Pathogen Chip for Respiratory Tract Infections

Overview

Journal J Clin Microbiol

Specialty Microbiology

Date 2013 Jan 11

PMID 23303493

Citations 13

Authors

Eric A F Simoes

Champa Patel

Wing-Kin Sung

Charlie W H Lee

Kuan Hon Loh

Marilla Lucero

Hanna Nohynek

Geraldine Nai

Pei Ling Thien

Chee Wee Koh

Yang Sun Chan

Jianmin Ma

Sebastian Maurer-Stroh

Phyllis Carosone-Link

Martin L Hibberd

Christopher W Wong

Affiliations

Soon will be listed here.

Abstract

Determining the viral etiology of respiratory tract infections (RTI) has been limited for the most part to specific primer PCR-based methods due to their increased sensitivity and specificity compared to other methods, such as tissue culture. However, specific primer approaches have limited the ability to fully understand the diversity of infecting pathogens. A pathogen chip system (PathChip), developed at the Genome Institute of Singapore (GIS), using a random-tagged PCR coupled to a chip with over 170,000 probes, has the potential to recognize all known human viral pathogens. We tested 290 nasal wash specimens from Filipino children <2 years of age with respiratory tract infections using culture and 3 PCR methods-EraGen, Luminex, and the GIS PathChip. The PathChip had good diagnostic accuracy, ranging from 85.9% (95% confidence interval [CI], 81.3 to 89.7%) for rhinovirus/enteroviruses to 98.6% (95% CI, 96.5 to 99.6%) for PIV 2, compared to the other methods and additionally identified a number of viruses not detected by these methods.

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References

Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H . Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol. 1986; 51 Pt 1:263-73. DOI: 10.1101/sqb.1986.051.01.032. View

Chen E, Miller S, DeRisi J, Chiu C . Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J Vis Exp. 2011; (50). PMC: 3169278. DOI: 10.3791/2536. View

Adegbola R . Childhood pneumonia as a global health priority and the strategic interest of the Bill & Melinda Gates Foundation. Clin Infect Dis. 2012; 54 Suppl 2:S89-92. DOI: 10.1093/cid/cir1051. View

Sakthivel S, Whitaker B, Lu X, Oliveira D, Stockman L, Kamili S . Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses. J Virol Methods. 2012; 185(2):259-66. PMC: 7119496. DOI: 10.1016/j.jviromet.2012.07.010. View

Pabbaraju K, Tokaryk K, Wong S, Fox J . Comparison of the Luminex xTAG respiratory viral panel with in-house nucleic acid amplification tests for diagnosis of respiratory virus infections. J Clin Microbiol. 2008; 46(9):3056-62. PMC: 2546709. DOI: 10.1128/JCM.00878-08. View

Nolte F, Marshall D, Rasberry C, Schievelbein S, Banks G, Storch G . MultiCode-PLx system for multiplexed detection of seventeen respiratory viruses. J Clin Microbiol. 2007; 45(9):2779-86. PMC: 2045250. DOI: 10.1128/JCM.00669-07. View

Yozwiak N, Skewes-Cox P, Stenglein M, Balmaseda A, Harris E, DeRisi J . Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis. 2012; 6(2):e1485. PMC: 3274504. DOI: 10.1371/journal.pntd.0001485. View

Gardner S, Jaing C, McLoughlin K, Slezak T . A microbial detection array (MDA) for viral and bacterial detection. BMC Genomics. 2010; 11:668. PMC: 3017867. DOI: 10.1186/1471-2164-11-668. View

Lee W, Wong C, Leong W, Miller L, Sung W . LOMA: a fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens. BMC Bioinformatics. 2008; 9:368. PMC: 2553803. DOI: 10.1186/1471-2105-9-368. View

10.

Hayden R, Gu Z, Rodriguez A, Tanioka L, Ying C, Morgenstern M . Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children. J Clin Virol. 2012; 53(4):308-13. PMC: 7108354. DOI: 10.1016/j.jcv.2011.12.020. View

11.

Leland D, Ginocchio C . Role of cell culture for virus detection in the age of technology. Clin Microbiol Rev. 2007; 20(1):49-78. PMC: 1797634. DOI: 10.1128/CMR.00002-06. View

12.

Liu Q, Bai Y, Ge Q, Zhou S, Wen T, Lu Z . Microarray-in-a-tube for detection of multiple viruses. Clin Chem. 2006; 53(2):188-94. PMC: 7108471. DOI: 10.1373/clinchem.2006.071720. View

13.

Liu L, Johnson H, Cousens S, Perin J, Scott S, Lawn J . Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012; 379(9832):2151-61. DOI: 10.1016/S0140-6736(12)60560-1. View

14.

Quan P, Palacios G, Jabado O, Conlan S, Hirschberg D, Pozo F . Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J Clin Microbiol. 2007; 45(8):2359-64. PMC: 1951265. DOI: 10.1128/JCM.00737-07. View

15.

Wong C, Heng C, Wan Yee L, Soh S, Kartasasmita C, Simoes E . Optimization and clinical validation of a pathogen detection microarray. Genome Biol. 2007; 8(5):R93. PMC: 1929155. DOI: 10.1186/gb-2007-8-5-r93. View

16.

Brunstein J, Thomas E . Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2. Diagn Mol Pathol. 2006; 15(3):169-73. DOI: 10.1097/01.pdm.0000210430.35340.53. View

17.

Merante F, Yaghoubian S, Janeczko R . Principles of the xTAG respiratory viral panel assay (RVP Assay). J Clin Virol. 2008; 40 Suppl 1:S31-5. PMC: 7128903. DOI: 10.1016/S1386-6532(07)70007-0. View

18.

Dacheux L, Berthet N, Dissard G, Holmes E, Delmas O, Larrous F . Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses. J Virol. 2010; 84(18):9557-74. PMC: 2937603. DOI: 10.1128/JVI.00771-10. View

19.

Urisman A, Fischer K, Chiu C, Kistler A, Beck S, Wang D . E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol. 2005; 6(9):R78. PMC: 1242213. DOI: 10.1186/gb-2005-6-9-r78. View

20.

Lucero M, Nohynek H, Williams G, Tallo V, Simoes E, Lupisan S . Efficacy of an 11-valent pneumococcal conjugate vaccine against radiologically confirmed pneumonia among children less than 2 years of age in the Philippines: a randomized, double-blind, placebo-controlled trial. Pediatr Infect Dis J. 2009; 28(6):455-62. DOI: 10.1097/INF.0b013e31819637af. View