Predictive modelling of clinical outcomes in acute tonsillitis based on microbiome analysis and machine learning algorithms
Acute tonsillitis is a common disease with high clinical variability. Traditional approaches based on clinical scores (e.g., Centor) are often insufficient for accurately predicting individual outcomes. The aim of the study was to determine the significance of integrating clinical parameters and oropharyngeal microbial composition data to construct a predictive model for disease duration and symptom severity using the random forest method. Fifty-two patients with acute tonsillitis were examined. Bacteriological analysis of oropharyngeal swabs, clinical assessment using the Centor score, and rapid testing for streptococcal and viral infections were performed. Random forest and linear discriminant analysis models were constructed and compared. The random forest model demonstrated higher accuracy compared to linear discriminant analysis, especially for predicting pain intensity (overall accuracy 81.8% vs 55.0%). For disease duration, the accuracy of the random forest was 72.7% vs 75.0% for linear discriminant analysis. Feature importance analysis revealed that integrating microbiome indices (pathogen/commensal ratio – Pathogen_ratio) with the Centor clinical score significantly improved predictive ability. Disease duration was associated with bacterial aetiology (positive streptococcal test) and smoking status, while pain intensity correlated with microbial dysbiosis parameters. The combination of clinical and microbiological data in machine learning models improves the accuracy of disease progression prediction and can be used to develop personalised treatment approaches
random forest model; oropharyngeal microbiome; Centor score; rapid diagnosis; clinical prognosis; group A streptococcus; viral antigens
https://doi.org/10.63341/ijmmr/2.2025.65- Pukhlik SM, Zaporozhchenko PO. Modern aspects of the treatment of different etiopathogenetic variants of chronic nasopharyngitis. Otorinolaringologiia. 2024;7(4–6):51–71. DOI: 10.37219/2528-8253-2024-4-6-7
- Bobruk SV. Rational antibiotic therapy in the treatment of bacterial tonsillitis in children. Bull Vinnytsia Natl Med Univ. 2018;22(2):301–5. DOI: 10.31393/reports-vnmedical-2018-22(2)-14
- Wu S, Hammarstedt-Nordenvall L, Jangard M, Cheng L, Radu SA, Angelidou P, et al. Tonsillar microbiota: A cross-sectional study of patients with chronic tonsillitis or tonsillar hypertrophy. mSystems. 2021;6(2):e01302-20. DOI: 10.1128/mSystems.01302-20
- Xu H, Tian B, Shi W, Tian J, Zhang X, Zeng J, et al. A correlation study of the microbiota between oral cavity and tonsils in children with tonsillar hypertrophy. Front Cell Infect Microbiol. 2022;11:724142. DOI: 10.3389/fcimb.2021.724142
- Katundu DR, Chussi D, van der Gaast-de Jongh CE, Rovers MM, de Jonge MI, Hannink G, et al. Bacterial colonisation of surface and core of palatine tonsils among Tanzanian children with recurrent chronic tonsillitis and obstructive sleep apnoea who underwent (adeno)tonsillectomy. J Laryngol Otol. 2024;138(1):89–92. DOI: 10.1017/S0022215123001147
- Jin Z, Ma F, Chen H, Guo S. Leveraging machine learning to distinguish between bacterial and viral induced pharyngitis using hematological markers: A retrospective cohort study. Sci Rep. 2023;13(1):22899. DOI: 10.1038/s41598-023-49925-1
- Alqaissi EY, Alotaibi FS, Ramzan MS. Modern machine-learning predictive models for diagnosing infectious diseases. Comput Math Methods Med. 2022;2022:6902321. DOI: 10.1155/2022/6902321
- Zhou X, Zhang J, Deng XM, Fu FM, Wang JM, Zhang ZY, et al. Using random forest and biomarkers to discriminate between COVID-19 and Mycoplasma pneumoniae infections. Sci Rep. 2024;14(1):22673. DOI: 10.1038/s41598-024-74057-5
- Xiong Y, Ma Y, Ruan L, Li D, Lu C, Huang L, et al. Comparing different machine learning techniques for predicting COVID-19 severity. Infect Dis Poverty. 2022;11:19. DOI: 10.1186/s40249-022-00946-4
- Hong W, Lu Y, Zhou X, Jin S, Pan J, Lin Q, et al. Usefulness of random forest algorithm in predicting severe acute pancreatitis. Front Cell Infect Microbiol. 2022;12:893294. DOI: 10.3389/fcimb.2022.893294
