Laboratory Technique 403
Fungal Targets 383
TABLE 3.1 Frequently used fungal molecular targets and primers for sequencebased species Identification 385
TABLE 3.2 Examples of fungal molecular targets and primers for multilocus sequence- based species identification 386 Classic Molecular Identification Methods 387
Polymerase Chain Reaction 387
Non-Sequencing-Based Identification Methods 389
MALDI-TOF Mass Spectrometry 389 Signal Amplification Methods 390
PNA FISH 390
Nucleic Acid Amplification Methods 390 T2 Magnetic Resonance 390
Broad-Panel Molecular Testing and Other Emerging Sample-to-Answer Technologies 391
Sequencing-Based Identification Methods 393
Sanger Sequencing 393 TABLE 3.3 Lane construction for traditional bidirectional Sanger sequencing 394
Massive Parallel or Next-Generation Sequencing 394
Applications of DNA Sequencing 397
Accurate Molecular Identification 397
TABLE 3.4 Commonly used databases for identification of medically important fungi
398 Phylogenetic Analysis 399
Organism Typing 401 Detection of Genetic Determinants of Resistance 401
PART IV
Laboratory Technique 403
Laboratory Procedures 405
Collection and Preparation of Specimens 406
TABLE 4.1 Common clinical sites for laboratory recovery of pathogenic fungi 409 Methods for Direct Microscopic Examination of Specimens 414
Primary Isolation 416 TABLE 4.2 Media for primary isolation of fungi 417 Macroscopic Examination of Cultures 419 Microscopic Examination of Growth 419 Procedure for Identification of Yeasts 421 Isolation of Yeast When Mixed with Bacteria 424 Germ Tube Test for the Presumptive Identification of Candida albicans 425 xiv CONTENTS