High Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Germany Revealed by Multitarget Genotyping
Abstract
1. Introduction
2. Results
2.1. Genotypes Identified, Origin, and Subdivision of C- and S-Type Strains
2.2. Individual Genotypes and Discriminatory Power of RFLP, MIRU-VNTR, and SSR Typing
2.2.1. Previously Detected and Novel Genotypes
2.2.2. Specific Sequence Pattern at VNTR7
2.2.3. Number and Frequency of Individual IS900-RFLP, MIRU-VNTR, and SSR Types
2.2.4. Discriminatory Power of Typing
2.3. Comparison of Combined Genotypes and Phylogeny
2.4. Distribution of Map Genotypes Among Different Herds, Hosts, and Federal States
2.5. Diversity of Isolates
2.6. Intra-Herd Diversity of Map
2.7. Mixed Genotypes and Co-Infection of Individual Animals
2.7.1. Mixed Genotypes in Individual Isolates
2.7.2. Different Genotypes in Isolates from Individual Animals
2.8. Suspected Epidemiological Linkages
3. Discussion
3.1. Genotyping Markers and Homoplasy
3.2. Phylogenetic Grouping and Comparison with WGS-Based SNP Analysis
3.3. Genotypes of Map S-Type Strains
3.4. Diversity of Map C-Type Strains
3.5. Intra-Herd Diversity of Map and Co-Infections of Herds and Individual Animals
3.6. Epidemiological Findings
4. Materials and Methods
4.1. Map Isolates
4.2. Map Strain Isolation, Cultivation, and Subspecies Identification
4.2.1. Strain Isolation, Cultivation, Sub-Cultivation
4.2.2. DNA Extraction for PCR Reactions
4.2.3. Molecular Map Identification
4.3. Molecular Genotyping
4.3.1. IS900-RFLP Analysis
4.3.2. MIRU-VNTR Typing
4.3.3. SSR Analysis
4.3.4. Analysis of Typing Results and Discriminatory Power
4.4. Comparison of Strains and Analysis of Phylogeny
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Glossary
References
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GT | RFLP a | VNTR b | INMV c | SSR d | [n] | Host |
---|---|---|---|---|---|---|
1 | C1-P1 | 42332228 | 1 | 7-4-4 | 17 | C, G |
2 | C1-P1 | 42332228 | 1 | 7-4-5 | 16 | C, S, D |
3 | C1-P1 | 42332228 | 1 | 8-4-5 | 1 | G |
4 | C1-P1 | 32332228 | 2 | 7-4-4 | 53 | C, G, S |
5 | C1-P1 | 32332228 | 2 | 7-4-5 | 13 | C, S |
6 | C1-P1 | 32332228 | 2 | 7-5-5 | 1 | C |
7 | C1-P1 | 32332228 | 2 | 9-5-5 | 2 | C |
8 | C1-P1 | 32332228 | 2 | 10-5-5 | 1 | C |
9 | C1-P1 | 32332228 | 2 | ≥11-5-5 | 7 | C |
10 | C1-P1 | 32332228 | 2 | ≥11-5-6 | 1 | C |
11 | C1-P1 | 32332218 | 3 | 7-4-4 | 3 | C |
12 | C1-P1 | 32332229 | 4 | 7-4-4 | 1 | C |
13 | C1-P1 | 42332218 | 5 | 7-4-4 | 1 | C |
14 | C1-P1 | 42332218 | 5 | 7-4-5 | 1 | C |
15 | C1-P1 | 32332128 | 6 | 7-4-5 | 1 | H |
16 | C1-P1 | 32332128 | 6 | ≥11-4-5 | 9 | C |
17 | C1-P1 | 32332(5) e 28 | 16 * | 7-4-4 | 2 | C |
