Tuberculosis (TB) remains one of the world deadliest communicable diseases.1Mycobacterium tuberculosis (Mtb) is broadly distributed across all five continents, although relatively few countries account for as much as 80% of all TB cases.1 To date, seven lineages of Mtb complex have been recognized and associated with particular geographical regions.2 There is evidence suggesting that these phylogeographic groups differ in their biological fitness and are best adapted to the sympatric human hosts.3,4

Three major spoligotyping families are most frequently found in Africa, Central America, Europe, and South America: Haarlem, Latin American-Mediterranean (LAM) and T from lineage 4 (which is defined by two deletions in the genome, one comprising the TbD1 region and another at the pks15/1 locus).2,5–7 The East African-Indian (EAI) spoligotyping family from lineage 1 (defined by the region of deletion RD239)2,5–7 is prevalent in Southeast Asia, particularly in the Philippines, Myanmar, Malaysia, Vietnam, Thailand, India, and East Africa, yet is relatively rare in the Americas.7

EAI, a mildly virulent group, possesses a reduced potential for transmissibility.8 Studies performed to characterize Mtb strains in circulation in Latin America have rarely identified EAI, and this family is considered to have limited distribution in comparison with other families in this region.7 Here we report the detection of one case of the EAI family in Salvador, Bahia-Brazil, an area endemic for TB, and we review previous reports of the occurrence of this family in Brazil.

In the survey conducted in Salvador, Bahia, only one case of EAI (0.3%) was identified among the 351 successfully genotyped isolates. This corresponded to a 31-year-old diabetic male presenting characteristic symptoms of TB: cough, hemoptysis, night sweats and weight loss. This patient was interviewed and reported that he had never changed residence, nor traveled outside the metropolitan area. He also reported that, in his adolescence, he had contact with a visiting relative from Italy who exhibited typical TB symptoms. The isolate retrieved from this patient was assigned to the EAI6-BGD1 SIT 702 clade in accordance with the spoligotyping profile observed (Fig. 1B). This unique EAI strain was identified by 15 of the 59 SNPs investigated in our series (Table 1, Fig. 1A). Lopes et al.12 showed that although 10 of these polymorphisms occur in other lineages, the presence of five SNPs: Rv 0629c_0870, Rv 1020_0256, Rv 2362c_0606, Rv 3644c_0726, and Rv 3644c_0735, serves as confirmation of EAI. The RFLP pattern showed 12 bands (Fig. 1C) and was unique in our series (data not published).

Fig. 1.

Genotypic profile of the isolate from Salvador, Bahia, Brazil assigned to the EAI6-BDG1 spoligotyping subfamily (SIT 702). (A) Single Nucleotide Polymorphisms (SNPs). Loci highlighted in blue show polymorphisms uniquely identified in the East African-Indian (EAI) strain as compared to the other 351 genotyped isolates in this series. Loci highlighted in orange show the SNPs that were also distinctive of EAI, according to Lopes et al.12 (B) Spoligotyping pattern. (C) Restriction-fragment length polymorphism (RFLP).

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Our systematic review of the literature regarding EAI occurrence in studies of Mtb diversity performed in Brazil yielded 175 articles, of which 14 were considered eligible for analysis (Fig. 2 and Table 2).14–27 Most of these were either based on bacterial collections maintained in reference laboratories that perform culturing for species identification and phenotypic drug-susceptibility testing,14,16–18,20,21,24,26,27 or on convenience sampling of TB patients at reference health care units responsible for TB diagnosis.15,22,23,25 One report consisted of a case-control study involving drug-sensitive versus drug-resistant TB patients.19

Fig. 2.

PRISMA31 flow diagram describing the systematic literature review performed. aRecords screened were excluded after reading the title and abstract if: (i) the study did not focus on M. tuberculosis; (ii) the isolates were not identified in Brazil; (iii) the strains analyzed were restricted to a non-East African-Indian (EAI) family of M. tuberculosis; (iv) the study did not focus on isolates from humans; (v) the full text was not available via the CAPES Consortium, or access to the article was not provided by Fiocruz. bFull-text articles were not included if: (i) they did not report EAI; (ii) spoligotyping was not performed; (iii) less than 10 isolates were described; (iv) the study analyzed records exclusively from the SITVIT database.

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Table 2.

Literature review summary of East African-Indian (EAI) isolates described in studies of Mycobacterium tuberculosis diversity performed in Brazil.

NA, not available.

aAmbiguous.

bPattern retrieved from the SITVIT WEB based on the SIT informed by the authors.

cAs described by the authors.

dNo match was found in the SITVIT WEB database; the closest matches found in the MIRU-VNTRplus database pertain to the LAM family.

The EAI family is rare in Brazil, occurring typically at frequencies below 2% of the datasets analyzed (Table 2). While EAI family isolates were found in the North,22,24 Northeast,19,22 South,14,16,26 and Southeast of Brazil,15,17,18,20–23,27 the highest circulation of this family was reported in the North (Pará)22 (Table 2). The number of EAI isolates varied from only one to as many as 15 in the studies reviewed (Table 2).

The EAI subfamilies most frequently reported in Brazil were EAI6-BGD1 (especially in Pará,22,24 SIT 129) and EAI5 (SIT 1983) (Fig. 3). Some orphan patterns similar to EAI6-BGD1 were also described in two studies performed in Pará (Fig. 3A). Strains of the EAI5 subfamily SIT 1983 were consistently reported (Table 2 and Fig. 3A).14,20–23 Furthermore, the spoligotyping patterns EAI3-IND SIT 11 and EAI1-SOM SIT 48 were also present in more than one study (Table 2 and Fig. 3A). These spoligotyping patterns are more similar to other EAI reported in the MIRU-VNTRplus database,28,29 while the EAI6-BGD1 isolates described in Pará and Bahia cluster with the Delhi/Central Asian (CAS) spoligotype (Fig. 3B).

Fig. 3.

Neighbor-joining trees depicting similarities between the East African-Indian (EAI) spoligotyping patterns in Brazil retrieved from the systematic review of the literature and the spoligotyping pattern described in Salvador, Bahia. (A) Dendrogram with corresponding binary spoligotyping patterns. (B) Radiation tree including the reference strains from the MIRU-VNTRplus database.

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The low frequency of EAI in Brazil suggests lower transmissibility of this phylogeographic group than what is observed in other Mtb families. Moreover, other authors have argued that immigration has resulted in the steady influx of particular EAI strains, which has been identified throughout Brazil. On the other hand, this broad distribution, taken together with the restricted genetic variability of the EAI isolates identified in the country, may indicate the endemic nature of this family, albeit at a low prevalence.

The most prevalent subfamilies found in Brazil were EAI6-BGD1 and EAI5. Despite the fact that these subfamilies include spoligotype patterns that are common worldwide, the EAI6-BGD1 SIT 702 and the EAI5 SIT 1983 clades described herein have restricted circulation outside Brazil. The SITVIT WEB database contains 21 isolates with the EAI6-BGD1 SIT 702 pattern, three of which are Brazilian samples from an outbreak in Pará.7,22 The remaining specimens were isolated in Cuba, French Guiana (from a patient of Brazilian origin), the United Kingdom, Malawi, Tunisia, and Zambia.7 For SIT 1983, the clade with the widest distribution in Brazil, the SITVIT WEB database contains data only from Brazil and India.7 Moreover, strains of the EAI6-BGD1 family (as well as orphan spoligotyping patterns similar to this subfamily, so far not described in the SITVIT WEB database) were previously reported in an outbreak in Pará,22,24 as well as in our series in Salvador, Bahia, which is indicative of ongoing transmission not restricted to a particular setting. While the EAI6-BGD1 SIT 129 pattern described in Pará has broader worldwide distribution, as isolates from this clade have been previously reported outside Brazil in Germany, the Republic of Congo, Malawi, Zimbabwe, South Africa, Zambia, French Guiana, and the United States,7 it was also identified in the context of the Pará outbreak. Finally, other widely distributed EAI clades, such as EAI3-IND SIT 11 and EAI1-SOM SIT 487 (as well as highly similar orphan patterns) were exclusively found in studies performed in southeastern Brazil. Taken together, these findings suggest that some specific clades of EAI may be better adapted to particular Brazilian populations.

Interestingly, EAI6-BGD1 and similar orphan spoligotyping patterns described in Salvador-Bahia and in the state of Pará, as well as the isolates obtained from the outbreak that occurred in this state, cluster with some strains of lineage 3 (defined by the combined deletion of the genomic regions TbD1 and RD750, including the Delhi/Central Asian (CAS) spoligotyping family2,5–7). Lineage 3 belongs to a group of modern Mtb lineages considered to be more virulent than EAI.2,5–7 Nonetheless, this finding should be interpreted with caution, due to the limited capacity of spoligotyping to accurately distinguish among monophyletic groupings of Mtb.30

In spite of the low detected prevalence, EAI may in fact be endemic in Brazil. The restricted worldwide distribution of some spoligotyping patterns described in multiple studies conducted in Brazil, together with the genetic relatedness found among isolates from different parts of the country and the occurrence of an outbreak in Pará, seem to suggest the increased fitness exhibited by some clades with respect to our population.

Conselho Nacional de Desenvolvimento Científico e Tecnológico (Edital MCT-CNPq/MS-SCTIE-DECIT – N° 25/2006).

The authors declare no conflicts of interest.