the phenotypic identification was inconclusive. Interms of the susceptibility pattern, 63.3% and 18.3% of the isolates were resistant tofluconazole and voriconazole, respectively. Candida albicans was also found to beresistant to amphotericin B.Conclusion: Molecular assay led to the identification of K. ohmeri, H. opuntiae, and C.orthopsilosis, which were multidrug-resistant. This study highlighted the need for theprompt and timely identification of clinical yeast isolates given the emergence of manyrare species and their capability of causing life-threatening infections and outbreaks. Inthe laboratories where molecular diagnostic methods are not available, alternativeservices of reference laboratories can be utilized as cost-effective measures. With regardto the growing prevalence of antifungal drug resistance, antifungal susceptibility testingshould be made mandatory for effective patient management.

Species distribution of yeasts recovered from different clinical samples Addiss Ababa,Ethiopia

10.21203/rs.2.9212/v2 ◽

2019 ◽

Author(s):

Elias Seyoum Deribe ◽

Adane Bitew ◽

Amete Mihret

Keyword(s):

Species Distribution ◽

Candida Species ◽

Fungal Infections ◽

Addis Ababa ◽

Antifungal Susceptibility ◽

Signs And Symptoms ◽

Cross Sectional Study ◽

Clinical Samples ◽

Cross Sectional ◽

Reported Data

Abstract Background Currently, fungal diseases of humans are among the most problematic illnesses is the result of an increase in opportunistic fungal infections caused by rise in the number of immune-compromised patients. Particularly, yeasts are the most common cause of fungal infections leading to a range superficial type to life-threatening invasive infections. The aim of this study is to determine species distribution of yeasts particularly of Candida species recovered from different clinical samples. Method A cross sectional study was conducted from January 01, 2018 –September 30, 2018 in Addis Ababa, Arsho laboratory. Oropharengial swabs, nail scrapings, sputum, corneal scrapings, and vaginal swabs were collected from patients with signs and symptoms of infections. Identification and antifungal susceptibility testing was performed by using YST card through VITEK 2 compact system. Data was entered and analyzed using SPSS version 20. Result A total of 209 yeasts were recovered of which 49.8% were Candida albicans, 43.1% were non-albicans candida species and 7.2% were yeasts other than Candida species. The current study, eighteen (18) different types of yeast species were identified from different clinical samples. All recognized yeast considered as a causative agent of fungal infection in previously reported data in worldwide. Conclusion C. albicans remaining the predominant species, but the emergence of non-albicans Candida and other than candida species have increased. Thus, more studies on Candida prevalence are needed throughout country.

Species distribution of yeasts recovered from different clinical samples Addiss Ababa,Ethiopia

10.21203/rs.2.9212/v1 ◽

2019 ◽

Author(s):

Elias Seyoum Deribe ◽

Adane Bitew ◽

Amete Mihret

Keyword(s):

Species Distribution ◽

Candida Species ◽

Fungal Infections ◽

Addis Ababa ◽

Antifungal Susceptibility ◽

Signs And Symptoms ◽

Cross Sectional Study ◽

Clinical Samples ◽

Cross Sectional ◽

Reported Data

Abstract Background Currently, fungal diseases of humans are among the most problematic illnesses is the result of an increase in opportunistic fungal infections caused by rise in the number of immune-compromised patients. Particularly, yeasts are the most common cause of fungal infections leading to a range superficial type to life-threatening invasive infections. The aim of this study is to determine species distribution of yeasts particularly of Candida species recovered from different clinical samples. Method A cross sectional study was conducted from January 01, 2018 –September 30, 2018 in Addis Ababa, Arsho laboratory. Oropharengial swabs, nail scrapings, sputum, corneal scrapings, and vaginal swabs were collected from patients with signs and symptoms of infections. Identification and antifungal susceptibility testing was performed by using YST card through VITEK 2 compact system. Data was entered and analyzed using SPSS version 20. Result A total of 209 yeasts were recovered of which 49.8% were Candida albicans, 43.1% were non-albicans candida species and 7.2% were yeasts other than Candida species. The current study, eighteen (18) different types of yeast species were identified from different clinical samples. All recognized yeast considered as a causative agent of fungal infection in previously reported data in worldwide. Conclusion C. albicans remaining the predominant species, but the emergence of non-albicans Candida and other than candida species have increased. Thus, more studies on Candida prevalence are needed throughout country.

