The rapid detection and differentiation of Mycobacterium tuberculosis complex members from cattle and water buffaloes in the delta area of Egypt, using a combination of real-time and conventional PCR.

Mycobacterium tuberculosis complex (MTBC) has the potential to cause infections in animals and human beings. The combination of real-time PCR targeting atpE or lpqT and RD1, and conventional PCR targeting regions of difference (RD) was rigorously evaluated as a descriptive molecular epidemiology tool. A total of 2100 cattle and buffaloes from the Menoufia, Sharkia, Gharbia, Dakahlia, Elbuhaira, and Cairo Governorates were tested by single intradermal comparative cervical tuberculin test (SICCT). The frequency was 74/2100 (3.5%); thereafter, on post-mortem examination (PM), 49/74 (66.21%) showed visible lesions, while only 25/74 (33.78%) were non-visible with a significant difference of (p < .0001). Real-time PCR using atpE or lpqT and RD1 similarly detected the frequency of infection, sensitivity, specificity, positive predictive value, negative predictive value, and accuracy, which represented 73/74 (98.65%), 98.65, 100, 100, 90.91, and 98.81%, respectively. Multiplex conventional PCR targeting RD1, 4, 9, and 12 confirmed that 49/74 (66.21%) were M.bovis, while the simplex conventional PCR targeting RD4 and RD9 confirmed mycobacteria in 71/74 (95.94%) samples, which included 61/74 (82.4%) M.bovis and 2/74 (2.7%) M.tuberculosis. Additionally, 8/74 (10.8%) exhibited mixed patterns of M.bovis and M.tuberculosis, and 3/74 (4.05%) were negative. There was a significant difference between the results of simplex and multiplex conventional PCR (p < .0001). Moreover, simplex conventional PCR targeting RD4 and RD9 proved higher sensitivity, specificity, positive predictive value, negative predictive value, and accuracy, which were 95.95, 100, 100, 76.92, and 96.43%, respectively, when compared with the values of multiplex conventional PCR targeting RD1,4,9, and 12 which were 66.22, 100, 100, 28.57, and 70.24%, respectively. The repeatability results of real-time PCR using atpE or lpqT and RD1, and simplex conventional PCR targeting RD4 and RD9 were acceptable. In conclusion, a combination of real-time PCR using atpE or lpqT and RD1 as the first step with simplex conventional PCR targeting RD4 and RD9 as the second step was reliable as a diagnostic tool.