Urinary tract infection (UTI) is the most typical and annoying human infection, and the most common causative agent is bacterial infection, which has high recurrence rates, high virulence, and growing resistance to antibiotics. UTI samples were collected from the patient’s nonresponse to antibiotic treatment, and bacteria were identified by morphological, biochemical, and molecular biosystematics. The isolated Streptomyces geysiriensis native actinomycetes strain obtained from Desert Research Center was grown on a starch nitrate broth medium, and the bio-guided active compound of metabolite was isolated and identified by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) and authentic sample. Bacterial isolates were identified as Bacillus cereus Ur-09, Pseudomonas aeruginosa Ur-14, and Escherichia coli Ur-33. Successive polarity solvents of cell-free filtrate of S. geysiriensis extract were tested against UTI-bacterial isolated strains for antimicrobial activity. The ethyl acetate (EA) extract is the most effective against bacteria isolated from the urinary tract, with mean inhibition zones of 21.67, 20.33, and 19.77 mm against B. cereus, P. aeruginosa, and E. coli, respectively. The lowest inhibitory concentration was recorded at 5 μg/ml against B. cereus and E. coli, while it was 10 μg/ml against P. aeruginosa. EA S. geysiriensis extract was used to identify by LC–MS/MS determined a major metabolite with potential antimicrobial activities, encompassing 3,4-dihydroxybenzoic acid. An isolated 3,4-dihydroxybenzoic acid is a promising compound with high antibacterial activity against UTI bacterial isolates and to overcome resistant bacteria. The research findings offer perspectives on finding new natural sources of native active isolated compounds as potential sources for pharmacological uses.
El-sakhawy MA, Hanora A, Zaky MM, Ateya AAS, Ibrahim HS, Bast RAA. Isolation, identification, and antimicrobial evaluation of bioactive metabolites from Streptomyces geysiriensis against UTI associated bacterial strains. J Appl Pharm Sci. 2025. Article in Press. http://doi.org/10.7324/JAPS.2025.250607
1. Mitrea L, Medeleanu M, Pop CR, Rotar AM, Vodnar DC. Biotics (Pre-, pro-, post-) and uremic toxicity: implications, mechanisms, and possible therapies. Toxins 2023;15(9):548. https://doi.org/10.3390/toxins15090548
2. Amiri F, Safiri S, Aletaha R, Sullman MJM, Hassanzadeh K, Kolahi AA, et al. Epidemiology of urinary tract infections in the Middle East and North Africa, 1990-2021. Trop Med Health 2025;53:16. https://doi.org/10.1186/s41182-025-00692-x
3. Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015;13(5):269-84. https://doi.org/10.1038/nrmicro3432
4. Mancuso G, Midiri A, Gerace E, Marra M, Zummo S, Biondo C. Urinary tract infections: the current scenario and future prospects. Pathogens 2023;12(4):623. https://doi.org/10.3390/pathogens12040623
5. Ahmed SS, Shariq A, Alsalloom AA, Babikir IH, Alhomoud BN. Uropathogens and their antimicrobial resistance patterns: relationship with urinary tract infections. Int J Health Sci (Qassim). 2019;13(2):48-55.
