Contribution of spoligotyping to the characterization of the population structure of Mycobacterium tuberculosis isolates in Portugal

David, Susana; Ribeiro, Diana Raposo; Antunes, Ana Vanessa; Portugal, Clara; Sancho, Luísa; Sousa, José Germano de

doi:10.1016/j.meegid.2007.05.007

Cited by 18 publications

(22 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In general, our observation are in accordance with regional (Borsuk et al, 2005;David et al, 2007) and worldwide (Brudey et al, 2006;Gagneux et al, 2006) earlier studies. MTBC diversity.…”

Section: Discussionsupporting

confidence: 93%

“…Lineage 2, in the other hand, is typically absent from South America. There has also been previous local-scale studies examining MTBC diversity in Portugal (David et al, 2007) and Southern regions of Brazil [Rio Grande do Sul (Borsuk et al, 2005;Scholante Silva et al, 2009), Parana (Malaghini et al, 2009) and São Paulo (Mendes et al, 2011)]. …”

Section: Introductionmentioning

confidence: 98%

See 1 more Smart Citation

SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil

Lopes

Marques

Soares

et al. 2013

Infection, Genetics and Evolution

View full text Add to dashboard Cite

Abstract:Human tuberculosis is an infectious disease caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Although Spoligotyping and MIRU-VNTR are standard methodology in MTBC genetic epidemiology, recent studies suggest that Single Nucleotide Polymorphisms (SNP) are advantageous in phylogenetics and strain identification. In this work we use a set of 79 SNPs to characterize 1915 MTBC isolates from Portugal and 141 from Northeast Brazil. All Brazilian samples and a subset of 111 Portuguese isolates were further characterized using Spolygotyping. Phylogenetic analysis against a reference set revealed that about 95% of the isolates in both populations were singly attributed to bacterial lineage 4. Within this lineage, the most frequent strain groups in both Portugal and Brazil were LAM, followed by Haarlem and then X. Contrarily to these groups, strain group T showed a very different prevalence between Portugal and Brazil, with a frequency of 7% and less than 1.5%, respectively. Taking the classification by SNPs as the most accurate, we analyze the performance of Spoligotyping in strain identification. The former marker shows about 12% of miss-matches and less than 1% of unidentifiable strains. The miss-matches are observed in the most represented groups of our sample set (i.e., LAM, Haarlem and T) in almost the same proportion. Besides being more accurate in strain identification, SNPs typing can also provide phylogenetic relationships between the strain groups. Indeed, using this molecular markers we were able to observe possible signs of rare recombination events in Mtb.Overall, the use of SNP typing revealed striking similarities between MTBC populations from Portugal and Brazil. In addition this marker suggest that, albeit rare, recombination events in MTBC are likely to occur.

show abstract

“…In general, our observation are in accordance with regional (Borsuk et al, 2005;David et al, 2007) and worldwide (Brudey et al, 2006;Gagneux et al, 2006) earlier studies. MTBC diversity.…”

Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 98%

SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil

Lopes

Marques

Soares

et al. 2013

Infection, Genetics and Evolution

View full text Add to dashboard Cite

show abstract

“…The main spoligotype families in this study, LAM and T (representing 69.4% of the isolates), were also found in the Hospital Fernando Fonseca in Lisbon, Portugal, where the predominance of the LAM family was noted in 51% of the isolates [19]. The preponderance of these M. tuberculosis families in São Paulo city and Lisbon is probably due to the close relationship between Brazil and Portugal, especially between the two cities.…”

Section: Discussionmentioning

confidence: 55%

“…The presence of the Beijing family (SIT1), representing 5.6% of all the identified SITs, may be due to the immigration of Asians to São Paulo city. In Portugal, the Beijing spoligotypes are less frequent (3%) [19]. Within the subfamily T1, we can highlight two isolates of a rare genotype SIT1905.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil

Mendes

Melo²,

Santos

et al. 2011

BMC Res Notes

Self Cite

View full text Add to dashboard Cite

BackgroundTuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis).FindingsSpoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International-types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated.ConclusionsOur data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients.

show abstract

“…They represent as much as 60% of M. tuberculosis strains isolated in Italy (31), 70% of the strains from Sweden (10), and 80% of the strains from France and Portugal (6,11). Thus, the population structure revealed in our study is characteristic of a European country.…”

mentioning

confidence: 57%

Spoligotype-Based Comparative Population Structure Analysis of Multidrug-Resistant and Isoniazid-Monoresistant Mycobacterium tuberculosis Complex Clinical Isolates in Poland

Jagielski¹,

Augustynowicz–Kopeć²,

Zozio

et al. 2010

J Clin Microbiol

View full text Add to dashboard Cite

The spoligotyping-based population structure of multidrug-resistant (MDR) Mycobacterium tuberculosis strains isolated in Poland (n ‫؍‬ 46), representing all culture-positive MDR tuberculosis (MDR-TB) cases, was compared to that of isoniazid (INH)-monoresistant strains (n ‫؍‬ 71) isolated in 2004. The latter data set from a previous study (E. Augustynowicz-Kopeć, T. Jagielski, and Z. Zwolska, J. Clin. Microbiol. 2008, 46:4041-4044) represented 87% of all INH-monoresistant strains. The clustering rates and genotypic-diversity indexes for the 2 subpopulations were not significantly different (P ‫؍‬ 0.05). The results were entered in the SITVIT2 database to assign specific shared type designations, corresponding genotypic lineages, and geographical distributions and compared to available data from neighboring countries (Germany, n ‫؍‬ 704; Czech Republic, n ‫؍‬ 530; Sweden, n ‫؍‬ 379; Kaliningrad, Russia, n ‫؍‬ 90) and strains from previous studies in Poland (n ‫؍‬ 317). MDR strains resulted in 27 patterns (20 unique strains within the study and 7 clusters containing 2 to 6 isolates per cluster with a clustering rate of 56.5%) and belonged to the following genotypic lineages: ill-defined T family (28.3%), Haarlem (17.4%), Latin American and Mediterranean (LAM) (13%), Beijing (8.7%), S family (4.35%), and the X clade (2.17%). Comparison of the genetic structure of the MDR strains with that of INH-monoresistant strains showed that a total of 9 patterns were shared by both groups; these represented 1/3 of the MDR strains and 2/3 of the INH-monoresistant strains. Interestingly, 76.1% of the MDR isolates and 71.8% of the INH-resistant isolates yielded spoligotypes that were previously reported from Poland. The observation that nearly half of the spoligotypes identified among both MDR (48.1%) and INH-monoresistant (43.3%) M. tuberculosis isolates were present in Poland's neighboring countries suggested that a significant proportion of MDR and INH-resistant TB cases in Poland were caused by strains actively circulating in Poland or its neighbors. Our results corroborate the leading role of the T and Haarlem genotypes in the epidemiology of drug-resistant TB in Poland. Nevertheless, the LAM and Beijing family strains that infected, correspondingly, 13% and 9% of patients with MDR-TB were absent among the strains from patients with INHmonoresistant TB, suggesting that a proportion of MDR-TB cases in Poland are due to ongoing transmission of MDR clones exhibiting specific genotypes. Study of the population genetic relationships between MDR and INH-monoresistant strains by drawing minimum spanning trees showed that ill-defined T1 sublineage strains (1/3 of all INH-monoresistant strains), represented by its prototype, SIT53, constituted the central node of the tree, followed by strains belonging to the well-defined H3, H1, and S subgroups. However, the MDR group, in addition, contained LAM (n ‫؍‬ 6) and Beijing (n ‫؍‬ 4) lineage isolates. With the exception of the 4 Beijing lineage strains in the latter group and a single orpha...

show abstract

Contribution of spoligotyping to the characterization of the population structure of Mycobacterium tuberculosis isolates in Portugal

Cited by 18 publications

References 19 publications

SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil

SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil

Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil

Spoligotype-Based Comparative Population Structure Analysis of Multidrug-Resistant and Isoniazid-Monoresistant Mycobacterium tuberculosis Complex Clinical Isolates in Poland

Contact Info

Product

Resources

About