In Silico Evaluation Reveals The Potential Risk of Antimicrobial Resistance in Bifidobacterium
Abstract
Abstract
Bifidobacteria have beneficial health effects for their hosts. However, they may acquire antibiotic-resistance genes. They may transfer antibiotic-resistance genes to pathogenic microbes found in the human intestine resulting in the emergence of antibiotic-resistant pathogens. This study aimed to predict their resistance to antibiotics by analyzing the whole genome sequence. The entire genome data of Bifidobacterium spp. were obtained from the National Center for Biotechnology Information (NCBI). This study included five Bifidobacterium strains of human origin, five strains of animal origin, and three strains isolated from the environment. The genomic sequences were analyzed using ResFinder and CARD web service. Antibiotic-resistance genes were detected in Bifidobacterium spp. from all sample sources. Bifidobacteria were potentially resistant to various antibiotics, such as tetracycline, rifamycin, chloramphenicol, macrolide, lincosamide, streptogramin, and mupirocin-like antibiotics. This study suggests the safety aspect consideration of applying Bifidobacterium spp. as a potential probiotic.
Abstrak
Bifidobacteria memiliki efek kesehatan yang menguntungkan bagi inangnya. Namun, sel Bifidobacteria dapat memperoleh gen resistensi antibiotik. Hal ini memunculkan potensi transfer gen resistensi antibiotik ke mikroba patogen yang ditemukan di usus manusia yang mengakibatkan munculnya patogen yang resisten terhadap antibiotik. Penelitian ini bertujuan untuk memprediksi resistensi Bifidobacteria terhadap antibiotik dengan menganalisis seluruh urutan genomnya. Seluruh data genom Bifidobacterium spp. diperoleh dari National Center for Biotechnology Information (NCBI). Penelitian ini melibatkan lima strain Bifidobacterium yang diisolasi dari manusia, lima strain yang berasal dari hewan, dan tiga strain yang diisolasi dari lingkungan. Sekuens genom dianalisis menggunakan ResFinder dan layanan web CARD. Gen resistensi antibiotik terdeteksi pada Bifidobacterium spp. dari semua sumber sampel. Bifidobacteria berpotensi menjadi resisten terhadap berbagai antibiotik, seperti tetrasiklin, rifamisin, kloramfenikol, makrolida, linkosamida, streptogramin, dan mupirocin-like antibiotics. Penelitian ini menyarankan pertimbangan aspek keamanan dalam menggunakan Bifidobacterium spp. sebagai probiotik potensial.
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Alcock, B. P., Huynh, W., Chalil, R., Smith, K. W., Raphenya, A. R., Wlodarski, M. A., … McArthur, A. G. (2023). CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Research, 51(D1), D690-D699. doi: 10.1093/nar/gkac920.
Babatunde, O. J., Okiti, A. F., Bayode, M. T., Babatunde, S. O., & Olaniran, A. M. (2022). Antibiogram profile prediction of selected bacterial strains by in silico determination of acquired antimicrobial resistance genes from their whole-genome sequence. Bulletin of the National Research Centre, 46(230). doi: 10.1186/s42269-022-00922-w.
Cao, L., Chen, H., Wang, Q., Li, B., Hu, Y., Zhao, C., … Yin, Y. (2020). Literature-based phenotype survey and in silico genotype investigation of antibiotic resistance in the genus Bifidobacterium. Current Microbiology, 77, 4104-4113. doi: 10.1007/s00284-020-02230-w.
Ding, D., Wang, B., Zhang, X., Zhang, J., Zhang, H., Liu, X., … Yu, Z. (2023). The spread of antibiotic resistance to humans and potential protection strategies. Ecotoxicology and Environmental Safety, 254, 114734. doi: 10.1016/j.ecoenv.2023.114734.
Duranti, S., Lugli, G. A., Mancabelli, L., Turroni, F., Milani, C., Mangifesta, M., … Ventura, M. (2017). Prevalence of antibiotic resistance genes among human gut-derived Bifidobacteria. Applied Environmental Microbiology, 83, e02894-16. doi: 10.1128/AEM.02894-16.
EFSA-FEEDAP Panel. (2018). Guidance on the characterization of microorganisms used as feed additives or as production organisms. EFSA Journal, 16(3), 5206. doi: 10.2903/j.efsa.2018.5206.
Erginkaya, Z., Turhan, E. U., & Tatli, D. (2018). Determination of antibiotic resistance of lactic acid bacteria isolated from traditional Turkish fermented dairy products. Iran Journal of Veterinary Research, 19, 53-56. doi: 10.22099/ijvr.2018.4769.
Florensa, A. F., Kaas, R. S., Clausen, P. T. L. C., Aytan-Aktug, D., & Aarestrup, F. M. (2022). ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microbial Genome, 8(1), 000748. doi: 10.1099/mgen.0.000748.
Gueimonde, M., Sanchez, B., de los Reyes-Gavilan, C. G., & Margolles, A. (2013). Antibiotic resistance in probiotic bacteria. Frontiers in Microbiology, 4(202). doi: 10.3389/fmich.2013.00202.
Hendrati, P. M., Kusharyati, D. F., Ryandini, D., & Oedjijono. (2017). Characterization of Bifidobacteria from infant feces with different modes of birth at Purwokerto, Indonesia. Biodiversitas, 18(3), 1265-1269. doi: 10.13057/biodiv/d180352.
