Molecular characterization and drug resistance patterns of strains of Mycobacterium tuberculosis isolated from patients in an AIDS counseling center in Port-au-Prince, Haiti: a 1-year study

Prevalence of multidrug-resistant tuberculosis in Latin America and the Caribbean: a systematic review and meta-analysis

OBJECTIVES

To evaluate the prevalence of multidrug-resistant tuberculosis (MDR-TB) in individuals living in Latin America and the Caribbean (LAC).

METHODS

We searched the MEDLINE, Embase and Literatura Latino Americana e do Caribe em Ciências da Saúde (Lilacs) databases until 08 August 2019 for all studies on the subject, without time or language restrictions. Original studies reporting the prevalence of infection with Mycobacterium tuberculosis resistant to isoniazid and rifampicin simultaneously (MDR) in LAC, the prevalence of resistance in cases with no previous treatment (new cases) and the prevalence of resistance in previously treated cases were selected. Considering the expected heterogeneity between studies, all analyses were performed using the random effects model, and heterogeneity was assessed using the I² statistic.

RESULTS

We included 91 studies from 16 countries. The estimated overall prevalence was 13.0% (95% CI 12.0-14.0%), and the heterogeneity between studies was substantial (I²  = 96.1%). In the subgroup analyses, it was observed that the prevalence of MDR-TB among new cases was 7.0% (95% CI 6.0-7.0%) and in previously treated cases was 26.0% (95% CI 24.0-28.0%).

CONCLUSIONS

This review highlights multidrug resistance to antituberculosis drugs in LAC, indicating that prevention strategies have not been effective. Government institutions should invest heavily in strategies for early diagnosis and the rapid availability of effective treatments and prioritise adequate protection for health professionals. In addition, screening programmes should be adopted to prevent secondary cases.

Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean

Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.

Spatiotemporal Clustering of Mycobacterium tuberculosis Complex Genotypes in Florida: Genetic Diversity Segregated by Country of Birth

Background

Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB control efforts.

Methods

We investigated the genetic diversity and spatiotemporal clustering of 2,510 MTBC strains isolated in Florida, United States, between 2009 and 2013 and genotyped using spoligotyping and 24-locus MIRU-VNTR. We mapped the genetic diversity to the centroid of patient residential zip codes using a geographic information system (GIS). We assessed transmission dynamics and the influence of immigration on genotype clustering using space-time permutation models adjusted for foreign-born population density and county-level HIV risk and multinomial models stratified by country of birth and timing of immigration in SaTScan.

Principal Findings

Among the 2,510 strains, 1,245 were reported among foreign-born persons; including 408 recent immigrants (<5 years). Strain allelic diversity (h) ranged from low to medium in most locations and was most diverse in urban centers where foreign-born population density was also high. Overall, 21.5% of cases among U.S.-born persons and 4.6% among foreign-born persons clustered genotypically and spatiotemporally and involved strains of the Haarlem family. One Haarlem space-time cluster identified in the mostly rural northern region of Florida included US/Canada-born individuals incarcerated at the time of diagnosis; two clusters in the mostly urban southern region of Florida were composed predominantly of foreign-born persons. Both groups had HIV prevalence above twenty percent.

Conclusions/Significance

Almost five percent of TB cases reported in Florida during 2009–2013 were potentially due to recent transmission. Improvements to TB screening practices among the prison population and recent immigrants are likely to impact TB control. Due to the monomorphic nature of available markers, whole genome sequencing is needed to conclusively delineate recent transmission events between U.S. and foreign-born persons.

