Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.

Restriction fragment length polymorphism (RFLP) analysis of 209Mycobacterium tuberculosis clinical isolates obtained from newly detected pulmonary tuberculosis patients (151 male and 58 female; mean age, 41 years) in Estonia during 1994 showed that 61 isolates (29%) belonged to a genetically closely related group of isolates, family A, with a predominant IS6110 banding pattern. These strains shared the majority of their IS6110 DNA-containing restriction fragments, representing a predominant banding pattern (similarity, >65%). This family A comprised 12 clusters of identical isolates, and the largest cluster comprised 10 strains. The majority (87.5%) of all multidrug-resistant (MDR) isolates, 67.2% of all isolates with any drug resistance, but only 12% of the fully susceptible isolates of M. tuberculosis belonged to family A. These strains were confirmed by spoligotyping as members of the Beijing genotype family. The spread of Beijing genotype MDR M. tuberculosis strains was also frequently seen in 1997 to 1999. The members of this homogenous group of drug-resistant M. tuberculosis strains have contributed substantially to the continual emergence of drugresistant tuberculosis all over Estonia.An increase in tuberculosis (TB) morbidity accompanied by an appearance of multidrug-resistant (MDR) TB has been documented in Estonia since the early 1990s. After a decline in incidence from 417 per 100,000 population in 1953 to 26 per 100,000 in 1992, the incidence showed a steady increase, which reached 52 per 100,000 in 1999 (26). This twofold increase in morbidity was accompanied by an increase in drug-resistant TB and particularly in MDR TB (i.e., TB that is resistant to at least isoniazid and rifampin) and has become a serious problem in Estonia. In 1994 and 1998, MDR TB comprised 10% (13) and 14% (25) of the new pulmonary cases detected. This places Estonia among the countries with the highest MDR TB rates in the world (24).To understand the epidemiology of tuberculosis, molecular methods such as restriction fragment length polymorphism (RFLP) analyses of the infecting organisms have proven to be very powerful tools (11,20,27). The RFLP method can detect genotypic variations between strains by using repetitive DNA sequences as probes in Southern hybridization analyses (12).In outbreak investigations (1, 14, 16), mutual association of IS6110 RFLP patterns and resistance profiles has often been described. However, in population-based studies, the molecular epidemiology and drug resistance pattern of the M. tuberculosis isolates (constituting a genetically closely related group of bacteria) have been studied only in very few geographical settings (23).In the epidemiology of drug-resistant disease, molecular epidemiological studies of resistant strains could help identify current and past failures in TB control and allow tracking of the transfer path of the resistant strains (6). In this study we explore the spread of M. tuberculosis strains in Estonia by molecular epidemiological methods and demonstrate that transmissio...

We have identified a globally important clonal complex of M. bovis by deletion analysis of over one thousand strains from over 30 countries. We initially show that over 99% of the strains of Mycobacterium bovis, the cause of bovine tuberculosis, isolated from cattle in the Republic of Ireland and the UK are closely related and are members of a single clonal complex marked by the deletion of chromosomal region RDEu,1 and we named this clonal complex European 1 (Eu1). Eu1 strains were present at less than

ABSTRACT:Tuberculosis has been diagnosed in wild boar (Sus scrofa) in several European countries during the last decade; however, almost no information has been reported to date for Portugal. This study aimed to investigate tuberculosis in wild boar in Portugal through characterization of Mycobacterium bovis infection and identification of disease risk factors. Tissue samples were obtained from hunted wild boar during the 2005 and 2006 hunting seasons. Samples were inspected for gross lesions and processed for culture. Acid-fast bacterial isolates were identified by polymerase chain reaction and spoligotyping. Associations between tuberculosis in wild boar and several variables linked to wild ungulate diversity and relative abundance, livestock density, and cattle tuberculosis incidence were investigated. Mycobacterium bovis isolates were identified in 18 of 162 wild boars from three of eight study areas. Infection rates ranged from 6% (95% confidence interval [CI P95% ]51-21%) to 46% (CI P95% 527-67%) in the three infected study areas; females in our sample were at greater risk of being infected than males (odds ratio54.33; CI P95% 53.31-5.68). Spoligotyping grouped the M. bovis isolates in three clusters and one isolate was a novel spoligotype not previously reported in international databases. Detection of M. bovis was most consistently associated with variables linked to wild ungulate relative abundance, suggesting that these species, particularly the wild boar, might act as maintenance hosts in Portugal.

