Design and validation of a supragenome array for determination of the genomic content of Haemophilus influenzae isolates

作者: Rory A Eutsey , N Hiller , Joshua P Earl , Benjamin A Janto , Margaret E Dahlgren

DOI: 10.1186/1471-2164-14-484

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摘要: Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of airway; it also less commonly invasive disease. Clinical isolates H. display extensive genomic diversity plasticity. The development strategies to successfully prevent, diagnose treat depends on tools ascertain gene content individual isolates. We describe validate supragenome hybridization (SGH) array that can be used characterize full genic complement any strain within species, well strains from several highly related species. contains 31,307 probes collectively cover essentially all alleles 2890 clusters identified whole genome sequencing 24 clinical strains. finite model predicts these data include greater than 85% non-rare genes (where rare are defined those present in 10% sequenced strains). veracity was tested by comparing sequences eight their obtained using array. predictions were correct reproducible for ~ 98% This technology then applied an investigation 193 geographically clinically diverse These came multiple locations five different continents Papua New Guinea from: middle ears persons otitis media otorrhea; lung aspirates sputum samples pneumonia COPD patients, blood specimens patients sepsis; cerebrospinal fluid meningitis, pharyngeal healthy persons. analyses provided most comprehensive detailed genomic/phylogenetic look at this species date, subset divergent form separate lineage provides cost-effective high-throughput tool determine isolate or lineage. Furthermore, method probe selection given group available sequences.

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