6. Zhou Y, Zhou Z, Zheng L, Gong Z, Li Y, Jin Y, et al. Urinary tract infections caused by uropathogenic Escherichia coli: mechanisms of infection and treatment options. Int J Mol Sci. 2023;24(13):10537. https://doi.org/10.3390/ijms241310537
7. Weigel LM, Anderson GJ, Tenover FC. DNA gyrase and topoisomerase IV mutations associated with fluoroquinolone resistance in Proteus mirabilis. Antimicrob Agents Chemother. 2002;46(8):2582-7. https://doi.org/10.1128/AAC.46.8.2582-2587.2002
8. Erdem I, Kara Ali R, Ardic E, Elbasan Omar S, Mutlu R, Topkaya AE. Community-acquired lower urinary tract infections: etiology, antimicrobial resistance, and treatment results in female patients. J Glob Infect Dis. 2018;10(3):129-32. https://doi.org/10.4103/jgid.jgid_86_17
9. Al-Qurashi E, Elbnna K, Ahmad I, Abulreesh HH. Antibiotic resistance in Proteus mirabilis: mechanism, status, and public health significance. J Pure Appl Microbiol. 2022;16(3):1550-61. https://doi.org/10.22207/JPAM.16.3.59
10. Kraszewska Z, Skowron K, Kwieci?ska-Piróg J, Grudlewska-Buda K, Przekwas J, Wiktorczyk-Kapischke N, et al. Antibiotic resistance of Enterococcus spp. isolated from the urine of patients hospitalized in the University Hospital in North-Central Poland, 2016-2021. Antibiotics (Basel). 2022;11(12):1749. https://doi.org/10.3390/antibiotics11121749
11. Li Y, Kumar S, Zhang L, Wu H, Wu H. Characteristics of antibiotic resistance mechanisms and genes of Klebsiella pneumoniae. Open Med (Wars). 2023;18(1):20230707. https://doi.org/10.1515/med-2023-0707
12. Mare? C, Petca RC, Popescu RI, Petca A, Mul?escu R, Bulai CA, et al. Update on urinary tract infection antibiotic resistance-a retrospective study in females in conjunction with clinical data. Life (Basel). 2024;14(1):106. https://doi.org/10.3390/life14010106
13. Salam MA, Al-Amin MY, Salam MT, Pawar JS, Akhter N, Rabaan AA, et al. Antimicrobial resistance: a growing serious threat for global public health. Healthcare (Basel). 2023;11(13):1946. https://doi.org/10.3390/healthcare11131946
14. Cag Y, Haciseyitoglu D, Ozdemir AA, Cag Y. Antibiotic resistance and bacteria in urinary tract infections in pediatric patients. Medeni Med J. 2021;36(3):217-24. doi: https://doi.org/10.5222/MMJ.2021.78535
15. Mechal T, Hussen S, Desta M. Bacterial profile, antibiotic susceptibility pattern and associated factors among patients attending adult OPD at Hawassa University comprehensive specialized hospital, Hawassa, Ethiopia. Infect Drug Resist. 2021;14:99-110. https://doi.org/10.2147/IDR.S287374
16. Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health. 2015;109(7):309- 18. https://doi.org/10.1179/2047773215Y.0000000030
17. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev. 2015;80(1):1-43. https://doi.org/10.1128/MMBR.00019-15
18. Alam K, Mazumder A, Sikdar S, Zhao YM, Hao J, Song C, et al. Streptomyces: the biofactory of secondary metabolites. Front Microbiol. 2022;13:968053. https://doi.org/10.3389/fmicb.2022.968053
19. Uddin TM, Chakraborty AJ, Khusro A, Zidan BR, Mitra S, Emran TB, et al. Antibiotic resistance in microbes: history, mechanisms, therapeutic strategies and future prospects. J Infect Public Health 2021;14(12):1750-66. https://doi.org/10.1016/j.jiph.2021.10.020
20. Khameneh B, Eskin NM, Iranshahy M, Fazly Bazzaz BS. Phytochemicals: a promising weapon in the arsenal against antibiotic-resistant bacteria. Antibiotics 2021;10(9):1044. https://doi.org/10.3390/antibiotics10091044
21. Pradeepa P. Secondary metabolites synthesis in microorganisms. Indian J Appl Microbiol. 2019;22(2):26-32. https://doi.org/10.46798/ijam.2019.v22i02.004
22. Donald L, Pipite A, Subramani R, Owen J, Keyzers RA, Taufa T. Streptomyces: still the biggest producer of new natural secondary metabolites, a current perspective. Microbiol Res. 2022;13(3):418-65. https://doi.org/10.3390/microbiolres13030031
23. Mohammadipanah F, Wink J. Actinobacteria from arid and desert habitats: diversity and biological activity. Front Microbiol. 2016;6:1541. https://doi.org/10.3389/fmicb.2015.01541
24. Yaradoddi JS, Kontro MH, Banapurmath NR, Ganachari SV, Sulochana MB, Hungund BS, et al. Extremophilic actinobacteria. In: Yaradoddi JS, Kontro MH, Ganachari SV, editors. Actinobacteria. Rhizosphere biology. Singapore: Springer; 2021. https://doi.org/10.1007/978-981-16-3353-9
25. Karthick Kumar SB, Akilandeswari P, Pradeep BV, Begam MS, Julbiharahamed K, Vijayaselvendran RK. Isolation and identification of Streptomyces geysiriensis IN7 from marine water and evaluating the efficiency of their bioactive compounds against commonly exposed multidrug-resistant pathogens. Biol Bull Rev. 2024;14(Suppl 3):S254-64. https://doi.org/10.1134/S2079086424600784
26. Abdel Bast RA, Hanora A, Zaky M, Kobisi A. Antibacterial activity of Streptomyces sp. AMM1 metabolites isolated from Marsa Matrouh soil. Alfarama J Basic Appl Sci. 2024;5(3):320-32. https://doi.org/10.21608/ajbas.2024.249275.1198
27. Graham JC, Galloway AA. ACP best practice No 167: the laboratory diagnosis of urinary tract infection. J Clin Pathol. 2001;54(12):911-9. https://doi.org/10.1136/jcp.54.12.911
28. Rohde M. The Gram-positive bacterial cell wall. Microbiol Spectr. 2019;7(3):10-128. https://doi.org/10.1128/microbiolspec.GPP3-0044-2018
29. Paray AA, Singh M, Mir MA, Kaur A. Gram staining: a brief review. Int J Res Rev. 2023;10(9):336-41. https://doi.org/10.52403/ijrr.20230934
30. Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol. 1962;5(1):109-18. https://doi.org/10.1016/S0022-2836(62)80066-7
31. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP, Xu LH, et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol. 2001;51(2): 357-63. https://doi.org/10.1099/00207713-51-2-357
32. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406-25.
33. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993;10(3):512-26.
34. Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, et al. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc. 2013;8(3):451-60. https://doi.org/10.1038/nprot.2013.004
35. Badawy SA, Hassan AR, Abu Bakr MS, Mohammed AEI. UPLC-qTOF-MS/MS profiling of phenolic compounds in Fagonia arabica L. and evaluation of their cholinesterase inhibition potential through in-vitro and in-silico approaches. Sci Rep. 2025;15:5244. https://doi.org/10.1038/s41598-025-86227-0
36. Hudzicki J. Kirby-Bauer disk diffusion susceptibility test protocol. Am Soc Microbiol. 2009;15(1):1-23.
37. Balouiri M, Sadiki M, Ibnsouda SK. Methods for in vitro evaluating antimicrobial activity: a review. J Pharm Anal. 2016;6(2):71-9. https://doi.org/10.1016/j.jpha.2015.11.005
38. Scorzoni L, Sangalli-Leite F, de Lacorte Singulani J, Costa-Orlandi CB, Fusco-Almeida AM, Mendes-Giannini MJ. Searching new antifungals: the use of in vitro and in vivo methods for evaluation of natural compounds. J Microbiol Methods. 2016;123:68-78. https://doi.org/10.1016/j.mimet.2016.02.005
39. Bader MS, Loeb M, Brooks AA. An update on the management of urinary tract infections in the era of antimicrobial resistance. Postgrad Med. 2017;129(2):242-58. https://doi.org/10.1080/00325481.2017.1246055
40. Bader MS, Loeb M, Leto D, Brooks AA. Treatment of urinary tract infections in the era of antimicrobial resistance and new antimicrobial agents. Postgrad Med. 2020;132(3):234-50. https://doi.org/10.1080/00325481.2019.1680052
41. Monciardini P, Iorio M, Maffioli S, Sosio M, Donadio S. Discovering new bioactive molecules from microbial sources. Microb Biotechnol. 2014;7(3):209-20. https://doi.org/10.1111/1751-7915.12123
42. Aslam B, Wang W, Arshad MI, Khurshid M, Muzammil S, Rasool MH, et al. Antibiotic resistance: a rundown of a global crisis. Infect Drug Resist. 2018;11:1645-58. https://doi.org/10.2147/IDR.S173867
43. El-Sakhawy MA, Soliman GA, El-Sheikh HH, Ganaie MA. Anticandidal effect of Eucalyptus oil and three isolated compounds on cutaneous wound healing in rats. Eur Rev Med Pharmacol Sci. 2023;27(1):26-37.
