Insights into global transcriptomic profile of biofilm producing Staphylococcus aureus clinical isolates from chronic foot ulcers
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Abstract
Background and Objectives: Staphylococcus aureus (S. aureus) is one of the predominant biofilm producing pathogen in leprosy foot ulcer (LFU). The objective of this study was to identify the transcriptome profile through Next Generation Sequencing (NGS) approach in mature biofilm of leprosy foot ulcer isolate of S. aureus.
Materials and Methods: A cross-sectional study was conducted from July 2019 to May 2022 and a total of twenty-seven S. aureus isolates were collected from the foot ulcers of leprosy patients. All S. aureus isolates were screened for biofilm formation in vitro. Initially, two potential biofilm producing isolates and two planktonic cells were selected for transcriptome comparison.
Results: With reference to transcriptome profile, out of 2,842 genes, 2,688 genes in mature biofilm and 2,685 genes in planktonic cells were expressed. Among them, forty-five differentially expressed genes with 32 and 13 genes showing up and down regulation respectively were obtained.
Conclusion: The research emphasizes the need for continued exploration into the mechanisms of biofilm formation by S. aureus, particularly in the context of leprosy foot ulcers. Understanding these pathways not only aids in grasping the complexity of chronic infections but also paves the way for innovative therapeutic approaches aimed at mitigating biofilm-related complications in clinical settings.
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7. Vestby LK, Grønseth T, Simm R, Nesse LL. Bacterial biofilm and its role in the pathogenesis of disease. Antibiotics (Basel) 2020; 9: 59.
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12. Lau K, Paus R, Tiede S, Day P, Bayat A. Exploring the role of stem cells in cutaneous wound healing. Exp Dermatol 2009; 18: 921-933.
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14. Ramos JM, Pérez-Tanoira R, García-García C, Prieto-Pérez L, Bellón MC, Mateos F, et al. Leprosy ulcers in a rural hospital of Ethiopia: pattern of aerobic bacterial isolates and drug sensitivities. Ann Clin Microbiol Antimicrob 2014; 13: 47.
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16. Ebineshan K, Pallapati MS, Srikantam A. Occurrence of bacterial biofilm in leprosy plantar ulcers. Lepr Rev 2020; 91: 130-138.
17. Zheng L, Zhang X, Lu Z, Ma W, Hu A, Zhou H, et al. Transcriptome sequencing reveals the difference in the expression of biofilm and planktonic cells between two strains of Salmonella Typhimurium. Biofilm 2022; 4: 100086.
18. Vlaeminck J, Lin Q, Xavier BB, De Backer S, Berkell M, De Greve H, et al. The dynamic transcriptome during maturation of biofilms formed by methicillin-resistant Staphylococcus aureus. Front Microbiol 2022; 13: 882346.
19. Fux CA, Costerton JW, Stewart PS, Stoodley P. Survival strategies of infectious biofilms. Trends Microbiol 2005; 13: 34-40.
20. Ranjith K, Arunasri K, Reddy GS, Adicherla H, Sharma S, Shivaji S. Global gene expression in Escherichia coli, isolated from the diseased ocular surface of the human eye with a potential to form biofilm. Gut Pathog 2017; 9: 15.
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24. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie2. Nat Methods 2012; 9: 357-359.
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28. Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data Integration and visualization. Bioinformatics 2013; 29: 1830-1831.
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30. Batista KT, Monteiro GB, Y-Schwartzman UP, de Sa aureliano roberti AFS, Rosa AG, Correia CZ, et al. Treatment of leprosy-induced plantar ulcers. Rev Bras Cir Plást 2019; 34: 497-503.
31. Metcalf DG, Bowler PG. Biofilm delays wound healing: a review of the evidence. Burns Trauma 2013; 1: 5-12.
32. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009; 10: 57-63.
33. Kaplan JB. Antibiotic-induced biofilm formation. Int J Artif Organs 2011; 34: 737-751.
34. Otto M. Staphylococcal infections: mechanisms of biofilm maturation and detachment as critical determinants of pathogenicity. Annu Rev Med 2013; 64: 175-188.
35. Carter CW Jr. Coding of class I and II Aminoacyl-tRNA synthetases. Adv Exp Med Biol 2017; 966: 103-148.
36. Coman V, Vodnar DC. Hydroxycinnamic acids and human health: Recent advances. J Sci Food Agric 2020; 100: 483-499.
37. El-Seedi HR, El-Said AM, Khalifa SA, Goransson U, Bohlin L, Borg-Karlson AK, et al. Biosynthesis, natural sources, dietary intake, pharmacokinetic properties, and biological activities of hydroxycinnamic acids. J Agric Food Chem 2012; 60: 10877-10895.
