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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

Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In...

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Autores principales: Arastehfar, Amir, Daneshnia, Farnaz, Kord, Mohammad, Roudbary, Maryam, Zarrinfar, Hossein, Fang, Wenjie, Hashemi, Sayed Jamal, Najafzadeh, Mohammad Javad, Khodavaisy, Sadegh, Pan, Weihua, Liao, Wanqing, Badali, Hamid, Rezaie, Sassan, Zomorodian, Kamiar, Hagen, Ferry, Boekhout, Teun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385604/
https://www.ncbi.nlm.nih.gov/pubmed/30828570
http://dx.doi.org/10.3389/fcimb.2019.00021
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author Arastehfar, Amir
Daneshnia, Farnaz
Kord, Mohammad
Roudbary, Maryam
Zarrinfar, Hossein
Fang, Wenjie
Hashemi, Sayed Jamal
Najafzadeh, Mohammad Javad
Khodavaisy, Sadegh
Pan, Weihua
Liao, Wanqing
Badali, Hamid
Rezaie, Sassan
Zomorodian, Kamiar
Hagen, Ferry
Boekhout, Teun
author_facet Arastehfar, Amir
Daneshnia, Farnaz
Kord, Mohammad
Roudbary, Maryam
Zarrinfar, Hossein
Fang, Wenjie
Hashemi, Sayed Jamal
Najafzadeh, Mohammad Javad
Khodavaisy, Sadegh
Pan, Weihua
Liao, Wanqing
Badali, Hamid
Rezaie, Sassan
Zomorodian, Kamiar
Hagen, Ferry
Boekhout, Teun
author_sort Arastehfar, Amir
collection PubMed
description Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In this study, 301 clinically isolated yeast strains recovered from various anatomical sites [Blood (n = 145), other sites (n = 156)] were used to assess the accuracy and practicality of API 20C AUX and 21-plex PCR compared to MALDI-TOF MS and large subunit rDNA (LSU rDNA). MALDI-TOF MS correctly identified 98.33% of yeast isolates, 100% of top five Candida species, 95.7% of rare yeast species, while 1.3% of isolates were misidentified. API 20C AUX correctly identified 83.7% of yeast isolates, 97.2% of top five Candida species, 61.8% of rare yeast species, while 16.2% of yeast isolates were misidentified. The 21-plex PCR, accurately identified 87.3% of yeast isolates, 100% of top five Candida species, 72% of rare yeast species, but it misidentified 1.3% of rare yeast species while 9.9% of whole yeast isolates were not identified. The combination of rapidity of 21-plex PCR and comprehensiveness of API 20C AUX, led to correct identification of 92% of included yeast isolates. Due to expensiveness of MALDI-TOF MS and sequencing, this combination strategy could be the most accurate and inexpensive alternative identification strategy for developing countries. Moreover, by the advent and development of cost-effective, reliable, and rapid PCR machines that cost 130 US dollars, 21-plex could be integrated in routine laboratories of developing and resource-limited countries to specifically identify 95% causative agents of yeast-related infections in human. Databases of MALDI-TOF MS, API 20C AUX, and the number of target species identified by 21-plex require further improvement to keep up with the diverse spectrum of yeast species.
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spelling pubmed-63856042019-03-01 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, Sayed Jamal Najafzadeh, Mohammad Javad Khodavaisy, Sadegh Pan, Weihua Liao, Wanqing Badali, Hamid Rezaie, Sassan Zomorodian, Kamiar Hagen, Ferry Boekhout, Teun Front Cell Infect Microbiol Cellular and Infection Microbiology Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In this study, 301 clinically isolated yeast strains recovered from various anatomical sites [Blood (n = 145), other sites (n = 156)] were used to assess the accuracy and practicality of API 20C AUX and 21-plex PCR compared to MALDI-TOF MS and large subunit rDNA (LSU rDNA). MALDI-TOF MS correctly identified 98.33% of yeast isolates, 100% of top five Candida species, 95.7% of rare yeast species, while 1.3% of isolates were misidentified. API 20C AUX correctly identified 83.7% of yeast isolates, 97.2% of top five Candida species, 61.8% of rare yeast species, while 16.2% of yeast isolates were misidentified. The 21-plex PCR, accurately identified 87.3% of yeast isolates, 100% of top five Candida species, 72% of rare yeast species, but it misidentified 1.3% of rare yeast species while 9.9% of whole yeast isolates were not identified. The combination of rapidity of 21-plex PCR and comprehensiveness of API 20C AUX, led to correct identification of 92% of included yeast isolates. Due to expensiveness of MALDI-TOF MS and sequencing, this combination strategy could be the most accurate and inexpensive alternative identification strategy for developing countries. Moreover, by the advent and development of cost-effective, reliable, and rapid PCR machines that cost 130 US dollars, 21-plex could be integrated in routine laboratories of developing and resource-limited countries to specifically identify 95% causative agents of yeast-related infections in human. Databases of MALDI-TOF MS, API 20C AUX, and the number of target species identified by 21-plex require further improvement to keep up with the diverse spectrum of yeast species. Frontiers Media S.A. 2019-02-15 /pmc/articles/PMC6385604/ /pubmed/30828570 http://dx.doi.org/10.3389/fcimb.2019.00021 Text en Copyright © 2019 Arastehfar, Daneshnia, Kord, Roudbary, Zarrinfar, Fang, Hashemi, Najafzadeh, Khodavaisy, Pan, Liao, Badali, Rezaie, Zomorodian, Hagen and Boekhout. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Arastehfar, Amir
Daneshnia, Farnaz
Kord, Mohammad
Roudbary, Maryam
Zarrinfar, Hossein
Fang, Wenjie
Hashemi, Sayed Jamal
Najafzadeh, Mohammad Javad
Khodavaisy, Sadegh
Pan, Weihua
Liao, Wanqing
Badali, Hamid
Rezaie, Sassan
Zomorodian, Kamiar
Hagen, Ferry
Boekhout, Teun
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
title 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_short 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
title_sort 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
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385604/
https://www.ncbi.nlm.nih.gov/pubmed/30828570
http://dx.doi.org/10.3389/fcimb.2019.00021
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