Integrative Biomedical Research
Advances in Molecular Diagnostics for Infectious Diseases: A Review of Technologies, Clinical Impact, and Future Directions
Bandar Awadh M Almutairi 1, Fahad Farej F Alshammari 1, Abdulrahman Abdulmohsen Salh Alyousef 1, Tariq Mohammed Ruwayshid Alrehaili 1, Ali Abdullah Ali Al Shehri 2, Mohammed Saeed Saleh Al Qahtani 1, Sultan Obaid Salem Alharbi 1, Abdullah Sabih Alanazi 1, Rashed Nasser Salem Aldawsari 1, Munawir Zinaf M Alqahtani 3, Majed Malfi Salem Al-Harbi 3*
Journal of Angiotherapy 8 (8) 1-13 https://doi.org/10.25163/angiotherpay.8810536
Submitted: 27 May 2024 Revised: 14 August 2024 Accepted: 20 August 2024 Published: 22 August 2024
Abstract
Molecular diagnostics has reshaped the landscape of infectious disease detection by offering clinicians the ability to identify pathogens with exceptional speed and precision. This review explores how technologies such as polymerase chain reaction (PCR), real-time PCR, next-generation sequencing (NGS), and isothermal amplification have transformed routine clinical practice. Unlike conventional culture-based tests that often require days to yield results, molecular tools can detect viral, bacterial, and emerging pathogens directly from patient samples—sometimes even before symptoms appear. This early detection capability not only supports prompt clinical decisions but also plays a vital role in breaking chains of transmission during outbreaks. Across the studies reviewed, several themes consistently emerged: improved diagnostic accuracy, enhanced capacity to track genetic mutations, and meaningful insights into antimicrobial resistance patterns. These strengths make molecular diagnostics indispensable for managing fast-moving infectious threats and guiding personalized treatment plans. However, the review also highlights practical challenges that limit widespread adoption, including high costs, the need for specialized laboratory infrastructure, quality-control requirements, and ongoing ethical concerns surrounding genomic data. Despite these barriers, innovations are rapidly advancing. Portable devices, point-of-care assays, and AI-assisted interpretation tools are expanding access and simplifying clinical workflows. Together, the evidence shows that molecular diagnostics is no longer a specialized technology reserved for advanced laboratories—it is becoming a foundational component of modern healthcare. Its continued development promises earlier detection, stronger surveillance systems, and more effective responses to global infectious disease challenges.
Keywords: Molecular diagnostics; PCR; qPCR; NGS; infectious diseases; early detection; antimicrobial resistance; outbreak surveillance; point-of-care testing; epidemiology.
References
Agnelli C., Bouza E., del Carmen Martínez-Jiménez M., et al. (2020). Clinical relevance and prognostic value of persistently negative (1,3)-β-D-glucan in adults with candidemia: A 5-year experience in a tertiary hospital. Clinical Infectious Diseases, 70(9), 1925–1932. https://doi.org/10.1093/cid/ciz555
Alquraan L., Alzoubi K. H., Rababa’h S. Y. (2023). Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity. Informatics in Medicine Unlocked, 39, 101256. https://doi.org/10.1016/j.imu.2023.101256
Anderson J., Do L. A. H., van Kasteren P. B., Licciardi P. V. (2024). The role of respiratory syncytial virus G protein in immune cell infection and pathogenesis. EBioMedicine, 107, 105318. https://doi.org/10.1016/j.ebiom.2024.105318
