Design of clone-specific probes from genome sequences for rapid PCR-typing of outbreak pathogens.

The genome sequence of one OXA-48-producing Klebsiella pneumoniae belonging to sequence type (ST) 405, and three belonging to ST11, were used to design and test ST-specific PCR assays for typing OXA-48-producing K. pneumoniae. The approach proved to be useful for in-house development of rapid PCR typing assays for local outbreak surveillance.

Rapid identification of yeasts from positive blood culture bottles by pyrosequencing.

We have developed a rapid protocol for the identification of Candida species from positive blood cultures by combining a simple method for nucleic acid extraction and preparation using microbial storage cardboards with polymerase chain reaction (PCR) and pyrosequencing of a small region of the 18 S rRNA gene. The protocol is robust and easy to implement and can be performed in 4 h. The method was tested against a collection of clinical blood cultures. Agreement of sequence identifications with standard microbiological methods was 100%.

Detection and characterization of Enterobacteriaceae producing metallo-beta-lactamases in a tertiary-care hospital in Spain.

Carbapenem-resistant or intermediate (MIC >or=1 mg/L) clinical isolates (n = 12) of three species of Enterobacteriaceae (Klebsiella pneumoniae, Klebsiella oxytoca and Escherichia coli) were characterized. The isolates harboured integrons containing the VIM-1 metallo-beta-lactamase gene together with other resistance gene cassettes. In particular, the CTX-M-2 gene was detected in four of the K. pneumoniae isolates. The patient population was mostly paediatric and characterized by severe underlying illnesses that involved long-term hospitalization, major surgery and/or immunosuppressive and broad-spectrum antibiotic therapy.

[Usefulness of etiologic studies in children hospitalized for pneumonia]. / Utilidad de los estudios etiológicos en pacientes pediátricos hospitalizados por neumonía.

OBJECTIVE: The aims of this study were: 1) To assess the effectiveness of viral culture and serology. 2) To check if there are clinical differences between patients with viral or bacterial infections. 3) Assessment of treatment, previous to and during the hospital stay. PATIENTS AND METHODS: A prospective study was carried out between January 1994 and June 1995 on 56 inpatients diagnosed of pneumonia. The mean age was 3 years (range: 2 months- 14 years). Viral cultures on cell monolayers was carried out in 46 patients. Serology was carried out in 33 patients older than six months of age. Blood cultures were obtained in 27 patients and a tuberculine reaction was studied in 15 patients. On the basis of microbiological results, three groups were formed (viral, bacterial and unknown) and clinical symptoms, thorax X-rays, and laboratory data were compared. RESULTS: The etiologic agent was detected in 36 patients (64%). The most frequent pathogens detected were adenovirus and respiratory syncytial virus with 11 patients (19%) each, followed by Mycoplasma pneumoniae with 9 patients (16%): Viral cultures were positive in 16 patients (35%) and serology in 22 patients (66%). Viral infection was detected in 20 patients (36%) and bacterial infection in 16 (28%). Mixed infection (bacterial/viral) was found in 5 patients (9%). The patients with viral infections showed significant differences (p < 0.01) for age (younger) and tachypnea compared with those with bacterial infections. Sixty-six percent of the patients had received antibiotic treatment previous to hospital admission and 87% during their hospitalization. CONCLUSIONS: Although the etiologic studies were positive in 64% of the patients, the delay in obtaining the results make them scarcely useful in determining whether to initiate or not antibiotic therapy (87% of inpatients). Clinical data, radiology results and leukocyte counts do not show any difference between viral and bacterial infections.