High-throughput mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping for Mycobacterium tuberculosis epidemiological studies

The emergence of drug-resistant forms of tuberculosis (TB) represents a major public health concern. Understanding the transmission routes of the disease is a key factor for its control and for the implementation of efficient interventions. Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) marker typing is a well-described method for lineage identification and transmission tracking. However, the conventional manual genotyping technique is cumbersome and time-consuming and entails many risks for errors, thus hindering its implementation and dissemination. We describe here a new approach using the QIAxcel system, an automated high-throughput capillary electrophoresis system that also carries out allele calling. This automated method was assessed on 1,824 amplicons from 82 TB isolates and tested with sets of markers of 15 or 24 loci. Overall allele-calling concordance between the methods from 140 to 1,317 bp was 98.9%. DNA concentrations and repeatability and reproducibility performances showed no biases in allele calling. Furthermore, turnaround time using this automated system was reduced by 81% compared to the conventional manual agarose gel method. In sum, this new automated method facilitates MIRU-VNTR genotyping and provides reliable results. Therefore, it is well suited for field genotyping. The implementation of this method will help to achieve accurate and cost-effective epidemiological studies, especially in countries with a high prevalence of TB, where the high number of strains complicates the surveillance of circulating lineages and requires efficient interventions to be carried out in an urgent manner.

Incidence and transmission patterns of tuberculosis among indigenous populations in Brazil

Approximately 10% of the Brazilian indigenous population lives in the state of Mato Grosso do Sul (MS), where a large number of new cases of tuberculosis (TB) are reported. This study was conducted to assess TB occurrence, transmission and the utility of TB diagnosis based on the Ogawa-Kudoh (O-K) culture method in this remote population. The incidence of TB was estimated by a retrospective review of the surveillance data maintained by the Notifiable Diseases Surveillance System for the study region. The TB transmission pattern among indigenous people was assessed by genotyping Mycobacterium tuberculosis isolates using the IS 6110 restriction fragment length polymorphism (RFLP) technique. Of the 3,093 cases identified from 1999-2001, 610 (~20%) were indigenous patients (average incidence: 377/100,000/year). The use of the O-K culture method increased the number of diagnosed cases by 34.1%. Of the genotyped isolates from 52 indigenous patients, 33 (63.5%) belonged to cluster RFLP patterns, indicating recently transmitted TB. These results demonstrate high, on-going TB transmission rates among the indigenous people of MS and indicate that new efforts are needed to disrupt these current transmissions.

Use of Luminex MagPlex magnetic microspheres for high-throughput spoligotyping of Mycobacterium tuberculosis isolates in Port-au-Prince, Haiti

Genotyping of Mycobacterium tuberculosis strains became indispensable for understanding tuberculosis transmission dynamics and designing measures to combat the disease. Unfortunately, typing involves sophisticated laboratory analysis, is expensive, and requires a high level of technical expertise, which limited its use in the resource-poor countries where the majority of tuberculosis cases occur. Spoligotyping is a PCR-based M. tuberculosis complex genotyping method with advantages of technical simplicity, numerical output, and high reproducibility. It is based on the presence or absence of 43 distinct "spacers" separating insertion elements in the direct repeat region of the M. tuberculosis genome. The spoligotyping assay involves reverse hybridization of PCR products to the capture spacers attached to nitrocellulose membranes or to microspheres. Here we report modification of the classic 43-spacer method using the new generation of Luminex multiplexing technology with magnetic microspheres. The method was successfully established and validated on strains with known spoligotypes in our laboratory in Haiti. The distribution of spoligotypes determined in a collection of 758 recent M. tuberculosis isolates was in accordance with previous data for Haitian isolates in the SITWITWEB international database, which were obtained with the traditional membrane-based method. In the present form, spoligotyping may be suitable as a high-throughput, first-line tool for genotyping of Mycobacterium tuberculosis in countries with limited resources.

Phospholipase C in Beijing strains of Mycobacterium tuberculosis

BACKGROUND AND OBJECTIVES

Phospholipase of Mycobacterium tuberculosis plays an important role in pathogenesis through breaking up phospholipids and production of diacylglycerol. In this study, we examined the Beijing strains of Mycobacterium tuberculosis isolated from Iranian patients for the genes encoding this enzyme.

