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|58||France||Unpublished||J. Maïsetti & B. Carbonnelle|
|5b||Spain||Unpublished||S. Semper & C. Martin|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.
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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=