In the past decade, potential pathogens, including Alcaligenes species, have been increasingly recovered from cystic fibrosis (CF) patients. Accurate identification of multiply antibiotic-resistant gram-negative bacilli is critical to understanding the epidemiology and clinical implications of emerging pathogens in CF. We examined the frequency of correct identification of Alcaligenes spp. by microbiology laboratories affiliated with American CF patient care centers. Selective media, an exotoxin A probe for Pseudomonas aeruginosa, and a commercial identification assay, API 20 NE, were used for identification. The activity of antimicrobial agents against these clinical isolates was determined. A total of 106 strains from 78 patients from 49 CF centers in 22 states were studied. Most (89%) were correctly identified by the referring laboratories as Alcaligenes xylosoxidans. However, 12 (11%) strains were misidentified; these were found to be P. aeruginosa (n ؍ 10), Stenotrophomonas maltophilia (n ؍ 1), and Burkholderia cepacia (n ؍ 1). Minocycline, imipenem, meropenem, piperacillin, and piperacillin-tazobactam were the most active since 51, 59, 51, 50, and 55% of strains, respectively, were inhibited. High concentrations of colistin (100 and 200 g/ml) inhibited 92% of strains. Chloramphenicol paired with minocycline and ciprofloxacin paired with either imipenem or meropenem were the most active combinations and inhibited 40 and 32%, respectively, of strains. Selective media and biochemical identification proved to be useful strategies for distinguishing A. xylosoxidans from other CF pathogens. Standards for processing CF specimens should be developed, and the optimal method for antimicrobial susceptibility testing of A. xylosoxidans should be determined.Cystic fibrosis (CF) is the most common life-shortening disease caused by a recessive autosomal gene in the Caucasian population and afflicts about 60,000 patients worldwide, approximately 30,000 of whom are cared for in the United States (21). While the genetic defect in CF is known, the relationship between abnormal CF transmembrane conductance regulator and chronic pulmonary disease is not yet fully understood (22). Chronic pulmonary disease is characterized by a vicious cycle of inflammation and infection and is the major cause of morbidity and mortality. The pathogens of CF are well characterized and include Staphylococcus aureus, nontypeable Haemophilus influenzae, Pseudomonas aeruginosa, and Burkholderia cepacia (10).During the past decade, several additional potential pathogens have been recovered from CF patients, including nontuberculous mycobacteria (19), Stenotrophomonas maltophilia (3), and Alcaligenes species, particularly Alcaligenes xylosoxidans (29). As reported to the U.S. Cystic Fibrosis Foundation's National Patient Registry in 1996 and 1997, 1.9 and 2.7% of all CF patients harbored Alcaligenes spp. (7,8). As determined by a research laboratory participating in a phase III trial of aerosolized tobramycin in CF patients who were Ն6 years of ...