Comparison of 21-Plex PCR and API 20C AUX, MALDI-TOF MS, and rDNA Sequencing for a Wide Range of Clinically Isolated Yeast Species: Improved Identification by Combining 21-Plex PCR and API 20C AUX as an Alternative Strategy for Developing Countries

Arastehfar, Amir; Daneshnia, Farnaz; Kord, Mohammad; Roudbary, Maryam; Zarrinfar, Hossein; Fang, Wenjie; Hashemi, Seyed Hossein; Najafzadeh, Mohammad Javad; Khodavaisy, Sadegh; Pan, Weihua; Liao, Wanqing; Badali, Hamid; Rezaie, Sassan; Zomorodian, Kamiar; Hagen, Ferry; Boekhout, Teun

doi:10.3389/fcimb.2019.00021

Cited by 30 publications

(18 citation statements)

References 39 publications

(65 reference statements)

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“…The majority of Fig. 2 The distribution of the yeast from VVC by years misidentified yeast isolates were among rare species (n = 45), and the majority (4/5) of Pichia kudriavzevii strains were misidentified [25]. The closely related Candida complex was identified from vaginal samples by using molecular methods [8,[16][17][18][19]26].…”

Section: Strain Identification and Distributionmentioning

confidence: 99%

Molecular identification and antifungal susceptibility profile of yeast from vulvovaginal candidiasis

et al. 2020

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Background: Accurate identification Candida is important for successful therapy and epidemiology study. The aim of research is to study API 20C yeast identification system identification rate by using molecular identification as gold standard and tested the antifungal susceptibility of Candida from patients with vulvovaginal candidiasis (VVC). Methods: In total, 3574 yeast isolates were obtained from patients with VVC. API 20C yeast identification, molecular identification and in vitro antifungal susceptibility were performed. Results: C. albicans was the predominant Candida species [2748 isolates, 76.9%] in VVC. The isolates from vaginal samples represented 22 species based on molecular identification. The API 20C system identifies only 11 of the species encountered during the study period. Based on the API 20C system, 3273 (91.58%) isolates were correctly identified to the species level. The correct identification rate of the API 20C system for rare yeast was 15.29% (26/ 170 isolates). Antifungal susceptibility was tested in a total of 1844 isolates of Candida from patients with VVC. C. albicans was susceptible to most of the tested antifungals. The MICs of azoles for C. glabrata were higher than those for C. albicans. The MICs of echinocandins for C. parapsilosis were higher than those for C. albicans. Conclusions: The API 20C yeast identification system can be used to reliably identify the most common Candida species while molecular methods are necessary for the identification of closely related, emerging, and rare yeast species. The results from this study suggest that much of the previous studies on the epidemiology of VVC should be rethought. C. albicans was susceptible to most of the tested antifungals.

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Section: Strain Identification and Distributionmentioning

confidence: 99%

Molecular identification and antifungal susceptibility profile of yeast from vulvovaginal candidiasis

et al. 2020

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“…The 21-plex PCR showed a higher degree of accuracy for the yeast species included in this study compared with the Vitek 2 system. A previous study found a higher degree of accuracy when 21-plex PCR, as the first line identification tool, was used in combination with API 20C AUX for isolates that were not identified by 21-plex PCR [ 17 ]. 21-plex PCR showed superiority over the Vitek 2 system and the vast majority of rare yeasts and even a few isolates of the main Candida species were not correctly identified by the Vitek 2 system.…”

Section: Discussionmentioning

confidence: 99%

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

Kord

Salehi

Khodavaisy

et al. 2020

Journal of Medical Microbiology

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Introduction. 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. Aim. 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. Methodology. 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). Results. 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. Candida albicans (58/137, 42.3 %), Candida glabrata (30/137, 21.9 %), Candida parapsilosis sensu stricto (23/137, 16.8 %), Candida tropicalis (10/137, 7.3 %) and Pichia kudriavzevii ( Candida krusei ) (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 %). Conclusion. C. albicans 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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“…Unfortunately, accurate and rapid identification tools, such as matrix-assisted laser desorption ionization time-of-flight and Sanger sequencing, which are common in Western countries, are largely unaffordable for most clinical laboratories of developing countries, and most of the identifications are performed by inaccurate and expensive phenotypic tools [ 123 ]. To help overcome this issue, a comprehensive multiplex PCR was introduced [ 230 ], which can identify the most clinically important yeast species causing infection in humans and numerous studies afterward showed its reproducibility in various epidemiological studies [ 92 , 231 , 232 ]. Although such techniques are far from ideal, their application can significantly shorten the turnaround time and improve the species identification accuracy.…”

Section: Optimizing Therapy By Species Identificationmentioning

confidence: 99%

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

et al. 2020

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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 Candida, Aspergillus, Cryptococcus, and Pneumocystis 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 Candida 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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Comparison of 21-Plex PCR and API 20C AUX, MALDI-TOF MS, and rDNA Sequencing for a Wide Range of Clinically Isolated Yeast Species: Improved Identification by Combining 21-Plex PCR and API 20C AUX as an Alternative Strategy for Developing Countries

Cited by 30 publications

References 39 publications

Molecular identification and antifungal susceptibility profile of yeast from vulvovaginal candidiasis

Molecular identification and antifungal susceptibility profile of yeast from vulvovaginal candidiasis

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

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

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