Asghari A., Wang C., Yoo K. M., Rostamian A., Xu X., Shin J. D., Dalir H., Chen R. T. (2021). Fast, accurate, point-of-care COVID-19 pandemic diagnosis enabled through advanced lab-on-chip optical biosensors: Opportunities and challenges. Applied Physics Reviews, 8, 031313. https://doi.org/10.1063/5.0022211
Balaji L., Manoharan H., Prabhakaran N., Manivannan N. (2024). Time-to-positivity for Candida in bloodstream infections: Prognostic implications for mortality. Cureus, 16(8), e66364. https://doi.org/10.7759/cureus.66364
Bassetti M., Giacobbe D. R., Vena A., et al. (2019). Incidence and outcome of invasive candidiasis in intensive care units (ICUs) in Europe: Results of the EUCANDICU project. Critical Care, 23(1), 219. https://doi.org/10.1186/s13054-019-2497-3
Bloos F., Held J., Schlattmann P., et al. (2018). (1,3)-β-D-glucan-based diagnosis of invasive Candida infection versus culture-based diagnosis in patients with sepsis and with an increased risk of invasive Candida infection (CandiSep): Study protocol for a randomized controlled trial. Trials, 19(1), 472. https://doi.org/10.1186/s13063-018-2868-0
Bongomin F., Gago S., Oladele R., Denning D. (2017). Global and multi-national prevalence of fungal diseases—Estimate precision. Journal of Fungi, 3(4), 57. https://doi.org/10.3390/jof3040057
Cafaro A., Barillari G., Moretti S., Palladino C., Tripiciano A., Falchi M., Picconi O., Pavone Cossut M. R., Campagna M., Arancio A., et al. (2020). HIV-1 Tat protein enters dysfunctional endothelial cells via integrins and renders them permissive to virus replication. International Journal of Molecular Sciences, 22, 317. https://doi.org/10.3390/ijms22010317
Cafaro A., Schietroma I., Sernicola L., Belli R., Campagna M., Mancini F., Farcomeni S., Pavone-Cossut M. R., Borsetti A., Monini P., et al. (2024). Role of HIV-1 Tat protein interactions with host receptors in HIV infection and pathogenesis. International Journal of Molecular Sciences, 25, 1704. https://doi.org/10.3390/ijms25031704
Ceconi M., Ariën K. K., Delputte P. (2024). Diagnosing arthropod-borne flaviviruses: Non-structural protein 1 (NS1) as a biomarker. Trends in Microbiology, 32, 678–696. https://doi.org/10.1016/j.tim.2023.11.016
Chang C. C., Harrison T. S., Bicanic T. A., et al. (2024). Global guideline for the diagnosis and management of cryptococcosis: An initiative of the ECMM and ISHAM in cooperation with the ASM. Lancet Infectious Diseases, 24(8), e495–e512. https://doi.org/10.1016/S1473-3099(23)00731-4
Chen Y. Q., Zhou Y., Wang Q. L., Chen J., Chen H., Xie H. H., Li L. (2022). Conciliatory anti-allergic decoction attenuates pyroptosis in RSV-infected asthmatic mice and lipopolysaccharide (LPS)-induced 16HBE cells by inhibiting TLR3/NLRP3/NF-κB/IRF3 signaling pathway. Journal of Immunology Research, 2022, 1800401. https://doi.org/10.1155/2022/1800401
Concha-Velasco F., González-Lagos E., Seas C., Bustamante B. (2017). Factors associated with early mycological clearance in HIV-associated cryptococcal meningitis. PLoS One, 12(3), e0174459. https://doi.org/10.1371/journal.pone.0174459
Egger M., Salmanton-García J., Barac A., et al. (2023). Predictors for prolonged hospital stay solely to complete intravenous antifungal treatment in patients with candidemia: Results from the ECMM Candida III multinational European observational cohort study. Mycopathologia, 188(6), 983–994. https://doi.org/10.1007/s11046-023-00776-4
