Antagonistic activity of native Streptomyces spp. against ESBL- and KPC- producing Enterobacteriaceae and MRSA

Actividad antagónica de Streptomyces spp. nativas frente a Enterobacteriaceae productoras de BLEE y KPC, y a MRSA

Published 2025-07-01

Open | Download
PDF (Spanish) FLIP
Issue
Vol. 24 No. 45 (2025): 2025-02
Section
Artículo Original
How to Cite
Osorio Echeverri, V. M., Mejía Muñoz, A., Correa Gómez, E., Ochoa Aristizábal, A. M., Rada Bravo, A. M., & Martínez, J. G. (2025). Antagonistic activity of native Streptomyces spp. against ESBL- and KPC- producing Enterobacteriaceae and MRSA. Revista Nova, 24(45). https://doi.org/10.22490/
DOI

https://doi.org/10.22490/
Dimensions
PlumX
Citations
Crossref
Citations in Crossref
Scopus
Citations in Scopus
Google Scholar
Europe PMC
Citations in Europe PMC
license
Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Victor Manuel Osorio Echeverri
Mr
    https://orcid.org/0000-0002-9134-2713

    Alejandro Mejía
      https://orcid.org/0000-0002-9530-2209

      Elizabeth Correa Gómez
        https://orcid.org/0000-0001-7659-7518

        Ana María Ochoa Aristizábal
          https://orcid.org/0000-0002-2661-9632

          Ana Mercedes Rada Bravo
            https://orcid.org/0000-0002-9624-4776

            José Gregorio Martínez
              https://orcid.org/0000-0002-0731-4358

              Show authors biography

              Victor Manuel Osorio Echeverri,

              BSc in Chemical Engineering and MSc in Biotechnology. He is a professor at I.U. Colegio Mayor de Antioquia in the Biotechnology bachelor’s degree program. With experience in the isolation, characterization and production of antimicrobial compounds and hydrolytic enzymes with filamentous bacteria, and the determination of the antimicrobial activity of compounds produced by microorganisms or extracted from plants.

              Alejandro Mejía

              Professional in Bacteriology and Clinical Laboratory from I.U. Colegio Mayor de Antioquia. PhD student in Biology at the University of Antioquia. Associated with the Biology and Control of Infectious Diseases (BCEI) research group at the University of Antioquia. He has experience in microbiology, molecular biology, bioinformatics, and next-generation sequencing (NGS) library development. His main areas of interest are transcriptomics, genomics, and insecticide resistance.

              Elizabeth Correa Gómez

              Professional in Bacteriology and Clinical Laboratory, M.Sc. in Biotechnology. With experience in control of pathogens through quorum sensing systems and antimicrobial peptides. She was a professor of Mycology, and mentor of the research hotbed program of the Faculty of Health Sciences of Colegio Mayor de Antioquia. Ph.D. student in Biology working in Corporation for Biological Research on evaluation of compounds for colorectal cancer control, both in vitro and animal models, in Medical and Experimental Mycology research group.

              Ana María Ochoa Aristizábal

              Biotechnology professional from the IU Colegio Mayor de Antioquia. Master's degree in Biotechnology from the National University of Colombia, Medellín campus. He has experience using bioinformatics tools and molecular species differentiation.

              Ana Mercedes Rada Bravo

              Proffesional in Bacteriology and Clinical Laboratory. PhD in Basic Biomedical Sciences with an emphasis on Molecular Biology. Professor and researcher in Clinical Microbiology in I.U. Colegio Mayor de Antioquia, with experience in interdisciplinary work in the areas of Basic Biomedical Sciences in Parasitology and Microbiology with an emphasis on Molecular Biology. She is currently involved in research projects in the area of ​​surveillance and molecular detection of bacterial resistance.

              José Gregorio Martínez

              Aquaculture Engineer with a Master's degree in Biotechnology and a PhD in Biotechnology from the Federal University of Amazonas (Brazil). He has research experience in the areas of fish sperm cryoconservation and reproductive biotechnology, with an emphasis on aquaculture and fisheries resources. His scientific publications focus on biotechnological tools such as molecular markers (SNPs, microsatellites, and mitochondrial sequences) for animal genomics studies (sex markers), phylogenomics, phylogeography, population genomics/genetics, and molecular identification of species and quantitative traits (QTLs), in addition to the use of second-generation sequencing technologies (IonTorrent, Illumina). 