18 | C1-P1 | 22522228 | 12 | 7-4-4 | 10 | C |
19 | C1-P1 | 22332228 | 13 | 7-4-4 | 2 | C |
20 | C1-P1 | 42332128 | 19 | 7-4-4 | 3 | C |
21 | C1-P1 | 32522(3) f 28 | 30 * | 7-4-4 | 1 | C |
22 | C1-P1 | 32522228 | 33 | 7-4-4 | 29 | C, G, S |
23 | C1-P1 | 22522226 | 80 | 7-4-4 | 4 | C |
24 | C1-P1 | 32322228 | 117 | 7-4-4 | 3 | C |
25 | C1-P1 | 12322226 | 132 | 7-4-4 | 1 | C |
26 | C1-P1 | 12522226 | 133 | 7-4-4 | 1 | C |
27 | C1-P1 | 12322126 | 134 | 7-4-4 | 1 | C |
28 | C1-P1 | 22522128 | 136 | 7-4-4 | 4 | C |
29 | C1-P1 | 52332228 | 139 | 9-4-5 | 1 | DO |
30 | C1-P1 | 42322228 | 141 | 7-4-4 | 1 | C |
31 | C1-P1 | 32422128 | 142 | 7-4-4 | 1 | C |
32 | C1-P1 | 22522218 | 217 | 7-4-4 | 1 | C |
33 | C1-P1 | 22322226 | 262 | 7-4-4 | 3 | C, G |
34 | C1-P1 | 42332226 | 263 | 7-4-5 | 1 | C |
35 | C1-P2 | 32332228 | 2 | 7-4-3 | 2 | C |
36 | C1-P2 | 22332228 | 13 | 7-4-3 | 1 | C |
37 | C1-P3 | 42332128 | 19 | 7-4-4 | 23 | C, G, D |
38 | C1-P3 | 42332128 | 19 | 8-4-4 | 1 | C |
39 | C1-P3 | 43332128 | 143 | 7-4-4 | 8 | C |
40 | C1-P3 | 43332118 | 264 | 7-4-4 | 1 | C |
41 | C1-P7 | 32332228 | 2 | 7-5-5 | 1 | D |
42 | C1-P10 | 42332128 | 19 | 7-4-4 | 1 | C |
43 | C2-P18 | 32522228 | 33 | 7-4-4 | 2 | C |
44 | C5-P1 | 32332228 | 2 | ≥11-5-5 | 1 | C |
45 | C5-P7 | 32332228 | 2 | 7-5-5 | 1 | D |
46 | C5-P8 | 42332228 | 1 | 7-4-4 | 1 | C |
47 | C9-P2 | 42332228 | 1 | 7-4-4 | 1 | C |
48 | C9-P2 | 32332228 | 2 | 7-4-4 | 1 | C |
49 | C10-P6 | 42332228 | 1 | 7-4-4 | 1 | C |
50 | C10-P6 | 42332218 | 5 | 7-4-4 | 2 | C |
51 | C10-P6 | 42322228 | 141 | 7-4-4 | 1 | C |
52 | C10-P17 | 42332218 | 5 | 7-4-4 | 1 | C |
53 | C12-P3 | 42332128 | 19 | 7-4-4 | 1 | C |
54 | C13-P18 | 32332227 | 191 | 7-4-4 | 1 | C |
55 | C16-P12 | 42332128 | 19 | 7-4-4 | 1 | C |
56 | C17-P8 | 42332228 | 1 | 7-4-4 | 12 | C |
57 | C17-P8 | 32332228 | 2 | 7-4-4 | 3 | C, D |
58 | C17-P8 | 42332226 | 263 | 7-4-4 | 1 | C |
59 | C17-P8 | 42342228 | 265 | 7-4-4 | 1 | C |
60 | C17-P9 | 42332228 | 1 | 7-4-4 | 1 | C |
61 | C17-P9 | 42332128 | 19 | 7-4-4 | 8 | C, S |
62 | C17-P9 | 12332228 | 248 | 7-4-4 | 1 | C |
63 | C18-P1 | 32522228 | 33 | 7-4-4 | 1 | C |
64 | C18-P16 | 42332228 | 1 | 7-4-5 | 7 | C |
65 | C18-P16 | 32332228 | 2 | 6-4-4 | 2 | C, D |
66 | C18-P16 | 32332228 | 2 | 7-4-4 | 1 | C |
67 | C18-P16 | 32332228 | 2 | 10-5-5 | 2 | C |
68 | C18-P16 | 42332218 | 5 | 7-4-4 | 1 | C |
69 | C18-P16 | 22332228 | 13 | ≥11-5-5 | 1 | C |
70 | C18-P16 | 22522226 | 80 | 7-4-4 | 2 | C |
71 | C22-P1 | 32332228 | 2 | 7-4-4 | 1 | D |
72 | C22-P11 | 42332128 | 19 | 7-4-4 | 1 | C |
73 | C22-P20 | 22522228 | 12 | 7-4-4 | 1 | C |
74 | C24-P19 | 32522228 | 33 | 7-4-4 | 4 | C |
75 | C27-P1 | 42332228 | 1 | 7-4-5 | 2 | C |