MATERIALS AND METHODS

DNA extraction was performed using CTAB (cetyltrimethylammonium bromide) from positive culture specimens in tuberculosis patients. PCR was then used to amplify the plcA, plcB, plcC genes of Beijing strain, and non-Beijing strains were identified by spoligotyping.

RESULTS

Of 200 specimens, 19 (9.5%) were Beijing strain and 181 (90.5%) were non-Beijing strains. The results of PCR for Beijing strains were as follows: 16 strains (84.2%) were positive for plcA, 17 (89.4%) were positive for plcB and 17 (89.4%) were positive for plcC genes. The standard strain (H37RV) was used as control.

CONCLUSION

The majority of Beijing strains have phospholipase C genes which can contribute to their pathogenesis but we need complementary studies to confirm the role of phospholipase C in pathogenecity of Mycobacterium tuberculosis.

Characterization of Mycobacterium tuberculosis complex isolated from iranian and afghani patients by spoligotyping method

Designing newer drugs, vaccines, and diagnostic techniques is dependent on better understanding of M. tuberculosis virulence mechanism. In this study the prevalence of pcaA gene was determined in M. tuberculosis strains typed by spoligotyping. The associated risk factors among patients with different nationalities residing in Iran were also determined. The isolated M. tuberculosis strains have been characterized by performing susceptibility tests against four first-line antituberculosis drugs and were then subjected to spoligotyping characterization. PCR was used for detection of pcaA gene and its nucleotide sequence was also determined. Spoligotyping of M. tuberculosis strains resulted in 140 different patterns. One hundred twenty two (87.1%) of these spoligotype isolates were unique and reported for the first time. The remaining18 (12.8%) spoligotype patterns were previously reported from other geographical regions of the world. Haarlem family was most prevalent than other genotype. Antibiotic resistances were higher in those isolated from the Iranian patients. The pcaA gene was detected in M. tuberculosis clinical isolates but not in saprophyte strains such as M. kansasi. The results showed that, spread of M. tuberculosis strains belonging to the Beijing family among Iranian patients has to be considered seriously. This study confirmed the widespread existence of pcaA gene in almost all the clinical isolates. It is also important to undertake studies to identify which factors are the most significant to consider in tuberculosis control program.

First insight into Mycobacterium tuberculosis epidemiology and genetic diversity in Trinidad and Tobago

This report is based on a 1-year recruitment of all of the culture-positive Mycobacterium tuberculosis cases in Trinidad and Tobago (n = 132). The study population was characterized by a high male-to-female sex ratio of 4 and a human immunodeficiency virus-tuberculosis (TB) coinfection rate of 30%. It mainly occurred among African descendants, who represent 37.5% of the total population but 69.7% of all TB cases (P < 0.001). Spoligotyping resulted in 25 different patterns and 12 clusters (2 to 74 strains per cluster), with the predominance of a highly conserved spoligotype international type clone, SIT566.

Epidemiology and treatment of multidrug resistant tuberculosis

Multidrug resistant tuberculosis is now thought to afflict between 1 and 2 million patients annually. Although significant regional variability in the distribution of disease has been recorded, surveillance data are limited by several factors. The true burden of disease is likely underestimated. Nevertheless, the estimated burden is substantial enough to warrant concerted action. A range of approaches is possible, but all appropriate interventions require scale-up of laboratories and early treatment with regimens containing a sufficient number of second-line drugs. Ambulatory treatment for most patients, and improved infection control, can facilitate scale-up with decreased risk of nosocomial transmission. Several obstacles have been considered to preclude worldwide scale-up of treatment, mostly attributable to inadequate human, drug, and financial resources. Further delays in scale-up, however, risk continued generation and transmission of resistant tuberculosis, as well as associated morbidity and mortality.

