Sociodemographic, microbial and phylogentic studies of Mycobacterium tuberculosis cases diagnosed in El-Minia governorate, Egypt

Egypt is considered one of the high-burden countries in WHO’s Eastern Mediterranean region. This study determined the sociodemographic, microbial and phylogentic characteristics for Mycobacterium tuberculosis cases diagnosed in El-Minia governorate in upper Egypt. Fifty clinical samples were collected (male-to-female sex ratio 1.5 and 50% within the 21- to 40-years old) with complete history of patients; samples were cultured and identified by biochemical tests. DNA was extracted and tested for plc gene. Seven isolates were subjected to sequencing analysis of the amplified plc fragment and a phylogentic tree for these strains was formed. Out of 50 samples, 24 samples were culture positive, all grown isolates were identified as M. tuberculosis according to physical characters, rate of growth, biochemical tests. Direct polymerase chain reaction (PCR) method based on the amplification of 350 bp region of plc gene was used for the detection of M. tuberculosis, to differentiate it from Mycobacterium bovis in clinical samples. It was found that all isolates were positive for plc gene. Direct sequencing of 350 bp region of plc gene revealed many substitution mutations along the entire sequenced fragment. The main cause for such condition may rely on inadequate treatment regimen. The phylogenetic tree of the seven sequenced isolates were classified into three distinct nodes. We concluded that all cases were positive for M. tuberculosis and most of them were from rural area. There was different substitution mutations in the plc gene which may be due to the intermittent treatment regimens that made the tested strains under stress resulting in mutation.