76 | C27-P3 | 42332128 | 19 | 7-4-4 | 1 | C |
77 | C29-P3 | 42332128 | 19 | 7-4-4 | 1 | C |
78 | C41-P1 | 32332228 | 2 | 7-5-5 | 2 | C |
79 | C41-P1 | 32332128 | 6 | 7-5-5 | 1 | C |
80 | C41-P7 | 32332228 | 2 | 7-5-5 | 14 | C, D, S, B |
81 | C41-P7 | 32332128 | 6 | 7-5-5 | 1 | C |
82 | C42-P3 | 42332128 | 19 | 7-4-4 | 1 | C |
83 | C43-P3 | 42332128 | 19 | 7-4-4 | 3 | C |
84 | C44-P1 | 32332228 | 2 | 7-4-4 | 1 | C |
85 | C44-P1 | 32522228 | 33 | 7-4-4 | 1 | C |
86 | C45-P1 | 32332228 | 2 | ≥11-5-5 | 1 | C |
87 | C46-P1 | 42332229 | 190 | 8-4-4 | 4 | C |
88 | C47-P1 | 42332228 | 1 | 7-4-4 | 1 | C |
89 | C48-P18 | 32522228 | 33 | 7-4-4 | 1 | C |
90 | C49-P17 | 42332218 | 5 | 7-4-4 | 1 | C |
91 | I2-P14 | 22331(1.5) g 18 | 220 | 7-3-4 | 1 | S |
92 | I6-P13 | 42131(1.5)18 | 266 | 7-3-4 | 4 | S, C |
93 | I7-P14 | 52331(1.5)18 | 267 | 7-3-3 | 1 | S |
INMV Code | INMV Profile | Map-Type | Host Origin | Herd, Location (Loc) a |
---|---|---|---|---|
22322226 | 262 | C | cattle, goat | BB-2, RP-29, BB/Loc3 |
42332226 | 263 | C | cattle | RP-33, RP-34 |
43332118 | 264 | C | cattle | SL-6 |
42342228 | 265 | C | red deer | NRW/Loc13 |
42131(1.5) b 18 | 266 | S | sheep, cattle | NRW/Loc11, TH/Loc24; BY-2, BY-5 |
52331(1.5) b 18 | 267 | S | sheep | NRW/Loc10 |
325223*28 | 30* | C | cattle | TH21 |
Genotype | IS900-RFLP/MIRU-VNTR/SSR | Herds * [n] | Federal State [n] |
---|---|---|---|
GT4 | C1-P1/INMV2 (32332228)/7-4-4 | 48 (20%) | 9 |
GT22 | C1-P1/INMV33 (32522228)/7-4-4 | 26 (11%) | 10 |
GT37 | C1-P3/INMV19 (42332128)/7-4-4 | 21 (9%) | 8 |
GT1 | C1-P1/INMV1 (42332228)/7-4-4 | 16 (7%) | 7 |
GT2 | C1-P1/INMV1 (42332228)/7-4-5 | 14 (6%) | 7 |
No. | INMV Code | INMV Profile a | SSR | IS900-RFLP b | GT c | Isolate (n) | Herd d (n) |
---|---|---|---|---|---|---|---|
1 | (3+4)2332228 | 2 + 1 | 7-4/5-4/5 | C1-(P1 + P3) | - | 1 | NRW-12 |
2 | (3+4)2332(1+2)28 | 2 + 19 | 7-4-3/4 | C1-(P2 + P3) | 35 + 37 | 1 | RP-23 |
3 | 42332(1+2)28 | 1 + 19 | 7-4-4/5 | C1-(P1 + P3) | 2 + 37 | 1 | RP-31 |
4 | 4233222(6+8) | 263 + 1 | 7-4-5 | C1-P1 | 34 + 2 | 1 | RP-33 |
5 | 4233222(6+8) | 263 + 1 | 7-4-4 | C17-P8 | 58 + 56 | 2 | RP-34 |
6 | 32(3+5)22228 | 117 + 33 | 7-4-4 | C1-P1 | 24 + 22 | 1 | SL-2 |
7 | 433321(1+2)8 | 264 + 143 | 7-4-4 | C1-P3 | 40 + 39 | 1 | SL-6 |
8 | 32332(5*+2)28 | 16 * + 2 | 7-4-4 | C1-P1 | 17 + 4 | 2 | TH-42,43 |
N° a | Host | Origin a | Isolate | Tissue Origin | RFLP b | INMV c | Code d | SSR e | GT |
---|---|---|---|---|---|---|---|---|---|
1 | Cattle | TH-1 | 01A0432 | Jejunal LN | C17-P9 | 19 | 42332128 | 7-4-4 | 61 |
01A0435 | Liver | C17-P9 | 19 | 42332128 | 7-4-4 | 61 | |||
01A0441 | Muscle | C1-P1 | 1 | 42332228 | 7-4-4 | 1 | |||