Ensoli B., Moretti S., Borsetti A., Maggiorella M. T., Buttò S., Picconi O., Tripiciano A., Sgadari C., Monini P., Cafaro A. (2021). New insights into pathogenesis point to HIV-1 Tat as a key vaccine target. Archives of Virology, 166, 2955–2974. https://doi.org/10.1007/s00705-021-05158-z
Faust T. B., Binning J. M., Gross J. D., Frankel A. D. (2017). Making sense of multifunctional proteins: Human immunodeficiency virus type 1 accessory and regulatory proteins and connections to transcription. Annual Review of Virology, 4, 241–260. https://doi.org/10.1146/annurev-virology-101416-041654
Feng Y., Liu G., La M., Liu L. (2022). Colorimetric and electrochemical methods for the detection of SARS-CoV-2 main protease by peptide-triggered assembly of gold nanoparticles. Molecules, 27, 615. https://doi.org/10.3390/molecules27030615
Finkelman M. A. (2020). Specificity influences in (1→3)-β-D-glucan-supported diagnosis of invasive fungal disease. Journal of Fungi, 7(1), 14. https://doi.org/10.3390/jof7010014
Flower T. G., Buffalo C. Z., Hooy R. M., Allaire M., Ren X., Hurley J. H. (2021). Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein. Proceedings of the National Academy of Sciences of the USA, 118, e2021785118. https://doi.org/10.1073/pnas.2021785118
Garcia-Effron G. (2020). Rezafungin—Mechanisms of action, susceptibility and resistance: Similarities and differences with the other echinocandins. Journal of Fungi, 6(4), 262. https://doi.org/10.3390/jof6040262
Guha S., Ghimire J., Wu E., Wimley W. C. (2019). Mechanistic landscape of membrane-permeabilizing peptides. Chemical Reviews, 119, 6040–6085. https://doi.org/10.1021/acs.chemrev.8b00520
Hall R. G., Liu S., Putnam W. C., Kallem R., Gumbo T., Pai M. P. (2023). Optimizing anidulafungin exposure across a wide adult body size range. Antimicrobial Agents and Chemotherapy, 67(11), e0082023. https://doi.org/10.1128/aac.00820-23
Hamza A., Samad A., Parray Z. A., Ara S., Ahmed A., Almajhdi F. N., Hussain T., Islam A., Parveen S. (2022). Mutation in the CX3C motif of G protein disrupts its interaction with heparan sulfate: A calorimetric, spectroscopic, and molecular docking study. International Journal of Molecular Sciences, 23, 1950. https://doi.org/10.3390/ijms23041950
Hamza A., Shafat Z., Parray Z. A., Hisamuddin M., Khan W. H., Ahmed A., Almajhdi F. N., Farrag M. A., Mohammed A. A., Islam A., et al. (2021). Structural characterization and binding studies of the ectodomain G protein of respiratory syncytial virus reveal the crucial role of pH with possible implications in host-pathogen interactions. ACS Omega, 6, 10403–10414. https://doi.org/10.1021/acsomega.1c00800
He J., Melnik L. I., Komin A., Wiedman G., Fuselier T., Morris C. F., Starr C. G., Searson P. C., Gallaher W. R., Hristova K., et al. (2017). Ebola virus delta peptide is a viroporin. Journal of Virology, 91, e00438-17. https://doi.org/10.1128/JVI.00438-17
Honoré P. M., Girardis M., Kollef M., et al. (2024). Rezafungin versus caspofungin for patients with candidaemia or invasive candidiasis in the intensive care unit: Pooled analyses of the ReSTORE and STRIVE randomised trials. Critical Care, 28(1), 348. https://doi.org/10.1186/s13054-024-05117-5
Jain S., Martynova E., Rizvanov A., Khaiboullina S., Baranwal M. (2021). Structural and functional aspects of Ebola virus proteins. Pathogens, 10, 1330. https://doi.org/10.3390/pathogens10101330
Kasbergen L. M. R., Nieuwenhuijse D. F., de Bruin E., Sikkema R. S., Koopmans M. P. G. (2023). The increasing complexity of arbovirus serology: An in-depth systematic review on cross-reactivity. PLOS Neglected Tropical Diseases, 17, e0011651. https://doi.org/10.1371/journal.pntd.0011651
Keane S., Geoghegan P., Povoa P., Nseir S., Rodriguez A., Martin-Loeches I. (2018). Systematic review on the first line treatment of amphotericin B in critically ill adults with candidemia or invasive candidiasis. Expert Review of Anti-Infective Therapy, 16(11), 839–847. https://doi.org/10.1080/14787210.2018.1528872
Kohyama M., Suzuki T., Nakai W., Ono C., Matsuoka S., Iwatani K., Liu Y., Sakai Y., Nakagawa A., Tomii K., et al. (2023). SARS-CoV-2 ORF8 is a viral cytokine regulating immune responses. International Immunology, 35, 43–52. https://doi.org/10.1093/intimm/dxac044
Kumar J., Dhyani S., Kumar P., Sharma N. R., Ganguly S. (2023). SARS-CoV-2-encoded ORF8 protein possesses complement inhibitory properties. Journal of Biological Chemistry, 299, 102930. https://doi.org/10.1016/j.jbc.2023.102930
Lass-Flörl C., Kanj S. S., Govender N. P., Thompson G. R., Ostrosky-Zeichner L., Govrins M. A. (2024). Invasive candidiasis. Nature Reviews Disease Primers, 10(1), 20. https://doi.org/10.1038/s41572-024-00503-3
Li J., Eagles D. A., Tucker I. J., Pereira Schmidt A. C., Deplazes E. (2024). Secondary structure propensities of the Ebola delta peptide E40 in solution and model membrane environments. Biophysical Chemistry, 314, 107318. https://doi.org/10.1016/j.bpc.2024.107318
Liang B., Kabatova B., Kabat J., Dorward D. W., Liu X., Surman S., Liu X., Moseman A. P., Buchholz U. J., Collins P. L., et al. (2019). Effects of alterations to the CX3C motif and secreted form of human respiratory syncytial virus (RSV) G protein on immune responses to a parainfluenza virus vector expressing the RSV G protein. Journal of Virology, 93, e02043-18. https://doi.org/10.1128/JVI.02043-18
Lin X., Fu B., Xiong Y., Xing N., Xue W., Guo D., Zaky M., Pavani K., Kunec D., Trimpert J., et al. (2023). Unconventional secretion of unglycosylated ORF8 is critical for the cytokine storm during SARS-CoV-2 infection. PLOS Pathogens, 19, e1011128. https://doi.org/10.1371/journal.ppat.1011128
Lin X., Fu B., Yin S., Li Z., Liu H., Zhang H., Xing N., Wang Y., Xue W., Xiong Y., et al. (2021). ORF8 contributes to cytokine storm during SARS-CoV-2 infection by activating IL-17 pathway. iScience, 24, 102293. https://doi.org/10.1016/j.isci.2021.102293
Locke J. B., Pillar C. M., Castanheira M., et al. (2024). Outcomes by Candida spp. in the ReSTORE phase 3 trial of rezafungin versus caspofungin for candidemia and/or invasive candidiasis. Antimicrobial Agents and Chemotherapy, 68(5), e0158423. https://doi.org/10.1128/aac.01584-23
Ma J., Chen Y., Wu W., Chen Z. (2021). Structure and function of N-terminal zinc finger domain of SARS-CoV-2 NSP2. Virologica Sinica, 36, 1104–1112. https://doi.org/10.1007/s12250-021-00431-6
Melnik L. I., Garry R. F. (2022). Enterotoxigenic Escherichia coli heat-stable toxin and Ebola virus delta peptide: Similarities and differences. Pathogens, 11, 170. https://doi.org/10.3390/pathogens11020170
Melnik L. I., Guha S., Ghimire J., Smither A. R., Beddingfield B. J., Hoffmann A. R., Sun L., Ungerleider N. A., Baddoo M. C., Flemington E. K., et al. (2022). Ebola virus delta peptide is an enterotoxin. Cell Reports, 38, 110172. https://doi.org/10.1016/j.celrep.2021.110172
Muñoz P., Vena A., Machado M., et al. (2018). T2Candida MR as a predictor of outcome in patients with suspected invasive candidiasis starting empirical antifungal treatment: A prospective pilot study. Journal of Antimicrobial Chemotherapy, 73(suppl_4), iv6–iv12. https://doi.org/10.1093/jac/dky047
