Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması

Yıl 2023, Cilt: 13 Sayı: 2, 932 - 940, 01.06.2023

Özge Ilıkkan

https://doi.org/10.21597/jist.1233617

Öz

Laktik asit bakterileri, endüstride starter kültür veya probiyotik olarak kullanılmaktadırlar. European Food
Safety Authority (EFSA) tarafından 2021 yılında yayımlanan raporda gıdalarda kullanılacak bakterilerin
tüm genom dizileri üzerinden risk değerlendirmesi yapılması gerekliliği vurgulanmıştır. Bu nedenle,
laktik asit bakterilerinde dirençlilik geni araştırmaları önem kazanmıştır. Çünkü antibiyotik direnç
genlerinin bağırsak sisteminde bulunan patojen bakterilere aktarılma olasılığı vardır ya da laktik asit
bakterilerini barındıran gıdalar aracılığıyla alınmaları olasıdır. Bu nedenle, çalışmada, farklı fermente
gıdalardan izole edilen dört laktik asit bakterisi (Lentilactobacillus buchneri Egmn17, Levilactobacillus
brevis Atlas17, Levilactobacillus namurensis Ozge01, Lactiplantibacillus plantarum Gmze16) ve
probiyotik bir bakteri olan Lactiplantibacillus plantarum 299v suşu kullanılmıştır. Çalışmada, laktik asit
bakterileri arasında en yaygın antibiyotik dirençliliği gözlenen tetrasiklin seçilmiştir. 3 bakterinin
tetrasiklin antibiyotiğine orta derecede dirençli (zon çapı 15-18 mm) (299v, Gmze16 ve Egmn17) ve 2
bakterinin duyarlı (zon çapı >19 mm) (Atlas17 ve Ozge01) olduğu belirlenmiştir. Laktik asit
bakterilerinin tüm genom sekanslarının incelenmesi sonucu, orta dirençli bakterilerin tetrasikline bağlı
antimikrobiyal direnç (AMR) genlerinden tetA (MFS dışa atım pompası) ve tetO’ya (ribozomal koruma
proteini) sahip oldukları görülmüştür. Levilactobacillus brevis Atlas17’de ise TetA proteini mevcutken
322. aminoasit sekansında M → T değişimi gözlenmiştir. Ayrıca probiyotik bakteri olan
Lactiplantibacillus plantarum 299v’nin direnç genlerine sahip olması bu genlerin bağırsaktaki patojenlere
aktarılma riskini de arttırmaktadır. tetA genine sahip olduğu gözlenen Levilactobacillus brevis Atlas17
gibi fenotipi duyarlı olan türler de sessiz dirençlilik genlerine sahip olduklarında bunu diğer bakterilere
aktarabilmeleri olasıdır. Bu nedenle genotip ve fenotip birlikte incelenmesi önemlidir

Anahtar Kelimeler

• Tetrasiklin direnci, • Laktik asit bakterisi, • Tüm genom sekansı, • MFS dışa atım pompası, • tetO geni

Destekleyen Kurum

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Proje Numarası

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Teşekkür

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Investigation of Tetracycline Resistance of Lactic Acid Bacteria by in silico Genotypically in Whole Genome Sequences and Phenotypically

Öz

Lactic acid bacteria are used in industry as starter cultures or probiotics. In the report published by the European Food Safety Authority in 2021, it was emphasized that risk assessment should be carried out on the whole genome sequences of bacteria to be used in foods. Therefore, resistance gene research in lactic acid bacteria has gained importance. Because antibiotic resistance genes are likely to be transmitted to pathogenic bacteria in the intestinal tract or are likely to be ingested through foods containing lactic acid bacteria. Therefore, in this study, four lactic acid bacteria (Lentilactobacillus buchneri Egmn17, Levilactobacillus brevis Atlas17, Levilactobacillus namurensis Ozge01, Lactiplantibacillus plantarum Gmze16) isolated from different fermented foods and Lactiplantibacillus plantarum, a probiotic bacterium, were used. In the study, tetracycline, which has the most common antibiotic resistance among lactic acid bacteria, was selected. It was determined that 3 bacteria were moderately resistant (zone diameter 15-18 mm) (299v, Gmze16 and Egmn17) to tetracycline antibiotic and 2 bacteria were susceptible (zone diameter >19 mm) (Atlas17 and Ozge01). As a result of examining the whole genome sequences of lactic acid bacteria, it was seen that intermediate resistant bacteria have tetracyclinedependent antimicrobial resistance (AMR) genes tetA (MFS efflux pump) and tetO (ribosomal protection protein). In Levilactobacillus brevis Atlas17, while TetA protein was present, M→T change was observed in the 322nd amino acid sequence. In addition, the fact that the probiotic bacteria Lactiplantibacillus plantarum 299v has resistance genes also increases the risk of transferring these genes to pathogens in the
intestine. Species that are susceptible to the phenotype, such as Levilactobacillus brevis Atlas17, which has been observed to have the tetA gene, are also likely to be able to pass it on to other bacteria when they have silent resistance genes. Therefore, it is important to examine genotype and phenotype together.