44. Newman DJ, Cragg GM, Snader KM. Natural products as sources of new drugs over the period 1981−2002. J Nat Prod. 2003;66(7):1022-37. https://doi.org/10.1021/np030096l
45. Sato K, Ichiyama S, Ohmura M, Takashi M, Agata N, Ohta M, et al. A case of urinary tract infection caused by Bacillus cereus. J Inf Secur. 1998;36:247-8. https://doi.org/10.1016/S0163-4453(98)80032-7
46. Çoban B, Ülkü N, Kaplan H, Topal B, Erdo?an H, Bask?n E. Five-year assessment of causative agents and antibiotic resistances in urinary tract infections. Turk Pediatri Arsivi. 2014;49:124-9. https://doi.org/10.5152/tpa.2014.1505
47. Vasudevan R. Urinary tract infection: an overview of the infection and the associated risk factors. J Microbiol Exp. 2014;1:42-54. https://doi.org/10.15406/jmen.2014.01.00008
48. Nakamura T, Ishikawa K, Matsuo T, Kawai F, Uehara Y, Mori N. Enterococcus hirae bacteremia associated with acute pyelonephritis in a patient with alcoholic cirrhosis: a case report and literature review. BMC Infect Dis. 2021;21:999. https://doi.org/10.1186/s12879-021-06707-2
49. Amaya-Tapia G, Ibarra-Nieto G, Rivas OC, Sánchez JLG. Urinary tract infection in HIV/AIDS patients. In: Hegazy DW, El FDAA, Lwegasila DLJ, editors. Urinary tract infections. Rijeka, Croatia: IntechOpen; 2023. https://doi.org/10.5772/intechopen.110017
50. Zhou G, Wang Q, Wang Y, Wen X, Peng H, Peng R, et al. Outer membrane porins contribute to antimicrobial resistance in gram-negative bacteria. Microorganisms 2023;11(7):1690. https://doi.org/10.3390/microorganisms11071690
51. Gebremedhin KB, Yisma E, Alemayehu H, Medhin G, Belay G, Bopegamage S, et al. Urinary tract infection among people living with human immunodeficiency virus attending selected hospitals in Addis Ababa and Adama, central Ethiopia. Front Public Health 2024;12:1394842. https://doi.org/10.3389/fpubh.2024.1394842
52. Al-Mathkhury H, Flayyih M, Alghrair Z. Pathological study on Staphylococcus xylosus isolated from patients with urinary tract infections. J Al-Nahrain Univ. 2008;11:123-30. https://doi.org/10.22401/JNUS.11.2.18
53. Husna A, Rahman MM, Badruzzaman ATM, Sikder MH, Islam MR, Rahman MT, et al. Extended-spectrum β-lactamases (ESBL): challenges and opportunities. Biomedicines 2023;11(11):2937. https://doi.org/10.3390/biomedicines11112937
54. Gaurav A, Bakht P, Saini M, Pandey S, Pathania R. Role of bacterial efflux pumps in antibiotic resistance, virulence, and strategies to discover novel efflux pump inhibitors. Microbiology (Reading) 2023;169(5):001333. https://doi.org/10.1099/mic.0.001333
55. Khattab AI, Babiker EH, Saeed HA. Streptomyces: isolation, optimization of culture conditions and extraction of secondary metabolites. Int Curr Pharm J. 2016;5(3):27-32. https://doi.org/10.3329/icpj.v5i3.26695
56. Rammali S, Rahim A, El Aalaoui M, Bencharki B, Dari K, Habach A, et al. Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco. Sci Rep. 2024;14(1):3359. https://doi.org/10.1038/s41598-024-53801-x
57. Selvameenal L, Radhakrishnan M, Balagurunathan R. Antibiotic pigment from desert soil actinomycetes; biological activity, purification and chemical screening. Indian J Pharm Sci. 2009;71(5):499. https://doi.org/10.4103/0250-474X.58174
58. Rante H, Alam G, Usmar U, Zahra S, Kurniawati A, Ali A. Antimicrobial activity of Streptomyces spp. sponge-associated isolated from Samalona Island of South Sulawesi, Indonesia. Biodiv J Biol Diversity. 2022 Mar 2;23(3):1392-8. https://doi.org/10.13057/biodiv/d230325
59. Apsari PP, Budiarti SR, Wahyudi AT. Actinomycetes of rhizosphere soil producing antibacterial compounds against urinary tract infection bacteria. Biodiv J Biol Diversity. 2019;20(5):1259-65. https://doi.org/10.13057/biodiv/d200504
