Microarray and respiratory tract infections

 Infecţiile de tract respirator şi tehnica microarray

First published: 15 noiembrie 2015

Editorial Group: MEDICHUB MEDIA


Respiratory Tract Infections (RTIs) involve complicated microbial diseases which rank among first four deathful diseases around the globe. Classical and traditional microbiologic and serologic assays are not useful for an accurate and definite diagnosis and treatment. The nucleic acid based and molecular technologies are capable to provide us an effective diagnostic tool for a definite treatment. Among a vast range of molecular diagnostic tools microarray is an invaluable technique with rapid, accurate, sensitive, specific and cost effective properties. For this reason, this review has paid an especial attention to application of microarray for diagnosing RTIs. This article has been prepared via searching different types of articles regarding to the topic throughout the Internet. Google Scholar and PubMed were used for the most. Simultaneously, the experiences of the authors were helpful for writing this review literature. The results from different surveys confirm the application of microarray technology as an accurate, rapid, sensitive, specific, and cost effective technology to have an accurate and definite diagnosis and treatment in association with RTIs. We conclude that microarray technology is an appropriate multiparametric diagnostic technique which may be used in large scale clinical applications to decrease the rate of mortality among patients with RTIs worldwide. 

microarray, respiratory tract, pathogens, infectious diseases


Infecţiile de tract respirator (ITR) includ afecţiuni microbiene complexe, care reprezintă primele patru afecţiuni mortale de pe glob. Testele serologice şi microbiologice clasice şi tradiţionale nu sunt suficiente pentru un diagnostic şi tratament specific. Tehnologiile moleculare şi cele bazate pe testarea acizilor nucleici şi-au dovedit utilitatea ca instrumente diagnostice necesare unui tratament specific. Din gama largă de instrumente de diagnostic molecular, tehnica microarray este deosebit de valoroasă, fiind o metodă de laborator rapidă, precisă, cu sensibilitate crescută şi cu raport cost-beneficiu bun. Din acest motiv, lucrarea-review de faţă a acordat o atenţie deosebită utilizării tehnicii microarray în diagnosticul ITR. Această lucrare se bazează pe evaluarea literaturii de specialitate accesibilă pe Internet, a articolelor referitoare la acest subiect. Google Scholar şi PubMed au fost cele mai utilizate site-uri web. De asemenea, experienţa autorilor a fost utilă în redactarea articolului prezent. Rezultatele altor articole de tip review confirmă şi ele utilizarea tehnicii microarray ca un instrument precis, rapid, cu sensibilitate şi specificitate diagnostică bună şi cu raport cost-beneficiu eficient în obţinerea unui diagnostic şi tratament specific necesar infecţiilor de tract respirator (ITR). În concluzie, tehnica microarray este o tehnică de diagnostic multiparametrică adecvată, care poate fi utilizată clinic pe scară largă, pentru a scădea rata mortalităţii în rândul pacienţilor cu ITR din întreaga lume.


The RT structure in human being is divided into upper and lower respiratory tract (URT and LRT, respectively). The RT is a border structure between human body’s inner side and outer side. Thus, RT works as a channel which mediates the movement of airstream from environment to the inside of the body and vice versa. The air depending on the geographic situation of the place may include different particles such as dust, salt, carbon and microorganisms(1-3).

Each person inhales about 104 L air within her/his lungs during a day. In normal people who own healthy immune system, pathogenic microorganisms are failed to colonize and grow within RT(2).

According to several investigations, RT infections (RTIs) rank as the first four human diseases with high mortality and morbidity. The most important causative microbial agents relating to RTIs are recognized as bacteria, fungi and viruses. There are two main acquisition forms for RTIs involving community and hospital. Hospital acquired RTIs may occur person-to-person or via improper ventilation. Previous studies indicate a broad range of opportunistic and pathogenic microbial agents that cause different types of URT and LRT infections.

Moreover, the appearance of multidrug resistant microorganisms has increased the complicated position of RTIs. Therefore, traditional routine microbiologic approaches are not appropriate for accurate, rapid and definite diagnosis(4,5).