An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

10.21203/rs.2.15836/v2 ◽

2019 ◽

Author(s):

Mohireh Taei ◽

Mostafa Chadeganipour ◽

Rasoul Mohammadi

Keyword(s):

Candida Species ◽

Systemic Infection ◽

Molecular Techniques ◽

Clinical Isolates ◽

Clinical Samples ◽

Molecular Tests ◽

Yeast Strains ◽

Etiologic Agents ◽

Pcr Multiplex ◽

Pcr Rflp

Abstract Objective: Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. Results: A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR-RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non-albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non-Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.

Enfeksiyon Etkeni Mantarların Zamana Göre Sıklık ve Tür Dağılımlarındaki Değişimler: 12 Yıllık (2008-2019) Mikoloji Laboratuvarı Verileri Ne Söylüyor?

Mikrobiyoloji Bulteni ◽

10.5578/mb.20156 ◽

2021 ◽

Vol 55 (1) ◽

pp. 53-66

Author(s):

Dolunay Gülmez ◽

Ali Korhan Sığ ◽

Nida Akar ◽

Serhat Duyan ◽

Sevtap Arıkan Akdağlı

Keyword(s):

Respiratory Tract ◽

Regional Differences ◽

Lower Respiratory Tract ◽

Fungal Infections ◽

Antifungal Susceptibility ◽

Epidemiological Data ◽

University Hospital ◽

Clinical Samples ◽

Fungal Strains ◽

Second Period

The frequency and variety of infections caused by fungi are increasing. However, changes and intercenter and regional differences are observed in the distribution of fungal species over the years. It is important to update the epidemiological data in order to enable early and appropriate treatment. In this retrospective study, the number of fungi isolated from clinical samples, their distribution at the genus/ species level and the variations over the years in Hacettepe University hospital which is a regional center for patients at risk of fungal infection were investigated. For this purpose, laboratory records from 2008- 2019 were examined and 21813 fungal strains isolated from 19636 clinical samples were detected. When the first (2008-2013) and second (2014-2019) six-year periods were compared, a 2.5 fold increase was observed in the number of specimens yielding fungal growth (first period; n= 5620, second period; n= 14016). Fungi were most frequently isolated from urine (45.0%), lower respiratory tract (30.7%) and blood (6.8%) samples. Mould isolation rate in all samples increased significantly in the second six-year period (from 8.3% to 10.6%, p≤ 0.001). As expected, the most frequent yeast was Candida albicans (57.0%) and mould was Aspergillus fumigatus complex (50.4%). In the second six-year period, isolation of C.albicans (59.3% to 56.0%, p≤ 0.001) among yeasts and A.fumigatus complex (58.1% to 48.0%, p≤ 0.001) among moulds decreased significantly. In urine specimens, most common fungi were C.albicans (49.8%), Candida glabrata complex (15.6%), Candida tropicalis (8.9%) and Candida kefyr (7.5%). In lower respiratory tract specimens, the most common mould was A.fumigatus complex (51.2%), which has decreased from 63.7% in the first six years to 47.1% in the second period (p≤ 0.001). Over the same period, other Aspergillus species (from 25.5% to 34.1%, p= 0.002) and non-Aspergillus moulds (from 36.3% to 52.9%, p≤ 0.001) were increased. In blood samples, C.albicans (44.4%), Candida parapsilosis complex (21.5%) and C.glabrata complex (13.0%) were the most frequent species. In the second six-year period, the frequency of C.albicans decreased from 47.3% to 42.2% (p= 0.059) and the frequency of C.glabrata complex increased from 9.5% to 15.5% (p≤ 0.001) when compared to the first period. For the sterile specimens other than blood, the most common species were C.albicans (37.8%), C.glabrata complex (9.1%) and C.parapsilosis complex (4.7%). However, the number of fungal isolates and the distribution of the species showed great variation over the years. In our center, a substantial increase in the number of fungal strains isolated from the clinical specimens were observed over a 12-years period. In addition and similar to previously published reports, the increase of strains belonging to species with decreased antifungal susceptibility and/or species with unknown susceptibility were detected. The use of local data is required in order to implement early and appropriate antifungal treatment because of inter-center and regional differences observed in epidemiological trends regarding the distributions of fungal genera and species. Surveillance studies to be conducted with the participation of large and sufficient numbers of centers in our country, as we have done for our center, will also contribute to approaches regarding the management of fungal infections by revealing the epidemiological data in a comprehensive manner.