Typing of Mycobacterium tuberculosis strains isolated in Community Health Centers of Rio de Janeiro City, Brazil

Fingerprinting of Mycobacterium tuberculosis strains from tuberculosis (TB) patients attended in Community Health Centers (CHCs) of Rio de Janeiro was performed to verify possible risk factors for TB transmission. A prospective community-based study was performed during the period of July 1996 to December 1996 by collecting sputum samples of 489 patients in 11 different CHCs in four different planning areas (APs) of the city. Bacteriological, clinical, and epidemiological information was collected and M. tuberculosis genotypes defined after restriction fragment length polymorphism (IS6110-RFLP) and double repetitive element (DRE) fingerprinting of RFLP-clustered cases. Risk factors for TB transmission were looked for using three levels of cluster stringency. Among 349 (71%) positive cultures obtained, IS6110-RFLP typing could be performed on strains from 153 different patients. When using identity of RFLP patterns as cluster definition, 49 (32%) of the strains belonged to a cluster and none of the clinical or epidemiologic characteristics was associated with higher clustering levels. However, higher clustering level was observed in the AP including the central region of the city when compared to others. This strongly suggests that more recent transmission occurs in that area and this may be related with higher incidence of TB and HIV in this region.

Evaluation and genotyping of multidrug-resistant cases of tuberculosis in southern Brazil

Sixty isolates of Mycobacterium tuberculosis identified as multidrug-resistant (MDR) at a reference laboratory in Rio Grande do Sul State during the years 1999 and 2000 were analyzed using the IS6110-restriction fragment length polymorphism (RFLP) technique. We also genotyped 202 susceptible strains to compare the genotyping results, as well as the clinical and demographic data. Spacer oligotyping (spoligotyping) analysis was performed for isolates presenting low IS6110 copy number. Patients with identical DNA pattern strains were considered clustered. From 262 isolates, 94 (36%) belonged to 20 distinct RFLP clusters, and after spoligotyping analysis, 89 of the isolates (34%) remained in cluster. MDR isolates did not differ statistically in clustering proportion from susceptible strains. A significant association between the occurrence of MDR and previous tuberculosis (TB) treatment was observed (p < 0.001), as well as failure on TB treatment (p < 0.001). Human immunodeficiency virus (HIV)-positive patients were associated with susceptible tuberculosis (p = 0.024). We also identified that unmarried patients were more likely to develop TB due to recent transmission than married patients (p < 0.005). The introduction of directly observed therapy short-course (DOTS) strategy will be important in decreasing default and failure rates and avoiding the development of new MDR strains.

Long-term population-based genotyping study of Mycobacterium tuberculosis complex isolates in the French departments of the Americas

The three French overseas departments of the Americas are characterized both by insular (Guadeloupe and Martinique) and continental (French Guiana) settings with a tuberculosis case detection rate that varies from less than 10 per 100,000 per year in insular areas to an estimated incidence of more than 55 per 100,000 in French Guiana. Under a long-term genotyping program, more than three-fourths of all the Mycobacterium tuberculosis isolates (n = 744) received from the three settings were fingerprinted over a 10-year period (1994 to 2003) by spoligotyping and variable number of tandem DNA repeats (VNTRs) in order to understand the current trends in their detection rates, drug resistance, and groups and subpopulations at risk of contracting the disease and to pinpoint the circulating phylogeographical clades of the bacilli. The major difference in the study populations was the nationality of the patients, with a high percentage of immigrants from high-incidence neighboring countries in French Guiana and a low but increasing percentage in the French Caribbean. The rate of recent transmission was calculated to be 49.3% in French Guiana, compared to 27.2% and 16.9% in Guadeloupe and Martinique, respectively. At the phylogeographic level, 77.9% of the isolates studied belonged to four major clades (Haarlem, Latin-American and Mediterranean, T, and X) which are already reported from neighboring Caribbean islands in an international database and may underline potential interregional transmission events.

