Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies

Mycopathologia. 2017 Aug;182(7-8):625-632. doi: 10.1007/s11046-017-0129-5. Epub 2017 Mar 21.

Abstract

The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.

Keywords: Filamentous fungi; Fungal infection; Fusarium; Molecular methods.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Fungemia / diagnosis
  • Fungemia / microbiology
  • Fusariosis / diagnosis*
  • Fusariosis / microbiology
  • Fusarium / classification
  • Fusarium / genetics
  • Fusarium / isolation & purification*
  • Hematologic Neoplasms / complications*
  • Humans
  • Molecular Diagnostic Techniques / methods*
  • Nucleic Acid Amplification Techniques / methods*
  • Nucleic Acid Hybridization / methods*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods*