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

Víctor Manuel  Osorio; Alejandro  Mejía; Elizabeth  Correa; Ana María  Ochoa; Ana  Mercedes Rada; José  Gregorio Martínez

doi:10.22490/24629448.10141

Vol. 23 No. 45 (2025): 2.

Published 2025-07-01

license

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

Research Article (before OJS)

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

DOI: https://doi.org/10.22490/24629448.10141

Víctor Manuel Osorio Institución Universitaria Colegio Mayor de Antioquia

Alejandro Mejía Institución Universitaria Colegio Mayor de Antioquia

Elizabeth Correa Institución Universitaria Colegio Mayor de Antioquia

Ana María Ochoa Institución Universitaria Colegio Mayor de Antioquia

Ana Mercedes Rada Institución Universitaria Colegio Mayor de Antioquia

José Gregorio Martínez Institución Universitaria Colegio Mayor de Antioquia

PDF (Spanish)

Abstract
References

Introduction. The search for microorganisms producing antimicrobial compounds repre sents 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 Entero bacteriaceae 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 te chniques.

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 iso lates.

Conclusions. Streptomyces with antibacterial activities against ESBL and KPC-pro ducing 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.

keywords: Actinobacteria, antibacterial agents, drug resistance, Extended-Spectrum Beta-Lactamases producers, MRSA, soil microbiology

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.

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

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.

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.

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.

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.

Moellering RC. Vancomycin: A 50-Year Reassessment. Clin Infect Dis. 2017; 42(S1): 3-4. doi: 10.1086/491708.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Clinical and Laboratory Standards Institute – CLSI. Performance standards for antimicrobial susceptibility testing: 35th edition. Wayne, PA: CLSI; 2025.

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

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

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

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

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

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

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

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.

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

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

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

Osorio-Echeverri VM, Martinez J. Streptomyces from rhizospheres and compost [dataset]. Mendeley Data, V1. 2022. Available from doi: 10.17632/r7pfw2kywj.1

Kelly KL, Judd DB. Color. Universal Language and Dictionary of Names. Washington, DC: National Bureau of Standards. 1955.

Centore P. ISCC-NBS Colour System [Internet]. 2016 [accessed 10 March 2025]. Available in: https://www.munsellcolourscienceforpainters.com/ISCCNBS/ISCCNBSSystem.html

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

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

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

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.

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.

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.

Kocher TD. Adaptive evolution and explosive speciation: the cichlid fish model. Nat Rev Genet. 2004; 5(4): 288-298. doi: 10.1038/nrg1316.

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.

Vilgalys R. Taxonomic misidentification in public DNA databases. New Phytol. 2003; 160(1): 4-5. doi: 10.1046/j.1469-8137.2003.00894.x

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.

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

Leibniz Institut DSMZ. Streptomyces microflavus Krainsky. BacDive. The Bacterial Diversity Metadatabase. 2020. doi: 10.13145/bacdive15404.20241212.9.2

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.

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

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

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:10.3923/pjbs.2024.469.478

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

license

How to Cite

Osorio, V. M., Mejía, A., Correa, E., Ochoa, A. M., Mercedes Rada, A., & Gregorio Martínez, J. (2025). Antagonistic activity of native Streptomyces spp. against ESBL -and KPC- producing Enterobacteriaceae and MRSA. NOVA Biomedical Sciences Journal, 23(45), 7-25. https://doi.org/10.22490/24629448.10141

Download Citation

Almétricas

Metrics

Metrics Loading ...

Declaración de privacidad.

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

How to Cite