Exploring the “Latin American Mediterranean” family and the RDRio lineage in Mycobacterium tuberculosis isolates from Paraguay, Argentina and Venezuela

Abstract

Background The Latin American & Mediterranean (LAM) spoligotype family is one of the most successful genotype of Mycobacterium tuberculosis worldwide and particularly prevalent in South-America. Within this family, a sublineage named Region of Difference Rio (RD Rio ) was reported initially in Brazil and is characterized by a genomic deletion of about 26.3 kb. This lineage seems to show a specific adaptation to the Euro-Latin American population. In this context, we sought to evaluate the LAM family and the presence of the RD Rio genotype in samples from three Latin American countries including Paraguay, Venezuela and Argentina. To detect LAM strains reliably we applied a typing scheme using spoligotyping, 12 loci MIRU-VNTR, the Ag85C 103 SNP and the regions of difference RD Rio and RD174. IS6110-RFLP results were also used when available. Results Genotyping of 413 M. tuberculosis isolates from three Latin-American countries detected LAM (46%) and the ill-defined T clade (16%) as the most frequent families. The highest clustering rate was detected in the sample population from the city of Caracas in Venezuela. We observed considerable differences in the presence of the RD Rio lineage, with high frequency in Caracas-Venezuela (55%) and low frequency in Buenos Aires-Argentina (11%) and Paraguay (10%). The molecular markers (RD174, Ag85C 103 , MIRU02-MIRU40 signature) of the RD Rio lineage were essentially confirmed. For the LAM family, the most polymorphic loci were MIRU40, MIRU31, MIRU10, MIRU26, MIRU16 and the least polymorphic MIRU24, MIRU20, MIRU04, MIRU23. Conclusions Our results suggest a differential adaptation of LAM-sublineages in neighboring populations and that RD Rio strains spread regionally with different rates of distribution. The Ag85C SNP and RDs (RD174, RD Rio ) tested in this study can in fact facilitate molecular epidemiological studies of LAM strains in endemic settings and low-income countries. Electronic supplementary material The online version of this article (10.1186/s12866-019-1479-6) contains supplementary material, which is available to authorized users.

Whole genome analysis of extensively drug resistant Mycobacterium tuberculosis strains in Peru

“…Our results establish that the LAM family was dominant among the Peruvian XDR-TB strains analysed, which is consistent with that evidenced in neighbouring South American countries 67 – 72 . However, it disagrees with a previous study also carried out on Peruvian XDR-TB strains in which it was established that the dominant family was Haarlem 12 .…”

Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era: a literature review

“…bovis (n = 5); 76 , 77 , 78 , 79 , 80 no data on genotyping were available (n = 6); 49 , 66 , 81 , 82 , 83 , 84 incomplete information on genetic diversity (n = 3) 85 , 86 , 87 or genotyping data is mixed with samples from other countries (n = 3). 84 , 88 , 89 …”

“…Regarding manuscripts on RFLP-IS 6110 , we excluded those with data on M. bovis only (n = 4); 90 , 91 , 92 , 93 without visible on genotyping (n = 8) 33 , 94 , 95 , 96 did not present data regarding genetic diversity (n = 9); 24 , 97 , 98 , 99 , 100 , 101 , 102 , 103 were related to nontuberculous mycobacteria (NTM) (n = 4); 104 , 105 , 106 , 107 were performed in other countries (n = 5); 88 , 108 , 109 , 110 , 111 did not target IS 6110 for RFLP (n = 7) 112 - 118 or were data presented as part of a thesis manuscript and had not been peer reviewed (n = 4).…”

Distribution of Mycobacterium tuberculosis lineages in South America

“…This dispersion is how the LAM sublineage appears in cities with high population concentrations, promoting a more severe disease due to its high mutation rate. In turn, a new mutation from this sublineage has been reported, giving rise to a new RD Rio strain that appears in the population of Rio de Janeiro with a clinical picture that has with high bacillary loads (Moraes et al, 2017); lineage 4 sublineages such as Haarlem and T are directly related to their stability and transmissibility in urban areas and the S sublineage in rural areas, especially in indigenous communities (Díaz Acosta et al, 2019;Garzon-Chavez et al, 2020). The Beijing sublineage is unique due to its high level of virulence, reduced inflammatory response and predisposition to antibiotic resistance.…”