MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates
2.2. MALDI-TOF MS Preparation of Isolates
2.3. Database Development
2.4. Biomarker Assignment and Principal Component Analysis
2.5. Presence of Biomarkers Identified in Previous Studies
2.6. Classifier Models Based on Machine Learning
3. Results
3.1. Database Development
3.2. Biomarker Assignment and Principal Component Analysis
3.3. Presence of Biomarkers Identified in Previous Studies
3.4. Classifier Models Based on Machine Learning
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Species and Serotype/O-Type | Training Set | Test Set | ||
---|---|---|---|---|
n | Origin | n | Origin | |
S. dysenteriae serotype 1 | 2 | CIP 57.28T; A1 | 1 | 1 ci 1 |
S. dysenteriae serotype 2 | 5 | A2, 4 ci 1 | 4 | 4 ci 1 |
S. dysenteriae serotype 3 | 5 | AMC-43-G-93; 4 ci 1 | 3 | 3 ci 1 |
S. dysenteriae serotype 4 | 2 | AMC 43-G-86; 1 ci 1 | 0 | |
S. dysenteriae serotype 5 | 1 | AMC 43-G-84 | 0 | |
S. dysenteriae serotype 6 | 1 | AMC 43-G-81 | 1 | 1 ci 1 |
S. dysenteriae serotype 7 | 1 | AMC 43-G-76 | 1 | 1 ci 1 |
S. dysenteriae serotype 9 | 2 | A58: 1646; 1 ci 1 | 1 | 1 ci 1 |
S. dysenteriae serotype 10 | 1 | A2050-52 | 0 | |
S. dysenteriae serotype 12 | 2 | 2 ci 1 | 1 | 1 ci 1 |
S. dysenteriae serotype 14 | 1 | NCTC 11867 | 0 | |
S. dysenteriae serotype 15 | 1 | NCTC 11868 | 0 | |
Total number of S. dysenteriae | 24 | 12 | ||
S. flexneri serotype 1a | 3 | B1A; 2 ci 1 | 0 | |
S. flexneri serotype 1b | 5 | B1B; 4 ci 1 | 5 | 5 ci 1 |
S. flexneri serotype 1c | 4 | 4 ci 1 | 3 | 3 ci 1 |
S. flexneri serotype 2a | 32 | CIP 82.48T; B2A; 30 ci 1 | 32 | 32 ci 1 |
S. flexneri serotype 2b | 1 | B2B | 3 | 3 ci 1 |
S. flexneri serotype 3a | 2 | B3A; 1 ci 1 | 14 | 14 ci 1 |
S. flexneri serotype 3b | 2 | B3B; B3C | 3 | 3 ci 1 |
S. flexneri serotype 4a | 1 | B4A | 4 | 4 ci 1 |
S. flexneri serotype 4av | 4 | 5 ci 1 | 0 | |
S. flexneri serotype 4b | 1 | B4B | 0 | |
S. flexneri serotype 4c | 3 | 3 ci 1 | 0 | |
S. flexneri serotype 5b | 1 | B5 | 1 | 1 ci 1 |
S. flexneri serotype 6 | 10 | B6; 9 ci 1 | 10 | 10 ci 1 |
S. flexneri serotype X | 1 | |||
S. flexneri serotype Y | 2 | 2 ci 1 | 2 | 2 ci 1 |
S. flexneri serotype Yv | 2 | 2 ci 1 | 0 | |
S. flexneri provisional | 5 | 5 ci 1 | 0 | |
Total number of S. flexneri | 79 | 77 | ||
S. boydii serotype 1 | 2 | AMC-43-G-58; 1 ci 1 | 3 | 3 ci 1 |
S. boydii serotype 2 | 3 | CIP 82.50T; P288; 1 ci 1 | 4 | 4 ci 1 |
S. boydii serotype 3 | 1 | D1 | 0 | |
S. boydii serotype 4 | 2 | AMC-43-G-63; 1 ci 1 | 2 | 2 ci 1 |
S. boydii serotype 5 | 2 | P143; 1 ci 1 | 0 | |
S. boydii serotype 6 | 1 | CDC 9771 (D19) | 0 | |
S. boydii serotype 7 | 1 | AMC 4006 (Lavington) | 0 | |
S. boydii serotype 8 | 0 | 1 | 1 ci 1 | |
S. boydii serotype 9 | 1 | 1296/7 | 0 | |
S. boydii serotype 10 | 1 | 430 | 1 | 1 ci 1 |
S. boydii serotype 11 | 1 | 34 | 0 | |
S. boydii serotype 12 | 0 | 1 | 1 ci 1 | |
S. boydii serotype 13 | 0 | 1 | 1 ci 1 | |
S. boydii serotype 14 | 0 | 1 | 1 ci 1 | |
S. boydii serotype 15 | 1 | CDC C-703 | 0 | |
S. boydii serotype 18 | 1 | 1 ci 1 | 1 | 1 ci 1 |
Total number of S. boydii | 17 | 15 | ||