38. Yan X, Xu Y, Shen C, Chen D. Inactivation of Staphylococcus aureus by levulinic acid plus sodium dodecyl sulfate and their antibacterial mechanisms on S. aureus biofilms by transcriptomic analysis. J Food Prot 2023; 86: 100050.
39. Tomlinson BR, Malof ME, Shaw LN. A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. Microb Genom 2021; 7: 000598.
40. Wu S, Yang T, Luo Y, Li X, Zhang X, Tang J, et al. Efficacy of the novel oxazolidinone compound FYL-67 for preventing biofilm formation by Staphylococcus aureus. J Antimicrob Chemother 2014; 69: 3011-3019.
41. Wood TK, Knabel SJ, Kwan BW. Bacterial persister cell formation and dormancy. Appl Environ Microbiol 2013; 79: 7116-7121.
42. Kunnath AP, Suodha Suoodh M, Chellappan DK, Chellian J, Palaniveloo K. Bacterial persister cells and development of antibiotic resistance in chronic infections: an update. Br J Biomed Sci 2024; 81: 12958.
2. Gibbs NK, Ochalek J, Napit IB, Shrestha D, Goncalves PS, Lilford RJ, et al. Health-related quality of life implications of plantar ulcers resulting from neuropathic damage caused by leprosy: An analysis from the trial of autologous blood products (TABLE trial) in Nepal. PloS One 2025; 20(2): e0315944.
3. Tiwari A, Suryawanshi P, Raikwar A, Arif M, Richardus JH. Household expenditure on leprosy outpatient services in the Indian health system: A comparative study. PLoS Negl Trop Dis 2018; 12(1): e0006181.
4. Govindasamy K, Darlong J, Watson SI, Gill P. Prevalence of plantar ulcer and its risk factors in leprosy: a systematic review and meta-analysis. J Foot Ankle Res 2023; 16: 77.
5. Everett E, Mathioudakis N. Update on management of diabetic foot ulcers. Ann N Y Acad Sci 2018; 1411: 153-165.
6. Macdonald KE, Boeckh S, Stacey HJ, Jones JD. The microbiology of diabetic foot infections: a meta-analysis. BMC Infect Dis 2021; 21: 770.
7. Vestby LK, Grønseth T, Simm R, Nesse LL. Bacterial biofilm and its role in the pathogenesis of disease. Antibiotics (Basel) 2020; 9: 59.
8. Di Domenico EG, Farulla I, Prignano G, Gallo MT, Vespaziani M, Cavallo I, et al. Biofilm is a major virulence determinant in bacterial colonization of chronic skin ulcers independently from the multidrug resistant phenotype. Int J Mol Sci 2017; 18: 1077.
9. Ashwini B, Nandakishore B, Jyothi J. A Study of the clinico-bacteriology and antibiotic sensitivity profile of plantar ulcers in leprosy. Int J Sci Res 2015; 4: 1170-1172.
10. Rabin N, Zheng Y, Opoku-Temeng C, Du Y, Bonsu E, Sintim HO. Biofilm formation mechanisms and targets for developing antibiofilm agents. Future Med Chem 2015; 7: 493-512.
11. Gelatti LC, Bonamigo RR, Becker AP, Eidt LM, Ganassini L, d’Azevedo PA. Phenotypic, molecular and antimicrobial susceptibility assessment in isolates from chronic ulcers of cured leprosy patients: a case study in Southern Brazil. An Bras Dermatol 2014; 89: 404-408.
12. Lau K, Paus R, Tiede S, Day P, Bayat A. Exploring the role of stem cells in cutaneous wound healing. Exp Dermatol 2009; 18: 921-933.
13. Majumdar M, Chakraborty U, Das J, Barbhuiya JN, Mazumdar G, Pal NK. Bacteriological study of aerobic isolates from plantar ulcers of paucibacillary leprosy patients. Indian J Dermatol 2010; 55: 42-43.
14. Ramos JM, Pérez-Tanoira R, García-García C, Prieto-Pérez L, Bellón MC, Mateos F, et al. Leprosy ulcers in a rural hospital of Ethiopia: pattern of aerobic bacterial isolates and drug sensitivities. Ann Clin Microbiol Antimicrob 2014; 13: 47.
15. Kranjec C, Ovchinnikov KV, Grønseth T, Ebineshan K, Srikantam A, Diep DB. A bacteriocin-based antimicrobial formulation to effectively disrupt the cell viability of methicillin-resistant Staphylococcus aureus (MRSA) biofilms. NPJ Biofilms Microbiomes 2020; 6: 58.
16. Ebineshan K, Pallapati MS, Srikantam A. Occurrence of bacterial biofilm in leprosy plantar ulcers. Lepr Rev 2020; 91: 130-138.
