Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges

Beata Krawczyk; Józef Kur

doi:10.1016/b978-0-12-813547-1.00016-9

Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges

Abstract

Staphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization. Analysis of the 16S rRNA gene, the gap gene (coding for glyceraldehyde-3-phosphate dehydrogenase), the hsp60 gene (encoding the heat shock protein Hsp60), the dnaJ gene (encoding the heat shock protein Hsp40), the tuf gene (encoding the elongation factor Tu), the sodA gene (encoding the superoxide dismutase), and the ropB gene (encoding the β subunit of the RNA polymerase) is used as a tool for identification of Staphylococcus isolates. Moreover, the PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of core genes (16S rRNA, gap, hsp60, dnaJ, tuf) is described, and attention is paid to new molecular methods such as real-time PCR and among non-genome-based assays, mass spectrometry. We are also presenting methods relying on whole genome analysis, including random amplified polymorphism DNA (RAPD), pulsed-field gel electrophoresis (PFGE), ligation-mediated PCR (LM PCR), multilocus sequence typing (MLST), spa typing, that are crucial to determine genotypical relatedness among strains of a same species. This is of paramount importance to define whether a local outbreak is due to a single or diverse strains, to investigate characteristics of unrelated bacterial isolates, as well as to compare isolates from a certain region or area with those collected worldwide. Finally, in phylogenetic research, genome-based comparisons are necessary to study relationship among strains. In addition, current knowledge of SCC (Staphylococcus Cassette Chromosome) mec classification of methicillin-resistant Staphylococcus aureus (MRSA) isolates and selected SCCmec typing methods are discussed.

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Authors (2)

Beata Krawczyk dr hab.
Józef Kur prof. dr hab.

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Keywords

IDENTIFICATION GENETIC DIVERSITY MOLECULAR METHODS SEQUENCING

Details

Category:

Monographic publication

Type:

rozdział, artykuł w książce - dziele zbiorowym /podręczniku w języku o zasięgu międzynarodowym

Title of issue:

W :Pet-to-man travelling staphylococci :a World in Progress strony 199 - 233

Language:

English

Publication year:

2018

Bibliographic description:

Krawczyk B., Kur J.: Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges// Pet-to-Man Travelling Staphylococci/ ed. Vincento Savini London : Elsevier, 2018, s.199-233

DOI: