Modern and ancestral genotypes of Mycobacterium tuberculosis from Andhra Pradesh, India

Abstract

Traditionally, the distribution of the Mycobacterium tuberculosis genotypes in India has been characterized by widespread prevalence of ancestral lineages (TbD1+ strains and variants) in the south and the modern forms (TbD1(-) CAS and variants) predominating in the north of India. The pattern was, however, not clearly known in the south-central region such as Hyderabad and the rest of the state of Andhra Pradesh where the prevalence of both tuberculosis (TB) and human immunodeficiency virus (HIV) infection is one of the highest in the country; this area has been the hotspot of TB vaccine trials. Spoligotyping of 101 clinical isolates obtained from Hyderabad and rural Andhra Pradesh confirmed the occurrence of major genogroups such as the ancestral (or the TbD1+ type or the East African Indian (EAI) type), the Central Asian (CAS) or Delhi type and the Beijing lineage in Andhra Pradesh. Sixty five different spoligotype patterns were observed for the isolates included in this study; these were further analyzed based on specific genetic signatures/mutations. It was found that the major genogroups, CAS and "ancestral," were almost equally prevalent in our collection but followed a north-south compartmentalization as was also reported previously. However, we observed a significant presence of MANU lineage in south Andhra Pradesh, which was earlier reported to be overwhelmingly present in Mumbai. This study portrays genotypic diversity of M. tuberculosis from the Indian state of Andhra Pradesh and provides a much needed snapshot of the strain diversity that will be helpful in devising effective TB control programs in this part of the world.

Figure 1. Genetic affinities within the M. tuberculosis isolates based on spoligotyping.

Different clades corresponding to prevalent genotypes are prominently highlighted. In the inset is the distance coding convention relevant to the genetic relatedness of different isolates within a clade.

Figure 2. PCR-RFLP analysis of the pncA gene after restriction digestion with BseLI.

The pncA gene was analyzed for a silent mutation in the 65^th codon at the 195th bp. Mutated alleles correspond to lanes 1, 5 and 6 (344 bp product and one minor fragment of 81 bp). Lanes 2, 3 and 7 denote wild type pattern (280 bp product and two minor fragments of 81 and 64 bp sizes) while lane 4 represents a negative control. Lane M corresponds to the profiling of a 100 bp DNA molecular weight marker.