S. sonnei | 117 | CIP 82.49T; 116 ci 1 | 115 | 115 ci 1 |
EIEC | 30 | DSM 9027; DSM 9028; CCUG 11335; CCUG 38080; CCUG 38092; CCUG 38093; EW227; 1624-56; 1184-68; 145/46; L119B-10; 19 ci 1 | 31 | 31 ci 1 |
Other E. coli pathotypes (human) | 11 | 7 STEC ci 1, 4 EPEC ci 1 | 11 | 8 STEC ci 1; 3 EPEC ci 1 |
Other E. coli pathotypes (animal) 2 | 10 | 5 mussel, 3 pigeon, 2 turkey | 10 | 4 mussel, 3 pigeon, 2 turkey, 1 oyster |
Biomarkers (m/z) | 2691 | 2877 | 3129 | 3636 | 3647 | 3930 | 3939 | 4163 | 4189 | 4368 | 4501 | 4769 | 4775 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
S. dysenteriae | (n = 24) | 92 | 4 | 100 | 0 | 0 | 0 | 100 | 0 | 100 | 100 | 100 | 0 | 100 |
S. flexneri | (n = 46) | 100 | 0 | 100 | 0 | 63 | 53 | 18 | 1 | 94 | 97 | 99 | 22 | 97 |
S. boydii | (n = 17) | 88 | 0 | 100 | 18 | 0 | 0 | 94 | 0 | 100 | 88 | 100 | 18 | 100 |
S. sonnei | (n = 117) | 56 | 49 | 59 | 22 | 0 | 1 | 56 | 17 | 89 | 68 | 56 | 23 | 98 |
EIEC | (n = 31) | 100 | 0 | 100 | 3 | 6 | 0 | 97 | 0 | 97 | 100 | 94 | 26 | 97 |
Other E. coli | (n = 21) | 52 | 24 | 52 | 71 | 0 | 5 | 62 | 38 | 90 | 67 | 57 | 67 | 100 |
Biomarkers (m/z) | 4784 | 5156 | 5239 | 5386 | 5415 | 6262 | 6322 | 6412 | 6488 | 7275 | 7295 | 7715 | 7868 | 7879 |
S. dysenteriae | 100 | 100 | 8 | 92 | 52 | 100 | 100 | 0 | 0 | 0 | 0 | 0 | 0 | 100 |
S. flexneri | 76 | 97 | 55 | 99 | 45 | 99 | 99 | 4 | 42 | 1 | 83 | 0 | 41 | 23 |
S. boydii | 76 | 94 | 18 | 88 | 59 | 100 | 88 | 18 | 6 | 18 | 0 | 6 | 12 | 88 |
S. sonnei | 69 | 86 | 27 | 73 | 0 | 74 | 62 | 13 | 1 | 17 | 0 | 28 | 18 | 75 |
EIEC | 71 | 100 | 39 | 100 | 42 | 94 | 97 | 19 | 0 | 23 | 6 | 3 | 16 | 84 |
Other E. coli | 19 | 86 | 0 | 67 | 0 | 57 | 67 | 48 | 10 | 52 | 0 | 24 | 43 | 33 |
Biomarkers (m/z) | 8326 | 8370 | 8379 | 9002 | 9227 | 9535 | 9546 | 9563 | 9739 | 10,300 | 10,310 | 10,488 | 10,934 | |
S. dysenteriae | 0 | 0 | 100 | 100 | 0 | 0 | 100 | 100 | 0 | 0 | 100 | 0 | 0 | |
S. flexneri | 5 | 4 | 90 | 94 | 4 | 17 | 82 | 92 | 8 | 9 | 86 | 0 | 0 | |
S. boydii | 0 | 18 | 82 | 88 | 12 | 18 | 82 | 88 | 6 | 18 | 82 | 0 | 12 | |
S. sonnei | 15 | 15 | 82 | 38 | 12 | 16 | 85 | 54 | 15 | 13 | 70 | 34 | 36 | |
EIEC | 6 | 16 | 77 | 87 | 13 | 23 | 77 | 81 | 6 | 19 | 77 | 0 | 0 | |
Other E. coli | 43 | 38 | 38 | 24 | 48 | 48 | 62 | 38 | 43 | 48 | 48 | 0 | 5 | |
8326 | 8370 | 8379 | 9002 | 9227 | 9535 | 9546 | 9563 | 9739 | 10,300 | 10,310 | 10,488 | 10,934 |
Correct Identification with MALDI-TOF, Direct Smear | Correct Identification with MALDI-TOF, Ethanol | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Bruker Databases 1, n (%) | Custom Databases 1, n (%) | Bruker Databases 1 + Custom, n (%) | Biomarker Assignment, n (%) | Classifier Models, n (%) | Bruker Databases 1, n (%) | Custom Databases 1, n (%) | Bruker Databases 1 + Custom, n (%) | Biomarker Assignment, n (%) | Classifier Models, n (%) | |||||||||||
Genus | ||||||||||||||||||||
Shigella (n = 217) | 19 | (9) | 205 | (94) | 205 | (94) | 10 | (5) | 209 | (96) | 12 | (6) | 207 | (95) | 205 | (94) | 15 | (7) | 217 | (100) |