2 | Cattle | TH-1 | 01A0534 | Jejunal LN f | C1-P1 | 2 | 32332228 | 7-4-5 | 5 |
01A0535 | Jejunal LN g | C17-P9 | 19 | 42332128 | 7-4-4 | 61 | |||
3 | Cattle | TH-1 | 02A0112 | Feces | C17-P9 | 19 | 42332128 | 7-4-4 | 61 |
02A0116 | Ileo-caecal LN | C17-P9 | 19 | 42332128 | 7-4-5 | - | |||
02A0117 | Jejunal LN | C17-P9 | 19 | 42332128 | 7-4-4 | 61 | |||
02A0118 | Liver | C17-P9 | 19 | 42332128 | 7-4-4 | 61 | |||
02A0119 | Liver LN | C17-P9 | 19 | 42332128 | 7-4-4 | 61 | |||
4 | Cattle | TH-1 | 02A1191 | Feces | C17-P9 | 19 | 42332128 | 7-4-4 | 61 |
02A1192 | Ileum | C17-P9 | 19 | 42332128 | 7-4-4 | 61 | |||
02A1194 | Caecum | C16-P12 | 19 | 42332128 | 7-4-4 | 55 | |||
5 | Cattle | TH-3 | 05A2326 | Feces | C9-P2 | 1 | 42332228 | 7-4-4 | 47 |
05A2327 | Ileum LN | C9-P2 | 1 | 42332228 | 7-4-4 | 47 | |||
05A2328 | Spleen LN | C9-P2 | 2 | 32332228 | 7-4-4 | 48 | |||
05A2330 | Lung of foetus | C9-P2 | 1 | 42332228 | 7-4-4 | 47 | |||
6 | Cattle | NRW-3 | 06A1283 | Feces 1 * | C17-P8 | 2 | 32332228 | 7-4-4 | 57 |
06A1284 | Feces 2 * | C41-P7 | 2 | 32332228 | 7-5-5 | 80 | |||
7 | Cattle | NRW-13 | 06A1281 | Feces 1 * | C17-P9 | 19 | 42332128 | 7-4-4 | 61 |
06A1282 | Feces 2 * | C17-P8 | 1 | 42332228 | 7-4-4 | 56 | |||
8 | Roe deer | NRW-Loc17 | 06A1278 | Feces 2 * | C5-P7 | 2 | 32332228 | 7-5-5 | 45 |
06A1279 | Feces 3 * | C1-P7 | 2 | 32332228 | 7-5-5 | 41 | |||
9 | Sheep | TH-Loc24 | 11MA0986 | Mesenteric LN | I6-P13 | 266 | 42131(1.5)18 | 7-3-4 | 92 |
11MA0987a | Feces 1 (LJ) | I6-P13 | 266 | 42131(1.5)18 | 7-3-4 | 92 | |||
11MA0987b | Feces 2 (Her) | n.d. | 2 | 32332228 | 7-5-5 | - |
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Möbius, P.; Price-Carter, M.; Köhler, H. High Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Germany Revealed by Multitarget Genotyping. Int. J. Mol. Sci. 2025, 26, 5273. https://doi.org/10.3390/ijms26115273
Möbius P, Price-Carter M, Köhler H. High Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Germany Revealed by Multitarget Genotyping. International Journal of Molecular Sciences. 2025; 26(11):5273. https://doi.org/10.3390/ijms26115273
Chicago/Turabian StyleMöbius, Petra, Marian Price-Carter, and Heike Köhler. 2025. "High Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Germany Revealed by Multitarget Genotyping" International Journal of Molecular Sciences 26, no. 11: 5273. https://doi.org/10.3390/ijms26115273
APA StyleMöbius, P., Price-Carter, M., & Köhler, H. (2025). High Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Germany Revealed by Multitarget Genotyping. International Journal of Molecular Sciences, 26(11), 5273. https://doi.org/10.3390/ijms26115273