| Literature DB >> 29691192 |
Daniel Karcher1, Rafaella C Grenfell1, Andrea Micke Moreno2, Luisa Zanolli Moreno2, Silvio Arruda Vasconcellos2, Marcos B Heinemann2, Joao N de Almeida Junior3, Luiz Juliano4, Maria A Juliano1.
Abstract
Matrix Assisted Laser Desorption/Ionization and Time of Flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the identification of bacteria through the detection and analysis of their proteins or fragments derived from ribosomes. Slight sequence variations in conserved ribosomal proteins distinguish microorganisms at the subspecies and strain levels. Characterization of Leptospira spp. by 16S RNA sequencing is costly and time-consuming, and recent studies have shown that closely related species (e.g., Leptospira interrogans and Leptospira kirschneri) may not be discriminated using this technology. Herein, we report an in-house Leptospira reference spectra database using Leptospira reference strains that were validated with a collection of well-identified Brazilian isolates kept in the Bacterial Zoonosis Laboratory at the Veterinary Preventive Medicine and Animal Health Department at Sao Paulo University. In addition, L. interrogans and L. kirschneri were differentiated using an in-depth mass spectrometry analysis with ClinProTools™ software. In conclusion, our in-house reference spectra database has the necessary accuracy to differentiate pathogenic and non-pathogenic species and to distinguish L. interrogans and L. kirschneri.Entities:
Keywords: Brazil; Identification; Leptospira; MALDI-TOF; Mass spectrometry
Mesh:
Substances:
Year: 2018 PMID: 29691192 PMCID: PMC6175718 DOI: 10.1016/j.bjm.2018.03.005
Source DB: PubMed Journal: Braz J Microbiol ISSN: 1517-8382 Impact factor: 2.476
Leptospira strains used as reference for MALDI-TOF MS measurements.
| Specie | Serogruop | Serovar | Strain | Pathogenicity |
|---|---|---|---|---|
| Ballum | Castellonis | Castellon 3 | Pathogenic | |
| Celledoni | Whitcombi | Whitcombi | ||
| Javanica | Javanica | Veldrat Batavia 46 | ||
| Mini | Mini | Sari | ||
| Sejroe | Hardjo | Hardjobovis | ||
| Tarassovi | Tarassovi | Perepelitsin | ||
| Australis | Australis | Ballico | ||
| Australis | Bratislava | Jez Bratislava | ||
| Autumnalis | Autumnalis | Akiyami A | ||
| Bataviae | Bataviae | Van Tienen | ||
| Canicola | Canicola | Hond Utrecht IV | ||
| Djasiman | Sentot | Sentot | ||
| Hebdomadis | Hebdomadis | Hebdomadis | ||
| Icterohaemorrhagiae | Copenhageni | M-20 | ||
| Icterohaemorrhagiae | Icterohaemorrhagiae | RGA | ||
| Pomona | Kennewicki | Fromm | ||
| Pomona | Pomona | Pomona | ||
| Pyrogenes | Pyrogenes | Salinem | ||
| Sejroe | Hardjo | Hardjoprajitno | ||
| Sejroe | Wolffi | 3705 | ||
| Autumnalis | Butembo | Butembo | ||
| Cynopteri | Cynopteri | 3522C | ||
| Grippotyphosa | Grippotyphosa | Moskova V | ||
| Panama | Panama | CZ 214K | ||
| Shermani | Shermani | 1342 K | ||
| Andamana | Andamana | CH 11 | Non-pathogenic | |
| Andamana | Bovedo | Bovedo | ||
| Doberdo | Rufino | RPE | ||
| Garcia | Garcia | Garcia | ||
| Nazare | Nazare | Nazaré | ||
| Seramanga | Patoc | Patoc-1 | ||
Collection at the Bacterial Zoonoses Laboratory, Department of Veterinary Preventive and Animal Health of School of Veterinary Medicine and Animal Science, São Paulo University, Brazil.
Fig. 1MALDI-TOF MS spectra obtained by analyzing the reference strains of Leptospira interrogans and Leptospira borgpetersenii with and without extraction as described in “Material and methods” section. These data show the importance of the protein extraction to obtain the better quality of spectra.
Fig. 2Comparison of the phylogenetic classification and MALDI-TOF dendrograms of the isolates of Leptospira spp. This figure contains only strains analyzed in this study.