E. coli (n = 52) | 49 | (94) | 26 | (50) | 29 | (56) | NA | 11 | (21) | 47 | (90) | 35 | (67) | 37 | (71) | NA | 4 | (8) | ||
Unassigned 2 | 2 | (1) | 1 | (0.4) | 3 | (1) | 257 | (96) | 0 | (0) | 1 | (0.4) | 0 | (0) | 3 | (1) | 250 | (93) | 0 | (0) |
Pathotype | ||||||||||||||||||||
Shigella/EIEC (n = 248) | NA | 233 | (94) | 241 | (97) | 217 | (88) | 145 | (58) | NA | 245 | (99) | 242 | (98) | 225 | (92) | 147 | (59) | ||
Other E. coli (n = 21) | 21 | (100) | 6 | (29) | 10 | (48) | NA | 14 | (67) | 21 | (100) | 11 | (52) | 13 | (62) | NA | 6 | (29) | ||
Unassigned 2 | 2 | 1 | (0.4) | 3 | (1) | 46 | (17) | 0 | (0) | 0 | (0) | 0 | (0) | 3 | (1) | 27 | (10) | 0 | (0) | |
Group | ||||||||||||||||||||
Shigella (n = 217) | 19 | (9) | 205 | (94) | 205 | (94) | 193 | (89) | 131 | (60) | 12 | (6) | 207 | (95) | 205 | (94) | 195 | (90) | 134 | (62) |
EIEC (n = 31) | NA | 9 | (29) | 8 | (26) | NA | 2 | (6) | NA | 19 | (61) | 19 | (61) | NA | 0 | (0) | ||||
Other E. coli (n = 21) | 21 | (100) | 6 | (29) | 10 | (48) | NA | 13 | (62) | 21 | (100) | 11 | (52) | 13 | (62) | NA | 7 | (33) | ||
Unassigned 2 | 2 | (1) | 1 | (0.4) | 3 | (1) | 49 | (23) | 0 | (0) | 1 | (0.4) | 0 | (0) | 3 | (1) | 36 | (13) | 0 | (0) |
Species | ||||||||||||||||||||
S. dysenteriae (n = 11) | 5 | (45) | 5 | (45) | 5 | (45) | 0 | (0) | 0 | (0) | 4 | (36) | 7 | (64) | 6 | (55) | 0 | (0) | 0 | (0) |
S. flexneri (n = 77) | NA | 70 | (91) | 70 | (91) | 24 | (31) | 6 | (8) | NA | 73 | (95) | 73 | (95) | 30 | (39) | 3 | (4) | ||
S. boydii (n = 14) | NA | 1 | (7) | 0 | (0) | 0 | (0) | 0 | (0) | NA | 0 | (0) | 0 | (0) | 0 | (0) | 0 | (0) | ||
S. sonnei (n = 115) | NA | 110 | (96) | 110 | (96) | 113 | (98) | 92 | (80) | NA | 112 | (97) | 112 | (97) | 108 | (94) | 101 | (88) | ||
EIEC (n = 31) | NA | 9 | (29) | 8 | (26) | 0 | (0) | 1 | (3) | NA | 19 | (61) | 19 | (61) | 1 | (3) | 3 | (10) | ||
Other E. coli (n = 21) | 21 | (100) | 6 | (29) | 10 | (48) | 0 | (0) | 12 | (57) | 21 | (100) | 11 | (52) | 13 | (62) | 0 | (0) | 4 | (19) |
Unassigned 2 | 2 | (1) | 1 | (0.4) | 3 | (1) | 85 | (32) | 0 | (0) | 1 | (0.4) | 0 | (0) | 3 | (1) | 97 | (36) | 0 | (0) |
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van den Beld, M.J.C.; Rossen, J.W.A.; Evers, N.; Kooistra-Smid, M.A.M.D.; Reubsaet, F.A.G. MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli. Microorganisms 2022, 10, 435. https://doi.org/10.3390/microorganisms10020435
van den Beld MJC, Rossen JWA, Evers N, Kooistra-Smid MAMD, Reubsaet FAG. MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli. Microorganisms. 2022; 10(2):435. https://doi.org/10.3390/microorganisms10020435
Chicago/Turabian Stylevan den Beld, Maaike J. C., John W. A. Rossen, Noah Evers, Mirjam A. M. D. Kooistra-Smid, and Frans A. G. Reubsaet. 2022. "MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli" Microorganisms 10, no. 2: 435. https://doi.org/10.3390/microorganisms10020435
APA Stylevan den Beld, M. J. C., Rossen, J. W. A., Evers, N., Kooistra-Smid, M. A. M. D., & Reubsaet, F. A. G. (2022). MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli. Microorganisms, 10(2), 435. https://doi.org/10.3390/microorganisms10020435