Épidémiologie moléculaire de la tuberculose en Guadeloupe de 1994 à 2000

In Guadeloupe, the incidence of tuberculosis decreased between 1994 and 2000. The rate of resistance to at least one antibiotic remained constant at 11%, whereas the rate of multiple-drug resistance increased from 0.9 to 2.4% in 2000. The proportion of patients of foreign origin (mainly from Haiti and the Dominican Republic) increased whereas the number of French patients decreased. These results show that the epidemiology of tuberculosis in Guadeloupe is similar to industrialized countries as older people, foreigners from countries where TB is endemic, and HIV+ patients are at a higher risk to declare tuberculosis disease. Molecular typing realized by spoligotyping showed the importance of previous successive colonizations and migrations as characterized by the presence of major phylogenetic families originating essentially from Northern Europe (Haarlem), Latin America and Mediterranean (LAM) and from Anglo-Saxon countries (X). The sub-typing of clustered strains by IS6110-RFLP and by a PCR method based on the variable number of tandem DNA repeats (VNTR), highlighted 29 clusters, corresponding to 44.8% of clustered strains, and allowed to estimate the rate of recent transmission at 32.2%. The epidemiologic data associated with fingerprinting results underlined the importance of reactivation cases among older people, a significant number of imported TB cases without evident links, and casual contacts.

Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains

In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.

Comparison between spoligotyping and IS6110 restriction fragment length polymorphisms in molecular genotyping analysis of Mycobacterium tuberculosis strains

Spoligotyping was compared with RFLP fingerprinting analysis in the identification of Mycobacterium tuberculosis strains. Spoligotyping sensitivity was 97.6% with a specificity of 47%. The global probability for two strains clustered with spoligotyping to be clustered also with RFLP analysis was 33%; the probability for two strains clustered with RFLP analysis to be clustered also with spoligotyping analysis was 95%. However, comparing the two methods in five outbreak episodes, full concordance was evidenced between spoligotyping and RFLP. Moreover, we evaluated the presence of our 17 largest spoligotyping clusters in spoligotyping databases from Caribbean countries, London and Cuba. Only five out of 17 patterns were present in all the cohorts. The conditional probability comparing spoligotyping and RFLP methods related to these patterns resulted in very low concordance (range from 2 to 38%). In conclusion, we confirm that spoligotyping when used alone overestimates the number of recent transmission and does not represent a suitable method for wide clinical practice application. However, it allows to get a first good picture of strain identity in a new setting and in more localized or confined settings, the probability of reaching the same result compared to RFLP was 100% confirming the usefulness of spoligotyping in the management of epidemic events, especially in hospitals, prisons and close communities.

Molecular characterization of Mycobacterium tuberculosis isolates in a region of Brazil with a high incidence of tuberculosis

One hundred and seventy Mycobacterium tuberculosis clinical isolates were characterized by spoligotyping to evaluate the biodiversity of tubercle bacilli in a region of Brazil with a high incidence of tuberculosis (Pelotas and Rio Grande cities - Rio Grande do Sul State). The spoligotyping results were compared to the World Spoligotyping Database (Institut Pasteur de Guadeloupe), which contains data from >14,000 worldwide isolates of M. tuberculosis. The isolates clustered by spoligotyping were further characterized by IS6110-RFLP to confirm the clonal relationship. Sixty-six different spoligotypes were identified, grouping 125 of the isolates (74%). Approximately half of the isolates belonged to seven of the most frequently occurring spoligotypes in the database. Three shared types (with two or more isolates) not previously identified were given the type numbers 826, 827 and 863. An additional 45 spoligotypes were identified that did not match any existing database pattern. RFLP characterization reduced the number of isolates in most of the clusters, thereby showing a higher differentiation capacity than spoligotyping. These results highlight the importance of molecular epidemiology studies of tuberculosis in insufficiently studied regions with a high TB burden, in order to uncover the true extent of genetic diversity of the pathogen.

Recent tuberculosis advances in Latin America

PURPOSE OF REVIEW

Tuberculosis kills more people than any other infection. Despite advances in diagnostic methods and greater understanding of the reasons for treatment failure, tuberculosis remains common throughout Latin America.

