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 Ag85C¹⁰³ 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, Ag85C¹⁰³, 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.

Keywords: Genotyping; LAM; Mycobacterium tuberculosis; Paraguay; South-America.

Fig. 1

Frequency of distribution of spoligotyping families in each study population. The LAM family subtypes are shown in the blue pie charts

Fig. 2

Distribution of the most frequent spoligotyping families in each sanitary region according to patient’s residence as notified to the National TB Control Program

Fig. 3

Distribution of the spoligotyping families of the SNP Ag85C positive strains among Paraguayan isolates

Fig. 4

Distribution of the spoligotyping families of the SNP Ag85C positive or negative strains from a Buenos Aires- Argentina b Caracas- Venezuela

Fig. 5

Minimum spanning Tree based on 12 loci MIRU-VNTR profiles of Ag85C SNP positive strains from Buenos Aires, Caracas and Paraguay. Each node represents a MIRU-VNTR type. The size of the circle is relative to the number of isolates with the MIRU pattern and the colors indicate clusters containing either RD^Rio (red), WT (green) genotypes or mixed pattern (blue). In orange are strains with RD^Rio deletion but no RD174 deletion. The theoretical progenitor MIRU-VNTR-type for RD^Rio (MIRU 224226153321) is present in complex 1