Identification of moaA3 gene in patient isolates of Mycobacterium tuberculosis in Kerala, which is absent in M. tuberculosis H37Rv and H37Ra

BACKGROUND: Tuberculosis is endemic to developing countries like India. Though the whole genome sequences of the type strain M. tuberculosis H37Rv and the clinical strain M. tuberculosis CDC1551 are available, the clinical isolates from India have not been studied extensively at the genome level. This study was carried out in order to have a better understanding of isolates from Kerala, a state in southern India. RESULTS: A PCR based strategy was followed making use of the deletion region primers to understand the genome level differences between the type strain H37Rv and the clinical isolates of M. tuberculosis from Kerala. PCR analysis of patient isolates using RD1 region primers revealed the amplification of a 386 bp region, in addition to the expected 652 bp amplicon. Southern hybridization of genomic DNA with the 386 bp amplicon confirmed the presence of this new region in a majority of the patient isolates from Kerala. Sequence comparison of this amplicon showed close homology with the moaA3 gene of M. bovis. In M. bovis this gene is present in the RvD5 region, an IS6110 mediated deletion that is absent in M. tuberculosis H37Rv. CONCLUSION: This study demonstrates the presence of moaA3 gene, that is absent in M. tuberculosis H37Rv and H37Ra, in a large number of local isolates. Whether the moaA3 gene provides any specific advantage to the field isolates of the pathogen is unclear. Field strains from Kerala have fewer IS6110 sequences and therefore are likely to have fewer IS6110 dependent rearrangements. But as deletions and insertions account for much of the genomic diversity of M. tuberculosis, the mechanisms of formation of sequence polymorphisms in the local isolates should be further examined. These results suggest that studies should focus on strains from endemic areas to understand the complexities of this pathogen

Dendrogram based on the AFLP profile for EO/MC primer pair showing clustering of clinical isolates of and laboratory strains of , and BCG

<p><b>Copyright information:</b></p><p>Taken from "Combined use of Amplified Fragment Length Polymorphism and IS-RFLP in fingerprinting clinical isolates of from Kerala, South India"</p><p>http://www.biomedcentral.com/1471-2334/7/86</p><p>BMC Infectious Diseases 2007;7():86-86.</p><p>Published online 28 Jul 2007</p><p>PMCID:PMC1950308.</p><p></p> IScopy numbers of various isolates/strains are indicated

AFLP profiles generated by primer combinations EO/MT (panel A) and EG/MC (panel B)

<p><b>Copyright information:</b></p><p>Taken from "Combined use of Amplified Fragment Length Polymorphism and IS-RFLP in fingerprinting clinical isolates of from Kerala, South India"</p><p>http://www.biomedcentral.com/1471-2334/7/86</p><p>BMC Infectious Diseases 2007;7():86-86.</p><p>Published online 28 Jul 2007</p><p>PMCID:PMC1950308.</p><p></p> Lanes1-8: clinical isolates of , lanes 9&10: non tuberculous mycobacteria. The non-tuberculous mycobacteria have a very different profile from each other as well as from isolates. The primer pair EG/MC (panel B) shows fewer bands and more differences between the isolates as compared to EO/MT primer pair (panel A

AFLP profiles showing differences (arrows) between H37Rv (lane1), H37Ra (lane 2), (lane 3) and BCG (lane 4)

<p><b>Copyright information:</b></p><p>Taken from "Combined use of Amplified Fragment Length Polymorphism and IS-RFLP in fingerprinting clinical isolates of from Kerala, South India"</p><p>http://www.biomedcentral.com/1471-2334/7/86</p><p>BMC Infectious Diseases 2007;7():86-86.</p><p>Published online 28 Jul 2007</p><p>PMCID:PMC1950308.</p><p></p> The profiles shown are for EO/MC (panel A) and EO/MT (panel B) primer combinations