Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections
Abstract
:1. Introduction
2. Results
2.1. Results of the Automated Ribotyping Analysis
2.2. Results of the MLST Analysis
2.3. Relatedness between Ribogroups, STs, MLST CCs and eBURST Groups
2.4. Relatedness between Ribogroups, spa Types, spa CCs and BURP Clusters
2.5. Ribogroups Association with agr Type, tst and mecA Genes, IS256 and Phenotypic Antibiotic Resistance
Ribogroup | Prev. agr type | tst | IS256 | mecA | OXA | PEN | AMP | GEN | ERY | CLI | CHL | SXT | CIP | VAN | MAR |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ribocluster | III 98% | 83% | 0% | 0% | 2% | 94% | 92% | 4% | 11% | 6% | 0% | 0% | 4% | 0% | 0.21 |
cra-94-S7 | II 94% | 6% | 94% | 88% | 88% | 94% | 94% | 94% | 94% | 94% | 6% | 0% | 94% | 0% | 0.66 |
cra-146-S8 | II 100% | 22% | 0% | 22% | 0% | 44% | 44% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0.11 |
cra-137-S4 | I 100% | 0% | 50% | 79% | 86% | 100% | 100% | 57% | 57% | 62% | 21% | 7% | 86% | 0% | 0.57 |
cra-157-S4 | I 85% | 0% | 0% | 0% | 0% | 77% | 77% | 8% | 8% | 8% | 8% | 0% | 0% | 0% | 0.18 |
cra-147-S6 | III 100% | 25% | 50% | 25% | 25% | 75% | 75% | 13% | 25% | 25% | 0% | 0% | 0% | 0% | 0.24 |
2.6. Uncommon STs and spa Types Atypically Found within Ribogroups
2.7. Hunter-Gaston Discriminatory Power Analysis
3. Discussion
3.1. MLST vs. Automated Ribotyping
3.2. spa Typing vs. Automated Ribotyping
3.3. Clonal Complexes
4. Conclusions
5. Materials and Methods
5.1. Bacterial Isolates
5.2. Antibiotic Susceptibility
5.3. Automated Ribotyping
5.4. Bacterial DNA Isolation
5.5. Detection of mecA, tst, IS256, and agr Typing
5.6. spa Typing
5.7. MLST
5.8. Discriminatory Power
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Ribogroup | ST (%) | MLST CC Founder (Breaker) | eBURST Groups ** |
---|---|---|---|
Ribocluster (48) | ST30 (64.6%) ST34 (20.8%) ST2954 * (6.2%) ST2957 * (2.1%) ST2960 * (2.1%) ST untypeable (2.1%) ST243 (2.1%) | CC30 (SLV) | Group 1 |
cra-94-S-7 (16) | ST228 (87.5%) ST2956 * (6.25%) ST46 (6.25%) | CC5 (DLV) CC5 (DLV) CC45 † (SLV) | Group 2 Group 2 ST46 singleton |
cra-146-S-8 (9) | ST5 (88.9%) ST2626 (11.1%) | CC5 CC5 (SLV) | Group 2 |
cra-137-S-4 (14) | ST8 (64.3%) ST247 (28.6%) ST241 (7.1%) | CC8 CC8 (DLV) CC8 (DLV) | Group 3 |
cra-157-S-4 (13) | ST7 (69.2%) ST2955 * (7.7%) ST109 (15.4%) ST101 (7.7%) | CC7 CC7 (DLV) CC1 † (TLV) CC not delivered† | Group 4 Group 4 ST109 singleton ST101 singleton |
cra-147-S-6 (8) | ST1 (100%) | CC1 | ST1 singleton |
Ribogroup | MLST CC | MLST | spa Type | spa CC | Cluster |
---|---|---|---|---|---|
Ribocluster (48) | CC30 (48) | ST30 (31) | t012 (12) t021 (8) t018 (3) t093 (1) t338 (3) t1382 (2) t5891 (1) t11956 (1) | CC021/012 (37) | Cluster 1 |
ST2954 ** (3) | t298 (2) t012 (1) | ||||
ST2957 ** (1) ST2960 ** (1) ST untyp. (1) | t021 (1) t021 (1) t338 (1) | ||||
ST34 (8) | t166 (4) t4437 (1) t369 (3) | CC166 (8) | Cluster 4 | ||
t3906 (1) | Singleton (1) | - | |||
ST34 (1) ST30 (1) | t13129 * (1) t13132 * (1) | spatypes with missing alignments (2) | - | ||
cra-94-S-7 (16) | CC5 (15) | ST228 (7) ST228 (6) ST2956 ** (1) | t001 (7) t041 (6) t109 (1) | CC002 (14) | Cluster 2 |
ST228 (1) | t1382 (1) | CC021/012 (1) | Cluster 1 | ||
CC45 (1) | ST46 (1) | t1646 (1) | Singleton (1) | - | |
cra-146-S-8 (9) | CC5 (9) | ST5 (8) | t002 (2) t179 (1) t548 (2) t985 (1) | CC002 (6) | Cluster 2 |
t045 (1) | Singleton (2) | - | |||
t5349 (1) | |||||
ST2616 (1) | t13130 * (1) | spatype with missing alignments (1) | - | ||
cra-137-S-4 (14) | CC8 (14) | ST8 (9) | t008 (5) t024 (2) t121 (1) t574 (1) | CC121 (13) | Cluster 3 |
ST247 (4) | t051 (4) | ||||
ST241 (1) | t037 †(1) | CC021/012 (1) | Cluster 1 | ||
cra-157-S-4 (13) | CC7 (10) | ST7 (9) ST2955 ** (1) | t091 (9) t091 (1) | Singleton (13) | - |