Molecular technologies are known as accurate and rapid diagnostic tools which include a wide range of methods. Polymerase Chain Reaction (PCR) tests are a group of molecular techniques that possess multifunctional characteristics. Although PCR assays seems to be a suitable choice for diagnosing RTIs, they are time consuming and are not cost effective for detecting and identifying high numbers of microorganisms and clinical samples. Today, microarray technologies give an excellent opportunity for diagnosing accurate, rapid and definite. Simultaneously, multidrug resistant microorganisms may be detectable throughout microarray techniques. In addition to diagnostic application of microarray, this technology enables us to provide gene profiles regarding to different types of pathogens and opportunistic microorganisms. The use of microarray relating to high numbers of specimens and microorganisms is cost effective and time consuming(4,6-9).

The aim of the present review article is to study the importance of microarray as an accurate, rapid and definite diagnostic tool for detecting and identifying RTIs.

The RT microflora

Prior to Human Microbiome Project (HMP) achieved by National Institutes of Health (NIH), the main part of LRT such as lung was reported as sterile and germfree structure. Indeed, it was the traditional culture based diagnostics faults.

After performance of HMP throughout advanced molecular diagnostic techniques, the lung’s microflora were detected and identified(10-12).

There are a large number of bacteria which belong to RT microflora.

The types of bacteria are directly related to environmental situations, climate characteristics and geographic position. But, generally LRT has its own normal flora such as Acinetobacter spp., Bacteroides spp., Fusobacterium spp., Haemophilus spp., Lactobacillus spp., Micrococcus sp., Prevotella spp., Pseudomonas spp., Streptococcus spp., and veillonella spp.

On the other hand, the URT microflora population is consisted of Corynebacterium spp. (commensal species), Haemophilus influenzae (sometimes), Neisseria spp. (commensal species), and Streptococcus spp. (a-haemolytic and non-haemolytic strains)(1,2,11,13-15).

According to recorded reports, lungs in healthy people have a low number of microflora with a wide range of varieties. Knowledge about the RT microbiome helps us to recognize RTIs in an easy way.

The types of microorganisms (bacteria, fungi, viruses) guide us to have an aware guess about the situation of RT: healthy, allergy, asthma, bronchitis, bronchopulmonary infections, cystic fibrosis, newborn RTIs, pneumonia, atypical pneumonia, Legionnaires disease  chronic obstructive pulmonary disease (COPD), sinusitis, tuberculosis, Tularemia, and viral RTIs. Moreover, the viral infections in association with RTIs may lead to predispose for bacterial adhesion and secondary bacterial RTIs(11,13,15-18).

Because of the high frequency of microbial diversity and complicated interactions among microbial populations within human RT, the application of accurate, rapid and reliable methodologic issues are unavoidable(2,4,11,15).

Diagnostic tools applied for detecting RTIs

Diagnostic test has the key role for an accurate and definite treatment. The reliability of diagnosis is the principle of accurate detection and appropriate identification to have a confident treatment to reduce the rate of morbidity and mortality(9,19).

Before the fulminant advances in diagnostic tech­niques for RTIs, the routine classical tests were consisted of direct microscopy of the raw and staining clinical sample like sputum and cultured base methods. Simultaneously, the use of serologic tests including ELISA, fluorescent antibody test, radioimmunoassay, agglutination, microbial antigen or/and antibody detection etc. were progressed without any considerable results for accurate and definite detection and identification of microbial causative agents of RTIs. The classical and traditional diagnostics are inaccurate, time consuming, indefinite. So, their results are neither valuable nor reliable(4,20,21).

By the advances in clinical diagnostics and the appearance of nucleic acid based tests and nucleic acid amplification techniques (NAATs) it was revealed that the microbial nucleic acids were present in all clinical samples taken from respiratory tract. PCR techniques, loop mediated amplification (LAMP) and microarray are the most applied nucleic acid based tools used as microbiologic diagnostic approaches in different fields of infectious diseases such as RTIs. PCR tools are accurate, specific and sensitive and cost effective, if the number of specimens, microorganisms or genes is low. Otherwise, PCR technologies are expensive and time consuming. However, PCR technologies are capable to detect all the pathogenic microorganisms such as bacteria, fungi and viruses. In the case of high numbers of samples, the microarray technology is substituted as an appropriate alternative(1,7,20,22,23)

Microarray technology

Microarray technologies and particularly DNA microarray techniques are based on miniaturized spots of immobilized nucleic acid probes on array slide (chip), labeling single stranded target DNA within sample, hybridization of probes and target sequences and finally scanning stage. Because of the high sensitivity, specificity, accuracy, rapidity and reliability relating to DNA microarray technologies, the use of microarray may be qualitative or quantitative.

