Isogeneic bacterial strains that differ only in the production of a single microbial factor have been invaluable in studying the pathogenesis of bacterial infections, The targeted, intentional inactivation of a gene encoding a potential virulence determinant generally requires homologous recombination to replace the gene with an inactivated allele. To determine whether the insertion and expression of a fragment of a bacterial gene in an antisense orientation could be used as a rapid alternative to allelic inactivation for producing paired isogeneic isolates, we inverted a 600-bp fragment of the Staphylococcus aureus gene encoding alpha-toxin, hla, behind its native promoter on an Escherichia coli-S, aureus shuttle vector. A transformant of an S, aureus strain carrying the antisense hla fragment produced antisense hla RNA and made 16-fold less alpha-toxin than either its parent or an isogeneic transformant containing vector DNA without kla. Also, intraperitoneal injection of 1,5 x 10(9) CFU of the antisense hla-containing transformant was significantly less lethal in a murine model than that of the parent (1 of 10 versus 7 of 10 mice expired [P < 0.02]) or the transformant without hla (1 of 10 versus 7 of 7 mice expired [P < 0.001]), We conclude that the expression of a fragment of hla in an antisense orientation in S, aureus on a plasmid vector reduces alpha-toxin production and the lethal activity of the strain in a murine model, The antisense strategy for creating isogeneic strains of bacteria may facilitate molecular investigations into the pathogenesis of infection, It also may be useful in creating novel live-attenuated strains of bacteria for use as vaccine candidates.