Before getting right into the details of how genomics can help in the detection of infectious diseases. Let’s start with the basics of what genomics is.
WHO defines genomics as the study of the genes, their functions and the relevant techniques. Moreover, unlike genetics which involves study of single gene and its properties, genomics is the study of all genes, their interrelationship and their synergistic effect on the growth and development of an individual.
Benefits offered by genomics
The study of genomics has numerous benefits and the most important being the identification of the genes responsible for causing any infectious disease. Other benefits include – development of new treatment modalities based on identification of drug target gene, developing new preventive techniques such as vaccines.
Genomics can aid in providing accurate diagnosis of several pathogens and is also able to predict the treatment strategies to control infectious diseases caused by these pathogens.
How genomics works
Genomics and bioinformatics are technological advances that can provide the microbiologists and researchers with new methods to characterize the genetic maps of disease-causing pathogens responsible for multiple infectious diseases. Genomics can assist in the prediction of pathogenic ability of the bacteria by using the RNA seq data or raw reads. By doing this it can help to identify various novel bacterial pathogens.
Different techniques in genomics like RNA sequence data that can provide a better understanding of infectious disease diagnosis include –whole genome sequencing (WGS) or new generation sequencing (NGS). New generation sequencing relates to terms like deep sequencing and parallel sequencing which are both DNA sequencing technologies. These techniques involving RNA seq data have caused a revolution in genomic research.
Genetic sequencing technologies can further our understanding of pathogenic diseases. The genomic sequences of pathogens like E. coli and staphylococcus can be used to understand their interactions and effects on their host. NGS can be used to produce RNA seq data in a single day whereas other techniques require 2 to 3 days for the same task.
Infectious diseases affect a very large population residing in various areas of our society and are also responsible for innumerable mortality and morbidity rates throughout the world. Infectious diseases are passed on from one individual to others through a variety of ways such as from human touch, waterborne, and vector borne. These diseases also vary by the type of pathogen causing them for example bacteria, fungi or virus. Infectious agents can be the cause of acute illness such as influenza or a chronic one for instance HIV and hepatitis B virus.
Diagnostic methods like PCR, microbial culturing, and serology are being used from decades for the detection of infectious diseases. They are also referred to as a gold standard of diagnostics. Although on one hand these standard and validated techniques have several benefits like robustness and cost effectiveness, they have some limitations as well.
They sometimes fail to detect the type of pathogens in a significant number of cases. This narrow scope of these standard techniques is countered by genomic techniques. Genomic techniques can help in amplifying the RNA seq data of the infectious agents. This RNA seq data is then used for their detection in the suspected host.
Next generation sequencing or NGS can help in the fast generation of thousands and millions of base pairs of DNAs sequences. The generation of RNA seq data makes it an attractive technique for detection of infectious agents and the diseases caused by them.
Infectious diseases can be confirmed by sequencing the pathogens. Also sequencing can help in distinguishing the different strains of pathogens and also aids in their classification. As compared to the examination of single pathogenic sequences, the analysis of multiple sequences can be more helpful in the evaluation of transmission history. This can be done by using phylogenetic methods. Phylogenetic methods help to portray the relations between a set of species and helps in molecular evaluation.
Techniques such as RDP (ribosomal database project) and QIME can be used to analyze both the raw sequences and the processed data. These databases contain sequence information of about 3,356,809 bacterial rRNAs.
Using these databases, the presence of virus or bacteria can be identified in the sample specimen by the use of sequence data. These databases acquire the rna seq data by using several bioinformatics tools to detect, amplify and generate chimeric sequences from various microorganisms. The generation of chimeric sequence is an essential step in the microbiome assay.
All infectious agents contain RNA or DNA genome, which provides the basic of detection by genomic techniques, making them an attractive approach for infectious disease diagnosis. The RNA seq data of viruses and bacteria can be identified and thus in turn most of the infectious diseases can easily be detected using genomic studies.
Various genomic data can be used for the detection of infectious agents by analysing the whole genomic sequence of the pathogens. NGS is an emerging technique for unbiased pathogenic detection as it detects the pathogens by amplifying their genomic sequences and provides insights to various infectious diseases.