Cytomegalovirus (CMV) often persists in the lungs of marrow transplant patients with CMV pneumonia, despite ganciclovir (GCV) treatment. To determine whether GCV resistance contributes to viral persistence, the susceptibilities of CMV isolates from diagnostic bronchoalveolar lavage samples and CMV isolates obtained during treatment or from autopsy lung tissue from 12 patients were compared by DNA hybridization. Resistance (50% effective dose, > 12 ,uM) was detected in an isolate from only one patient who had also received several courses of GCV. GCV resistance did not explain the persistence of CMV in the lung.Although the combination of ganciclovir (GCV) and intravenous immunoglobulin (i.v.-Ig) has decreased the rate of mortality from cytomegalovirus (CMV) pneumonia in marrow transplant recipients, mortality remains high at 30 to 50% (3, 20), and as many as 10% of treated patients have relapses (2). CMV was still detected in 80% of patients with CMV pneumonia at our institution in a routine follow-up bronchoalveolar lavage (BAL) specimens after 9 days of treatment (22), without a reduction in viral titer (23). These findings raised the question of whether resistance to GCV could explain the persistence of CMV in the lungs of some patients, despite treatment.All 12 patients examined in the present study were allogeneic bone marrow transplant recipients with CMV pneumonia. CMV pneumonia was defined as described previously (23) and was treated with GCV, 5 mg/kg of body weight twice daily for 2 weeks, and i.v.-Ig (Cutter Biological, Miles Laboratories Inc., Berkeley, Calif.), 500 mg/kg on alternate days for 2 weeks. GCV was continued at 5 mg/kg daily for up to 30 days. Relapse was defined as the recurrence of symptoms, worsening pulmonary infiltrates on chest radiograph (20), and detection of CMV in BAL specimens after the completion of a course of treatment for the initial episode. Only two patients had received GCV prior to the episode of CMV pneumonia being studied. With the exception of one patient, all patients had received acyclovir (ACV) intravenously as CMV prophylaxis; ACV was given at 500 mg/M2 every 8 h from the day of pretransplant conditioning to the day of discharge from the hospital (17).CMV isolates were obtained from the initial diagnostic BAL specimens, from follow-up BAL specimens 9 days after starting GCV and i.v.-Ig, when routine follow-up BAL was being performed to assess the subsequent duration of GCV therapy, or from autopsy lung tissue after 7 to 32 days of treatment. Samples from urine, throat, and blood were obtained weekly for culture of CMV. All For susceptibility testing, isolates from patients and isolates 8708 and 8704 were first thawed and were then reinoculated into tube cultures of human foreskin fibroblasts and passaged one to four times until the cytopathic effect had progressed to 75 to 100% of the monolayer. CMV-infected cells were then removed with 0.05% trypsin and were resuspended in Dulbecco's modification of Eagle's medium with 10% fetal bovine serum (DME-10). Fifty mil...