Chapter 1 - Staphylococcal Taxonomy

Abstract

Staphylococcus was initially believed to belong to the family Micrococcaceae. Later, molecular and phylogenetic analysis revealed that staphylococci are not closely related to Micrococci anymore, and are thus classified in a new family, named Staphylococcaceae. An accurate identification of staphylococcal species in microbial communities is highly recommended to ensure a detailed determination of the host-pathogen relationships of staphylococci. Since 1962, when only 3 staphylococcal species were identified, an extensive revision of staphylococcal taxonomy has been performed. Overall, 45 staphylococcal species and 24 subspecies have been described so far in the genus by using molecular methods to identify all different species. An accurate identification of staphylococci to the species level is quite laborious, with phenotypic methods that, in several cases, may fail. For this reason, various molecular biology methods have been introduced. These molecular techniques may include sequencing of specific genes, hybridization probes, and may necessitate the restriction of enzymes. Such is the case for PCR-restriction fragment length polymorphism analysis; otherwise it may be accomplished by the whole-genome DNA-DNA hybridization analysis, although this latter methodology has proved unsuitable for routine use at this time. In addition to the 16S rRNA gene, several other gene targets have proven to be useful markers for accurate identification of staphylococcal species, such as the heat shock protein 60 (hsp60) gene, the sodA gene, the tuf gene, the rpoB gene, and the gap gene. By DNA-DNA hybridization studies and by hsp60 and the sodA gene sequence analysis, the Staphylococcus species could be divided into eight distinct species groups. With rpoB-based data, nine clusters were found, and with the gap sequences, Staphylococcus species could be classified into four clusters. The gap sequence analysis proved to be useful for distinguishing the staphylococcal species, and more discriminative compared with the other genes. Therefore, the determination of the sequences of several genes is an important tool for pathogen identification and phylogenetic studies within staphylococci. Although all gene-derived data differs, it has been found that groups obtained with two different sequences with high similarity are stable and reliable.