Mylonakis E., Zacharioudakis I. M., Clancy C. J., Nguyen M. H., Pappas P. G. (2018). Efficacy of T2 magnetic resonance assay in monitoring candidemia after initiation of antifungal therapy: The serial therapeutic and antifungal monitoring protocol (STAMP) trial. Journal of Clinical Microbiology, 56(4), e01756-17. https://doi.org/10.1128/JCM.01756-17
Pappas P. G., Lionakis M. S., Arendrup M. C., Ostrosky-Zeichner L., Kullberg B. J. (2018). Invasive candidiasis. Nature Reviews Disease Primers, 4(1), 18026. https://doi.org/10.1038/nrdp.2018.26
Pfaller M. A., Diekema D. J., Turnidge J. D., Castanheira M., Jones R. N. (2019). Twenty years of the SENTRY antifungal surveillance program: Results for Candida species from 1997–2016. Open Forum Infectious Diseases, 6(Supplement_1), S79–S94. https://doi.org/10.1093/ofid/ofy358
Pokhrel R., Pavadai E., Gerstman B. S., Chapagain P. P. (2019). Membrane pore formation and ion selectivity of the Ebola virus delta peptide. Physical Chemistry Chemical Physics, 21, 5578–5585. https://doi.org/10.1039/C8CP07323F
Ponde N. O., Shoger K. E., Khatun M. S., Sarkar M. K., Dey I., Taylor T. C., Cisney R. N., Arunkumar S. P., Gudjonsson J. E., Kolls J. K., et al. (2023). SARS-CoV-2 ORF8 mediates signals in macrophages and monocytes through MyD88 independently of the IL-17 receptor. Journal of Immunology, 211, 252–260. https://doi.org/10.4049/jimmunol.2300110
Pristov K. E., Ghannoum M. A. (2019). Resistance of Candida to azoles and echinocandins worldwide. Clinical Microbiology and Infection, 25(7), 792–798. https://doi.org/10.1016/j.cmi.2019.03.028
Rodriguez-Rodriguez B. A., Ciabattoni G. O., Duerr R., Valero-Jimenez A. M., Yeung S. T., Crosse K. M., Schinlever A. R., Bernard-Raichon L., Rodriguez Galvan J., McGrath M. E., et al. (2023). A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8. Nature Communications, 14, 3026. https://doi.org/10.1038/s41467-023-38783-0
Salmanton-García J., Cornely O. A., Stemler J., et al. (2024). Attributable mortality of candidemia—Results from the ECMM Candida III multinational European observational cohort study. Journal of Infection, 89(3), 106229. https://doi.org/10.1016/j.jinf.2024.106229
Shaaban A., Du Y. C. (2023). An optical universal plasmon-based biosensor for virus detection. Journal of Medical and Biological Engineering, 28, 1–8. https://doi.org/10.1007/s40846-023-00788-x
Sofjan A. K., Mitchell A., Shah D. N., et al. (2018). Rezafungin (CD101), a next-generation echinocandin: A systematic literature review and assessment of possible place in therapy. Journal of Global Antimicrobial Resistance, 14, 58–64. https://doi.org/10.1016/j.jgar.2018.02.013
Soriano A., Honore P. M., Puerta-Alcalde P., et al. (2023). Invasive candidiasis: Current clinical challenges and unmet needs in adult populations. Journal of Antimicrobial Chemotherapy, 78(7), 1569–1585. https://doi.org/10.1093/jac/dkad139
Su Z., Luo C., Dai K., et al. (2023). Failure of early mycological clearance in HIV-negative cryptococcal meningitis. Open Forum Infectious Diseases, 10(4), ofad158. https://doi.org/10.1093/ofid/ofad158
Theodore D. A., Henneman A. D., Loo A., et al. (2024). Initial micafungin treatment does not improve outcomes compared to fluconazole treatment in immunocompromised and critically ill patients with candidaemia. Journal of Antimicrobial Chemotherapy, 79(8), 1877–1884. https://doi.org/10.1093/jac/dkae175