Diagnostic applications of microarray include physiologic and biochemical diseases, infectious diseases, and genetic malfunctions and dysregulations in which the produced data are qualitative. The microarray data provided in gene profiling and gene expression profiling are quantitative(6-9,19,23,24).

Choosing correct platforms and suitable probe sets in microarray technologies lead to get accurate and reliable results. The rapidity and multiparametric characterizations of microarray are the other useful properties relating to microarray technologies(4,9,19,23,24)

By the progression of microarray technologies, several online databases have been designed and activated for the users worldwide for free and without any charges. This important revolution has increased the application of microarray techniques in the field of infectious diseases(8).

The importance of microarray methodologies in RTIs

Respiratory tract infections are known as multi-microbial infectious diseases. There are different opportunistic and pathogenic bacterial, fungal and viral causative agents which can lead to a vast range of respiratory disorders, diseases and infections. Because of complicated condition relating to RTIs, classical and traditional microbiologic and serologic tests are not useful in the most cases.

The outcome of applied classical diagnostics is high mortality in patients with RTIs. In parallel with high diversity of microbial infectious agents causing RTIs, several studies indicate the increase of multi drug resistant microorganisms which cause RTIs. Hence, for challenging with a huge number of deathful outcomes in association with RTIs; rapid, accurate, sensitive, specific and reliable diagnostic tools are needed to overcome the problems(20,21,25).

Microarray enables us to detect tens, hundreds and thousands of microbial pathogens causing RTIs. The commercial microarray products such as resequencing microarray, Lawrence Livermore Microbial Detection Array (LLMDA), GreeneChip, ViroChip, and PathChip are capable to detect a wide range of pathogens in clinical specimens of patients with RTIs(18,24,26-28).

On the other hand, the presence of different pathotypes and strains among microbial agents of RTIs, and multidrug resistant microorganisms, provoke us to profile genes and their expressions to categorize all the strains to have an appropriate diagnosis and definite treatment. Microarray has the capability of gene and gene expression profiling with high sensitivity and specificity. Microarray technology is able to study hundred of thousands genes at the same time(4,6-9,12,18-21,23,24,26-28).     


The RTIs involve a vast range of diseases and microorganisms. RTIs are categorized into acute, mild and chronic groups. Some of RTI such as tularemia are deathful. Moreover, the microbial nucleic acids are spread within clinical samples.

There are a huge diversity of gram positive and gram negative bacterial, fungal and viral agents which some of them predispose other diseases and infections.

Furthermore, the high progression of multidrug resistant microorganisms among causative agents of RTIs around the world is a big threat in global public health.

According to aforementioned reasons, there is a need for a rapid, accurate, reliable, sensitive, specific, and cost effective diagnostic technology. Although, the use of PCR technologies for limited diagnostics may be helpful, but regarding to vast diagnostic applications are ineffective, expensive and time consuming.

The use of microarray in large scale applications gives us a diversity of possibilities including gene and gene expression profiling, genotyping, fragile and precise classifications of pathotypes and microbial strains to have a rapid, accurate, cost effective and definite diagnosis and treatment regarding to RTIs to reduce to level of mortality worldwide.


  1. Behzadi P, Behzadi E. Environmental Microbiology. 1st ed. Tehran: Niktab; 2007.

  2. Cullen L, McClean S. Bacterial Adaptation during Chronic Respiratory Infections. Pathogens. 2015;4(1):66-89.

  3. Wozniak-Kosek A, Kosek J, Zielnik-Jurkiewicz B. Detection of Respiratory Tract Pathogens with Molecular Biology Methods.  Respiratory Infections: Springer; 2015. p. 9-13.

