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


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.

Share and Cite:

Herrera-Rodriguez, S. , Elizondo-Quiroga, D. and Alvarez-Maya, I. (2013) Infectious diseases detection by microarray: An overview of clinical relevant infections. Journal of Biomedical Science and Engineering, 6, 1006-1013. doi: 10.4236/jbise.2013.610125.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Yoo, S.M. and Lee, S.Y. (2008) Diagnosis of pathogens using DNA microarray. Recent Patents on Biotechnology, 2, 124-129.
[2] Mikhailovich, V., Gryadunov, D., Kolchinsky, A., Makarov, A.A. and Zasedatelev, A. (2008) DNA microarrays in the clinic: Infectious diseases. BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, 30, 673-682.
[3] Wilson, W.J., Strout, C.L., DeSantis, T.Z., Stilwell, J.L., Carrano, A.V., et al. (2002) Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Molecular and Cellular Probes, 16, 119-127.
[4] Leski, T.A., Malanoski, A.P., Stenger, D.A. and Lin, B. (2010) Target amplification for broad spectrum microbial diagnostics and detection. Future Microbiology, 5, 191-203.
[5] Hook, A.L., Chang, C.Y., Yang, J., Atkinson, S., Langer, R., et al. (2013) Discovery of novel materials with broad resistance to bacterial attachment using combinatorial polymer microarrays. Advanced Materials, 25, 2542-2547.
[6] Fux, C.A., Shirtliff, M., Stoodley, P. and Costerton, J.W. (2005) Can laboratory reference strains mirror “realworld” pathogenesis? Trends in Microbiology, 13, 58-63.
[7] Fukushima, M., Kakinuma, K., Hayashi, H., Nagai, H., Ito, K., et al. (2003) Detection and identification of Mycobacterium species isolates by DNA microarray. Journal of Clinical Microbiology, 41, 2605-2615.
[8] Aragon, L.M., Navarro, F., Heiser, V., Garrigo, M., Espanol, M., et al. (2006) Rapid detection of specific gene mutations associated with isoniazid or rifampicin resistance in Mycobacterium tuberculosis clinical isolates using non-fluorescent low-density DNA microarrays. The Journal of Antimicrobial Chemotherapy, 57, 825-831.
[9] Mancini, N., Carletti, S., Ghidoli, N., Cichero, P., Burioni, R., et al. (2010) The era of molecular and other non-culture-based methods in diagnosis of sepsis. Clinical Microbiology Reviews, 23, 235-251.
[10] Monecke, S. and Ehricht, R. (2005) Rapid genotyping of methicillin-resistant Staphylococcus aureus (MRSA) isolates using miniaturised oligonucleotide arrays. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 11, 825-833.
[11] Gryadunov, D., Mikhailovich, V., Lapa, S., Roudinskii, N., Donnikov, M., et al. (2005) Evaluation of hybridisation on oligonucleotide microarrays for analysis of drugresistant Mycobacterium tuberculosis. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 11, 531-539.
[12] Zimenkov, D.V., Antonova, O.V., Kuz’min, A.V., Isaeva, Y.D., Krylova, L.Y., et al. (2013) Detection of secondline drug resistance in Mycobacterium tuberculosis using oligonucleotide microarrays. BMC Infectious Diseases, 13, 240.
[13] Corless, C.E., Kaczmarski, E., Borrow, R. and Guiver, M. (2008) Molecular characterization of Neisseria meningitidis isolates using a resequencing DNA microarray. The Journal of Molecular Diagnostics: JMD, 10, 265-271.
[14] Crompton, P.D., Kayala, M.A., Traore, B., Kayentao, K., Ongoiba, A., et al. (2010) A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proceedings of the National Academy of Sciences of the United States of America, 107, 6958-6963.
[15] Su, X.Z., Jiang, H., Yi, M., Mu, J. and Stephens, R.M. (2009) Large-scale genotyping and genetic mapping in Plasmodium parasites. The Korean Journal of Parasitology, 47, 83-91.
[16] Leland, D.S. and Ginocchio, C.C. (2007) Role of cell culture for virus detection in the age of technology. Clinical Microbiology Reviews, 20, 49-78.
[17] Elnifro, E.M., Ashshi, A.M., Cooper, R.J. and Klapper, P.E. (2000) Multiplex PCR: Optimization and application in diagnostic virology. Clinical Microbiology Reviews, 13, 559-570.