Anahtar Kelimeler

• Tetracycline resistance, • Lactic acid bacteria, • Whole genome sequence, • MFS efflux pump, • tetO gene

Proje Numarası

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Kaynakça

• Catalano, A., Iacopetta, D., Ceramella, J., Scumaci, D., Giuzio, F., Saturnino, C., … Sinicropi, M. S. 2022. "Multidrug Resistance ( MDR ): A Widespread Phenomenon in Pharmacological Therapies". Molecules, 1–18.
• CDC. 2019. "Antibiotic Resistance Threats in The United States 2019". Atlanta, GA: U.S. Department of Health and Human Services, 10(1).
• Chopra, I., Roberts, M. 2001. "Tetracycline Antibiotics : Mode of Action , Applications , Molecular Biology , and Epidemiology of Bacterial Resistance", 65(2), 232–260.
• Colautti, A., Arnoldi, M., Comi, G., Iacumin, L. 2022. "Antibiotic resistance and virulence factors in lactobacilli : something to carefully consider". Food Microbiology, 103(February 2021), 103934.
• Das, D. J., Shankar, A., Johnson, J. B., Thomas, S. 2020. "Critical insights into antibiotic resistance transferability in probiotic Lactobacillus". Nutrition, 69, 110567.
• Dec, M., Nowaczek, A., St, D., Wawrzykowski, J., Urban-chmiel, R. 2018. "Identification and antibiotic susceptibility of lactobacilli isolated from turkeys". BMC Microbiology, 18(168), 1–15.
• EFSA. 2012. "Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance". European Food Safety Authority Journal, 10(6), 1–10.
• EFSA. 2021. "EFSA statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain". European Food Safety Authority journal, 19(March).
• EFSA, Aguilera, J., Aguilera-gomez, M., Barrucci, F., Cocconcelli, P. S., Davies, H., … Matthew, C. 2018. "EFSA Scientific Colloquium 24 – ’ omics in risk assessment : state of the art and next steps". European Food Safety Authority Journal, EN-1512(November), 30.
• EFSA, Amore, G., Beloeil, P.-A., Fierro, R. G., Guerra, B., Papanikolaou, A., … Stoicescu, A.-V. 2021. "Manual for reporting 2021 antimicrobial resistance data within the framework of Directive 2003 / 99 / EC and Decision 2020 / 1729 / EU European Food Safety Authority ( EFSA ),". European Food Safety Authority Journal, EN-6652(April), 31.
• Franklin R. Cockerill, Wikler, M. A., Alder, J., Dudley, M. N., Eliopoulos, G. M., Ferraro, M. J., … Hecht, D. W. 2012. "Performance Standards for Antimicrobial Disk Susceptibility Tests ; Approved Standard — Eleventh Edition". Clinical and Laboratory Standards Institute, 32(1).
• Høg, B. B., Sönksen, U. W., Duarte, A. S. R., Müller-Pebody, B., Attauabi, M., Lindegaard, M. 2021. "Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark-Danmap". National Food Institute, Technical University of Denmark.
• Kaya, N. M., Sarıbaş, Z. 2012. "Mikobakterilerde Dışa Atım Pompaları ve İlaç Direnci". Türk Mikrobiyol Cem Derg, 42(3), 81–84.
• Ma, Q., Pei, Z., Fang, Z., Wang, H., Zhu, J., Lee, Y. K., … Chen, W. 2021. "Evaluation of tetracycline resistance and determination of the tentative microbiological cutoff values in lactic acid bacterial species". Microorganisms.
• Narvhus, A., Axelsson, L. 2003. "Lactic acid bacteria". Encyclopedia of Food Sciences and Nutrition, (1989), 3465–3472.
• Nikodinoska, I., Heikkinen, J., Moran, C. A. 2023. "Antimicrobial Susceptibility Data for Six Lactic Acid Bacteria Tested against Fifteen Antimicrobials". Data, 8(1), 1–7.
• 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(February), 103999.
