Personalized selection of topical antibacterial agents in patients with microbial eczema based on whole genome sequencing data: A prospective сomparative randomized study

Background. Each individual has a unique skin microbiota that includes a diverse resident and transient community displaying an individualized composition. This study focuses on the identification of skin microbial genomes in patients with chronic microbial eczema.

Objective. To evaluate the clinical efficacy of complex therapy in patients with microbial eczema using personalized selection of topical antibacterial agents while taking into account the determination of antibiotic resistance by whole genome sequencing.

Methods. The prospective сomparative randomized study involved 60 patients with microbial eczema in the exacerbation stage, who were randomly divided into two groups of 30 people each: main and control groups. In the control group (group 2, n = 30) patients were treated according to the Federal Clinical Guidelines. In the main group (group 1, n = 30) patients were also treated with conventional therapy, while topical antibacterial agents were selected in a personalized manner based on antibiotic resistance data. On the 21st day of therapy, an emollient with a probiotic component was added to the treatment regimen for patients of both groups. The patients underwent therapy, observation, and examination at the Department of Dermatovenerology of the Kuban State Medical University of the Ministry of Health of the Russian Federation. The clinical study was performed between December 2023 and December 2024. The observation periods in the study were divided into several stages: before the start of therapy, on days 14, 21, and six months after treatment. In this study, the microbiome of the affected skin areas of the patients was analyzed comparatively, and the effect of topical antibacterial preparation selected on the basis of whole genome sequencing data was evaluated. The laboratory stage of the present study was conducted at two sites: CL Lab Clinical Diagnostic Laboratory (“СL Medicalgroup” LLC) in Krasnodar and Serbalab Genetic Laboratory (“Serbalab” LLC) in St. Petersburg. The Eczema Area and Severity Index (EASI) was used to evaluate the skin pathologic process. Statistical processing of data was performed using the Statistica 12.0 software package (StatSoft, USA) and Microsoft Exel 2010 (Microsoft, USA). Quantitative parameters were statistically described using median and quartiles (Me (Q1;Q3)), along with mean with standard deviation (M ± SD). Differences were considered statistically significant at the error level of p < 0.05.

Results. During exacerbation in patients with chronic microbial eczema, the microbial equilibrium shifted towards an increase in microorganisms Staphylococcus aureus, Clostridioides difficile, Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli that were present on the affected skin areas, while the number of functional bacteria was limited. A more pronounced tendency to restoration of healthy microbiome in the patients of the main group was observed as soon as the 14th day. By the 6th month of treatment, the patients of the main group experienced a greater decrease in microbial colonization in the foci of microbial eczema lesions than in the control group, whereas the proportion of Bifidobacterium and Lactobacillus functionalis was increased compared to the pre-treatment values by 2.31 and 2.10 times, respectively. In addition, the disease relapse occurred in two patients in the main group (versus five in the control group), which may indicate the higher efficacy of the therapy method proposed in the study.

Conclusion. Whole genome sequencing method identifies the taxonomic diversity of the microbiome. Personalized application of topical antibacterial agent in complex therapy in the main group of patients promotes faster restoration of healthy skin microbiome than in the control group.

1. Silina LV, Schwartz NE. Skin microbiome in case of microbial eczema (in Russian only). Russian Journal of Clinical Dermatology and Venereology. 2019;18(1):49–55 (In Russ.). https://doi.org/10.17116/klinderma20191801149

2. Hülpüsch C, Rohayem R, Reiger M, Traidl-Hoffmann C. Exploring the skin microbiome in atopic dermatitis pathogenesis and disease modification. J Allergy Clin Immunol. 2024;154(1):31–41. https://doi.org/10.1016/j.jaci.2024.04.029

3. Salem I, Ramser A, Isham N, Ghannoum MA. The Gut Microbiome as a Major Regulator of the Gut-Skin Axis. Front Microbiol. 2018;9:1459. https://doi.org/10.3389/fmicb.2018.01459

4. Widhiati S, Purnomosari D, Wibawa T, Soebono H. The role of gut microbiome in inflammatory skin disorders: A systematic review. Dermatol Reports. 2021;14(1):9188. https://doi.org/10.4081/dr.2022.9188

5. Ahmad F, Alam MA, Ansari AW, Jochebeth A, Leo R, Al-Abdulla MN, Al-Khawaga S, AlHammadi A, Al-Malki A, Al Naama K, Ahmad A, Buddenkotte J, Steinhoff M. Emerging Role of the IL-36/IL-36R Axis in Multiple Inflammatory Skin Diseases. J Invest Dermatol. 2024;144(2):206–224. https://doi.org/10.1016/j.jid.2023.11.004

6. Rozhivanova TA, Polesko IV, Shcherbakova MYu. Modern concepts of the microbiocenosis of the skin and intestine in patients with eczema and metabolic syndrome. Russian Journal of Clinical Dermatology and Venereology. 2015;14(2):11–16 (In Russ.). https://doi.org/10.17116/klinderma201514211-16

7. Kobayashi T, Nagao K. Host-microbial dialogues in atopic dermatitis. Int Immunol. 2019;31(7):449–456. https://doi.org/10.1093/intimm/dxz026

8. Kovaleva YuS, Komkina NG. Microbic eczema — trigger points of influence. Meditsinskiy Sovet. 2023;17(2):37–44 (In Russ.). https://doi.org/10.21518/ms2022-031.

9. Baviera G, Leoni MC, Capra L, Cipriani F, Longo G, Maiello N, Ricci G, Galli E. Microbiota in healthy skin and in atopic eczema. Biomed Res Int. 2014;2014:436921. https://doi.org/10.1155/2014/436921

10. Murzina E, Kaliuzhna L, Bardova K, Yurchyk Y, Barynova M. Human Skin Microbiota in Various Phases of Atopic Dermatitis. Acta Dermatovenerol Croat. 2019;27(4):245–249.

11. Kuznetsov KO, Tukbaeva LR, Kazakova VV, Mirzoeva KR, Bogomolova EA, Salakhutdinova AI, Ponomareva DYu, Garipova AR, Mutsolgova MSM, Galimkhanov AG, Sakhibgareev MI, Guzhvieva ER. The Role of COVID-19 in Antibiotic Resistance in Pediatric Population. Pediatric pharmacology. 2022;19(6):503–513 (In Russ). http://dx.doi.org/10.15690/pf.v19i6.2465

12. Shah RA, Hsu JI, Patel RR, Mui UN, Tyring SK. Antibiotic resistance in dermatology: The scope of the problem and strategies to address it. J Am Acad Dermatol. 2022;86(6):1337–1345. https://doi.org/10.1016/j.jaad.2021.09.024

13. Miller AC, Adjei S, Temiz LA, Tyring SK. Antibiotic Resistance in Dermatology Part 1: Mechanisms of Resistance. Skin Therapy Lett. 2023;28(1):7–10

14. Stracy M, Snitser O, Yelin I, Amer Y, Parizade M, Katz R, Rimler G, Wolf T, Herzel E, Koren G, Kuint J, Foxman B, Chodick G, Shalev V, Kishony R. Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections. Science. 2022;375(6583):889–894. https://doi.org/10.1126/science.abg9868

15. Bin L, Malley C, Taylor P, Preethi Boorgula M, Chavan S, Daya M, Mathias M, Shankar G, Rafaels N, Vergara C, Potee J, Campbell M, Hanifin JM, Simpson E, Schneider LC, Gallo RL, Hata T, Paller AS, De Benedetto A, Beck LA, Ong PY, Guttman-Yassky E, Richers B, Baraghoshi D, Ruczinski I, Barnes KC, Leung DYM, Mathias RA. Whole genome sequencing identifies novel genetic mutations in patients with eczema herpeticum. Allergy. 2021 Aug;76(8):2510–2523. https://doi.org/10.1111/all.14762

16. Olisova OYu, Svitich OA, Poddubikov AV, Vartanova NA, Potapova MB. Microbiological assessment of the effectiveness of standard therapy in atopic dermatitis. Vestnik Dermatologii i Venerologii. 2023;99(3):44–52 (In Russ). https://doi.org/10.25208/vdv1364

