The wide diversity of microbial flora in sputum from cystic fibrosis (CF) patients raises special laboratory challenges in detecting opportunistic pathogens outside the typically recognised bacteria such as S. aureus, P. aeruginosa, H. influenzae and S. pneumoniae. The majority of these emerging pathogens are environmental, multi-resistant Gram-negative bacteria. New technology such as MALDI-TOF may facilitate identification of these less frequently recognised bacteria.

A Gram- negative bacillus was isolated from sputum from a 10 year-old boy on 2 occasions, 14 months apart. He had a history of CF, with 1-2 admissions for exacerbations yearly, bilateral lower lobe bronchiectasis and was on the 3rd percentile for height and weight.
Isolation was facilitated by growth on a B. cepacia selective plate which suppressed coexistent +++oral flora and P. aeruginosa. Microbiological characteristics were: oxidase positive, no growth on MacConkey agar, nitrate, TRP, glucose, ADH, urease and esculin negative, OF alkaline reversion. No identification was obtained by Vitek or API 20NE. MALDI-TOF identification (score 2.5) was Inquilinus limosus and this was confirmed by 16S rRNA sequence analysis. The organism was sensitive to ciprofloxacin and meropenem, but resistant to aminoglycosides, colistin, piperacillin-tazobactam, aztreonam and cefepime.

This isolate demonstrates the importance of careful laboratory detection of unusual Gram negative bacteria in CF patients as well as the utility of MALDI-TOF, which is likely to become the primary method for identification of sputum isolates in CF.