Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism
Abstract
:1. Introduction
2. Materials and Methods
2.1. In Silico Evaluation of Restriction Enzymes
2.2. Pneumococcal Isolates
2.3. PCR Amplification of S. pneumoniae cps Genes
2.4. Analysis of Fragments Obtained from Enzyme Digestions
2.5. Serotyping of Clinical Isolates
3. Results
3.1. In Silico Analysis of GenBank Sequences
3.2. Generation of a Preliminary Database of Fragment Patterns.
3.3. PCR-RFLP Analysis of S. pneumoniae Collection Type Strains
3.4. Serotype Identification of Clinical Isolates by PCR-RFLP Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Strain |
---|
S. pneumoniae serotype 1 CCUG 2839A a |
S. pneumoniae serotype 2 CCUG 8435 a |
S. pneumoniae serotype 3 GB05 b |
S. pneumoniae serotype 4 CCUG 2226 a |
S. pneumoniae serotype 5 CCUG 2541 a |
S. pneumoniae serotype 6B CCUG 1350 a |
S. pneumoniae serotype 7A CCUG 8436 a |
S. pneumoniae serotype 9A CCUG 3506 a |
S. pneumoniae serotype 10B Sri Lanka b |
S. pneumoniae serotype 10C/1 Sanger b |
S. pneumoniae serotype 10F CCUG 5697 a |
S. pneumoniae serotype 11A CCUG 36617 a |
S. pneumoniae serotype 11B CCUG 8440 a |
S. pneumoniae serotype 11D Sanger 70/86 b |
S. pneumoniae serotype 12A CCUG 8444 a |
S. pneumoniae serotype 12B Gambia 1/81 b |
S. pneumoniae serotype 14 CCUG 1086B a |
S. pneumoniae serotype 18C Sanger 4593/4 b |
S. pneumoniae serotype 19A Sanger 1773/39 b |
S. pneumoniae serotype 19C Sanger 408/41 b |
S. pneumoniae serotype 19F CCUG 1407 a |
S. pneumoniae serotype 20 CCUG 8451 a |
S. pneumoniae serotype 21 CCUG 1697 a |
S. pneumoniae serotype 22F Sanger 1772/40 b |
S. pneumoniae serotype 24F CCUG 8457 a |
S. pneumoniae serotype 27 CCUG 5898 a |
S. pneumoniae serotype 31 CCUG 6956 a |
S. pneumoniae serotype 32A CCUG 8458 a |
S. pneumoniae serotype 33D India b |
S. pneumoniae serotype 33F Sanger 3077/37 b |
S. pneumoniae serotype 34 CCUG 2399 a |
S. pneumoniae serotype 35A CCUG 3556 a |
S. pneumoniae serotype 36 CCUG 5906 a |
S. pneumoniae serotype 40 CCUG 8468 a |
S. pneumoniae serotype 42 CCUG 6568 a |
S. pneumoniae serotype 45 CCUG 8472 a |
S. pneumoniae serotype 48 CCUG 8476 a |
Serotype | Nº Isolates | Origin | Nº Concordant Patterns (nº Strains) | Nº New Patterns (nº Strains) |
---|---|---|---|---|
1 | 3 | aSPRL | 3 (3) | |
2 | 1 | bHUCA | 1 (1) | |
3 | 8 | SPRL | 8 (8) | |
4 | 4 | HUCA, SPRL | 4 (4) | |
6A | 1 | HUCA | 1 (1) | |
6B | 3 | HUCA | 2 (3) | |
7F | 8 | cUA, SPRL | 7 (7) | 1(1) |
8 | 4 | UA, SPRL | 4 (4) | |
9N | 2 | HUCA, SPRL | 2 (2) | |
9V | 3 | HUCA, SPRL | 3 (3) | |
10A | 1 | SPRL | 1 (1) | |
11A | 4 | HUCA, SPRL | 4 (4) | |
12F | 3 | dCNM, SPRL | 2 (2) | 1 (1) |
13 | 1 | HUCA | 1(1) | |
14 | 7 | HUCA, SPRL | 6 (6) | 1 (1) |
15A | 2 | SPRL | 1 (1) | 1 (1) |
15B | 1 | CNM | 1 (1) | |
16F | 2 | SPRL | 2 (2) | |
17F | 1 | CNM | 1 (1) | |
18C | 1 | SPRL | 1 (1) | |
19A | 11 | SPRL | 3 (3) | 3 (8) |
19F | 1 | HUCA | 1 (1) | |
22F | 3 | HUCA, SPRL | 3 (3) | |
23B | 2 | SPRL | 2 (2) | |
23F | 7 | HUCA, SPRL | 7 (7) | |
24F | 2 | SPRL | 1 (1) | 1 (1) |
28A | 1 | SPRL | 1 (1) | |
29 | 1 | SPRL | 1 (1) | |
33F | 2 | SPRL | 2 (2) | |
34 | 2 | HUCA, SPRL | 2 (2) | |
35B | 2 | SPRL | 2 (2) | |
35F | 2 | HUCA, SPRL | 2 (2) | |
NT | 2 | SPRL | 2 (2) | |
Total | 98 | 77 (77) | 15 (21) |
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García-Suárez, M.d.M.; González-Rodríguez, I.; Cima-Cabal, M.D.; Yuste, J.E.; Vazquez, F.; Santiago, E. Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism. Diagnostics 2019, 9, 196. https://doi.org/10.3390/diagnostics9040196
García-Suárez MdM, González-Rodríguez I, Cima-Cabal MD, Yuste JE, Vazquez F, Santiago E. Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism. Diagnostics. 2019; 9(4):196. https://doi.org/10.3390/diagnostics9040196
Chicago/Turabian StyleGarcía-Suárez, María del Mar, Irene González-Rodríguez, María Dolores Cima-Cabal, Jose Enrique Yuste, Fernando Vazquez, and Enrique Santiago. 2019. "Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism" Diagnostics 9, no. 4: 196. https://doi.org/10.3390/diagnostics9040196