Plasmids, transposons (Tn), insertion sequences (IS), bacteriophages, pathogenic islands, and staphylococcal cassette chromosomes. These elements play a central role in the pathogen’s adaptation process to different stresses, and are means to transfer genetic information among and within bacterial species [3]. Each S. aureus lineage carries a unique combination of genomic islands. In the genome of S. aureus Mu50, nine genomic islands have been identified, including vSa3, vSa4, vSaa, vSab, vSac, SCCmec, phage wSa1, phage wSa3, andTn5801 [4]. The carriage of genomic islands in S. aureus can alter the pathogenic and resistance potential of the strains. The dissemination of particular clones in a specific environment or host in favor of other strains, or the replacement of clones in a single environment suggests a genetic basis for epidemics related to genomic islands. This has fuelled efforts to identify novel genomic islands associated with the evolution of antibiotic resistance and host adaptation in Chinese S. aureus. Comparative genome hybridization (CGH) is an efficient method to identify critical gene clusters. When applied to pathogenic S. aureus, CGH unveils the variability in terms of gene content in regions related to pathogenicity and gives new insights into the evolutionary aspects of S. aureus. The high discriminatory power of this technique has been used to distinguish major MRSA lineages, community-associated MRSA strains, and predominant S. aureus lineages [5,6,7,8]. This study aimed to compare the genetic repertoire of different S. aureus clones through microarray-based comparative genomics to identify the gene clusters that may explain the evolutionaryComparative Genomics of Staphylococcus aureusmystery of S. aureus: (i) Many articles reported that human MRSA may originate in animals [9], but host-specific genes or gene clusters were rarely found. (ii) MSSA showed more diverse patterns compared with the relative preponderance of a few MRSA clones. (iii) ST239 and ST5 were the most predominant MRSA clones in China [1]. From 1994 to 2000 in Beijing, CB 5083 ST239spa t030 rapidly replaced t037 and became the major MRSA clone [10]. In this study, we identified 13 gene clusters in the S. aureus genome associated with the evolution of antibiotic resistance and host specificity by using CGH microarray. The gene clusters were confirmed by large-scale validation via polymerase chain reaction (PCR) in 160 clinical strains. Among these clusters, several critical genes and four novel gene clusters related to the evolution of resistance and host specificity in Chinese S. aureus have not yet been reported.Results Overall Genome Diversity in S. aureusThe microarray comprised all the genetic information found in only two S. aureus genomes, Mu50 and CN79. CGH microarray analysis revealed extensive genome diversity within the S. aureus species. Within the 2,457 genes buy HIV-RT inhibitor 1 present on the S. aureus microarray, all of the 50 strains shared 1,738 genes (70.7 ) and 719 (29.3 ) genes were absent in at least one strain. An average of 260 (10.6 ) genes were absent per strain compared to the genes present on the microarray. Cluster analysis indicated that all of the 50 strains were clustered into seven different complexes (Fig. 1). Strains in the same complex showed similar backgrounds such as isolation time, location, species, and lineage. Different complexes represented different backgrounds. Complex 1 included 11 MRSA (ST239-spa t037) isolated in Beijing bef.Plasmids, transposons (Tn), insertion sequences (IS), bacteriophages, pathogenic islands, and staphylococcal cassette chromosomes. These elements play a central role in the pathogen’s adaptation process to different stresses, and are means to transfer genetic information among and within bacterial species [3]. Each S. aureus lineage carries a unique combination of genomic islands. In the genome of S. aureus Mu50, nine genomic islands have been identified, including vSa3, vSa4, vSaa, vSab, vSac, SCCmec, phage wSa1, phage wSa3, andTn5801 [4]. The carriage of genomic islands in S. aureus can alter the pathogenic and resistance potential of the strains. The dissemination of particular clones in a specific environment or host in favor of other strains, or the replacement of clones in a single environment suggests a genetic basis for epidemics related to genomic islands. This has fuelled efforts to identify novel genomic islands associated with the evolution of antibiotic resistance and host adaptation in Chinese S. aureus. Comparative genome hybridization (CGH) is an efficient method to identify critical gene clusters. When applied to pathogenic S. aureus, CGH unveils the variability in terms of gene content in regions related to pathogenicity and gives new insights into the evolutionary aspects of S. aureus. The high discriminatory power of this technique has been used to distinguish major MRSA lineages, community-associated MRSA strains, and predominant S. aureus lineages [5,6,7,8]. This study aimed to compare the genetic repertoire of different S. aureus clones through microarray-based comparative genomics to identify the gene clusters that may explain the evolutionaryComparative Genomics of Staphylococcus aureusmystery of S. aureus: (i) Many articles reported that human MRSA may originate in animals [9], but host-specific genes or gene clusters were rarely found. (ii) MSSA showed more diverse patterns compared with the relative preponderance of a few MRSA clones. (iii) ST239 and ST5 were the most predominant MRSA clones in China [1]. From 1994 to 2000 in Beijing, ST239spa t030 rapidly replaced t037 and became the major MRSA clone [10]. In this study, we identified 13 gene clusters in the S. aureus genome associated with the evolution of antibiotic resistance and host specificity by using CGH microarray. The gene clusters were confirmed by large-scale validation via polymerase chain reaction (PCR) in 160 clinical strains. Among these clusters, several critical genes and four novel gene clusters related to the evolution of resistance and host specificity in Chinese S. aureus have not yet been reported.Results Overall Genome Diversity in S. aureusThe microarray comprised all the genetic information found in only two S. aureus genomes, Mu50 and CN79. CGH microarray analysis revealed extensive genome diversity within the S. aureus species. Within the 2,457 genes present on the S. aureus microarray, all of the 50 strains shared 1,738 genes (70.7 ) and 719 (29.3 ) genes were absent in at least one strain. An average of 260 (10.6 ) genes were absent per strain compared to the genes present on the microarray. Cluster analysis indicated that all of the 50 strains were clustered into seven different complexes (Fig. 1). Strains in the same complex showed similar backgrounds such as isolation time, location, species, and lineage. Different complexes represented different backgrounds. Complex 1 included 11 MRSA (ST239-spa t037) isolated in Beijing bef.
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