Week 1: What is Gene Sequencing?

Hi everyone, welcome back to my blog! This week, I will be focusing on what gene sequencing is and how the data can be further analyzed in public health scenarios. 

What is Gene Sequencing?

Gene sequencing determines the precise order of the nucleotides – adenine, thymine, cytosine, and guanine – of a DNA molecule found within an organism’s cell. First, the DNA molecules are extracted from liquid or solid samples of tissues before the fragmentation process takes place and adapters are attached to help with sequencing. Depending on the type of technology used within the gene sequencer, millions of short reads or multiple long reads of these nucleotide base pairs are carried out. Afterward, these short or long reads are aligned to a reference genome (which, in some cases, can be E. Coli for bacteria reads or GRCh38 for human reads). Now, the sequence is fully constructed and ready for any computational or manual analysis. 

Gene sequencing retains importance throughout medical fields such as oncology, research spheres such as microbiology and evolutionary biology, and agriculture. It betters the scientific understanding of genetic diseases, targeted therapies, and evolutionary relationships among organisms.

Public Health Scenarios: Applications of Gene Sequencing

In my first blog post, I mentioned one specific instance of gene sequencing being used to help contain agricultural and medical outbreaks of foodborne illnesses. The 2011 E. Coli O104:H4 outbreak took place in Northern Germany and was caused by mutations within an enteroaggregative E. Coli (EAEC) strain that produced Shiga toxins. Whole genome sequencing (WGS) was utilized to identify the presence of mutations causing unusually virulent characteristics and antibiotic resistance and tracing its origins to Central Africa; however, it also highlighted how targeted diagnostics tests can be created to contain the spread of the disease more effectively. 

This is not the only historical example of gene sequencing being used to help contain the spread of E. Coli, but this next instance had to do with the 2018 E. coli O157:H7 outbreak within romaine lettuce in the United States. The CDC utilized WGS to analyze the bacteria found within infected patients to determine that the outbreak had been caused by the Shiga toxin-producing E. coli (STEC) O157:H7. Through a comparison to genetic sequences from various sources across the country, the origin of the outbreak was traced back to Arizona. This situation demonstrated how gene sequencing is necessary and incredibly helpful for containing the spread of the disease, identifying the source, and determining the cause. 

However, these public health scenarios also highlight an emergent need for computer algorithms to help streamline the comparison process of bacterial gene sequences. This will help ensure that mutations can be identified at a quicker pace and also allow for a more established understanding of the impact that mutations may have on patients, animals, and plants. Therefore, the literature review covered in this blog post emphasizes the need for a computer algorithm to compare gene sequences for medical, research, and agricultural applications. 

Links for Further Research:

• https://www.cdc.gov/advanced-molecular-detection/about/what-is-genomic-sequencing.html#:~:text=The%20genome%20of%20an%20organism,with%20unique%20genetic%20%22fingerprints.%22 
• https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6250a3.htm
• https://pubmed.ncbi.nlm.nih.gov/30062592/
• https://pmc.ncbi.nlm.nih.gov/articles/PMC8796143/