Whole Genome Sequencing (WGS) Arianna Lee

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Background
The process of identifying an organism's
whole genome sequence and comparing
it to a standardized reference sequence
in a database of all other genomes
(Icahn School of Medicine, 2012).
CHEM 53.10
Purpose
It can be used for the following:
Identification of an organism
Drug susceptibility and resistance profiling
Tracing an organism's genealogy
Determining a pathogen's epidemiology
(Argimón et al., 2020).

An organism's DNA sample is taken to be analyzed at the lab

1 (Openstax, n.d.).

CHAIN TERMINATION METHOD

2 also known as dideoxy method, the DNA is first replicated

using a primer and deoxynucleotides (Openstax, n.d.).

CHAIN TERMINATION METHOD

3 The primer and deoxynucleotides are mixed with fluorescent-
labelled dideoxynucleotides (Openstax, n.d.).

CHAIN TERMINATION METHOD

Dideoxynucleotides are used because of their missing 3'
4
hydroxyl group terminates the DNA replication, leading to
multiple short DNA fragments (Openstax, n.d.).

GEL ELECTROPHORESIS
DNA fragments are separated by band size. The color-coded
5
dideoxynucleotides then reveal the template strand's sequence
(Openstax, n.d.).

Antimicrobial Resistance and in the Philippines

Antimicrobial resistance (AMR) is a growingly significant threat to the economy and public
health that demands for coordinated response among nations, government agencies, NGOs,
and other sectors. Without AMR management, healthcare expenses, the global GDP,
livestock output, and international trade would all suffer (Argimón et al., 2020).
The DOH has the
The ARSP utilizes WGS to
Antimicrobial Resistance Carbapenem is an antibiotic
identify the pathogen culture's
Surveillance Program used against numerous
drug resistance, reporting to
(ARSP) where they survey bacteria; and in the last 10
national and international
common pathogens, focusing years, pathogens have
institutions. The data
on those causing infectious increasingly become
collected is then used for
diseases as they are one of resistant to antibiotics--with
clinical guidelines on the
the leading causes of carbapenem being one of
local and international level to
morbidity and infant them (Argimón et al.,
combat AMR (Argimón et
mortality (Argimón et al., 2020).
al., 2020).
2020).

Event Response

WGS was used to identify an NICU

outbreak of drug-resistant K. Findings were disseminated to
pneumoniae. It was found that the hospitals and staff, allowing infection
Local
ST340 gene contributed to the control to take place (Argimón et al.,
pathogen's drug-resistance (Argimón 2020).
et al., 2020).

WGS helped map out the Information dissemination on a

epidemiology and geographic national level took place. Genomic
National distribution of K. pneumoniae ST147 data is now being considered to be
in the Philippines (Argimón et al., added to surveillance reports
2020). (Argimón et al., 2020).

AMR data collection is gradually

WGS helped map out the
becoming standardized. The spread of
transmission of E. coli ST410 variants
Global AMR is now better monitored and
in the Philippines and other Asian
allows for better control response
countries (Argimón et al., 2020).
(Argimón et al., 2020).

Benefits Weaknesses

WGS can trace a pathogen strain's lineage and WGS supplies and equipment can be difficult
find mutations that enable AMR (Argimón et to acquire, more so for low- or middle-income
al., 2020). countries (Argimón et al., 2020).

WGS can map the spread and epidemiology Institutions and staff may feel like they lack
of resistant pathogens, and develop infection training or are understaffed to conduct WGS
control strategies. (Argimón et al., 2020) (Argimón et al., 2020).

WGS can help monitor AMR development, AMR surveillance standardization is

which can help improve local prevention and developing, giving genetic data a more varied
response (Argimón et al., 2020) identification (Argimón et al., 2020).
Supplementary Video

ETHICS OF WGS

Confidentiality and Data Security

With concerns on who has access to one's genetic data, institutions and staff conducting WGS
should adhere to research ethics and minimize public harm (Damon, 2014).

Decision and Autonomy

Patients have autonomy to decide on who may or may not access their data. Furthermore, the
genetic data collected can be depersonalized or made anonymous through encryption, in turn,
minimizing risks of confidentiality breaches (Damon, 2014).

Public beneficence and Intellectual Freedom

Aside from developing personalized treatments, research for public health may improve due to
scientists having creative freedom to study and the rising societal and governmental duty.
Furthermore, more jobs and investments related to WGS can be provided (Damon, 2014).

POV: I am a medical practitioner

On the one hand, with reference to the ethical considerations of WGS, I would promote it. This
method can significantly improve the Philippines' surveillance of diseases and development of the
medical field. For one, WGS is already being used to track tuberculosis in the country, so it leaves
much potential for tracing other common pathogens here. However, Philippine healthcare is already
underfunded, underequipped, and understaffed. Furthermore, the current state of our healthcare calls
for bigger prioritization of primary care (Argimón et al., 2020). Hence, WGS should be gradually
integrated into Philippine medicine and be further developed in the country in accordance to the
country's resources.
References
Argimón, S., Masim, M. A. L., Gayeta, J. M., Lagrada, M. L., Macaranas, P. K. V., Cohen, V.,
Limas, M. T., Espiritu, H. O., Palarca, J. C., Chilam, J., Jamoralin, M. C., Jr, Villamin, A. S.,
Borlasa, J. B., Olorosa, A. M., Hernandez, L. F. T., Boehme, K. D., Jeffrey, B., Abudahab, K.,
Hufano, C. M., … Carlos, C. C. (2020). Integrating whole-genome sequencing within the National
Antimicrobial Resistance Surveillance Program in the Philippines. Nature Communications, 11(1),
2719. https://doi.org/10.1038/s41467-020-16322-5
Damon, J. P. (2014). Whole Genome Sequencing: Privacy and security in an era of gnomic and
advancements. Nova Science Publishers, Inc.
Icahn School of Medicine. (2012, November 9). Whole genome sequencing and you [Video].
YouTube. https://www.youtube.com/watch?v=IXamRS85hXU
Whole-Genome Sequencing. (n.d.). OpenStaxCollege. https://pressbooks-
dev.oer.hawaii.edu/biology/chapter/whole-genome-sequencing/