• PHAC. 2021. "Canadian Antimicrobial Resistance Surveillance System Report-2021". Public Health Agency of Canada, 1–118. Tarihinde adresinden erişildi https://www.canada.ca/en/public-health/services/publications/drugs-health-products/canadian-antimicrobial-resistance-surveillance-system-report-2016.html
• Piddock, L. J. V. 2006. "Multidrug-resistance efflux pumps — not just for resistance", 4(August), 629–636.
• Reenen, C. A. Van, Dicks, L. M. T. 2011. "Horizontal gene transfer amongst probiotic lactic acid bacteria and other intestinal microbiota : what are the possibilities ? A review". Archives of Microbiology, 193, 157–168.
• Rezac, S., Kok, C. R., Heermann, M., Hutkins, R. 2018. "Fermented foods as a dietary source of live organisms". Frontiers in Microbiology, 9(AUG).
• Roberts, M. C. 2005. "Update on acquired tetracycline resistance genes". FEMS Microbiology Letters, 245(2), 195–203.
• Samtiya, M., Matthews, K. R., Dhewa, T., Puniya, A. K. 2022. "Antimicrobial Resistance in the Food Chain: Trends, Mechanisms, Pathways, and Possible Regulation Strategies". Foods, 11(19), 1–20.
• Sapunaric, M., Levy, S. B., Levy, S. B. 2005. "Substitutions in the interdomain loop of the Tn10 TetA efflux transporter alter tetracycline resistance and substrate specificit". Microbiology, 151, 2315–2322.
• Shen, Y., Stedtfeld, R. D., Guo, X., Bhalsod, G. D., Jeon, S., Tiedje, J. M., … Zhang, W. 2019. "Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce". Environment International, 131(June), 105031.
• Sirichoat, A., Flórez, A. B., Vázquez, L., Buppasiri, P., Panya, M., Lulitanond, V., Mayo, B. 2020. "Antibiotic susceptibility profiles of lactic acid bacteria from the human vagina and genetic basis of acquired resistances". International Journal of Molecular Sciences, 21(7).
• Thaker, M., Spanogiannopoulos, P., Wright, G. D. 2010. "The tetracycline resistome". Cellular and Molecular Life Sciences, 67, 419–431.
• Thumu, S. C. R., Halami, P. M. 2012. "Presence of erythromycin and tetracycline resistance genes in lactic acid bacteria from fermented foods of Indian origin", 541–551.
• Tóth, A. G., Csabai, I., Judge, M. F., Maróti, G., Becsei, Á., Spisák, S., Solymosi, N. 2021. "Mobile Antimicrobial Resistance Genes in Probiotics". Antibiotics, 10, 1–16.
• Villedieu, A., Diaz-Torres, M. L., Hunt, N., McNab, R., Spratt, D. A., Wilson, M., Mullany, P. 2003. "Prevalence of tetracycline resistance genes in oral bacteria". Antimicrobial Agents and Chemotherapy, 47(3), 878–882.
• Wang, T., Yao, L., Qu, M., Wang, L., Li, F., Tan, Z., … Jiang, Y. 2022. "Whole genome sequencing and antimicrobial resistance analysis of Vibrio parahaemolyticus Vp2015094 carrying an antimicrobial-resistant plasmid". Journal of Global Antimicrobial Resistance, 30(106), 47–49.
• WHO. 2022. "Antimicrobial resistance surveillance in Europe-2022". World Health Organization.
• Yamaguchi, A., Adachi, K., Akasaka, T., Ono, N., Sawai, T. 1991. "Metal-tetracycline/H+ antiporter of Escherichia coli encoded by a transposon Tn10. Histidine 257 plays an essential role in H+ translocation.". Journal of Biological Chemistry, 266(10), 6045–6051.
• Yörük, Gamze Nuray; Güner, A. 2010. "Laktik Asit Bakterilerinin Sınıflandırılması ve Weissella Türlerinin Gıda Mikrobiyolojisinde Önemi". Atatürk Üniversitesi Veteriner Bilimleri Dergisi, 6(2), 163–176.