Molecular Detection of Multiple Emerging Pathogens in Sputa from Cystic Fibrosis Patients

Background: There is strong evidence that culture-based methods detect only a small proportion of bacteria present in the respiratory tracts of cystic fibrosis (CF) patients. Methodology/Principal Findings: Standard microbiological culture and phenotypic identification of bacteria in sputa from CF patients have been compared to molecular methods by the use of 16S rDNA amplification, cloning and sequencing. Twenty-five sputa from CF patients were cultured that yield 33 isolates (13 species) known to be pathogens during CF. For molecular cloning, 760 clones were sequenced (7.263.9 species/sputum), and 53 different bacterial species were identified including 16 species of anaerobes (30%). Discrepancies between culture and molecular data were numerous and demonstrate that accurate identification remains challenging. New or emerging bacteria not or rarely reported in CF patients were detected including Dolosigranulum pigrum, Dialister pneumosintes, and Inquilinus limosus. Conclusions/Significance: Our results demonstrate the complex microbial community in sputa from CF patients, especially anaerobic bacteria that are probably an underestimated cause of CF lung pathology. Metagenomic analysis is urgentl

Ciprofloxacin resistance in clinical isolates of Salmonella typhimurium obtained from two patients.

Two patients (patients A and B) infected with Salmonella typhimurium failed ciprofloxacin therapy, and the posttherapy isolates had reduced susceptibilities to quinolones; 6 of 11 isolates from patient B were also cross-resistant to chemically unrelated agents. No transferable resistance, chloramphenicol-acetylating enzymes, or beta-lactamases were detected. For 13 of 14 isolates, the concentrations of ciprofloxacin that inhibited DNA synthesis by 50% were similar to the MICs, suggesting a mutation in gyrA. Insertion of pNJR3-2 (gyrA) in the posttherapy isolate from patient A and 5 of 11 of the posttherapy isolates from patient B resulted in lower quinolone MICs, also suggesting that resistance was due to a mutation in gyrA. Three of the five isolates also had reduced levels of accumulation of quinolones. All six cross-resistant isolates from patient B had reduced levels of accumulation of quinolones, but only one isolate had increased susceptibility when pNJR3-2 was inserted. Despite the lack of OmpF seen in five isolates from patient B, there was no correlation with decreased levels of quinolone accumulation. All isolates had identical smooth lipopolysaccharide profiles. The mechanism of apparently reduced accumulation has yet to be determined