Fighting infectious disease with genomics

The rapidly developing field of genomics is not only uncovering potential treatments and cures for diseases, but is playing a major role in preventing and treating infectious diseases.

 

‘Genome sequencing’ is the latest approach to the study of infectious diseases; in simple terms, genome sequencing determines the order of Deoxyribonucleic Acid (DNA) nucleotides — or bases — in a genome by using a piece of equipment, a ‘sequencer’, capable of analysing loaded DNA to study the structure and function of genes, in both human and pathogen.^{1, 2}

Forensic sciences have also incorporated genomics into its activities. Microbial genomes of pathogens involved in severe historical pandemics such as the Spanish flu and Bubonic Plague have been recovered and sequenced, tracing the origin and virulence of those past epidemics.^{3, 4}

It was mid-1995 when Haemophilus influenzae was recognised as the first organism to have its entire genome sequenced.⁵ By 2001, with over a hundred scientists, and about $3 billion, a draft of the entire human genome sequence was published⁶; this will always be an unprecedented milestone in the history of medical sciences.

Genomics and infectious disease

A growing body of evidence has indicated that a better knowledge of pathogen genomics and their vectors is likely to play a major role in preventing and treating infectious diseases.⁷ Various viral genomes have already been sequenced; by knowing their structure and action mechanisms at the molecular level, it has been possible to design antiviral drugs that can disrupt the viral genome, interfere with protein synthesis, or block the spread of viruses from cell to cell.⁸ Numerous genomic studies from the 2014 Ebola outbreak used benchtop and portable sequencing platforms to characterise this epidemic, analysis of which actively contributed to the public health response.⁹

Genomics is also being utilised by the One Health concept, a worldwide strategy aiming to expand interdisciplinary collaborations in all aspects of health care for humans, animals and the environment. Most emerging infectious diseases (EID) are zoonotic in origin, with the human population being affected due to demographic changes and/or increases in farming activity.¹⁰ The study of the human–animal interface has been a direct beneficiary of the genomics movement, particularly in foodborne outbreaks where accurately identifying related cases and point source (from paddock to plate) are crucial for developing early intervention strategies.¹¹

Faster identification processes

In the past, surveillance relied on clinical laboratories to identify pathogens from patient isolates, report the results or send isolates to health-department laboratories for additional characterisation that took days, even weeks.

Today, sequencing is starting to replace traditional microbiology techniques. High resolution sequencing is capable of differentiating related from non-related cases even with a lack of complete epidemiological information; it allows public health personnel to connect related illnesses and stop outbreaks earlier, even across continents, which would have been missed without access to this technology.¹²

A number of health systems have established pathogen genomics whole genome sequencing (WGS) infrastructure and services to meet the ongoing demand to manage infectious diseases at national and international levels. In the US, the Food and Drug Administration (FDA) has developed GenomeTrakr, a WGS-based surveillance network for detecting and investigating foodborne disease outbreaks. Public Health England (PHE) is routinely using WGS for Salmonella spp. surveillance and outbreak investigation, among a range of other pathogens of national importance.

Genomics in Australia

Australia has not been absent from the genomics movement. Various successful initiatives across the country have seen an increased use of this technology at the clinical level, identifying individual patients’ risk, as well as on the public health field for prevention and control of infectious diseases among the population. New South Wales (NSW) in particular has developed the NSW Public Health Genomics Partnership (NSW-PGP), led by the Centre for Infectious Diseases and Microbiology – Public Health at Westmead Hospital and the Marie Bashir Institute for Infectious Diseases and Biosecurity at the University of Sydney. Its main goal is to develop NSW capacity in public health pathogen genomics and to facilitate its translation into clinical practice.

It has allowed clinicians and scientists in Sydney to become some of the leading groups nationally in genomic surveillance and disease control. Since its inception in mid-2015, thousands of pathogens recovered from patient and environmental samples in NSW have been sequenced and analysed using next generation sequencing techniques.

There are some limitations to the use of genomics. Many regions, nationally and internationally, lack the laboratory capacity to implement this technology. Additionally, several ethical, legal and social issues, particularly on the application of this technology in human DNA and the release of genomic-related information, are still being raised as dilemmas. Nevertheless, it has proven it has the potential to have an important impact on health care for the future. It is fundamental that society is prepared for the many new concepts that are coming with it. Genomics are here to stay.

*Dr Cristina Sotomayor-Castillo is a Senior Research Officer at the Susan Wakil School of Nursing and Midwifery and Marie Bashir Institute for Infectious Diseases and Biosecurity.

**Professor Ramon Shaban is the inaugural Clinical Chair and Professor of Infection Prevention and Disease Control at the University of Sydney and Western Sydney Local Health District, within the Marie Bashir Institute for Infectious Diseases and Biosecurity and the Susan Wakil School of Nursing and Midwifery.

References

1. Struelens MJ, Brisse S. From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases. Euro Surveill. 2013;18(4):20386.
2. Kwong JC, McCallum N, Sintchenko V, Howden BP. Whole genome sequencing in clinical and public health microbiology. Pathology. 2015;47(3):199-210.
3. Massey SE. Comparative Microbial Genomics and Forensics. Microbiol Spectr. 2016;4(4).
4. Andam CP, Worby CJ, Chang Q, Campana MG. Microbial Genomics of Ancient Plagues and Outbreaks. Trends Microbiol. 2016;24(12):978-90.
5. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995;269(5223):496-512.
6. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science. 2001;291(5507):1304-51.
7. Gilmour MW, Graham M, Reimer A, Van Domselaar G. Public health genomics and the new molecular epidemiology of bacterial pathogens. Public Health Genomics. 2013;16(1-2):25-30.
8. Relman DA. Microbial genomics and infectious diseases. N Engl J Med. 2011;365(4):347-57.
9. Gardy JL, Loman NJ. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat Rev Genet. 2018;19(1):9-20.
10. Harding JC. Genomics, animal models, and emerging diseases: relevance to One Health and food security. Genome. 2015;58(12):499-502.
11. Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol. 2016;7:353-74.
12. Ronholm J, Nasheri N, Petronella N, Pagotto F. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev. 2016;29(4):837-57.

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