Streptococcus pyogenes Cas9 (SpCas9) has been widely adapted for genetic manipulation in numerous microbes . However, it is restricted for application in mycobacteria because of the notable cellular toxicity and low DNA targeting efficiency . To develop an active CBE in mycobacterium, we screened different CBEs composed of the fusion of rat APOBEC1 cytosine deaminase and different Cas nucleases, including dSpCas9 (catalytically inactive Streptococcus pyogenes Cas9), dLbCpf1 (catalytically inactive Lachnospiraceae bacterium Cpf1) and dSt1Cas9 (catalytically inactive Streptococcus thermophilus Cas9). The expression of the Cas nucleases was under the control of an anhydrotetracycline (ATc)-inducible promoter while the expression of the corresponding gRNAs was under the control of a synthetic constitutive promoter J23119.