              Introduction. The search for microorganisms producing antimicrobial compounds represents a strategy to address the global crisis of antibiotic resistance. Identification of bacteria of the genus Streptomyces with antagonistic activity against resistant bacteria is the initial step for the subsequent recovery of effective antibacterial metabolites for the inhibition of these resistant organisms. Objectives. Recognize promising sources to isolate filamentous bacteria able to inhibit clinical isolates, including ESBL- and KPC- producing Enterobacteriaceae and MRSA. Methods.  Actinobacteria were isolated from rhizospheres and a compost system. MRSA, Escherichia coli, and Klebsiella pneumoniae clinical isolates were chosen to address antagonism tests. Antibacterial activity was recorded by a cross-streak method. Streptomyces isolates were characterized according to International Streptomyces Project and the native isolates with antimicrobial activity were identified by molecular techniques. Results. Nine isolates of actinobacteria with activity against resistant-antibiotic bacteria were obtained, two from the avocado rhizosphere, four from a living fence and three from a composting system. Two of the isolates showed activity against all the tested antibiotic-resistant bacteria. Molecular taxonomic identification found S. jumonjinensis, S. bacillaris, S. prasinus, S. microflavus, and S. cadmiisoli as putative species for native isolates. Conclusions. Streptomyces with antibacterial activities against ESBL and KPC-producing Enterobacteria and MRSA have been isolated and the potential of rhizospheres and compost systems for obtaining antibiotic-producing bacteria was validated. Native isolates exhibited common traits for Streptomyces; although NCBI's Blast did not show a resolution to identification, EzBioCloud 16S-based identification was able to accurately detect the identity of the isolates down to the species level.

