Development of a PCR assay for identification of staphylococci at genus and species levels

Rapid molecular theranostics in infectious diseases

The increasing availability of rapid and sensitive nucleic acid testing assays for infectious diseases will revolutionize the practice of medicine by gradually reducing the need for standard culture-based microbiological methods that take at least two days. Molecular theranostics in infectious diseases is an emerging concept in which molecular biology tools are used to provide rapid and accurate diagnostic assays to enable better initial management of patients and more efficient use of antimicrobials. Essential conditions and the quality control required for the development and validation of such molecular theranostic assays are reviewed.

"Staphylococcus pettenkoferi," a novel staphylococcal species isolated from clinical specimens

In this report we describe a novel species of coagulase-negative novobiocin susceptible staphylococci obtained from an epidemiologically unrelated blood culture and a wound infection. These isolates significantly differed from all other validated Staphylococcus species based on phenotypic characteristics and 16S rRNA gene sequencing. Both isolates had identical 16S rRNA sequences and phylogenetic trees constructed from evolutionary distances showed that this species formed a distinct and deep subline that was most closely related to members of the Staphylococcus saprophyticus cluster group (S. kloosii, S. gallinarum, S. arlettae, S. saprophyticus, S. xylosus, S. equorum, S. succinus and S. cohnii) and Staphylococcus auricularis. Furthermore these strains could each be distinguished from all other staphylococci based on at least one phenotypic trait. Therefore we propose the designation of "Staphylococcus pettenkoferi" a novel species of coagulase-negative staphylococci.

Molecular characterization of methicillin-resistant Staphylococcus epidermidis clones: evidence of geographic dissemination

Denmark and Iceland are countries where the frequency of methicillin-resistant Staphylococcus aureus is very low due to strict infection control and restrictive antibiotic use policies. In contrast, methicillin-resistant S. epidermidis (MRSE) continues to be isolated as a nosocomial pathogen. The molecular typing by pulsed-field gel electrophoresis (PFGE) of 136 MRSE isolates from five hospitals in Denmark and 94 MRSE isolates from one hospital in Iceland collected in 1997 and 1998 defined 40 different patterns. Closely related PFGE types were found in isolates recovered in Iceland, Denmark, Mexico, Uruguay, Greece, and Cape Verde, evidencing for the first time the geographic clonal dissemination of MRSE strains. The large majority (87.4%) of the MRSE isolates studied were multiresistant.

Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target

Simple PCR and sequencing assays that utilize a single pair of degenerate primers were used to characterize a 429-bp-long DNA fragment internal (sodA(int)) to the sodA gene encoding the manganese-dependent superoxide dismutase in 40 coagulase-negative staphylococcal (CNS) type strains. The topology of the phylogenetic tree obtained was in general agreement with that which was inferred from an analysis of their 16S rRNA or hsp60 gene sequences. Sequence analysis revealed that the staphylococcal sodA genes exhibit a higher divergence than does the corresponding 16S ribosomal DNA. These results confirm that the sodA gene constitutes a highly discriminative target sequence for differentiating closely related bacterial species. Clinical isolates that could not be identified at the species level by phenotypical tests were identified by use of this database. These results demonstrate the usefulness of this method for rapid and accurate species identification of CNS isolates, although it does not allow discrimination of subspecies. The sodA sequence polymorphisms observed with staphylococcal species offer good opportunities for the development of assays based on DNA chip technologies.