Indrawati, A., Khoirani, K., Setiyaningsih, S., Safika, U. A., & Ningrum, S. G. (2021). Detection of tetracycline resistance genes among Escherichia coli isolated from layer and broiler breeders in West Java, Indonesia. Tropical Animal Science Journal, 44(3), 267-272. doi: 10.5398/tasj.2021.44.3.267
Kusharyati, D. F., Pramono, H., Ryandini, D., Manshur, T. A., Dewi, M. A., Khatimah, K., & Rovik, A. (2020). Bifidobacterium from infant stool: The diversity and potential screening. Biodiversitas, 21(6), 2506-2513. doi: 10.13057/biodiv/d210623.
Larsson, D. G. K., & Flach, C. F. (2022). Antibiotic resistance in the environment. Nature Reviews, 20, 257. doi: 10.1038/s41579-021-00649-x.
Liu, Z., Roy, N. C., Guo, Y., Jia, H., Ryan, L., Samuelsson, L., … Young, W. (2016). Human breast milk and infant formulas differentially modify the intestinal microbiota in human infants and host physiology in rats. Nutrients, 146, 191-199. doi: 10.3945/jn.115.223552.
McArthur, A. G., Waglechner, N., Nizam, F., Yan, A., Azad, M. A., Baylay, A. J., … Wright, G. D. (2013). The comprehensive antibiotic resistance database. Antimicrobial Agents and Chemotherapy, 57(7), 3348-3357. doi: 10.1128/AAC.00419-13.
Nunziata, L., Brasca, M., Morandi, S., & Silvetti, T. (2022). Antibiotic resistance in wild and commercial non-enterococcal lactic acid bacteria and Bifidobacteria strains of dairy origin: An update. Food Microbiology, 104, 103999. doi: 10.1016/j.fm.2022.103999.
Pedersen, S. K., Wagenaar, J. A., Vigre, H., Roer, L., Mikoleit, M., Aidara-Kane, A., … Hendriksen, R. S. (2018). Proficiency of WHO Global Foodborne Infections Network external quality assurance system participants in the identification and susceptibility testing of thermotolerant Campylobacter spp. from 2003 to 2012. Journal of Clinical Microbiology, 56(11), e01066-18. doi: 10.1128/JCM.01066-18.
Peiris, C., Gunatilake, S. R., Mlsna, T. E., Mohan, D., & Vithanage, M. (2017). Biochar based removal of antibiotic sulfonamides and tetracyclines in aquatic environments: A critical review. Bioresource Technology, 246, 150-159. doi: 10.1016/j.biortech.2017.07.150.
Rozman, V., Lorbeg, P. M., Acetto, T., & Matijasic, B. B. (2020). Characterization of antimicrobial resistance in lactobacilli and Bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data. International Journal of Food Microbiology, 314, 108388. doi: 10.1016/j.ijfoodmicro.2019.108388.
Sakanaka, M., Gotoh, A., Yoshida, K., Odamaki, T., Koguchi, H., Xiao, J-Z., … Katayama, T. (2020). Varied pathways of infant gut-associated Bifidobacterium to assimilate human milk oligosaccharides: prevalence of the gene set and its correlation with Bifidobacteria-rich microbiota formation. Nutrients, 12(71). doi: 10.3390/nu12010071.
Shreiner, A. B., Kao, J. Y., & Young, V. B. (2015). The gut microbiome in health and disease. Current Opinion on Gastroenterology, 31(1), 69-75. doi: 10.1097/MOG.0000000000000139.
Sirilun, S., Takahashi, H., Boonyaritichaikij, S., Chaiyasut, C., Lertruangpanya, P., Koga, Y., & Mikami, K. (2015). Impact of maternal Bifidobacteria and the mode of delivery on Bifidobacterium microbiota in infants. Beneficial Microbes, 6, 767-774. doi: 10.3920/BM2014.0124.
Su, M., Satola, S. W., & Read, T. D. (2019). Genome-based prediction of bacterial antibiotic resistance. Journal of Clinical Microbiology, 57(3), e01405-18. doi: 10.1128/JCM.01405-18.
World Health Organization. (2002). Guidelines for the evaluation of probiotics in food. London: FAO/WHO Working Group.
Yan, S., Zhao, G., Liu, X., Zhao, J., Zhang, H., & Chen, W. (2017). Production of exopolysaccharide by Bifidobacterium longum isolated from elderly and infant feces and analysis of priming glycosyltransferase genes. RSC Advance, 7, 31736-31744. doi: 10.1039/C7RA03925E.
Yasmin, I., Saeed, M., Khan, W. A., Khaliq, A., Chughtai, M. F. J., Iqbal, R., … Tanweer, S. (2020). In vitro probiotic potential and safety evaluation (Hemolytic, cytotoxic activity) of bifidobacterium strains isolated from raw camel milk. Microorganisms, 8(3), 354. doi: 10.3390/microorganisms8030354.
Zankari, E., Allesoe, R., Joensen, K. G., Cavaco, L. M., Lund, O., & Aarestrup, F M. (2017). PointFinder: A novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. Journal of Antimicrobial Chemotherapy, 72, 2764-2768. doi:10.1093/jac/dkx217.
Zarzecka, U., Chajęcka-Wierzchowska, W., & Zadernowska, A. (2022). Microorganisms from starter and protective cultures-occurrence of antibiotic resistance and conjugal transfer of tet genes in vitro and during food fermentation. LWT-Food Science and Technology, 153, 112490. doi: 10.1016/j.lwt.2021.112490.
DOI: https://doi.org/10.15408/kauniyah.v1i1.34873 Abstract - 0 PDF - 0
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