Abstract Background: Early identification of organisms from respiratory specimens of cystic fibrosis (CF) patients is important to guide therapeutic decisions. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) has emerged as a rapid and powerful tool for routine identification of bacteria. The objective was to identify common bacterial isolates including non-fermenting Gram-negative bacteria (NFGNB) in a cohort of CF patients by MALDI-TOF MS. Methods: Fifty CF patients were enrolled between July and December, 2012, where sputum samples or deep-oropharyngeal swabs were prospectively collected at each CF clinic visit or hospital admission from both pediatric and adult CF patients. Bacterial isolates were identified using MALDI-TOF MS in parallel with conventional phenotypic methods. Discrepant strains were confirmed by 16S rDNA gene sequencing. Results: A total of 124 CF isolates from 83 samples representing 15 bacterial species were identified. The MALDI-TOF MS correctly identified bacterial isolates 123/124 (99.2%) [Log (score) <2 and =1.7] to the genus level and 119/124 (96%) [Log (score) =2] to the species level. The MALDI-TOF MS results were 100% consistent to the species level with conventional phenotypic identification for isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenzae, streptococcus pyogenes, Achromobacter xylosoxidans, Stentrophomonas maltophilia, Chryseobacterium gleum, and Enterobacter cloacae. Discrepant isolates 6/124 (4.8%) were all Gram negative isolates. Conclusions: MALDI-TOF MS provided reliable, rapid, and an efficient method for the identification of bacteria in routine clinical laboratory in the setting of CF which exhibited large species diversity. This instant identification of microorganisms will lead to early antimicrobial therapy in CF patients.


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