1
GLOSSARY
Caenorhabditis elegans: This nematodelives in soil and eats environmental bacteria. It is a simple and easy to handlemodel that ca be used to evaluate the virulence of bacterial pathogens. It is increasingly being usedto study host-pathogen interactions and has helped identify basic evolutionarily conserved pathways associated with microbial pathogenesis. In particular, this has revealed important factors of the host response with remarkable parallels in higher organisms. This organism’s short (2–3-weeks) life span facilitates host-bacteria interaction analysis, offering an ideal compromise between complexity and tractability.
Staphylococcal cassette chromosome mec (SCCmec) elements: MRSA strains belonging to multidrug resistant bacteria, produce penicillin binding protein 2a (PBP2a), which is poorly acylated by ß-lactam antibiotics. The mecA gene, encoding PBP2a, is carried on a peculiar typeof mobile genetic element inserted into the SCCmec. SCCmec elements typically share four characteristics: first,they carry the mec gene complex (mec) consisting of the methicillinresistance determinant mecA and its regulatory genes and insertionsequences; second, they carry the ccr gene complex (ccr) consistingof ccr genes that are responsible for the mobility of the element andits surrounding sequences; third, they have characteristic directly repeatednucleotide sequences and inverted complementary sequences at bothends; and last, they integrate into the 3' end of an open readingframe (ORF), orfX.
The junkyard (J) region: The SCCmec element type has been defined by the combinationof ccr type and mec class. In MRSA strains, six types of SCCmecelements, that is, six combinations of ccr and mec, have beenreported. These six SCCmec elements have been furtherclassified by differences in regions other than ccr and mec,which are designated junkyard regions. The J regions comprisethree parts: J1 (the region between ccr and the right-flanking chromosomalregion), J2 (the region between mec and ccr), and J3 (the regionbetween orfX and mec).
spa sequence typing: The spa gene of Staphylococcus aureus encodes protein A andis used for typing of MRSA. The sequence typing of the spa gene repeat region allowsstudying the epidemiology of these strains. The repeatregion of the spa gene is subject to spontaneous mutations,as well as loss and gain of repeats. Repeats are assigned analpha-numerical code, and the spa type is deduced from the orderof specific repeats. Repeats and spa types weredetermined by Ridom StaphType, a software tool allowingrapid repeat determination, data management and retrieval, andInternet-based assignment of new spa types following automaticquality control of DNA sequence chromatograms.sis, offering an ideal compromise between complexity and tractability