Comparison of genotypic and phenotypic methods for species identification of coagulase-negative staphylococcal isolates from blood cultures

Rapid and accurate identification of coagulase-negative staphylococci by real-time PCR

Biprobe identification assays based on real-time PCR were designed for 15 species of coagulase-negative staphylococci (CNS). Three sets of primers and four biprobes were designed from two variable regions of the 16S rRNA gene. An identification scheme was developed based on the pattern of melting peaks observed with the four biprobes that had been tested on 24 type strains. This scheme was then tested on 100 previously identified clinical isolates and 42 blindly tested isolates. For 125 of the 142 clinical isolates there was a perfect correlation between the biprobe identification and the result of the ID 32 Staph phenotypic tests and PCR. For 12 of the other isolates a 300-bp portion of the 16S rRNA gene was sequenced to determine identity. The remaining five isolates could not be fully identified. LightCycler real-time PCR allowed rapid and accurate identification of the important CNS implicated in infection.

Characterization of coagulase-negative staphylococci by primer-specific polymerase chain reaction and ribotyping

OBJECTIVE: To analyze, by primer-specific polymerase chain reaction (PCR) and ribotyping, coagulase-negative staphylococci (CNS). METHODS: Forty-five clinical isolates of CNS were identified by the API ID32 STAPH system and ribotyping. Additionally, primer-specific PCR was evaluated for identification of clinical strains of Staphylococcus epidermidis. RESULTS: Forty-five isolates of CNS from neonates with nosocomial bacteremia were studied. The results of the S. epidermidis-specific PCR were compared with those obtained using ribotyping and the API ID32 STAPH system. Excellent congruence was found between primer-specific PCR and ribotyping. Primer-specific PCR proved to be a fast and reliable method for the identification of S. epidermidis strains. According to the primer-specific PCR and ribotyping analysis, a few CNS isolates were found to be incorrectly identified by the API ID32 STAPH system. CONCLUSIONS: Primer-specific PCR is a fast and reliable method for the identification of S. epidermidis. Primer-specific PCR in combination with ribotyping is a promising approach for studying the epidemiology of S. epidermidis and other CNS species in hospital.

Phylogenetic analyses of Staphylococcus based on the 16S rDNA sequence and assignment of clinical isolates from animals

The nucleotide sequences of the 16S rDNA in 17 strains of 16 taxa of the genus Staphylococcus were determined. The sequences were compared phylogenetically together with the gene sequences of 10 (including 7 other species) Staphylococcus species retrieved from the DNA Data Bank of Japan. Although the primary and secondary structures of most of Staphylococcus species were very similar (homology values 96.4% or more) except for S. caseolyticus MAFF 911387T (homology values 95.4% or less), the 23 staphylococcal species were divided into 10 groups based on similarity, evolutionary distance and phylogenetic tree analysis. Nucleotide stretches in several variable domains in the 16S rDNA sequences appeared to be specific for the bacterial groups or the species. By comparing such characteristics in the sequence and phylogenies of 5 staphylococcal clinical isolates from bovine mastitis, canine and feline pyoderma, and feline urogenital syndrome with the information obtained in this study, the species level of each organism was identified.

A comparison of methods to determine whether clinical isolates of Staphylococcus epidermidis from the same patient are related

Staphylococcus epidermidis is a major cause of hospital-acquired infections but also part of the normal skin flora. A common clinical question is whether repeated isolation of S. epidermidis from one patient represents the same strain; because if different strains are isolated, they are often thought to be contaminants. In this study, different typing methods were compared to answer this question. Twenty isolates of S. epidermidis from five different patients were investigated. The isolates from each patient had identical or very similar antibiograms, and were recovered on different occasions. Typing was performed by antibiogram, biotype, slime production, plasmid profile, and pulsed-field gel electrophoresis (PFGE) banding pattern of SmaI digests of chromosomal DNA. In addition, the level of resistance to methicillin was determined by growth curves in broth containing methicillin for a series of different inocula for each isolate. The results showed that the isolates from each patient belonged to the same clone, but examples of instabilities in their antibiograms, plasmid profiles, as well as their PFGE banding patterns were seen. A change in the level of methicilli, resistance was observed in one strain; otherwise this characteristic was found to be strain-specific and stable in vivo. It was concluded that in combination with biotyping and antibiotic resistance testing the level of resistance to methicillin could be used as an aid to distinguish between two or more clinical isolates of S. epidermidis from the same patient.