[18] Zimmer, S.M. and Burke, D.S. (2009) Historical perspective—Emergence of influenza A (H1N1) viruses. The New England Journal of Medicine, 361, 279-285.
[19] World Health Organization (2009) Assessing the severity of an influenza pandemic.
[20] Donnelly, C.A., Ghani, A.C., Leung, G.M., Hedley, A.J., Fraser, C., et al. (2003) Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong. Lancet, 361, 1761-1766.
[21] Ryabinin, V.A., Kostina, E.V., Maksakova, G.A., Neverov, A.A., Chumakov, K.M., et al. (2011) Universal oligonucleotide microarray for sub-typing of influenza A virus. PloS One, 6, Article ID: e17529.
[22] Mehlmann, M., Dawson, E.D., Townsend, M.B., Smagala, J.A., Moore, C.L., et al. (2006) Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus. Journal of Clinical Microbiology, 44, 2857-2862.
[23] Townsend, M.B., Dawson, E.D., Mehlmann, M., Smagala, J.A., Dankbar, D.M., et al. (2006) Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance. Journal of Clinical Microbiology, 44, 2863-2871.
[24] Zhu, H., Hu, S., Jona, G., Zhu, X., Kreiswirth, N., et al. (2006) Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proceedings of the National Academy of Sciences of the United States of America, 103, 4011-4016.
[25] Wang, D., Urisman, A., Liu, Y.T., Springer, M., Ksiazek, T.G., et al. (2003) Viral discovery and sequence recovery using DNA microarrays. PLoS Biology, 1, Article ID: E2.
[26] Drosten, C., Kummerer, B.M., Schmitz, H. and Gunther, S. (2003) Molecular diagnostics of viral hemorrhagic fevers. Antiviral Research, 57, 61-87.
[27] Nordstrom, H., Falk, K.I., Lindegren, G., Mouzavi-Jazi, M., Walden, A., et al. (2005) DNA microarray technique for detection and identification of seven flaviviruses pathogenic for man. Journal of Medical Virology, 77, 528-540.
[28] Garcia-Monco, J.C. (2010) Acute encephalitis. Neurologia, 25, 11-17.
[29] Boriskin, Y.S., Rice, P.S., Stabler, R.A., Hinds, J., AlGhusein, H., et al. (2004) DNA microarrays for virus detection in cases of central nervous system infection. Journal of Clinical Microbiology, 42, 5811-5818.
[30] Bryant, B.J. and Klein, H.G. (2007) Pathogen inactivation: The definitive safeguard for the blood supply. Archives of Pathology & Laboratory Medicine, 131, 719-733.
[31] Khodakov, D.A., Zakharova, N.V., Gryadunov, D.A., Filatov, F.P., Zasedatelev, A.S., et al. (2008) An oligonucleotide microarray for multiplex real-time PCR identification of HIV-1, HBV, and HCV. BioTechniques, 44, 241-246, 248.
[32] Songok, E.M., Luo, M., Liang, B., McLaren, P., Kaefer, N., et al. (2012) Microarray analysis of HIV resistant female sex workers reveal a gene expression signature pattern reminiscent of a lowered immune activation state. PloS One, 7, Article ID: e30048.
[33] Xu, W.W., Han, M.J., Chen, D., Chen, L., Guo, Y., et al. (2013) Genome-wide search for the genes accountable for the induced resistance to HIV-1 infection in activated CD4+ T cells: Apparent transcriptional signatures, coexpression networks and possible cellular processes. BMC Medical Genomics, 6, 15.
[34] Chen, E.C., Miller, S.A., DeRisi, J.L. and Chiu, C.Y. (2011) Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. Journal of Visualized Experiments: JoVE.
[35] Palacios, G., Quan, P.L., Jabado, O.J., Conlan, S., Hirschberg, D.L., et al. (2007) Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerging Infectious Diseases, 13, 73-81.
[36] Gardner, S.N., Jaing, C.J., McLoughlin, K.S. and Slezak, T.R. (2010) A microbial detection array (MDA) for viral and bacterial detection. BMC Genomics, 11, 668.
[37] Mays, S.R., Bogle, M.A. and Bodey, G.P. (2006) Cutaneous fungal infections in the oncology patient: Recognition and management. American Journal of Clinical Dermatology, 7, 31-43.
[38] Dimopoulos, G., Frantzeskaki, F., Poulakou, G. and Armaganidis, A. (2012) Invasive aspergillosis in the intensive care unit. Annals of the New York Academy of Sciences, 1272, 31-39.
