If I understood your question properly although is not very clear to me. If you mean genomics and proteomics in host, I will prioritize proteomics since we can check the affected proteins, newly synthesized, immune system function, microbes' toxins ect... While host genomics could be indicative but is not relevant to my opinion for the first diagnosis. However, if you mean microbial genomics on other hand, it is very informative to know the microbe origin, specie, pathogenicity ect..

Hello Bankole Abdul-Quadri

Genomics can improve diagnostic accuracy, predict which drugs are likely to be effective in patients, and contribute to the monitoring, treatment and control of infectious disease in individuals and in populations. One may explore the genomic structure of infectious agents, the implication of acquisition or loss of nucleotides, genes and plasmids on pathogenicity, evaluate how sequencing of the genome of infective organisms can be used for diagnosis, sub-classification and strain identity, and the sensitivity of a pathogen to drug treatment.

Few examples of genomics in clinical diagnosis of infectious diseases.

A. The application of nucleic acid sequencing and sequence-dependent detection methods may be used for the diagnosis and management of viral infections such as the blood-borne viruses human immunodeficiency virus (HIV) and hepatitis C virus (HCV).

B. Integration of genomic technologies into routine antimicrobial resistance (AMR) surveillance in health-care facilities has the potential to generate rapid, actionable information for patient management and inform infection prevention and control measures. Detection of drug resistance in plasma-borne viruses using DNA sequencing has been a mainstay for the clinical management of HIV-infected patients. This method is reliable and fast compared to the alternative, gold standard, cell-based phenotyping in culture and is also used to manage other viral infections that are treated with antivirals including HCV, hepatitis B virus, influenza and herpesviruses.

Proteomics expression provides biomarker identification by comparing the profile of protein expression between normal samples and those affected by the disease. When protein expression changes in biological pathways during disease conditions, monitoring of these altered proteins in tissue, blood, urine, or other biological samples can provide indicators of the disease.

Disease-specific biomarkers can be categorized into diagnostic for early detection; prognostic to predict disease recurrence; and treatment-predictive biomarkers. Predictive biomarkers classify patients into categories of responders and non-responders. This classification also is important in drug design applications. So, these biomarkers, in general, could reflect how patients feel and survive.

Few examples of proteomics in clinical diagnosis of infectious diseases.

A. Proteomic methods can be applied for the diagnosis of tuberculosis. Proteomic methods enable for the establishment of proteins secreted by the clinical isolates in vitro. Among these, rRv0566c, rRv3874, and rRV3369 have shown potential as sero-diagnostic antigens with a sensitivity of 43%, 74%, and 60%, and a specificity of 84%, 97%, and 96%, respectively. Therefore, kit-based serum screening test can be performed by using such groups of proteins.

B. Proteomics has played a significant role in the diagnosis of sera proteins during periods of SARS-CoV-2 outbreak. Severe acute respiratory syndrome is a viral infectious disease which was the cause of a number of deaths. For the treatment and control of this disease, a precise diagnostic approach would be important. Therefore, MS-based proteomic techniques can be used to detect SARS-CoV-2 viral proteins. Sera proteomic study of SARS patients can reveal possible protein markers of truncated forms of α 1-antitrypsin (TF-α 1-AT) that are consistently detected with higher concentrations in SARS patients than healthy individuals. These markers are proven useful as therapeutic targets, vaccine targets, and diagnostic tool for SARS patients.

The article attached below will be helpful!

https://onlinelibrary.wiley.com/doi/10.1155/2023/5510791#:~:text=Proteomics%20expression%20provides%20biomarker%20identification,those%20affected%20by%20the%20disease.

Best.