TABLE 5.

Molecular and proteomic methods used to identify Paracoccidioides isolates to the species level^e

Method	Sample type used in molecular assays				Identification power			Reference(s)
	Culture	Biopsy specimena	Biological fluidsb	Soil	Genus level	Species complex levelc	5-species systemd
DNA barcoding (ITS1/2 + 5.8S)	Yes	No	No	No	Yes	Yes	No	313
DNA sequencing (MLSA)	Yes	No	No	No	Yes	Yes	Yes	8–10, 32, 291
Single-plex PCR	Yes	Yes	Yes	Yes	Yes	No	No	10, 294–300
Duplex PCR	Yes	Yes	Yes	Yes	Yes	Yes	No	284
Nested PCR	Yes	Yes	Yes	Yes	Yes	No	No	54, 301–306
qPCR	Yes	Yes	Yes	Yes	Yes	Yes	No	32, 309–312
RAPD	Yes	No	No	No	Yes	No	No	17
PCR-RFLP	Yes	No	No	No	Yes	Yes	No	293
AFLP	Yes	No	No	No	Yes	Yes	Yes	293
Microsatellites (SSR)	Yes	No	No	No	Yes	Yes	No	20
SNaPshot	Yes	No	No	No	Yes	Yes	No	32
LAMP	Yes	Yes	Yes	No	Yes	No	No	307, 308
FISH/ISH	Yes	No	No	Yes	Yes	Yes	No	53, 318, 319
Whole-genome sequencing	Yes	No	No	No	Yes	Yes	Yes	12, 34, 316, 322
MALDI-TOF MS	Yes	No	No	No	Yes	Yes	No	321

^aFresh tissue or formalin-fixed, paraffin-embedded (FFPE) tissue.

^bBiological samples include sputum, bronchoalveolar lavage fluid, and serum, etc.

^cDifferentiation between the P. brasiliensis complex (S1, PS2, PS3, and PS4) and P. lutzii.

^dFive species of Paracoccidioides: S1 (P. brasiliensis sensu stricto), PS2 (P. americana), PS3 (P. restrepiensis), PS4 (P. venezuelensis), and P. lutzii.

^eMLSA, multilocus sequence analysis; qPCR, quantitative real-time PCR; RAPD, random amplified polymorphic DNA; PCR-RFLP, restriction fragment length polymorphism; AFLP, amplified fragment length polymorphism; SSR, simple-sequence repeat; LAMP, loop-mediated isothermal amplification; FISH, fluorescence in situ hybridization; MALDI-TOF MS, matrix-assisted laser desorption ionization–time of flight mass spectrometry.