An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

10.21203/rs.2.15836/v3 ◽

2019 ◽

Author(s):

Mohireh Taei ◽

Mostafa Chadeganipour ◽

Rasoul Mohammadi

Keyword(s):

Candida Species ◽

Systemic Infection ◽

Molecular Techniques ◽

Clinical Isolates ◽

Clinical Samples ◽

Molecular Tests ◽

Yeast Strains ◽

Etiologic Agents ◽

Pcr Multiplex ◽

Pcr Rflp

Abstract Objective: Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. Results: A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR-RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non- albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non- Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.

An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

10.21203/rs.2.15836/v4 ◽

2019 ◽

Author(s):

Mohireh Taei ◽

Mostafa Chadeganipour ◽

Rasoul Mohammadi

Keyword(s):

Candida Species ◽

Systemic Infection ◽

Molecular Techniques ◽

Clinical Isolates ◽

Clinical Samples ◽

Molecular Tests ◽

Yeast Strains ◽

Etiologic Agents ◽

Pcr Multiplex ◽

Pcr Rflp

Abstract Objective: Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. Results: A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR-RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non- albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non- Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.

Isolation, Identification, and In Vitro Antifungal Susceptibility Testing of Dermatophytes from Clinical Samples at Sohag University Hospital in Egypt

Electronic physician ◽

10.19082/2557 ◽

2016 ◽

Vol 8 (6) ◽

pp. 2557-2567 ◽

Cited By ~ 8

Author(s):

Mona Fattouh Mohamed Shalaby ◽

Asmaa Nasr El-din ◽

Mohammed Abu El-Hamd

Keyword(s):

Susceptibility Testing ◽

Antifungal Susceptibility ◽

Antifungal Susceptibility Testing ◽

University Hospital ◽

Clinical Samples ◽

In Vitro Antifungal Susceptibility

Distribution and antifungal susceptibility of Candida species in patients with increased risk for fungal infections

Macedonian Pharmaceutical Bulletin ◽

10.33320/maced.pharm.bull.2016.62.01.006 ◽

2016 ◽

Vol 62 (1) ◽

pp. 65-76

Author(s):

Gordana Mirchevska ◽

Maja Jurhar Pavlova ◽

Elena Trajkovska-Dokic ◽

Zaklina Cekovska ◽

Gordana Jankoska ◽

...

Keyword(s):