17. Fölster-Holst R. The role of the skin microbiome in atopic dermatitis - correlations and consequences. J Dtsch Dermatol Ges. 2022;20(5):571– 577. https://doi.org/10.1111/ddg.14709

18. Tlish MM, Kuznetsova TG, Naatyzh ZhYu, Psavok FA. Microbial eczema: possibilities of correction at the present stage. Vestnik Dermatologii i Venerologii. 2018;94(4):60–67 (In Russ). https://doi.org/10.25208/0042-4609-2018-94-4-60-67

19. Hanifin JM, Baghoomian W, Grinich E, Leshem YA, Jacobson M, Simpson EL. The Eczema Area and Severity Index-A Practical Guide. Dermatitis. 2022;33(3):187–192. https://doi.org/10.1097/DER.0000000000000895

20. Muravyova AS, Lykov IN. Medical and environmental aspects of antibiotic resistance of the skin microbiome in family members. Problemy Regional’noi Ekologii. 2023;3:27–31 (In Russ). https://doi.org/10.24412/1728-323X-2023-3-27-32

21. Piruzyan AL, Niewozinska ZA, Korsunskaya IM. Skin bacterial infections — always a topical problem. Medical Council. 2021;8:63–66 (In Russ.). https://doi.org/10.21518/2079-701X-2021-8-63-66

22. Tarasko AD. Chronic deep recurrent pyoderma in the outpatient practice of the surgeon. Ambulatory Surgery (Russia). 2021;18(2):144–150 (In Russ.). https://doi.org/10.21518/1995-1477-2021-18-2-144-150

23. Tlish MM, Popandopulo EK. Evaluation of the effectiveness of ultratonotherapy in patients with microbial eczema. Problems of Balneology, Physiotherapy and Exercise Therapy. 2022;99(5):48–53 (In Russ.). https://doi.org/10.17116/kurort20229905148

24. Mlynarczyk-Bonikowska B, Kowalewski C, Krolak-Ulinska A, Marusza W. Molecular Mechanisms of Drug Resistance in Staphylococcus aureus. Int J Mol Sci. 2022;23(15):8088. https://doi.org/10.3390/ijms23158088

25. Xie J, Li M, Yang S, Dong Q. Topical administration of mupirocin ointment and fusidic acid in bacterial infection-induced skin diseases. Postepy Dermatol Alergol. 2025;42(1):42–46. https://doi.org/10.5114/ada.2024.145185

26. Chu DK, Chu AWL, Rayner DG, Guyatt GH, Yepes-Nuñez JJ, Gomez-Escobar L, Pérez-Herrera LC, Díaz Martinez JP, Brignardello-Petersen R, Sadeghirad B, Wong MM, Ceccacci R, Zhao IX, Basmaji J, MacDonald M, Chu X, Islam N, Gao Y, Izcovich A, Asiniwasis RN, Boguniewicz M, De Benedetto A, Capozza K, Chen L, Ellison K, Frazier WT, Greenhawt M, Huynh J, LeBovidge J, Lio PA, Martin SA, O’Brien M, Ong PY, Silverberg JI, Spergel JM, Smith Begolka W, Wang J, Wheeler KE, Gardner DD, Schneider L. Topical treatments for atopic dermatitis (eczema): Systematic review and network meta-analysis of randomized trials. J Allergy Clin Immunol. 2023;152(6):1493–1519. https://doi.org/10.1016/j.jaci.2023.08.030

27. Kotsur YuM, Chernykh TF, Flisyuk EV, Narkevich IA. Development of a topical formulation of a thiadiazole derivative. Drug development & registration. 2024;13(4):121–128 (In Russ.). https://doi.org/10.33380/2305-2066-2024-13-4-1931

28. Lax SJ, Van Vogt E, Candy B, Steele L, Reynolds C, Stuart B, Parker R, Axon E, Roberts A, Doyle M, Chu DK, Futamura M, Santer M, Williams HC, Cro S, Drucker AM, Boyle RJ. Topical Anti-Inflammatory Treatments for Eczema: A Cochrane Systematic Review and Network Meta-Analysis. Clin Exp Allergy. 2024;54(12):960–972. https://doi.org/10.1111/cea.14556