Thompson G. R., Soriano A., Honore P. M., et al. (2024). Efficacy and safety of rezafungin and caspofungin in candidaemia and invasive candidiasis: Pooled data from two prospective randomised controlled trials. Lancet Infectious Diseases, 24(3), 319–328. https://doi.org/10.1016/S1473-3099(23)00551-0
Tripiciano A., Picconi O., Moretti S., Sgadari C., Cafaro A., Francavilla V., Arancio A., Paniccia G., Campagna M., Pavone-Cossut M. R., et al. (2021). Anti-Tat immunity defines CD4+ T-cell dynamics in people living with HIV on long-term cART. EBioMedicine, 66, 103306. https://doi.org/10.1016/j.ebiom.2021.103306
Urbinati C., Milanesi M., Lauro N., Bertelli C., David G., D’Ursi P., Rusnati M., Chiodelli P. (2021). HIV-1 Tat and heparan sulfate proteoglycans orchestrate the setup of in cis and in trans cell-surface interactions functional to lymphocyte trans-endothelial migration. Molecules, 26, 7488. https://doi.org/10.3390/molecules26247488
Varghese J., De Silva I., Millar D. S. (2023). Latest advances in arbovirus diagnostics. Microorganisms, 11, 1159. https://doi.org/10.3390/microorganisms11051159
Vinjamuri S., Li L., Bouvier M. (2022). SARS-CoV-2 ORF8: One protein, seemingly one structure, and many functions. Frontiers in Immunology, 13, 1035559. https://doi.org/10.3389/fimmu.2022.1035559
Wan Ismail W. N. A., Jasmi N., Khan T. M., Hong Y. H., Neoh C. F. (2020). The economic burden of candidemia and invasive candidiasis: A systematic review. Value in Health Regional Issues, 21, 53–58. https://doi.org/10.1016/j.vhri.2019.07.002
Wang X., Wang W., Wang T., Wang J., Jiang Y., Wang X., Qiu Z., Feng N., Sun W., Li C., et al. (2023). SARS-CoV-2 ORF8 protein induces endoplasmic reticulum stress-like responses and facilitates virus replication by triggering calnexin: An unbiased study. Journal of Virology, 97, e0001123. https://doi.org/10.1128/jvi.00011-23
Wei H., Zhang C., Du X., Zhang Z. (2023). Research progress of biosensors for detection of SARS-CoV-2 variants based on ACE2. Talanta, 251, 123813. https://doi.org/10.1016/j.talanta.2022.123813
Widoretno Sjahrurachman A., Dewi B. E., Lischer K., Pratami D. K., Flamandita D., Sahlan M. (2020). Surface plasmon resonance analysis for detecting non-structural protein 1 of dengue virus in Indonesia. Saudi Journal of Biological Sciences, 27, 1931–1937. https://doi.org/10.1016/j.sjbs.2020.06.018
Winkler M. L., Rhomberg P., Klauer A. L., Edeker S., Castanheira M. (2024). The in vitro activity of rezafungin against uncommon species of Candida. Mycoses, 67(11), e70001. https://doi.org/10.1111/myc.70001
Wu X., Manske M. K., Ruan G. J., Witter T. L., Nowakowski K. E., Abeykoon J. P., Tang X., Yu Y., Gwin K. A., Wu A., et al. (2023). Secreted ORF8 induces monocytic pro-inflammatory cytokines through NLRP3 pathways in patients with severe COVID-19. iScience, 26, 106929. https://doi.org/10.1016/j.isci.2023.106929
Xu Z., Choi J. H., Dai D. L., Luo J., Ladak R. J., Li Q., Wang Y., Zhang C., Wiebe S., Liu A. C. H., et al. (2022). SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation. Proceedings of the National Academy of Sciences of the USA, 119, e2204539119. https://doi.org/10.1073/pnas.2204539119
Zhang C., Zheng W., Huang X., Bell E. W., Zhou X., Zhang Y. (2020). Protein structure and sequence reanalysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1. Journal of Proteome Research, 19, 1351–1360. https://doi.org/10.1021/acs.jproteome.0c00129
Save
Citation
View
Share