Blood Culture ◽

Amphotericin B ◽

Critically Ill Patients ◽

Candida Species ◽

Antifungal Agents ◽

Fungal Infections ◽

Antifungal Susceptibility ◽

Clinical Specimens ◽

Fourth Group ◽

Increased Risk

Candida species are opportunistic yeasts that can be a serious threat for immunocompromised and critically ill patients, and a cause for increased morbidity and mortality in hospitalized patients. The aim of this study was to determine the frequency and distribution of different Candida species in clinical specimens in patients with increased risk for fungal infections, and to determine the antifungal susceptibility profile of invasive Candida species to antifungal agents. During a two year period, clinical specimens from 120 patients divided into 4 groups were analysed at the Institute of microbiology and parasitology, Faculty of Medicine, Skopje, Republic of Macedonia. Each of these 4 groups consisted of specimens from 30 patients, with primary immune deficiency, critically ill patients treated in the intensive care units (ICU), patients with mucosal candidiasis only, and patients with cystic fibrosis. All specimens were investigated with conventional mycological methods. Identification of Candida species was performed with VITEK-2 system (bioMérieux, France). E-test strips of fluconazole, voriconazole, amphotericin B and caspofungin (AB bioMerieux, France) were used for determination of the antifungal susceptibility profile. In this study, a total of 115 isolates of Candida species were confirmed in different clinical specimens (91 isolates from mucosal surfaces and 24 isolates from blood culture). Colonisation of mucosal membranes of gastrointestinal, respiratory and/or urinary tracts was registered in 56.67% (17/30), 56.67% (17/30), 90% (27/30) and 100% (30/30) of the specimens in the first, second, third and fourth group respectively. In all four groups of patients, the following Candida species were confirmed: C. albicans - 55%, C. glabrata - 17.6%, C. parapsilosis - 7.7%, C. tropicalis - 6.6%, unidentified Candida species - 4.4%, C. dubliniensis - 3.3%, C. kefyr - 2.2%, and one isolate of C. rugosa, C. pelliculosa and C. krusei each. Positive blood culture was registered in 23.33% specimens from the first group, 43.33% in the second group, 23.08% of the third group, and in one specimen of the fourth group. The most frequent isolates from blood culture were C. tropicalis and C. krusei, followed by C. albicans, C. parapsilosis and C. tropicalis, and in the second group C. albicans and C. pelliculosa were equally distributed, followed by C. parapsilosis and C. glabrata. All invasive isolates of Candida species were susceptible to amphotericin B, voriconazole and caspofungin. Resistance to fluconazole was registered in 8.3% (2/24) of all confirmed Candida species. Dose-dependent susceptibility to fluconazole was confirmed in 46% (11/24) of the isolates. Our study confirms high prevalence of colonisation and candidemia with non-albicans Candida species. Resistance to antifungal agents was registered only in two isolates of C. krusei. An epidemiological study is necessary for surveillance of dynamics of candidemia and antifungal susceptibility profile of invasive isolates of Candida species in our patients.

Multiplex PCR Based Strategy for Detection of Fungal Pathogen DNA in Patients with Suspected Invasive Fungal Infections

Journal of Fungi ◽

10.3390/jof6040308 ◽

2020 ◽

Vol 6 (4) ◽

pp. 308

Author(s):

Joana Carvalho-Pereira ◽

Filipa Fernandes ◽

Ricardo Araújo ◽

Jan Springer ◽

Juergen Loeffler ◽

...

Keyword(s):

Fungal Infections ◽

Fungal Species ◽

Cross Reactivity ◽

Invasive Fungal Infections ◽

Clinical Samples ◽

Correct Identification ◽

Colony Pcr ◽

Pcr Multiplex ◽

Pathogen Dna ◽

Species Specific

A new and easy polymerase chain reaction (PCR) multiplex strategy, for the identification of the most common fungal species involved in invasive fungal infections (IFI) was developed in this work. Two panels with species-specific markers were designed, the Candida Panel for the identification of Candida species, and the Filamentous Fungi Panel for the identification of Aspergillus species and Rhizopusarrhizus. The method allowed the correct identification of all targeted pathogens using extracted DNA or by colony PCR, showed no cross-reactivity with nontargeted species and allowed identification of different species in mixed infections. Sensitivity reached 10 to 1 pg of DNA and was suitable for clinical samples from sterile sites, with a sensitivity of 89% and specificity of 100%. Overall, the study showed that the new method is suitable for the identification of the ten most important fungal species involved in IFI, not only from positive blood cultures but also from clinical samples from sterile sites. The method provides a unique characteristic, of seeing the peak in the specific region of the panel with the correct fluorescence dye, that aids the ruling out of unspecific amplifications. Furthermore, the panels can be further customized, selecting markers for different species and/or resistance genes.