  4. Reddington K, Tuite N, Barry T, O’Grady J, Zumla A. Advances in multiparametric molecular diagnostics technologies for respiratory tract infections. Current opinion in pulmonary medicine. 2013;19(3):298-304.

  5. Zumla A. Killer respiratory tract infections: time to turn the tide. Current opinion in pulmonary medicine. 2012;18(3):173-4.

  6. Behzadi P, Najafi A, Behzadi E, Ranjbar R. Detection and Identification of Clinical Pathogenic Fungi by DNA Microarray. Infectioro. 2013;35(3):6-10.

  7. Behzadi P, Ranjbar R, Alavian SM. Nucleic Acid-Based Approaches for Detection of Viral Hepatitis. 2015.

  8. Behzadi P, Behzadi E, Ranjbar R. Microarray data analysis. Albanian medical journal. 2014;4:84-90.

  9. Behzadi P, Behzadi E, Ranjbar R. The application of Microarray in Medicine. ORLro. 2014;24(3):24-6.

  10. Kiley JP. Advancing respiratory research. CHEST Journal. 2011;140(2):497-501.

  11. Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Translational Research. 2012;160(4):258-66.

  12. Proctor LM. The human microbiome project in 2011 and beyond. Cell host & microbe. 2011;10(4):287-91.

  13. Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. American journal of respiratory and critical care medicine. 2011;184(8):957-63.

  14. Zakharkina T, Heinzel E, Koczulla RA, Greulich T, Rentz K, Pauling JK, et al. Analysis of the airway microbiota of healthy individuals and patients with chronic obstructive pulmonary disease by T-RFLP and clone sequencing. PloS one. 2013;8(7):e68302.

  15. Bosch AA, Biesbroek G, Trzcinski K, Sanders EA, Bogaert D. Viral and bacterial interactions in the upper respiratory tract. PLoS pathogens. 2013;9(1):e1003057.

  16. Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, et al. Analysis of the lung microbiome in the “healthy” smoker and in COPD. PloS one. 2011;6(2):e16384.

  17. Medscape: emedicine; 2015. Available from:

  18. Schnee C, Schulsse S, Hotzel H, Ayling RD, Nicholas RA, Schubert E, et al. A novel rapid DNA microarray assay enables identification of 37 Mycoplasma species and highlights multiple Mycoplasma infections. PloS one. 2012;7(3):e33237.

  19. Yoo SM, Choi JH, Lee SY, Yoo NC. Applications of DNA microarray in disease diagnostics. J Microbiol Biotechnol. 2009;19(7):635-46.

  20. Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, et al. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections—needs, advances, and future prospects. The Lancet Infectious Diseases. 2014;14(11):1123-35.

  21. Donatin E, Drancourt M. DNA microarrays for the diagnosis of infectious diseases. Médecine et maladies infectieuses. 2012;42(10):453-9.

  22. Speers DJ. Clinical applications of molecular biology for infectious diseases. Clinical Biochemist Reviews. 2006;27(1):39.

  23. Miller MB, Tang Y-W. Basic concepts of microarrays and potential applications in clinical microbiology. Clinical microbiology reviews. 2009;22(4):611-33.

  24. Najafi A, Ram M, Ranjbar R. Microarray: Principles & applications 1st ed. Tehran: Persian Science & Research Publisher; 2012.

  25. Behzadi P, Behzadi E, Ranjbar R. Multidrug-Resistant Bacteria. 2014;39(3):29-31.

  26. Simões EA, Patel C, Sung W-K, Lee CW, Loh KH, Lucero M, et al. Pathogen chip for respiratory tract infections. Journal of clinical microbiology. 2013;51(3):945-53.

  27. Lin B, Wang Z, Vora GJ, Thornton JA, Schnur JM, Thach DC, et al. Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome research. 2006;16(4):527-35.

  28. Rodrigo MAM, Zitka O, Krejcova L, Hynek D, Masarik M, Kynicky J, et al. Electrochemical Microarray for Identification Pathogens: A. Int J Electrochem Sci. 2014;9:3431-9.