- Cappelli F, Castronuovo G, Grimaldi S, Telesca V. Random forest and feature importance measures for discriminating the most influential environmental factors in predicting cardiovascular and respiratory diseases. Int J Environ Res Public Health. 2024;21(7):867. DOI: 10.3390/ijerph21070867
- Zhao W, Sun P, Li W, Shang L. Machine learning-based prediction model for multidrug-resistant organisms infections: Performance evaluation and interpretability analysis. Infect Drug Resist. 2025;18:2255–69. DOI: 10.2147/IDR.S459830
- Yang X, Li Y, Liu L, Zang Z. Prediction of respiratory diseases based on random forest model. Front Public Health. 2025;13:1537238. DOI: 10.3389/fpubh.2025.1537238
- Unified clinical protocol for primary, secondary (specialised) and tertiary (highly specialised) medical care Tonsillitis [Internet]. 2021 April 6 [cited 2025 June 1]. Available from: https://www.dec.gov.ua/mtd/tonzylit/
- The World Medical Association. Declaration of Helsinki: Ethical Principles for Medical Research Involving Human Subjects [Internet]. [cited 2025 June 1]. Available from: https://www.wma.net/what-we-do/medical-ethics/declaration-of-helsinki/
- Order of the Ministry of Health of Ukraine No. 690. On Approval of the Procedure for Conducting Clinical Trials of Medicinal Products and Examination of Clinical Trial Materials and the Model Regulation on Ethics Committees [Internet]. 2009 September 23 [cited 2025 June 1]. Available from: https://zakon.rada.gov.ua/laws/show/z1010-09#Text
- Klymnyuk SI, Sytnyk IO, Shirobokov VP, Tvorko MS, Tkachuk NI, Romaniuk LB, et al. Practical microbiology: A textbook. Vinnytsia: Nova Knyha; 2018. 576 P.
- El Hachem EJ, Sokolovska N, Soula H. Latent dirichlet allocation for double clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework. BMC Bioinformatics. 2023;24(1):61. DOI: 10.1186/s12859-023-05177-4
- Wang J, Yu H, Hua Q, Jing S, Liu Z, Peng X, et al. Descriptive study of random forest algorithm for predicting COVID-19 patients outcome. PeerJ. 2020;8:e9945. DOI: 10.7717/peerj.9945
- Sharif MS, Raj Theeng Tamang M, Fu CHY, Baker A, Alzahrani AI, Alalwan N. An innovative random-forest-based model to assess the health impacts of regular commuting using non-invasive wearable sensors. Sensors. 2023;23(6):3274. DOI: 10.3390/s23063274
- Thapelo TS, Mpoeleng D, Hillhouse G. Informed random forest to model associations of epidemiological priors, government policies, and public mobility. MDM Policy Pract. 2023;8(2):23814683231218716. DOI: 10.1177/23814683231218716
- Galli J, Calò L, Ardito F, Imperiali M, Bassotti E, Fadda G, et al. Biofilm formation by Haemophilus influenzae isolated from adeno-tonsil tissue samples, and its role in recurrent adenotonsillitis. Acta Otorhinolaryngol Ital. 2007;27(3):134–8.
- García Callejo FJ, Núñez Gómez F, Sala Franco J, Marco Algarra J. Management of peritonsillar infections. An Pediatr. 2006;65(1):37–43. DOI: 10.1157/13090896
- Aalbers J, O’Brien KK, Chan WS, Falk GA, Teljeur C, Dimitrov BD, et al. Predicting streptococcal pharyngitis in adults in primary care: A systematic review of the diagnostic accuracy of symptoms and signs and validation of the Centor score. BMC Med. 2011;9:67. DOI: 10.1186/1741-7015-9-67
- Jääskeläinen J, Renko M, Kuitunen I. Centor scores associated poorly with rapid antigen test findings in children with sore throat. Eur J Pediatr. 2024;184(1):4. DOI: 10.1007/s00431-024-05863-2
- Guntinas-Lichius O, Geißler K, Mäkitie AA, Ronen O, Bradley PJ, Rinaldo A, et al. Treatment of recurrent acute tonsillitis – a systematic review and clinical practice recommendations. Front Surg. 2023;10:1221932. DOI: 10.3389/fsurg.2023.1221932
- Siabrenko GP, Kyrychenko II, Shklyar AS, Tereshchenko GA, Prykhodko EO, Demikhov AO. Psychological and metabolic features of young people with stage 1 hypertension and disgarmonious fat component. Bull Med Biol Res. 2021;3(1):92–9. DOI: 10.11603/bmbr.2706-6290.2021.1.12094
- Osiejewska A, Gorajek A, Kudan M, Gradzik A, Mikut K. Acute tonsillopharyngitis – a review. J Educ Health Sport. 2022;12(7):873–82. DOI: 10.12775/JEHS.2022.12.07.08
- Dickson RP, Schultz MJ, van der Poll T, Schouten LR, Falkowski NR, Luth JE, et al. Lung microbiota predict clinical outcomes in critically ill patients. Am J Respir Crit Care Med. 2020;201(5):555–63. doi: 10.1164/rccm.201907-1487OC