| Literature DB >> 31269718 |
Patrick Schwarz1,2, Houssem Guedouar3, Farah Laouiti3, Frédéric Grenouillet4, Eric Dannaoui3,5.
Abstract
More than 20 different species of Mucorales can be responsible for human mucormycosis. Accurate identification to the species level is important. The morphological identification of Mucorales is not reliable, and the currently recommended identification standard is the molecular technique of sequencing the internal transcribed spacer regions. Nevertheless, matrix-assisted laser desorption ionization time-of-flight mass spectrometry has been shown to be an accurate alternative for the identification of bacteria, yeasts, and even filamentous fungi. Therefore, 38 Mucorales isolates, belonging to 12 different species or varieties, mainly from international collections, including 10 type or neo-type strains previously identified by molecular methods, were used to evaluate the usefulness of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for the identification of human pathogenic Mucorales to the species level. One to three reference strains for each species were used to create a database of main spectrum profiles, and the remaining isolates were used as test isolates. A minimum of 10 spectra was used to build the main spectrum profile of each database strain. Interspecies discrimination for all the isolates, including species belonging to the same genus, was possible. Twenty isolates belonging to five species were used to test the database accuracy, and were correctly identified to the species level with a log-score >2. In summary, matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a reliable and rapid method for the identification of most of the human pathogenic Mucorales to the species level.Entities:
Keywords: MALDI-TOF mass spectrometry; identification; mucorales; mucormycosis
Year: 2019 PMID: 31269718 PMCID: PMC6787577 DOI: 10.3390/jof5030056
Source DB: PubMed Journal: J Fungi (Basel) ISSN: 2309-608X
List of isolates used for the construction of the database.
| Species | Strain Number | Source | ITS Sequence Accession Number |
|---|---|---|---|
|
| CBS 112.07T | Human, lung | DQ119031 |
|
| IP 4.77 | Human, brain | DQ119024 |
| CBS 112589 | Environment, tempeh | DQ119011 | |
| CBS 631.72T | Environment, bread | DQ119009 | |
|
| CBS 429.75NT | Environment, soil | FJ719407 |
|
| CBS 100.31 | Animal, aborted cow | FJ19398 |
|
| CBS 269.65 | Environment, hay | FJ19405 |
|
| CBS 270.65 | Unknown | FJ19406 |
|
| CBS 582.65NT | Seed, | GQ342909 |
|
| CBS 291.66T | Animal, dung of bird | GQ342891 |
| CBS 195.68NT | Environment, air | DQ118991 | |
|
| CBS 384.95(T) | Human, skin | DQ119007 |
|
| CBS 226.29T | Unknown | DQ118994 |
|
| CBS 182.67T | Environment, plant | DQ118995 |
|
| CBS 354.68NT | Environment, cornmeal | DQ119005 |
|
| IP 3.77 | Animal, brain of cat | DQ119001 |
|
| CBS 441.59 | Animal, dung | HM999985 |
|
| CBS 190.84 | Human, heart | HM849701 |
ITS, internal transcribed spacer; IP, Institut Pasteur; CBS, Westerdijk Fungal Biodiversity Institute; T, type strain; (T), formerly type strain of Rhizomucor variabilis var. regularior; NT, neo-type strain.
Identification and corresponding log-score value for 20 Mucorales isolates used for the accuracy test of the database.
| Isolate | Collection No. | Identified Species | Score |
|---|---|---|---|
|
| IP 1443.83 |
| 2.18 |
|
| CBS 120808 |
| 2.04 |
|
| CBS 120809 |
| 2.13 |
|
| IP 1129.75 |
| 2.17 |
|
| IP 1279.81 |
| 2.16 |
|
| IP 1280.81 |
| 2.09 |
|
| CBS 101040 |
| 2.21 |
|
| CBS 120581 |
| 2.04 |
|
| CBS 120580 |
| 2.45 |
|
| BES 335 |
| 2.2 |
|
| PS 1.1 |
| 2.07 |
|
| HEGP-3473 |
| 2.42 |
|
| BES 362 |
| 2.29 |
|
| BES 228 |
| 2.46 |
|
| CBS 120585 |
| 2.06 |
|
| IP 1127.75 |
| 2.42 |
|
| IP 1956.90 |
| 2.38 |
|
| CBS 120587 |
| 2.42 |
|
| CBS 120586 |
| 2.53 |
|
| CBS 120588 |
| 2.31 |
IP, Institut Pasteur; CBS, Westerdijk Fungal Biodiversity Institute; BES, Centre hospitalier régional universitaire de Besançon; PS; Center for Invasive Mycoses and Antifungals Marburg; HEGP, Hôpital Européen Georges-Pompidou.
