Both control strains yielded standard patterns of spacer arrangements; absence of spacers 20-21 and 33-36 and presence of spacers 39-43 for M. tuberculosis H37Rv and absence of spacers 3, 9, 16 and 39-43 for M. bovis BCG P3. Figure 1 presents spoligotype patterns and frequency of occurrence of M. bovis spoligotypes in the whole material.
The latter include patterns belonging to H4 sublineage that were relabeled "Ural-2" and some patterns previously classified as H3 sublineage but with an additional specific signature (presence of spacer 2, absence of spacers 29 to 31 and 33 to 36), which are now relabeled "Ural-1".
In fact, those genotypes are from different families, i.e. Haarlem (classification rule: absence of spacer 31 and spacers 33 36), LAM (absence of spacers 21 24 and spacers 33 36) and Beijing clades (absence of spacers 1 34) respectively [ 32].
dRule A, absence of spacers 29 32, presence of spacer 33 and absence of spacer 34; rule B, absence of spacers 21 24 and spacers 33 36; rule C : absence of spacer 18 and spacers 33 36; rule D, absence of spacers 39 43; rule E, absence of spacer 31 and spacers 3 -36; rule F, absence of spacers 33 36.
SB1186 and SB1187 differed from the ubiquitous SB140 by absence of spacer 35 and spacers 35 and 37, respectively.
Eighteen patterns were not previously reported in the SpolDB4 international database fifteen of which presenting the typical signature of the East African-Indian (EAI) family (absence of spacers 29-32, presence of spacer 33, absence of spacer 34) [ 10].
In addition to the absence of spacer 30, most of the strains from Mali (12/13) also lack spacer 6, a characteristic not seen in isolates from Central African countries [ 14- 16].
This may be an artefact, as the spoligotype that we have designated ST59c, which differs from 59 only in the absence of spacer 15 was found only up to 1994 p<0.0011), and it was previously noted that hybridisation of spacer 15 was not consistent.
Beijing strains were defined as isolates with a spoligotype showing the absence of spacers 1 34 and presence of at least 3 spacers among spacers 35 43 (26, 27 ).
It is characterized by the absence of spacers 33 and 34, two spacers likely to be of high phylogenetic importance in group I organisms since they permit distinguishing between 1) East African Indian (EAI) superfamily (presence of spacer 33, absence of 34), 2) CAS family (absence of 33 and 34), and 3) M. bovis (presence of 33 and 34).
