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Bacterial culture of sputum is frequently positive in patients with pulmonary tuberculosis (TB). However, it remains to be clarified whether detection of potential pathogenic microorganisms (PPM) in sputum represents bacterial infection or only colonization of the respiratory tract. In the present study, we investigated the clinical significance of PPM in patients with pulmonary TB.Sputum culture for PPM was studied in 174 pulmonary TB patients (117 males and 57 females, mean age of 71 years) on the day of admission. Ninety-seven patients (63 males and 34 females, mean age of 67.1 years) also underwent transtracheal aspirates (TTA). Quantitative culture of sputum and TTA was performed to distinguish infection from colonization. The results were evaluated as follows: more than 106 or 105 c.f.u./mL indicated infection in the case of sputum or TTA samples, respectively. We also compared various clinical parameters between patients with PPM and patients with non-potential pathogenic microorganisms (non-PPM).Potential pathogenic microorganisms were positive in 44% and 24% of sputum and TTA specimens, respectively. However, quantitative culture for PPM showed positive findings in only 11% and 3% of sputum and TTA specimens, respectively. A comparative study of the clinical features revealed that PPM patients had a lower bodyweight and lower serum albumin levels than non-PPM patients. A fatal outcome was also more common in PPM patients than in non-PPM patients. Logistic regression analysis further confirmed that PPM clearly contributed to a fatal outcome in addition to the previously established parameters including age, performance status, haemoglobin, albumin and radiographic disease extent.Although sputum PPM represent only colonization of the upper respiratory tract in TB patients, they are associated with a poor prognosis.