Journal Article

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

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

2019

Overview

Occurrence of non- (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 ( = 145), other sites ( = 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 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 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 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.

• Publisher: Frontiers Media SA,Frontiers Media S.A
• Subject: 21-plex PCR / API 20C AUX / Assimilation / Candida / Candida - chemistry / Candida - classification / Candida - genetics / Candida - isolation & purification / Candidiasis / Candidiasis - diagnosis / Candidiasis - microbiology / Cellular and Infection Microbiology / Developing Countries / DNA/methods / Epidemiology / Ethics / Humans / Identification / Industrialized nations / Kappa coefficient / Laboratories / LDCs / LSU rDNA sequencing / MALDI-TOF MS / Mass / Matrix-Assisted Laser Desorption-Ionization/methods / Medical research / Microbial Sensitivity Tests / Microbiology / Molecular Diagnostic Techniques / Molecular Diagnostic Techniques - methods / Multiplex Polymerase Chain Reaction / Multiplex Polymerase Chain Reaction - methods / Mycological Typing Techniques / Mycological Typing Techniques - methods / QR1-502 / Rare species / Sensitivity and Specificity / Sequence Analysis / Sequence Analysis, DNA / Sequence Analysis, DNA - methods / Spectrometry / Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods / Yeast