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. 2012 Feb;78(4):1132–1139. doi: 10.1128/AEM.06812-11

Table 1.

Molecular characteristics of 53 Mycobacterium avium subsp. paratuberculosis isolates originating from different hosts within and outside Eifel National Park and assumed cross-species and intraspecies Mycobacterium avium subsp. paratuberculosis transmissions

Geographic region (distance from park [km]) Regional origin/herda Host animal No. of isolates Strain no.b SSR genotypec MIRU-VNTR genotyped INMV no.e IS900-RFLP type after digestion withf:
 Genotype transmittedg
BstEII PstI
Eifel National Park A Red deer 1 05A0159 7–[10]–4–4 42332128 19 C1 P3 I*
1 06A0820 7–[11]–4–4 42332128 19 C1 P3 I*
2 06A0821, 06A0822 7–[10]–5–5 32332228 2 Cn1 P7 II*
B Red deer 3 06A0815, 06A0818, 06A1285 7–[10]–5–5 32332228 2 Cn1 P7 II*
1 06A0816 7–[10]–4–4 32332228 2 C17 P8 III*
1 06A0817 7–[11]–4–4 32332228 2 C17 P8 III*
1 06A0819 7–[12]–4–4 32332228 2 C17 P8 III*
1 06A1280 7–[10]–4–4 42332228 1 C17 P8 IV*
1 06A0813 7–[11]–4–4 42342228 C17 P8
1 06A0814 7–[11]–4–4 32332228 2 C22 P7
C Cattle 1 06A0826 7–[13]–4–4 42332128 19 C1 P3 I*
1 06A0830 7–[10]–5–5 32332228 2 Cn1 P7 II*
1 06A1107 7–[11]–4–4 42332128 19 Cn2 P3
D Cattle 1 06A1108 7–[10]–4–4 42332128 19 Cn3 P3
1 05A2674 7–[11]–4–4 42332128 19 Cn3 P3
E Cattle 1 06A1100 7–[10]–4–4 42332228 1 C17 P8 IV*
1 06A1097 7–[15]–4–4 32332228 2 C1 P1 V
F Cattle 1 06A0997 7–[09]–4–4 32332228 2 C17 P8 III*
1 06A0993 7–[10]–4–4 32332228 2 C17 P8 III*
3 06A0996, 06A1264, 06A1265 7–[11]–4–4 32332228 2 C17 P8 III*
2 06A0990, 06A0994 7–[12]–4–4 32332228 2 C17 P8 III*
2 06A1263, 06A0995 7–[13]–4–4 32332228 2 C17 P8 III*
1 06A0991 7–[14]–4–4 32332228 2 C17 P7
1 06A0998 7–[12]–4–4 32332228 2 C1 P1 V
G Cattle 2 06A1268, 06A1271 7–[10]–4–4 42332128 19 C1 P3 I*
1 06A1270 7–[10]–4–4 42332228 1 C17 P8 IV*
H Cattle 1 05A3269 7–[10]–4–4 32332228 2 C1 P1 V
1 05A3271 7–[11]–4–4 32332228 2 C1 P1 V
Aachen (40) Ih Cattle 1 04A1398 7–[9]–4–4 42332228 1 C17 P8 IV*
1 04A1382 7–[10]–4–4 42332228 1 C17 P8 IV*
2 04A1384, 04A1387 7–[9]–4–4 42332128 19 C1 P10
2 04A1381, 05A3258 7–[10]–4–4 42332128 19 C1 P10
1 04A1383 7–[10]–4–4 43332128 19 C1 P3
1 05A2669 7–[11]–4–4 43332128 19 C1 P3
1 05A2670 7–[12]–4–4 43332128 19 C1 P3
Bergischer Kreis, northeast of Cologne (120) J Cattle 1 05A0158 7–[11]–4–4 42332228 1 C1 P1
K Cattle 1 05A3268 7–[9]–4–4 12322226 new C1 P1
1 05A3267 7–[10]–4–4 12322226 new C1 P1
1 05A3265 7–[10]–4–4 12522226 new C1 P1
1 05A3263 7–[12]–4–4 12322126 new C1 P1
L Cattle 1 05A2760 7–[10]–5–5 32332228 2 Cn1 P7 II*
M Cattle 1 05A2765 7–[12]–4–4 32332228 2 C1 P1 V
1 05A2763 7–[12]–4–4 22522228 12 C1 P1
a

Regional origins of red deer/cattle herds are shown in detail in Fig. 1.

b

Strain number within the strain collection of the Friedrich-Loeffler-Institut in Jena, Germany.

c

Short sequence repeat genotypes were indicated by the numbers of G1 and G2 repeats (loci 1 and 2, respectively), GGT repeats (locus 8), and TGC repeats (locus 9) according to Amonsin et al. (1). Genotypes are listed in the format 1-[2]-8-9, with the number of repeats of each locus in the place of the locus number. G2 repeats (locus 2) were enclosed in brackets because of polymerase slippage during genotyping and the suspicion that they are not conserved enough for epidemiological studies.

d

Number of tandem repeats at MIRU-VNTR loci 292, X3, 25, 47, 3, 7, 10, and 32, according to Thibault et al. (36). The first number in the 8-digit genotype corresponds to the number of repeats at locus 292, the second number corresponds to the number of repeats at locus X3, etc.

e

Designation according to the INRA Nouzilly MIRU-VNTR nomenclature (36) for MIRU-VNTR patterns.

f

After digestion with BstEII, IS900-RFLP types C1, C17, and C22 were designated according to the nomenclature of Pavlik et al. (26) and Cn1 was designated according to Möbius et al. (21). Two novel profiles were detected (Cn2 and Cn3). After digestion with PstI, types P1 and P3 were designated according to the nomenclature of Whipple et al. (42) and types P7, P8, and P10 were designated according to Möbius et al. (21).

g

Genotypes which were detected in more than one herd or forest district and assumed to show cross-species (additionally designated by an asterisk) and intraspecies Mycobacterium avium subsp. paratuberculosis transmission were designated with roman numerals. Results of SSR G2 repeats were excluded.

h

Nine isolates from a total of 15 included in a herd previously examined by Möbius et al. (21) without SSR genotyping were again subcultivated and genotyped, and the isolates were included in the current study as part of a herd originating from North Rhine-Westphalia but far from Eifel National Park.