              Article visits 14 | PDF visits 7

              Downloads

              Download data is not yet available.
              1. World Health Organization. Report of the 6th Meeting: WHO Advisory Group on Integrated Surveillance of Antimicrobial Resistance with AGISAR 5-year strategic framework to support implementation of the global action plan on antimicrobial resistance (2015-2019). Seoul: WHO Press; 2015.
              2. World Health Organization. WHO bacterial priority pathogens list, 2024: Bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance [Internet]. Geneva: WHO Press; 2024 [accessed 4 June 2025]. Available in: https://www.who.int/publications/i/item/9789240093461
              3. Procópio REL, da Silva IR, Martins MK, de Azevedo JL, de Araújo JM. Antibiotics produced by Streptomyces. Braz J Infect Dis. 2012; 16(5): 466-471. doi: 10.1016/j.bjid.2012.08.014.
              4. Asagbra AE, Sanni AI, Oyewole OB. Solid-state fermentation production of tetracycline by Streptomyces strains using some agricultural wastes as substrate. World J Microbiol Biotechnol. 2015; 21: 107-114. doi: 10.1007/s11274-004-2778-z.
              5. Higgens CE, Kastner RE. Streptomyces clavuligerus sp. nov., a b-Lactam antibiotic producer. Int J Syst Microbiol. 1971; 21(4): 326-331. doi: 10.1099/00207713-21-4-326.
              6. Arora A, Nain L, Gupta JK. Solid-state fermentation of wood residues by Streptomyces griseus B1, a soil isolate, and solubilization of lignins. World J Microbiol Biotechnol. 2005; 21: 303-308. doi: 10.1007/s11274-004-3827-3.
              7. Moellering RC. Vancomycin: A 50-Year Reassessment. Clin Infect Dis. 2017; 42(S1): 3-4. doi: 10.1086/491708.
              8. Thakur D, Yadav A, Gogoi BK, Bora TC. Isolation and screening of Streptomyces in soil of protected forest areas from the states of Assam and Tripura, India, for antimicrobial metabolites. J Mycol Med. 2007; 17(4): 242-249. doi: 10.1016/j.mycmed.2007.08.001.
              9. Ceylan O, Okmen G, Ugur A. Isolation of soil Streptomyces as source antibiotics active against antibiotic-resistant bacteria. EurAsian J Biosci. 2008; 2: 73-82.
              10. Ryandini D, Pramono H, Sukanto S. Antibacterial activity of Streptomyces SAE4034 isolated from Segara Anakan mangrove rhizosphere against antibiotic resistant bacteria. Biosaintifika. 2018; 10(1): 117-124. doi: 10.15294/biosaintifika.v10i1.12896.
              11. Dazzo F, Ganter S. Rhizosphere. In: Schaechter M, editor. Encyclopedia of Microbiology. San Diego: Academic Press; 2009. p. 335-349. doi: 10.1016/B978-012373944-5.00287-X.
              12. Crawford DL, Lynch JM, Whipps JM, Ousley MA. Isolation and characterization of actinomycete antagonists of a fungal root pathogen. Appl Environ Microbiol. 1993; 59(11), 3899-3905. doi: 10.1128/aem.59.11.3899-3905.1993.
              13. Trinidad-Cruz JR, Rincón-Enríquez G, Evangelista-Martínez Z, Guízar-González C, Enríquez-Vara JN, López-Pérez L et al. Actinobacteria from avocado rhizosphere: antagonistic activity against Colletotrichum gloeosporioides and Xanthomonas sp. Rev Terra Latinoam. 2021; 39: e802. doi: 10.28940/terra.v39i0.802.
              14. Tello T. Dosis de gallinaza y distanciamiento de siembra de plantones de Swinglea glutinosa como cerco vivo y su efecto en las características agronómicas en Yurimaguas – Perú [internet] [Thesis]. Iquitos: Universidad Nacional de la Amazonía Peruana; 2015. Available in: http://repositorio.unapiquitos.edu.pe/handle/20.500.12737/4444.
              15. Al-Dhabi NA, Esmail GA, Mohammed Ghilan AK, Arasu MV. Composting of vegetable waste using microbial consortium and biocontrol efficacy of Streptomyces sp. Al-Dhabi 30 isolated from the Saudi Arabian environment for sustainable agriculture. Sustainability. 2019; 11(23): 6845. doi: 10.3390/su11236845.
              16. Kämpfer P. Order XIV. Streptomycetales ord. nov. In: Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K, Ludwig W, et al., editors. Bergey’s Manual of Systematic Bacteriology. Volume 5. The Actinobacteria, Part A and B. Athens, USA: Springer; 2012. p. 1446-1804. doi: 10.1007/978-0-387-68233-4.
              17. Mackay SJ. Improved enumeration of Streptomyces spp. on a starch casein salt medium. Appl Environ Microbiol. 1977; 33(2): 227-230. doi: 10.1128/aem.33.2.227-230.1977.
              18. Clinical and Laboratory Standards Institute – CLSI. Performance standards for antimicrobial susceptibility testing: 35th edition. Wayne, PA: CLSI; 2025.
              19. Velho-Pereira S, Kamat NM. Antimicrobial screening of actinobacteria using a modified cross-streak method. Indian J Pharm Sci. 2011; 73(2): 223-228. doi: 10.4103/0250-474X.91566
              20. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol. 1966; 16(3): 313-40. doi: 10.1099/00207713-16-3-313
              21. Sharma D, Kaur T, Chadha BS, Manhas RK. Antimicrobial activity of actinomycetes against multidrug resistant Staphylococcus aureus, E. coli and various other pathogens. Trop J Pharm Res. 2011; 10(6): 801-808. doi: 10.4314/tjpr.v10i6.14
              22. Santos ÉR, Teles ZNS, Campos NM, Souza DAJ, Bispo ASR, Nascimento RP. Production of α-amylase from Streptomyces sp. SLBA-08 strain using agro-industrial by-products. Brazilian Arch Biol Technol. 2012; 55(5): 793-800. doi: 10.1590/S1516-89132012000500020
              23. Prasad P, Singh T, Bedi S. Characterization of the cellulolytic enzyme produced by Streptomyces griseorubens (Accession No. AB184139) isolated from Indian soil. J King Saud Univ – Sci. 2013; 25: 245–250. doi: 10.1016/j.jksus.2013.03.003