Log-score values obtained when the main spectrum profiles were identified by the database itself. For each isolate, the log-score values for the first 10 best matches are shown.
| Isolate Number and Identification | Log-Score Values for Strain | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | |
| 3 | 0.57 | 0.42 | ND | 0.43 | 0.38 | ND | 0.38 | ND | ND | ND | 0.52 | 0.35 | ND | ND | ND | 0.28 | 0.58 | |
| 0.47 | 3 | 2.39 | 0.85 | ND | 0.18 | 0.66 | 0.6 | ND | 0.39 | ND | ND | ND | 0.23 | 0.35 | ND | ND | ND | |
| 0.44 | 2.41 | 3 | 1.14 | 0.12 | 0.6 | ND | ND | ND | ND | 0.48 | 0.37 | 0.25 | 0.26 | ND | ND | ND | ND | |
| ND | 0.8 | 1.13 | 3 | 0.35 | 0.67 | 0.67 | ND | ND | 0.91 | ND | ND | ND | 0.54 | ND | 0.4 | 0.38 | ND | |
| 0.39 | ND | ND | 0.58 | 3 | 1.78 | 1.04 | 0.44 | 0.21 | 0.58 | ND | ND | ND | 0.51 | ND | ND | 0.37 | ND | |
| 0.41 | ND | 0.58 | 0.6 | 1.76 | 3 | 0.87 | ND | ND | ND | 0.52 | ND | ND | 0.4 | 0.47 | ND | 0.44 | ND | |
| ND | 0.42 | ND | 0.65 | 1.07 | 0.98 | 3 | ND | ND | 0.27 | ND | 0.7 | 0.34 | 0.38 | 0.32 | ND | ND | ND | |
| 0.58 | ND | ND | ND | 0.44 | 0.29 | ND | 3 | 0.87 | 0.98 | ND | ND | ND | 0.9 | 0.75 | 0.28 | ND | ND | |
| 0.14 | ND | ND | 0.1 | 0.1 | ND | ND | 0.9 | 3 | 0.63 | ND | ND | ND | 0.76 | 0.25 | ND | 0.31 | 0.13 | |
| ND | ND | ND | 0.95 | 0.55 | 0.66 | ND | 0.98 | 0.62 | 3 | ND | 0.59 | 0.98 | 0.53 | ND | 0.9 | ND | ND | |
| 0.23 | 0.16 | 0.04 | ND | ND | 0.54 | ND | ND | ND | 0.19 | 3 | 0.05 | 0.27 | 0.23 | ND | ND | ND | 0.22 | |
| 0.48 | ND | ND | ND | ND | 0.27 | 0.71 | ND | ND | 0.57 | 0.09 | 3 | 2.82 | 0.38 | 0.64 | 0.31 | ND | ND | |
| 0.3 | ND | 0.33 | ND | ND | ND | 0.35 | ND | ND | 1.01 | 0.29 | 2.82 | 3 | 0.33 | 0.47 | 0.04 | ND | ND | |
| ND | ND | ND | 0.61 | 0.53 | 0.38 | ND | 0.94 | 0.78 | 0.57 | ND | 0.38 | ND | 3 | 1.54 | ND | 0.43 | ND | |
| ND | ND | ND | ND | ND | 0.47 | 0.31 | 0.81 | 0.24 | 0.42 | ND | 0.66 | 0.5 | 1.54 | 3 | ND | ND | 0.3 | |
| ND | ND | ND | 0.41 | ND | 0.66 | ND | 0.31 | ND | 0.92 | 0.05 | 0.21 | ND | ND | ND | 3 | 0.47 | 0.58 | |
| 0.33 | ND | ND | 0.42 | 0.5 | 0.45 | 0.25 | ND | 0.3 | ND | ND | ND | ND | 0.45 | 0.11 | 0.41 | 3 | ND | |
| 0.62 | ND | ND | ND | 0.16 | 0.3 | ND | ND | 0.14 | 0.3 | 0.27 | ND | ND | ND | 0.25 | 0.81 | 0.46 | 3 | |
IP, Institut Pasteur; CBS, Westerdijk Fungal Biodiversity Institute; ND, not determined.
Figure 1Typical spectra patterns obtained for five different species of Mucorales.
Figure 2Plot of log-score values obtained for the isolates, belonging to four species, were used for the accuracy test of the database. On each graph, the left panel plots the log-scores values obtained for isolates belonging to the same species (as a marker of intraspecies variability), and the right panel plots the log-scores values obtained for isolates belonging to different species (as a marker of interspecies variability).