1997 (11, 45). This rise was largely due to a 20% increase in the incidence of TB in African countries that are heavily affected by the human immunodeficiency virus (HIV) infection and AIDS epidemic (45). HIVinfected persons have an increased risk of developing clinical TB (20). This risk was previously attributed mainly to an increased risk of reactivation of a latent infection (15, 34). DNA fingerprinting of the Mycobacterium tuberculosis genome has been used extensively to explore the dynamics of TB transmission (5, 40). In general, the simultaneous accumulation of mycobacterial isolates with identical fingerprints, i.e., clusters, has been attributed to recent infection, whereas isolates with unique fingerprints are most commonly associated with endogenous reactivation (23,40). Studies from industrialized countries in which DNA fingerprinting of insertion element IS6110 of the M. tuberculosis genome has been used (37) have shown that nearly two-thirds of M. tuberculosis isolates from HIVinfected patients appear in clusters, suggesting recent infection (2, 36). Further support for this suggestion is provided by DNA fingerprinting of nosocomial TB outbreaks, including transmission of multidrug-resistant strains (6,7,12). These studies have demonstrated rapid progression to clinical disease in immunosuppressed HIV-infected individuals.In population-based studies from sub-Saharan Africa, where the rate of M. tuberculosis transmission is very high, the proportion of clustered M. tuberculosis isolates from patients with smear-positive TB has varied from 38 to 47% (18, 28, 29, 44). The proportion of isolates appearing in clusters was even higher (67%) for isolates from male patients in a gold-mining community in South Africa with a particularly high incidence of TB (16). In those studies, however, isolates appearing in clusters were equally distributed among HIV-positive and HIV-negative TB patients.During the 1990s Ethiopia experienced a severe HIV epidemic, with the prevalence of pregnant women in Addis Ababa infected with HIV rising from 6% in 1989 to 18% in 1997 (13). A TB epidemic has coincided with this development, and in 1999, Ethiopia was ranked number 8 among the 23 countries with the highest total TB burden (45). In 1997, about 30% of all new TB cases were believed to occur in HIV-positive individuals (11). In areas such as Ethiopia where HIV infection is highly endemic, the relative importance of reactivation and recent infection is not known. Information in this field may

Background: The poor peri-urban areas of developing countries with inadequate living conditions and a high prevalence of HIV infection have been implicated in the increase of tuberculosis (TB). Presence of different lineages of Mycobacterium tuberculosis has been described in different parts of the world. This study determined the predominant strain lineages that cause TB in Rubaga division, Kampala, Uganda, and the prevalence of resistance to key anti-tuberculosis drugs in this community.

The Guinea-Bissau family of strains is a unique group of the Mycobacterium tuberculosis complex that, although genotypically closely related, phenotypically demonstrates considerable heterogeneity. We have investigated 414 M. tuberculosis complex strains collected in Guinea-Bissau between 1989 and 2008 in order to further characterize the Guinea-Bissau family of strains. To determine the strain lineages present in the study sample, binary outcomes of spoligotyping were compared with spoligotypes existing in the international database SITVIT2. The major circulating M. tuberculosis clades ranked in the following order: AFRI (n = 195, 47.10%), Latin-American-Mediterranean (LAM) (n = 75, 18.12%), ill-defined T clade (n = 53, 12.8%), Haarlem (n = 37, 8.85%), East-African-Indian (EAI) (n = 25, 6.04%), Unknown (n = 12, 2.87%), Beijing (n = 7, 1.68%), X clade (n = 4, 0.96%), Manu (n = 4, 0.97%), CAS (n = 2, 0.48%). Two strains of the LAM clade isolated in 2007 belonged to the Cameroon family (SIT61). All AFRI isolates except one belonged to the Guinea-Bissau family, i.e. they have an AFRI_1 spoligotype pattern, they have a distinct RFLP pattern with low numbers of IS6110 insertions, and they lack the regions of difference RD7, RD8, RD9 and RD10, RD701 and RD702. This profile classifies the Guinea-Bissau family, irrespective of phenotypic biovar, as part of the M. africanum West African 2 lineage, or the AFRI_1 sublineage according to the spoligtyping nomenclature. Guinea-Bissau family strains display a variation of biochemical traits classically used to differentiate M. tuberculosis from M. bovis. Yet, the differential expression of these biochemical traits was not related to any genes so far investigated (narGHJI and pncA). Guinea-Bissau has the highest prevalence of M. africanum recorded in the African continent, and the Guinea-Bissau family shows a high phylogeographical specificity for Western Africa, with Guinea-Bissau being the epicenter. Trends over time however indicate that this family of strains is waning in most parts of Western Africa, including Guinea-Bissau (p = 0.048).

BackgroundMozambique is one of the countries with the highest burden of tuberculosis (TB) in Sub-Saharan Africa, and information on the predominant genotypes of Mycobacterium tuberculosis circulating in the country are important to better understand the epidemic. This study determined the predominant strain lineages that cause TB in Mozambique.ResultsA total of 445 M. tuberculosis isolates from seven different provinces of Mozambique were characterized by spoligotyping and resulting profiles were compared with the international spoligotyping database SITVIT2.The four most predominant lineages observed were: the Latin-American Mediterranean (LAM, n = 165 or 37%); the East African-Indian (EAI, n = 132 or 29.7%); an evolutionary recent but yet ill-defined T clade, (n = 52 or 11.6%); and the globally-emerging Beijing clone, (n = 31 or 7%). A high spoligotype diversity was found for the EAI, LAM and T lineages.ConclusionsThe TB epidemic in Mozambique is caused by a wide diversity of spoligotypes with predominance of LAM, EAI, T and Beijing lineages.