              24. Manivasagan P, Gnanam S, Sivakumar K, Thangaradjou T, Vijayalakshmi S, Balasubramanian T. Isolation, identification and characterization of multiple enzyme producing actinobacteria from sediment samples of Kodiyakarai coast, the Bay of Bengal. J Microbiol. 2010; 4(14): 1550–1559. doi: 10.5897/AJMR.9000470
              25. Ugur A, Sarac N, Boran R, Ayaz B, Ceylan O, Okmen G. New lipase for biodiesel production: partial purification and characterization of LipSB 25-4. ISRN Biochem. 2014; 289749. doi: 10.1155/2014/289749
              26. Zarith N, Zin M, Tasrip NA, Nasir M, Desa M, Kqueen CY, et al. Characterization and antimicrobial activities of two Streptomyces isolates from soil in the periphery of Universiti Putra Malaysia. Trop Biomed. 2011; 28(3): 651-660.
              27. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12): 1647-1649. doi: 10.1093/bioinformatics/bts199
              28. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22): 4673-4680. doi: 10.1007/978-1-4020-6754-9_3188
              29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3): 403-410. doi: 10.1016/S0022-2836(05)80360-2
              30. Osorio-Echeverri VM, Martinez J. Streptomyces from rhizospheres and compost [dataset]. Mendeley Data, V1. 2022. Available from doi: 10.17632/r7pfw2kywj.1
              31. Kelly KL, Judd DB. Color. Universal Language and Dictionary of Names. Washington, DC: National Bureau of Standards. 1955.
              32. Centore P. ISCC-NBS Colour System [Internet]. 2016 [accessed 10 March 2025]. Available in: https://www.munsellcolourscienceforpainters.com/ISCCNBS/ISCCNBSSystem.html
              33. Pérez N, Jaramillo DF, Ruiz OS, Parra LN. Caracterización de un Andisol de la cuenca alta de la quebrada Santa Elena, Oriente Antioqueño, Colombia. Rev Fac Cienc. 2017; 6(1): 24-38. doi: 10.15446/rev.fac.cienc.v6n1.60628
              34. Wemheuer F, Berkelmann D, Wemheuer B, Daniel R, Vidal S, Bisseleua HB. Agroforestry management systems drive the composition, diversity, and function of fungal and bacterial endophyte communities in Theobroma cacao leaves. Microorganisms. 2020; 8(3): 405. doi: 10.3390/microorganisms8030405
              35. Williams HTP, Lenton TM. Artificial selection of simulated microbial ecosystems. Proc Natl Acad Sci USA. 2007; 104(21), 8918-8923. doi: 10.1073/pnas.0610038104
              36. Rebollido R, Martínez J, Aguilera Y, Melchor K, Koerner I, Stegmann R. Microbial populations during composting process of organic fraction of municipal solid waste. Appl Ecol Environ Res. 2008; 6(3), 61-67. doi: 10.15666/aeer/0603_061067.
              37. Salamoni SP, Mann MB, Campos FS, Franco AC, Germani JC, van der Sand ST. Preliminary characterization of some Streptomyces species isolated from a composting process and their antimicrobial potential. World J Microbiol Biotechnol. 2010; 26: 1847-1856. doi: 10.1007/s11274-010-0366-y.
              38. Kiepas AB, Hoskisson PA, Pritchard L. 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces. Microb Genom. 2024; 10(9):001287. doi: 10.1099/mgen.0.001287.
              39. Kocher TD. Adaptive evolution and explosive speciation: the cichlid fish model. Nat Rev Genet. 2004; 5(4): 288-298. doi: 10.1038/nrg1316.
              40. Lai YP, Loerger TR. Exploiting homoplasy in genome-wide association studies to enhance identification of antibiotic-resistance mutations in bacterial genomes. Evol Bioinform Online. 2020; 16: 1176934320944932. doi: 10.1177/1176934320944932.
              41. Vilgalys R. Taxonomic misidentification in public DNA databases. New Phytol. 2003; 160(1): 4-5. doi: 10.1046/j.1469-8137.2003.00894.x
              42. Chorlton SD. Ten common issues with reference sequence databases and how to mitigate them. Front Bioinform. 2024; 4:1278228. doi: 10.3389/fbinf.2024.1278228.
              43. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017; 67(5):1613-1617. doi: 10.1099/ijsem.0.001755
              44. Leibniz Institut DSMZ. Streptomyces microflavus Krainsky. BacDive. The Bacterial Diversity Metadatabase. 2020. doi: 10.13145/bacdive15404.20241212.9.2
              45. Atta HM, Yassen AM. Antimicrobial activities of a Streptomyces microflavus isolated from KSA: taxonomy, fermentation, extraction and biological activities. Int J Life Sci. 2015; 4(4): 260-269.
              46. Cho E, Kwon O-S, Chung B, Lee J, Sun J, Shin J, et al. Antibacterial activity of Chromomycins from a marine-derived Streptomyces microflavus. Mar Drugs. 2020; 18(10):522. doi: 10.3390/md18100522
              47. Chung B, Kwon O-S, Shin J, Oh K-B. Antibacterial activity and mode of action of Lactoquinomycin A from Streptomyces bacillaris. Mar Drugs. 2021; 19(1):7. doi: 10.3390/md19010007
              48. Taechowisan T, Chuen-Im T, Phutdhawong WS. Antibacterial and anticancer properties of Endophenazines from Streptomyces prasinus ZO16, an endophyte in Zingiber officinale Rosc. Pak J Biol Sci. 2024; 27:469-478. doi:1 0.3923/pjbs.2024.469.478
              49. Li K, Tang X, Zhao J, Guo Y, Tang Y, Gao J. Streptomyces cadmiisoli sp. nov., a novel actinomycete isolated from cadmium-contaminated soil. Int J Syst Evol Microbiol. 2019; 69(4). doi: 10.1099/ijsem.0.003262
              Tutorials

              Autors:

              How send article?

              Evaluator pair

              How to evaluate an article?

              Information

              Keywords

              Google Scholar profile

              Is part of
               
              Más leídos en los últimos 30 días

              Current Issue

              Sistema OJS 3.4.0.5 - Metabiblioteca |