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Chapter 5 : The Staphylococci: A Postgenomic View
Category: Genomics and Bioinformatics; Bacterial Pathogenesis
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Staphylococci that can cause disease in humans are Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. saprophyticus, S. hominis, S. warneri, S. lugdunensis, S. schleiferi subsp. schleiferi, S. capitis subsp. ureolyticus, and S. simulans. This chapter briefly discusses the often complex biology of the organism before the genomic insights determined from the sequence. One of the most valuable tools that can arise from whole genome sequences are whole-genome microarrays. A study on core variable genes revealed new information about the S. aureus genome and its evolution. S. haemolyticus are generally more resistant to antiobiotics than other staphylococci, and it could be that they accumulate more of these genes than other species. As the methods for classifying strains into dominant types become more widespread, further epidemiological patterns and associations between certain lineages, toxins, and the infections they cause are being considered. Unlike the genomic islands in other staphylococci that are often associated with virulence, the arginine catabolism mobile element (ACME) island is associated with drug resistance. Each of the sequenced staphylococcal genomes carries genes common to all other sequenced staphylococci, genes specific to particular species, genes specific to particular lineages, and mobile genetic elements (MGEs).
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Phylogenetic relationships of staphylococcal species based on 16S rRNA sequences. Symbols after the names of the species indicate the host association: *, human; +, animals and birds; no symbol, other. Maximum-likelihood tree built from 16S rRNA sequences downloaded from the Ribosomal Database Project-I (http://rdp.cme.msu.edu) ( 19 ) by ClustalX ( 81 ), Phylip (version 3.6) ( 29 ) and NJplot ( 70 ). The numbers at the tree branches are percentage bootstrap values indicating the confident levels at that node where congruent ( 28 ). The bar indicates the genetic distance between species (1 nucleotide substitution per 100) as displayed in the branch lengths. Sequences used to construct the tree are S. aureus (accession number X68417), S. sciuri (AJ421446), S. condimenti (Y15750), S. nepalensis (AJ517414), S. muscae (S83566), S. arlettae (AB009933), S. carnosus (AB009934), S. caprae (AB009935), S. cohnii (AB009936), S. capitis (AB009937), S. delphini (AB009938), S. equorum (AB009939), S. kloosii (AB009940), S. lugdunensis (AB009941), S. piscifermentans (AB009943), S. schleiferi (AB009945), S. vitulinus (AB009946), S. succinus (AF004220), S. auricularis (D83358), S. chromogenes (D83360), S. epidermidis (D83363), S. felis (D83364), S. gallinarum (D83366), S. haemolyticus (D83367), S. hyicus (D83368), S. intermedius (D83369), S. lentus (D83370), S. saprophyticus (D83371), S. simulans (D83373), S. xylosus (D83374), S. hominis (L37601), S. saccharolyticus (L37602), S. warneri (L37603), S. pasteuri (AF041361), S. simiae (AY727530), and S. pseudintermedius (AJ780976). Currently recognized Staphylococcus species missing from the tree are Staphylococcus fleurettii ( 84 ) and Staphylococcus lutrae ( 33 ); these species were not included in the tree because the 16S rRNA sequences available for these species are <600 bp.
Pairwise comparisons of S. aureus NCTC8325, USA300, COL, Mu50, N315, MW2, MSSA476, MRSA252, and RF122 chromosomes displayed using the Artemis Comparison Tool (ACT) ( 14 ). The sequences have been aligned from the predicted replication origins (oriC; right), with the terminus of replication in the center. The dark gray bars separating each genome represent orthologous matches identified by reciprocal FASTA analysis ( 69 ), with an identity cutoff of 30% and a length-of-match cutoff of 80%. Variable regions of the chromosomes containing mobile genetic elements such as prophages, plasmids, transposons, SaPIs, and other genomic islands are marked as boxes within the genomes and vary significantly between each strain.
Distribution of orthologous CDSs in S. aureus. Venn diagram showing the number of genes unique or shared between three S. aureus strains (MRSA252, MSSA476, and N315). The associated pie charts show the breakdown of the functional groups assigned for CDSs in relevant sections of the Venn diagram. Orthologous matches were identified as previously described for Fig. 2 . Grayscale code for the functional groups in the pie charts is displayed.
Pairwise comparisons of the S. aureus MRSA252, S. epidermidis ATCC 12228, S. epidermidis RP62A, S. haemolyticus, and S. saprophyticus chromosomes. The comparisons are displayed using the Artemis Comparison Tool (ACT) ( 14 ). The sequences have been aligned from the predicted replication origins (oriC; right). The gray bars separating each genome represent orthologous matches identified by reciprocal FASTA analysis as previously described for Fig. 2 . The intensity of the gray matches indicates the relative identity of the orthologous match; the darker the gray, the higher the identity.
Distribution of orthologous CDSs in staphylococci. (A) Circular diagrams show the number of genes unique or shared between S. aureus MRSA252 and S. epidermidis RP62A; S. aureus MRSA252 and S. haemolyticus; and S. aureus MRSA252 and S. saprophyticus. (B) Functional distribution of orthologous CDSs. Orthologous matches were identified as previously described for Fig. 2 .
Clonal complex (CC) and sequence type (ST) of the sequenced isolates