RECENT FINDINGS

The impact of HIV and multidrug resistance on tuberculosis control has been enormous. HIV-positive patients may be at 10 times greater risk of multidrug resistant tuberculosis than HIV-negative patients. Hopefully, improved diagnostic techniques will allow more rapid diagnosis of tuberculosis and new colorimetric systems are being developed that will enable expedited drug-sensitivity testing. However, in alarming reports, only 58% of patients were treated with the recommended treatment regime in a Brazilian study, and dropout from treatment in parts of Bolivia was common. Many failings could be combated by rigorous education of patients and physicians. In an encouraging advance, multidrug resistant tuberculosis was successfully treated in a community-based programme, saving an estimated 90% of the cost of hospital-based treatment. An opportunity to identify treatment failure earlier is demonstrated by the finding that 2 months after the initiation of therapy, positive smears were found in only 3% of those whose treatment was successful, but 74% of those whose treatment failed.

SUMMARY

The importance of inexpensive and widely available drugs to treat HIV and multidrug resistant tuberculosis in Latin America is clear. The need for rapid, affordable tests for tuberculosis diagnosis, and for easy drug sensitivity testing is also evident. Finally, improving treatment success is achievable even in the resource poor setting.

Diagnosis and management of isolated pancreatic tuberculosis: recent experience and literature review

The increased reporting of tuberculosis of the pancreas is related to a worldwide increase in tuberculosis and an increase in emigration from countries where tuberculosis is endemic into countries where more sophisticated healthcare and radiological imaging are available. Three recent cases of pancreatic tuberculosis in Auckland, New Zealand, emphasize that tuberculosis should now be included in the differential diagnosis of a pancreatic mass. Diagnostic indicators include emigration from, or recent travel to, a country where tuberculosis is endemic, the association of a pancreatic mass with fever, the presence of abdominal pain and a cystic pancreatic mass in a younger male. Radiological appearances might be similar to a mucinous cystic neoplasm or could show a pancreatic mass with involvement of peripancreatic lymph nodes or a mass centred in a peripancreatic lymph node. When the diagnosis is suspected an human immunodeficiency virus test and a comprehensive screening for tuberculosis at other sites should be performed. If tuberculosis is unable to be diagnosed then pancreatic biopsy and culture is indicated. Endoscopic ultrasound with fine needle aspiration for cytology is likely to become the preferred technique. Most patients have an excellent clinical response to standard antituberculosis regimens.

Phylogenetic reconstruction of Mycobacterium tuberculosis within four settings of the Caribbean region: tree comparative analyse and first appraisal on their phylogeography

In order to compare phylogenetic methods and to reconstruct the evolutionary history of the tubercle bacilli, a set of macro-array-based genotyping data of Mycobacterium tuberculosis clinical isolates (called spoligotyping for spacer oligonucleotide typing, which assays the variability of the Direct Repeat -DR- locus), was analyzed in four settings of the Caribbean region (Guadeloupe, Martinique, Cuba and Haiti). A set of 47 alleles, split into 26 shared and 21 unique alleles) representative of 321 individual M. tuberculosis clinical isolates from patients residing in the above regions was studied. The following methods (and software in brackets) were investigated: numerical taxonomy distance methods (TAXOTRON), maximum parsimony procedure (PAUP), median-joining networks (NETWORK), and nested clade analysis (GEODIS). Results using these methods were analyzed, compared and discussed. The latter method (GEODIS) was investigated in detail by introducing geographical data together with genetic variability results to detect a link between population structure and population history, and to test the null hypothesis of no association between geography and genotypes. Irrespective of the methods used, our findings demonstrate that a core structure of four families (or clades) of M. tuberculosis strains is highly prevalent within the islands studied, indirectly reflecting passed colonization history of these different settings. Specificity of M. tuberculosis genotypes in each of the islands is discussed in the light of their respective colonial and contemporary histories.