Volume 7, Number 3—June 2001
Spoligotype Database of Mycobacterium tuberculosis: Biogeographic Distribution of Shared Types and Epidemiologic and Phylogenetic Perspectives
|No. of isolates||Origina||Year||Reference|
|58||France||Unpublished||J. Maïsetti & B. Carbonnelle|
|5b||Spain||Unpublished||S. Semper & C. Martin|
|69||Far East Asia||1995||44|
aAlthough a potential sampling bias cannot be excluded, the sampling of isolates and their representativeness (in order of description) was as follows: Denmark, of 249 isolates described with a low copy number of IS6110 collected since 1992 (exhaustivity 93%), 24 shared types, representing 136 spoligotypes, were retained (9 other shared types, representing 49 isolates that were found exclusively in Denmark (S1,S2,S4,S19,S22,S23,S27,S30,S33), were not included in the present analysis; Italy, of 158 isolates from 156 patients in Verona collected during 1996-1997, 147 spoligotypes were retained; Cuba, of 160 isolates typed (obtained from a pool of 578 smear-positive sputa collected during 1994-1995), 157 spoligotypes described (exhaustivity 36%) were retained; Philippines, no data except for a single spoligotype available; Peru, of 29 strains isolated during 1995-1996 from the sputa of patients in Lima and Cuzco, only 3 were retained in this study since the remaining isolates shared spoligotypes with patients in Texas (12) and are included in the 1,283 Texan profiles; USA, 18 clinical isolates from the collection of R. Frothingham (representativeness unknown); France, 111 isolates from 105 hospitalized patients in Paris obtained during 1993 (patients were from three major hospitals that represented 5% of the total public hospital beds in Paris); United Kingdom, 167 isolates from all the culture-positive tuberculosis (TB) patients from three large hospitals in northwest London (without any indication of period of recruitment); France, 296 isolates sent for reference purposes during a 3-year period to the Centre National de Référence des Mycobactéries, Institut Pasteur, Paris; Zimbabwe, 28 spoligotypes obtained directly from sputum samples during a 1-month recruitment period (December 1995) of sputum-positive TB cases representing 20% of all cases; Guinea-Bissau, of 229 spoligotypes obtained from samples of 900 patients with suspected TB cases during 1989-1994, only 32 spoligotypes were fully described by the authors, and were retained for the analysis; the Netherlands, 118 isolates of unspecified representativeness from the collection of National Institute of Health (RIVM, Bilthoven); International multicenter study, 68 of 90 isolates from 38 countries representing the five continents; France, 58 isolates during a 1-year (1999) recruitment in the University Hospital of Angers; Russia, 62 isolates representing the St. Petersburg area collected during 1997-1999; West Africa, 84 isolates from Ivory Coast and around Dakar, Senegal, collected during 1994-1995; Thailand, 5 isolates from northern Thailand (unknown representativeness); Romania, 14 isolates of unknown representativeness; Brazil, 17 spoligotypes out of 91 isolates from a São Paulo hospital in 1995 (unknown representativeness); Spain, 5 multidrug-resistant isolates (unknown representativeness); USA, 1,429 clinical isolates from 1,283 patients during 1994-1999 that are part of an ongoing population-based study in Houston, Texas; United Kingdom, a single spoligotype from ancient DNA extracted from a bone sample; the Netherlands, 19 spoligotypes obtained from paraffin-wax embedded tissue samples previously collected during 1983-1993 (unknown representativeness); the Netherlands, a single spoligotype from a previous study (unknown representativeness); Far East Asia, 69 isolates from China and Mongolia obtained during 1992-1994 (unknown representativeness); Caribbean, 425 clinical isolates from a population-based ongoing study that includes all cultures isolated in Guadeloupe, Martinique, and French Guiana since 1994 and covers a 1 million population (exhaustivity 100%). Some isolates in this pool came from patients from other countries (essentially neighboring countries such as Haiti, Dominican Republic, Brazil, Commonwealth of Dominica, Barbados, and Surinam).
bDescription of a given spoligotype without precise number of isolates within this type.
1For this purpose, the independent sampling sizes for Europe and the USA were taken as n1 and n2, the number of individuals within a given shared-type "x" was k1 and k2, and in this case, the representativeness of the two samples was p1=k1/n1 and P2=k2/n2, respectively. To assess if the divergence observed between p1 and p2 was due to sampling bias or the existence of two distinct populations, the percentage of individuals (p0) harboring shared-type "x" in the population studied was estimated by the equation p0= k1+k2/n1+n2=n1p1+n2p2/n1+n2. The distribution of the percentage of shared-type "x" in the sample sizes n1 and n2 follows a normal distribution with a mean p0 and a standard deviation of and respectively, and the difference d=p1-p2 follows a normal distribution of mean p0-p0=0 and of variance σd2=σp12+σp22 = p0q0/n1+p0q0/n2 or σd2=p0q0 (1/n1+1/n2). The two samples being independent, the two variances were additive; the standard deviation σd=