Fig 1.
Spoligotype patterns of MTBC circulating in Assam.
Table 1.
Distribution of different lineages of MTBC Spoligotypes isolated from Assam in the study based on the classification by SITVITWEB.
Fig 2.
A two dimensional scatter plot based on principal component analysis (PCA).
Geographical regions having similarity in patterns of spoligotypes tend to clusters together.
Table 2.
The allelic profiles and Hunter Gaston Discriminatory Index (HGDI) of each of the 24 MIRU-VNTR loci in Mycobacterium tuberculosis isolates (n = 189) from Assam.
Table 3.
Hunter Gaston Discriminatory Index (HGDI) and cluster results based on MIRU-VNTR loci analysis of 189 Mycobacterium tuberculosis complex (MTBC) isolates from Assam.
Fig 3.
Neighbour-Joining (NJ) tree showing genetic diversity of 67 Beijing isolates from Assam based on 24 MIRU-VNTR loci.
Two major clusters (Group A and Group B) and their sub-lineages can be seen from this figure.
Fig 4.
Genotypic diversity of 78 Non-Beijing and Non-orphan MTBC isolates from Assam.
A MIRU-VNTR based dendrogram was generated using NJ tree analysis. M. tuberculosis strain lineages were identified using MIRU-VNTRplus identification database. 24-loci MIRU-VNTR alleles and spoligotypes from 78 isolates are also represented along with MIRU-VNTR NJ tree.
Fig 5.
Comparison of Beijing MTBC isolates from Assam with Beijing isolates from other countries (Singapore, Cambodia, Hong Kong, China, Taiwan, South Africa and rest of India) where Beijing isolates are also reported.
The radiation tree was constructed based on 24-MIRU-VNTR loci data using Neighbour-Joining method. Beijing isolates from Assam group into two well defined clusters, one major MTBC cluster which is close to some Beijing strains from Hong Kong, China, Taiwan and rest of India whereas the Beijing strains in the minor cluster were phylogenetically more close to a few Beijing strains from South Africa and Taiwan.
Fig 6.
A three dimensional scatter plot based on principal component analysis (PCA) showing relatedness of different geographical regions based on their similarity in patterns of 12-loci MIRU-VNTR diversity in MTBC from Assam and other geographical localities.
Different geographical areas were clustered in three groups and the state of Assam clustered with other Asian countries.
Fig 7.
Fig 7 showing phylogenetic relationship of orphan strains of MTBC from Assam with reference MTBC isolates available at the database MIRU-VNTRplus.
The NJ tree was constructed using 24-loci MIRU-VNTR data. 24-loci MIRU-VNTR alleles and spoligotypes from 44 isolates are also represented along with MIRU-VNTR NJ tree. This phylogenetic tree clearly shows that the orphan strains of MTBC from Assam represent two new well defined sub-clades namely Assam/EAI and Assam/CAS.