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In this study, 1500 buffaloes and 2200 cattle were tested by single intradermal comparative cervical tuberculin test and compared with the detection rates of <jats:italic>M. bovis<\/jats:italic> isolation, real-time and simplex PCR, and flow Cytometry.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The tuberculin test is the reference test in Egypt, the positive rate was 54\/3700 (1.5%) composed of 18\/1500 (1.2%) buffaloes and 36\/2200 (1.6%) cattle which were mandatorily slaughtered under the Egyptian legislation, after postmortem examination the non-visible-lesion proportion was 39\/54 (72.2%) which surpassed the visible-lesion rate 15\/54 (27.8%) with (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.0001). The samples from each case were pooled into one sample representing the case, and the isolation rate of <jats:italic>M. bovis<\/jats:italic> was 25\/54 (46.3%). Real-time PCR using <jats:italic>atp<\/jats:italic>E was positive for mycobacteria on the genus level in 18\/18 (100%) and 5\/5 (100%) of tissue samples and isolates, respectively; simplex PCR detected <jats:italic>M. bovis<\/jats:italic> in 44\/54 (81.5%) and 25\/25 (100%) of tissue samples and isolates, respectively. Flow Cytometry evaluation of the CD4<jats:sup>+<\/jats:sup>, CD8<jats:sup>+<\/jats:sup>, WC1<jats:sup>+<\/jats:sup>\u03b4\u03b3, and CD2<jats:sup>+<\/jats:sup> cell phenotypes showed increased counts in the tuberculin-positive cases compared with negative cases (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.0001), and these phenotypes in the tuberculin-positive cases increased after antigen stimulation than in the negative cases (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.0001). Detection rates of PCR techniques and flow Cytometry exceeded that of bacterial isolation (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.0001) and exhibited a strong correlation.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The skin test suffers from interference from non-tuberculous mycobacteria able to cause false-positive reactions in cattle and other species. Real-time PCR using <jats:italic>atp<\/jats:italic>E, conventional PCR targeting RDs, and flow Cytometry are rapid and accurate methods that correlate with the isolation and can be promising for detection and confirmation of infected live and slaughtered cases.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-022-02568-0","type":"journal-article","created":{"date-parts":[[2022,6,11]],"date-time":"2022-06-11T03:31:48Z","timestamp":1654918308000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Real-time PCR using atpE, conventional PCR targeting different regions of difference, and flow cytometry for confirmation of Mycobacterium bovis in buffaloes and cattle from the Delta area of Egypt"],"prefix":"10.1186","volume":"22","author":[{"given":"Mohamed Sabry Abd Elraheam","family":"Elsayed","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed","family":"Salah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed Abd","family":"Elbadee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamer","family":"Roshdy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,6,11]]},"reference":[{"issue":"1","key":"2568_CR1","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1099\/ijsem.0.002507","volume":"68","author":"MA Riojas","year":"2018","unstructured":"Riojas MA, McGough KJ, Rider-Riojas CJ, Rastogi N, Hazbon MH. 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