CC1 (2) | ST109 (2) | t209 (2) | |||
CC n.d. | ST101 (1) | t7956 (1) | |||
cra-147-S-6 (8) | CC1 | ST1 (8) | t127 (5) t2478 (1) | Singleton (6) | - |
t693 (1) t1252 (1) | Excluded CC no founder (2) | Cluster 5 |
Ribogroup | STs | MLST Allele Succession (arc-aroe-glpf-gmk-pta-tpi-yiql) | agr Type | spa Types-spa CC | spa Repeats Succession |
---|---|---|---|---|---|
cra-94-S-7 (16) | ST228 (14) ST46 (1) | 01-04-01-04-12-24-29 10–14-08–06-14-03-02 | II I | t001-CC002 (7) t041-CC002 (6) t1646–singleton (1) | 26-30-17-34-17-20-17-12-17-16 26-30-17-34-17-20-17-34-17-20-17-12-17-16 09-20-16-34-13-17-34-16-34 |
cra-157-S-4 (13) | ST7 (9) ST109 (2) ST101 (1) | 05-04–01-04-04-06-03 03-27-01-01–01-01-1003-01-14-15-11-19-03 | I II I | t091-singleton (9) t209-singleton (2) t7956-singleton (1) | 07-23-21-17-34-12-23-02-12-23 07-16-12-23-3404-13-21-12-17-20-17-12-17-17-17 |
cra-137-S-4 (14) | ST8 (9) ST241 (1) | 03-03-01-01-04–04–03 02-03-01-01-04–04–03 | I I | t008 (5 CC121) t037 (1 CC021/012) | 11-19-12-21-17-34-24-34-22-25 15-12-16-02-25-17-24 |
Spa Typing | MLST | Ribotyping | spa CC | MLST CC | |
---|---|---|---|---|---|
MSSA (79) | 0.936 | 0.802 * | 0.596 | 0.746 † | 0.590 ** |
MRSA (29) | 0.879 | 0.751 | 0.636 | 0.594 | 0.567 |
TOTAL (108) | 0.955 | 0.869 * | 0.744 | 0.817 † | 0.721 ** |
Ribogroup 1 | MLST CC 1 | MLST ST | spa Type | spa CC | IS256 |
---|---|---|---|---|---|
Ribocluster (48/48) | CC30 (48/48) | ST30 (31), ST34 (10), ST2954 (3), ST2957 (1), ST2960 (1), ST243 (1), ST non-typeable (1) | t012 (13), t021 (10), t018 (3), t093 (1), t166 (4), t298 (2), t338 (4), t369 (3), t1382 (2), t3906(1), t4437 (1), t5891 (1), t11956 (1), t13129 * (1), t13132 * (1) | CC021/012 (37) CC166 (8) singleton and missing alignments (3) | neg (44) |
cra-94-S7 (2/16) cra-146-S8 (7/9) | CC5 (8/25) CC45 (1/25) | ST5 (6), ST228 (1), ST2626 (1) ST46 (1) | t1382 (1), t1646 (1), t002 (1), t045 (1), t179(1), t548 (2), t5349 (1), t13130 * (1) | CC002 (5) CC021/012 (1) singletons (3) | neg (8) pos (1) |
cra-137-S4 (3/14) | CC8 (3/14) | ST8 (3) | t008 (1), t024 (1), t574 (1) | CC121 (3) | neg (3) |
cra-157-S4 (13/13) | CC7 (10/13) CC1 (2/13) CC not delivered (1/13) | ST7 (9)–ST2955 (1) ST109 (2) ST101 (1) | t091 (10), t209 (2), t7956 (1) | singletons (13) | neg (13) |
cra-147-S6 (6/8) | CC1 (6/8) | ST1 (6) | t127 (3), t693 (1), t1252 (1), t2478 (1) | excluded (2) singletons (4) | neg (4) pos (2) |
Ribogroup 1 | MLST CC 1 | MLST ST | spa Type | spa CC | IS256 |
---|---|---|---|---|---|
cra-94-S7 (14/16) cra-146-S8 (2/9) | CC5 (16/25) | ST228 (13) ST5 (2) ST2956 (1) | t001 (7), t041 (6), t109 (1), t002 (1), t985 (1) | CC002 (16) | pos (14) neg (2) |
cra-137-S4 (11/14) | CC8 (11/14) | ST8 (6) ST247 (4) ST241 (1) | t008 (4), t051 (4), t024 (1), t037 (1), t121 (1) | CC121 (10) singleton (1) | pos (7) neg (4) |
cra-147-S6 (2/8) | CC1 (2/8) | ST1 (2) | t127 (2) | singletons (2) | pos (2) |
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Ravaioli, S.; Campoccia, D.; Ruppitsch, W.; Allerberger, F.; Poggi, A.; Chisari, E.; Montanaro, L.; Arciola, C.R. Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections. Int. J. Mol. Sci. 2022, 23, 1660. https://doi.org/10.3390/ijms23031660
Ravaioli S, Campoccia D, Ruppitsch W, Allerberger F, Poggi A, Chisari E, Montanaro L, Arciola CR. Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections. International Journal of Molecular Sciences. 2022; 23(3):1660. https://doi.org/10.3390/ijms23031660
Chicago/Turabian StyleRavaioli, Stefano, Davide Campoccia, Werner Ruppitsch, Franz Allerberger, Alessandro Poggi, Emanuele Chisari, Lucio Montanaro, and Carla Renata Arciola. 2022. "Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections" International Journal of Molecular Sciences 23, no. 3: 1660. https://doi.org/10.3390/ijms23031660