ArticleApplied and environmental microbiology2005
Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics.
Article in Applied and environmental microbiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 77 citations in OpenAlex.
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- Identification of commonly expressed exoproteins and proteolytic cleavage events by proteomic mining of clinically relevant UK isolates ofMicrobial genomics · 2016Article
- High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom.Journal of clinical microbiology · 2015Article
- Cross-talk between two nucleotide-signaling pathways in Staphylococcus aureus.The Journal of biological chemistry · 2015Article
- Solid and Suspension Microarrays for Microbial Diagnostics.Methods in microbiology · 2015Article
- Identification of staphylococcal phage with reduced transcription in human blood through transcriptome sequencing.Frontiers in microbiology · 2015Article
- Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.BMC research notes · 2014Article
- Staphylococcal phenotypes induced by naturally occurring and synthetic membrane-interactive polyphenolic β-lactam resistance modifiers.PloS one · 2014Article
- The skin microbiome: current perspectives and future challenges.Journal of the American Academy of Dermatology · 2013Review
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- DNA microarray profiling of a diverse collection of nosocomial methicillin-resistant staphylococcus aureus isolates assigns the majority to the correct sequence type and staphylococcal cassette chromosome mec (SCCmec) type and results in the subsequent identification and characterization of novel SCCmec-SCCM1 composite islands.Antimicrobial agents and chemotherapy · 2012Article
- Antistaphylococcal activity of DNA-interactive pyrrolobenzodiazepine (PBD) dimers and PBD-biaryl conjugates.The Journal of antimicrobial chemotherapy · 2012Article
- The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated.BMC microbiology · 2012Article
- Transcriptome analysis of responses to rhodomyrtone in methicillin-resistant Staphylococcus aureus.PloS one · 2012Article
- Host- and microbe determinants that may influence the success of S. aureus colonization.Frontiers in cellular and infection microbiology · 2012Review
- Staphylococcus aureus temperate bacteriophage: carriage and horizontal gene transfer is lineage associated.Frontiers in cellular and infection microbiology · 2012Article
- Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites.Frontiers in microbiology · 2012Article
- Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray.The ISME journal · 2011Article
- Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus.BMC systems biology · 2011Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Bacterial comparative genomics has been revolutionized by microarrays, but the power of any microarray is dependent on the number and diversity of gene reporters it contains. Staphylococcus aureus is an important human pathogen causing a wide range of invasive and toxin-mediated diseases, and more than 20% of the genome of any isolate consists of variable genes. Seven whole-genome sequences of S. aureus are available, and we exploited this rare opportunity to design, build, and validate a comprehensive, nonredundant PCR product microarray carrying reporters that represent every predicted open reading frame (3,623 probes). Such a comprehensive microarray necessitated a novel design strategy. Validation with the seven sequenced strains showed correct identification of 93.9% of genes present or absent/divergent but was dependent on the method of analysis chosen. Microarray data were highly reproducible, reducing the need for many replicate slides. Interpretation of microarray data was enhanced by focusing on the major areas of variation--the presence or absence of mobile genetic elements (MGEs). We compiled "composite genomes" of every individual MGE and visualized their distribution. This allowed the sensitive discrimination of related isolates, including the first clear description of how isolates of the same clone of epidemic methicillin-resistant S. aureus differ substantially in their carriage of MGEs. These MGEs carry virulence and resistance genes, suggesting differences in pathogenic potential. The novel methods of design and interpretation of data generated from this microarray will enable further studies of S. aureus evolution, epidemiology, and pathogenesis.
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Registered trials
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