60. Ambarwati A, Wahyuono S, Moeljopawiro S, Yuwono T. Antimicrobial activity of ethyl acetate extracts of Streptomyces sp. CRB46 and the prediction of their bioactive compounds chemical structure. Biodiv J Biol Diversity. 2020;21(7):3380-90. https://doi.org/10.13057/biodiv/d210763
61. Shah I, Uddin Z, Hussain M, Khalil AAK, Amin A, Hanif F, et al. Streptomyces sp. from desert soil as a biofactory for antioxidants with radical scavenging and iron chelating potential. BMC Microbiol. 2024;24(1):419. https://doi.org/10.1186/s12866-024-03586-w
62. Kowalska-Krochmal B, Dudek-Wicher R. The minimum inhibitory concentration of antibiotics: methods, interpretation, clinical relevance. Pathogens 2021;10(2):165. https://doi.org/10.3390/pathogens10020165
63. Maiti PK, Das S, Sahoo P, Mandal S. Streptomyces sp SM01 isolated from Indian soil produces a novel antibiotic picolinamycin effective against multi drug resistant bacterial strains. Sci Rep. 2020;10(1):10092. https://doi.org/10.1038/s41598-020-66984-w
64. Chanthasena P, Hua Y, Rosyidah A, Pathom-Aree W, Limphirat W, Nantapong N. Isolation and identification of bioactive compounds from Streptomyces actinomycinicus PJ85 and their in vitro antimicrobial activities against methicillin-resistant Staphylococcus aureus. Antibiotics (Basel) 2022;11(12):1797. https://doi.org/10.3390/antibiotics11121797
65. Cha JW, Piao MJ, Kim KC, Zheng J, Yao CW, Hyun CL, et al. Protective effect of 3,4-dihydroxybenzoic acid isolated from Cladophora wrightiana harvey against ultraviolet B radiation-induced cell damage in human HaCaT keratinocytes. Appl Biochem Biotechnol. 2014;172:2582-92. https://doi.org/10.1007/s12010-013-0711-3
66. Westervelt P, Bloom ML, Mabbott GA, Fekete FA. The isolation and identification of 3, 4-dihydroxybenzoic acid formed by nitrogen-fixing Azomonas macrocytogenes. FEMS Microbiol Lett. 1985;30(3):331-5. https://doi.org/10.1111/j.1574-6968.1985.tb01105.x
67. Guria M, Mitra P, Ghosh T, Gupta S, Basu B, Mitra PK. 3, 4-dihydroxybenzoic acid Isolated from the leaves of Ageratum conyzoides L. Eur J Biotechnol Biosci. 2013;1:25-8.
68. Ebrahimi-Zarandi M, Bonjar GH, Riseh RS, El-Shetehy M, Saadoun I, Barka EA. Exploring two Streptomyces species to control Rhizoctonia solani in tomato. Agronomy 2021;11(7):1384. https://doi.org/10.3390/agronomy11071384
69. Khan A, Haque E, Mukhlesur RM, Mosaddik A, Rahman M, Sultana N. Isolation of antibacterial constituent from rhizome of Drynaria quercifolia and its sub-acute toxicological studies. Daru J Pharm Sci. 2007;15:205-11.
70. Syafni N, Putra DP, Arbain D. 3, 4-dihydroxybenzoic acid and 3, 4-dihydroxybenzaldehyde from the fern Trichomanes chinense L.; isolation, antimicrobial and antioxidant properties. Indones J Chem. 2012;12(3):273-8. https://doi.org/10.22146/ijc.21342
71. Kakkar S, Bais S. A review on protocatechuic acid and its pharmacological potential. ISRN Pharmacol. 2014;2014:952943. https://doi.org/10.1155/2014/952943
72. Song J, He Y, Luo C, Feng B, Ran F, Xu H, et al. New progress in the pharmacology of protocatechuic acid: a compound ingested in daily foods and herbs frequently and heavily. Pharmacol Res. 2020;161:105109. https://doi.org/10.1016/j.phrs.2020.105109
73. Liang S, Zhao Z, Liu L, Zhang Y, Liu X. Research progress on the mechanisms of protocatechuic acid in the treatment of cognitive impairment. Molecules 2024;29(19):4724 https://doi.org/10.3390/molecules29194724
74. Mangzira Kemung H, Tan LT, Chan KG, Ser HL, Law JW, Lee LH, et al. Streptomyces sp. strain MUSC 125 from mangrove soil in Malaysia with anti-MRSA, anti-biofilm and antioxidant activities. Molecules 2020;25(15):3545. https://doi.org/10.3390/molecules25153545
75. Panda L, Duarte-Sierra A. Recent advancements in enhancing antimicrobial activity of plant-derived polyphenols by biochemical means. Horticulturae 2022;8(5):401. https://doi.org/10.3390/horticulturae8050401
Year
Month