Identification results of 22 leptospiral field isolates by MALDI-TOF MS and 16S rRNA gene sequencing.
| Strain identification | Genome species (16S rRNA Identification) | Serogroup | MALDI-TOF-MS Identification | |
|---|---|---|---|---|
| Species | Score values | |||
| Ranarum | Semaranga | 2.355 | ||
| M85/06 | 2.565 | |||
| M46/07 | Icterohaemorrhagiae | 2.070 | ||
| M67/07 | Icterohaemorrhagiae | 2.535 | ||
| M71/07 | Icterohaemorrhagiae | 2.643 | ||
| M5/90 | Icterohaemorrhagiae | 2.342 | ||
| M64/06 | Icterohaemorrhagiae | 2.542 | ||
| 61H | Pomona | 1.898 | ||
| M110/06 | 1.866 | |||
| 16CAP | Grippotyphosa | 2.828 | ||
| 19CAP | Grippotyphosa | 3.000 | ||
| LO9 | 2.574 | |||
| M52/08-12 | 2.359 | |||
| M52/08-19 | 1.833 | |||
| U160 | 2.017 | |||
| U164 | Tarassovi | 2.093 | ||
| An776 | Bataviae | 2.366 | ||
| 10ACAP | Grippotyphosa | 2.525 | ||
| 6BCAP | Grippotyphosa | 2.457 | ||
| 21CAP | Grippotyphosa | 2.614 | ||
| M4/98 | Sejroe | 2.370 | ||
| BOV 6 | Sejroe | 2.434 | ||
Collection at the Bacterial Zoonoses Laboratory, Department of Veterinary Preventive and Animal Health of School of Veterinary Medicine and Animal Science, São Paulo University, Brazil.
Fig. 3Principal component analysis (PCA) using tools ClinProTool™. In (A), PCA of strains analyzed, for data standardization by species, data from different serovars were used. In (B), we have PCA of different serovars of the L. kirchneri and in (C), we have PCA of different serovars of L. interrogans.
Complete results derived from the classification models.
| Classification model | Cross validation (CV) (%) | Recognition capability (RC) (%) | Integration regions used for classification | ||||
|---|---|---|---|---|---|---|---|
| Peak #1 (Da) | Peak #2 (Da) | Peak #3 (Da) | Peak #4 (Da) | Peak #5 (Da) | |||
| GA | 97.2 | 100.0 | 8057 | 4671 | 5472 | 8084 | 8305 |
| SNN | 55.6 | 100.0 | 8057 | 8097 | 6710 | 8084 | 12,679 |
| QC | 92.6 | 93.7 | 8057 | – | – | – | – |
Results obtained by analyzing of ClinProTools.
Genetic Algorithm.
Supervised Neural Network.
Quick Classifier.
Fig. 4Strain distribution map corresponding to Leptospira interrogans (red) and Leptospira kirschneri (green). The x-axis shows the peak area/intensity values with respect to the most relevant peak (8057 Da) to distinguish Leptospira interrogans (red) from Leptospira kirschneri (green). The y-axis shows the peak area/intensity values with respect to the peak with (6711 Da) from Leptospira interrogans (red) and Leptospira kirschneri (green). The ellipses represent the spectra with greater distinction between the two groups, whereas prominent peaks in the x-axis and y-axis.
Single-peak analysis for the discrimination of L. kirschneri and L. interrogans.
| Peaks ( | ClinProTools | FlexAnalysis | Sensitivity (%) | Specificity (%) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| AUC | Dave | PWKW | PAD | Ave | Ave | AUC | Cutoff | |||
| 8059 | 0.99 | 3.68 | 0 | 0.00226 | 16.72 | 20.63 | 0.99 | 6.96 | 98 | 95 |
| 3090 | 0.92 | 2.90 | <0.0001 | 0.000001 | 7.81 | 7.51 | 0.74 | 3.93 | 96 | 48 |
| 3074 | 0.91 | 4.14 | <0.0000 | <0.000001 | 7.13 | 8.04 | 0.83 | 5.41 | 100 | 59 |
| 3118 | 0.90 | 12.03 | <0.0001 | <0.000001 | 8.38 | 9.47 | 0.83 | 14.00 | 100 | 56 |
| 6710 | 0.87 | 2.85 | 0 | <0.000001 | 14.26 | 16.36 | 0.87 | 3.22 | 85 | 86 |
Peaks with the best performances according to ClinProTools™ and FlexAnalysis™ softwares.
AUC, area under the curve.
Dave, difference between the maximal and the minimal average peak area/intensity of the groups.
PWKW, p-value of Wilcoxon/Kruskal–Wallis test (range:0–1; 0 D good).
PAD: p-value of Anderson–Darling test, <0.05 indicates data not normally distributed; gives information about the normal distribution (range: 0–1; 0 = not normally distributed).
Ave, area/intensity average of a group from Leptospira kirschneri.
Ave, area/intensity average of a group from Leptospira interrogans.
AUCs and signal-to-noise cut off values were obtained from an ROC curve constructed using SPSS Version18.0 and FlexAnalysis.
Fig. 5Representative spectra of Leptospira interrogans and Leptospira kirschineri. The representative peaks that allow differentiation of the strains in the spectra are showed, in red for L. interrogans, and in blue for L. kirschneri. The peak with m/z = 8059 in L. interrogans we detected as shown in Table 3 by ClinPro Tools analysis. The peak m/z = 8098 in L. kirschineri was previously identified by Rettinger et al.