17. Zheng L, Zhang X, Lu Z, Ma W, Hu A, Zhou H, et al. Transcriptome sequencing reveals the difference in the expression of biofilm and planktonic cells between two strains of Salmonella Typhimurium. Biofilm 2022; 4: 100086.
18. Vlaeminck J, Lin Q, Xavier BB, De Backer S, Berkell M, De Greve H, et al. The dynamic transcriptome during maturation of biofilms formed by methicillin-resistant Staphylococcus aureus. Front Microbiol 2022; 13: 882346.
19. Fux CA, Costerton JW, Stewart PS, Stoodley P. Survival strategies of infectious biofilms. Trends Microbiol 2005; 13: 34-40.
20. Ranjith K, Arunasri K, Reddy GS, Adicherla H, Sharma S, Shivaji S. Global gene expression in Escherichia coli, isolated from the diseased ocular surface of the human eye with a potential to form biofilm. Gut Pathog 2017; 9: 15.
21. Andrews S (2010). FastQC: A quality control tool for high throughput sequence data.
https://www.scirp.org/reference/referencespapers?referenceid=2781642
22. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32: 3047-3048.
23. Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34: i884-i890.
24. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie2. Nat Methods 2012; 9: 357-359.
25. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15: 550.
26. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014; 30: 923-930.
27. Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters. OMICS 2012; 16: 284-287.
28. Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data Integration and visualization. Bioinformatics 2013; 29: 1830-1831.
29. Silva-Tinoco R, Cuatecontzi-Xochitiotzi T, Reyes-Paz Y, Vidal-Santos B, Galíndez-Fuentes A, Castillo-Martínez L. Improving foot ulcer risk assessment and identifying associated factors: results of an initiative enhancing diabetes care in primary settings. Diabet Epidemiol Manag 2024; 14: 100195.
30. Batista KT, Monteiro GB, Y-Schwartzman UP, de Sa aureliano roberti AFS, Rosa AG, Correia CZ, et al. Treatment of leprosy-induced plantar ulcers. Rev Bras Cir Plást 2019; 34: 497-503.
31. Metcalf DG, Bowler PG. Biofilm delays wound healing: a review of the evidence. Burns Trauma 2013; 1: 5-12.
32. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009; 10: 57-63.
33. Kaplan JB. Antibiotic-induced biofilm formation. Int J Artif Organs 2011; 34: 737-751.
34. Otto M. Staphylococcal infections: mechanisms of biofilm maturation and detachment as critical determinants of pathogenicity. Annu Rev Med 2013; 64: 175-188.
35. Carter CW Jr. Coding of class I and II Aminoacyl-tRNA synthetases. Adv Exp Med Biol 2017; 966: 103-148.
36. Coman V, Vodnar DC. Hydroxycinnamic acids and human health: Recent advances. J Sci Food Agric 2020; 100: 483-499.
37. El-Seedi HR, El-Said AM, Khalifa SA, Goransson U, Bohlin L, Borg-Karlson AK, et al. Biosynthesis, natural sources, dietary intake, pharmacokinetic properties, and biological activities of hydroxycinnamic acids. J Agric Food Chem 2012; 60: 10877-10895.
38. Yan X, Xu Y, Shen C, Chen D. Inactivation of Staphylococcus aureus by levulinic acid plus sodium dodecyl sulfate and their antibacterial mechanisms on S. aureus biofilms by transcriptomic analysis. J Food Prot 2023; 86: 100050.
39. Tomlinson BR, Malof ME, Shaw LN. A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. Microb Genom 2021; 7: 000598.
40. Wu S, Yang T, Luo Y, Li X, Zhang X, Tang J, et al. Efficacy of the novel oxazolidinone compound FYL-67 for preventing biofilm formation by Staphylococcus aureus. J Antimicrob Chemother 2014; 69: 3011-3019.
41. Wood TK, Knabel SJ, Kwan BW. Bacterial persister cell formation and dormancy. Appl Environ Microbiol 2013; 79: 7116-7121.
42. Kunnath AP, Suodha Suoodh M, Chellappan DK, Chellian J, Palaniveloo K. Bacterial persister cells and development of antibiotic resistance in chronic infections: an update. Br J Biomed Sci 2024; 81: 12958.
| Files | ||
| Issue | Vol 17 No 2 (2025) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v17i2.18394 | |
| Keywords | ||
| Leprosy foot ulcer; Staphylococcus aureus; Biofilm; Confocal microscopy; Transcriptome | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Ebineshan K, Srikantam A, Pallapati MS. Insights into global transcriptomic profile of biofilm producing Staphylococcus aureus clinical isolates from chronic foot ulcers. Iran J Microbiol. 2025;17(2):211-219.
