A chromobacter is an emerging pathogen in cystic fibrosis (CF) patients, but accurate species identification of isolates is difficult. Most Achromobacter clinical isolates are designated as Achromobacter xylosoxidans; however, the commonly used phenotypic tests are not reliable (1-3). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis is used in clinical microbiology laboratories as an emerging technology for bacterial species identification (4-8). Genotypic methods have also been developed for Achromobacter species. The amplification of an inner fragment of the bla OXA-114 gene has been proposed for A. xylosoxidans identification (9). Furthermore, the presence of bla , bla , and bla OXA-243 has been detected in Achromobacter ruhlandii, Achromobacter dolens, and Achromobacter insuavis, respectively (2, 3). Multilocus sequence typing (MLST) schemes that increase the accuracy of the characterization and identification of Achromobacter strains and species have also been developed (10,11). This study compares the identification of Achromobacter species from CF patients by bla OXA-114 gene sequencing, MLST, and MALDI-TOF MS.Twenty-eight archived isolates that had been collected between 2003 and 2008 from 16 CF patients attending two reference centers in Rio de Janeiro, Brazil, were included. The isolates were identified as A. xylosoxidans by 16S rRNA gene sequencing (12, 13); bla OXA-114-like gene amplification and sequencing were performed as described by Turton et al. (9). MLST analysis by sequencing of seven housekeeping genes (nusA, rpoB, eno, gltB, lepA, nuoL, and nrdA) was performed as described previously (11). Allelic profiles and sequence types (STs) were analyzed according to the PubMLST databases (http://pubmlst.org/achromobacter). MALDI-TOF MS identification was performed with a Microflex LT instrument (Bruker Daltonics, GmbH, Germany) using FlexControl 3.0 software (Bruker Daltonics). Scores of Ն2.0 indicated species-level identification, scores of 1.7 to 1.9 indicated genuslevel identification, and scores of Ͻ1.7 indicated no reliable identification (14, 15).Positive bla OXA-114 amplification was obtained for 26 isolates. In 17 isolates, amplicons showed 99 to 100% identity with the bla OXA-114 reference sequence. In 9 isolates, identified as A. ruhlandii, sequences displayed 99% identity with bla OXA-258 . Two isolates (isolates 4530 and 7393) were negative for bla OXA . As observed by Papalia et al. (2), in our study not only A. xylosoxidans but also A. ruhlandii yielded positive amplification for the A. xylosoxidans species-specific marker bla . Amplification of the inner fragment without sequence analysis, as initially described by Turton et al. (9), thus may result in the misidentification of some Achromobacter species; by this criterion, we would have identified 26 isolates instead of 17 as A. xylosoxidans. MALDI-TOF MS identified 89% of the isolates (25/28 isolates) as A. xylosoxidans, while 7% (2/28 isolates) were identified at the probable ge...

GeneXpert GBS is an acceptable test for the identification of GBS colonization in HIV-infected pregnant women and represents a reasonable option to detect GBS colonization in settings where culture is not feasible.

The application of next-generation sequencing tools revealed that the cystic fibrosis respiratory tract is a polymicrobial environment. We have characterized the airway bacterial microbiota of five adult patients with cystic fibrosis during a 14-month period by 16S rRNA tag sequencing using the Illumina technology. Microbial diversity, estimated by the Shannon index, varied among patient samples collected throughout the follow-up period. The beta diversity analysis revealed that the composition of the airway microbiota was highly specific for each patient, showing little variation among the samples of each patient analyzed over time. The composition of the bacterial microbiota did not reveal any emerging pathogen predictor of pulmonary disease in cystic fibrosis or of its unfavorable clinical progress, except for unveiling the presence of anaerobic microorganisms, even without any established clinical association. Our results could potentialy help us to translate and develop strategies in response to the pathobiology of this disease, particularly because it represents an innovative approach for CF centers in Brazil.