[39] Ustianowski, A.P., Sieu, T.P. and Day, J.N. (2008) Penicillium marneffei infection in HIV. Current Opinion in Infectious Diseases, 21, 31-36.
[40] Morrison, C.J. and Lindsley, M.D. (2002) Serological approaches to the diagnosis of invasive fungal infections. In: R. Calderone and R. Cihlar, Eds., Fungal Pathogenesis: Principles and Practice, Marcel Dekker, New York, 667-716.
[41] Hamilton, A.J. (1998) Serodiagnosis of histoplasmosis, paracoccidioidomycosis and penicilliosis marneffei; cur-rent status and future trends. Medical Mycology: Official Publication of the International Society for Human and Animal Mycology, 36, 351-364.
[42] Ramos-e-Silva, M., Lima, C.M., Schechtman, R.C., Trope, B.M. and Carneiro, S. (2012) Systemic mycoses in immunodepressed patients (AIDS). Clinics in Dermatology, 30, 616-627.
[43] Aidorevich, L., Morrison, C.J., Reiss, E. and Choi, J.S. (2006) Nucleic acids for detecting fusarium species. 30 de Mayo. US 7052836 B2.
[44] Choi, J., Lindsley, M., Morrison, C. and Qin, Z. (2002) Nucleic acids for the identification of fungi and methods for using the same cross-reference to related application. US Patent App. 10/490, 726, US20050260584 A1.
[45] Tang, Y.W., Ellis, N.M., Hopkins, M.K., Smith, D.H., Dodge, D.E., et al. (1998) Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. Journal of Clinical Micryobiology, 36, 3674-3679.
[46] Hsiao, C.R., Huang, L., Bouchara, J.P., Barton, R., Li, H.C., et al. (2005) Identification of medically important molds by an oligonucleotide array. Journal of Clinical Microbiology, 43, 3760-3768.
[47] Huang, A., Li, J.W., Shen, Z.Q., Wang, X.W. and Jin, M. (2006) High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray. Journal of Clinical Microbiology, 44, 3299-3305.
[48] Leinberger, D.M., Schumacher, U., Autenrieth, I.B. and Bachmann, T.T. (2005) Development of a DNA microbarray for detection and identification of fungal pathogens involved in invasive mycoses. Journal of Clinical Microbiology, 43, 4943-4953.
[49] Spiess, B., Seifarth, W., Hummel, M., Frank, O., Fabarius, A., et al. (2007) DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients. Journal of Clinical Microbiolog, 45, 3743-3753.
[50] Ponton, J., Morgues, M.D. and Quindos, G. (2002) Nonculture based diagnostics. In: Calderone, R., Ed., Candida and Candidiasis, American Society for Microbiology, Washington DC, 395-425.
[51] Yeo, S.F. and Wong, B. (2002) Current status of nonculture methods for diagnosis of invasive fungal infections. Clinical Microbiology Reviews, 15, 465-484.
[52] Quindos, G., Moragues, M.D. and Ponton, J. (2004) Is there a role for antibody testing in the diagnosis of invasive candidiasis. Revista Iberoamericana de Micologia, 21, 10-14.
[53] Lorenz, M.C. and Fink, G.R. (2001) The glyoxylate cycle is required for fungal virulence. Nature, 412, 83-86.
[54] Barker, K.S., Crisp, S., Wiederhold, N., Lewis, R.E., Bareither, B., et al. (2004) Genome-wide expression profiling reveals genes associated with amphotericin B and fluconazole resistance in experimentally induced antifungal resistant isolates of Candida albicans. The Journal of Antimicrobial Chemotherapy, 54, 376-385.
[55] Lorenz, M.C., Bender, J.A. and Fink, G.R. (2004) Transcriptional response of Candida albicans upon internalization by macrophages. Eukaryotic Cell, 3, 1076-1087.
[56] Saville, S.P., Thomas, D.P. and Lopez-Ribot, J.L. (2005) Use of genome information for the study of the pathogenesis of fungal infections and the development of diagnostic tools. Revista Iberoamericana de Micologia, 22, 238-241.
[57] Garaizar, J., Brena, S., Bikandi, J., Rementeria, A. and Ponton, J. (2006) Use of DNA microarray technology and gene expression profiles to investigate the pathogenesis, cell biology, antifungal susceptibility and diagnosis of Candida albicans. FEMS Yeast Research, 6, 987-998.

Copyright © 2023 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.