Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases

Palacios, Gustavo; Quan, Phenix‐Lan; Jabado, Omar; Conlan, Sean; Hirschberg, David L.; Liu, Yang; Zhai, Jing; Renwick, Neil; Hui, Jeffrey; Hegyi, Hédi; Grolla, Allen; Strong, James E.; Towner, Jonathan S.; Geisbert, Thomas W.; Jahrling, Peter B.; Büchen-Osmond, C.; Ellerbrok, Heinz; Sánchez-Seco, María Paz; Lussier, Yves A.; Formenty, Pierre; Nichol, Stuart T.; Feldmann, Heinz; Briese, Thomas; Lipkin, W. Ian

doi:10.3201/eid1301.060837

Cited by 304 publications

(274 citation statements)

References 21 publications

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“…Numerous potential pathogens are also part of the normal commensal flora. Methods for characterization of the human microbiome have included large scale ''universal'' 16S (bacterial) and 5.8 S and 28S (fungal) DNA sequencing (for review, see Petrosino et al 2009), array-based techniques for detection of viral sequences (Wang et al 2002a;Palacios et al 2007), large scale shotgun sequencing (Qin et al 2010), and shotgun proteomics (Verberkmoes et al 2009). These techniques are all powerful methods for determination of the members of a microbiome community, but all make significant assumptions about the nature of members (i.e., bacterial, fungal, viral).…”

Section: Discussionmentioning

confidence: 99%

Biome representational in silico karyotyping

Muthappan¹,

Lee²,

Lamprecht³

et al. 2011

Genome Res.

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Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping—biome representational in silico karyotyping (BRISK)—as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery.

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Section: Discussionmentioning

confidence: 99%

Biome representational in silico karyotyping

Muthappan¹,

Lee²,

Lamprecht³

et al. 2011

Genome Res.

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“…GreeneChipVr (only for viruses) version 1.0 contained 9477 probes to address all vertebrate viruses (1710 species, including all reported isolates). GreeneChipPm version 1.0 contained 29,495 probes that included probes comprising GreeneChipVr, as well as 11,479 16S rRNA bacterial probes, 1120 18S rRNA fungal probes, and 848 18S rRNA parasite probes [35].…”

Section: Perspectives: Viral Identification Platformsmentioning

confidence: 99%

Infectious diseases detection by microarray: An overview of clinical relevant infections

Herrera-Rodríguez¹,

Elizondo-Quiroga²,

Álvarez-Maya³

2013

JBiSE

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Microarray technology is a powerful tool to investigate whole genome expression profiles to study the crosstalk between pathogens and associated hosts that cause illness. Microarrays have been used in several comparative genome hybridization studies of pathogens. In addition to detection and identification of pathogens, microarrays are ideal for characterizing genetic differences between bacteria isolates of the same species to the strain level. Furthermore, the use of microarrays has been gaining importance in the detection of viral agents. Here we explore the use of microarrays for simultaneous detection of viruses and modifications made over these techniques. Microarray technology has also been incorporated to compensate for time-consuming sequencing. The procedure of fungi identification based on sequences and studies reported the use of microarrays to identify pathogenic yeasts and molds by targeting the internal transcribed spacer regions in fungal rRNA genes. The remarkable advancement in genomics over the last decade has made it possible for microarray technology to evolve towards being the best option for clinical diagnostics because they have several advantages.

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“…Previously developed microarrays either use small subunit RNA probes for low-resolution identification of bacteria (4), have probes for viruses only (5), or use a combination of these approaches (6). The LLMDA, by contrast, has several dozen probes for each of the thousands of bacteria and viruses sequenced to date, so it can simultaneously examine multiple genomic regions from each organism.…”

Section: Current Pathogen Detection Techniquesmentioning

confidence: 99%

“…In designing probes for our array, we sought to balance the goals of conservation and uniqueness, prioritizing oligo sequences that were conserved, to the extent possible, within the family of the targeted organism, and unique relative to other families and kingdoms. We designed arrays with larger numbers of probes per sequence (50 or more for viruses, 15 or more for bacteria) than previous arrays having only [2][3][4][5][6][7][8][9][10] probes per target (5,6). The large number of probes per target was expected to improve sensitivity, an important consideration given possible amplification bias in the random PCR sample preparation protocol, which could result in non-amplification of genome regions targeted by some probes.…”

Section: Llmda Probe Design For Broad Spectrum Detection Of Viruses Amentioning

confidence: 99%

Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array

Jaing¹,

Gardner²,

McLoughlin³

et al. 2011

PDA Journal of Pharmaceutical Science and Technology

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ABSTRACT:We designed the Lawrence Livermore Microbial Detection Array (LLMDA), which contains 388,000 DNA probes. This array can detect any sequenced viruses or bacteria within 24 hours. In addition, the oligonucleotide probes were selected to enable detection of novel, divergent species with homology to sequenced organisms. We recently used this array to identify an adventitious virus from a vaccine product. We have also used this array to detect viral and bacterial infections from various human clinical samples. Broad spectrum microbial detection microarrays are efficient and cost-effective tools to rapidly screen cell bank samples, raw materials, vaccine samples and clinical samples to ensure drug, food and health safety in the United States and worldwide.

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Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases

Cited by 304 publications

References 21 publications

Biome representational in silico karyotyping

Biome representational in silico karyotyping

Infectious diseases detection by microarray: An overview of clinical relevant infections

Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array

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