Genotypic and Phenotypic Analyses of Antibiotic Resistance in Indonesian Indigenous Lactobacillus Probiotics
Applied Food Biotechnology,
Vol. 8 No. 4 (2021),
2 October 2021
,
Page 267-274
https://doi.org/10.22037/afb.v8i4.34448
Abstract
Abstract
Background and Objective: In the authors’ previous study, four unique Lactobacillus strains (Lactobacillus plantarum Dad-13, Lactobacillus plantarum Mut-7, Lactobacillus plantarum T-3 and Lactobacillus paracasei SNP-2) from Indonesian fermented foods and healthy feces have been studied as probiotic agents. In the current study, antibiotic resistance phenotypes of the highlighted Lactobacillus plantarum and Lactobacillus paracasei against eight antibiotics (amoxicillin, tetracycline, erythromycin, clindamycin, chloramphenicol, streptomycin, kanamycin, ciprofloxacin) and antibiotic resistance genes of these strains were investigated.
Material and Methods: The bacterial antibiotic susceptibility to eight antibiotics was assessed using disk diffusion method. Genome sequencing was carried out using NovaSeq 6000 sequencing platform. Genome was annotated using Rapid Annotation using Subsystem Technology v.2.0. Each group of the predicted products of resistance genes was further aligned using multiple sequence comparison by log-expectation and their functions were verified using comprehensive antibiotic resistance database 2020.
Results and Conclusion: All strains showed resistance to aminoglycoside and ciprofloxacin but sensitive to amoxicillin, clindamycin and erythromycin. Resistance to chloramphenicol and tetracycline varied within the strains. Two strains were sensitive and others were intermediate resistance to chloramphenicol. One strain was resistant to tetracycline, while the other three strains demonstrated intermediate resistance to the antibiotic. Genome sequence of the four strains verified the presence of the tetracycline, β-lactamase and ciprofloxacin resistance genes as well as multidrug resistance efflux systems. Occurrence of the resistance genes was correlated to the phenotype results, except for amoxicillin and aminoglycosides. Rapid Annotation using Subsystem Technology annotation showed that all Lactobacillus strains did not include transposable elements, gene transfer agents and plasmid linked functions; thus, horizontal transfer of the antibiotic resistance genes unlikely occurred.
Conflict of interest: The authors declare no conflict of interest.
- ▪ Antibiotic resistance ▪ Genomics ▪ Lactobacillus ▪ Probiotics
How to Cite
References
Nuraida L. A review: Health promoting lactic acid bacteria in traditional Indonesian fermented foods. Food Sci Hum Wellness. 2015; 4(2): 47-55.
doi: 10.1016/j.fshw.2015.06.001
Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Girones R, Koutsoumanis K, Herman L, Lindqvist R, Nørrung B, Robertson L, Ru G, Sanaa M, Simmons M, Skandamis P, Snary E, Speybroeck N, Ter Kuile B, Threlfall J, Wahlstrom H, Cocconcelli PS, Klein (deceased) G, Peixe L, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Correia S, Fernandez Escamez PS. Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 5: Suitability of taxonomic units notified to EFSA until September 2016. Eur Food Saf Authority J. 2017; 15(3): 1-20.
doi: 10.2903/j.efsa.2017.4663
Vieco-Saiz N, Belguesmia Y, Raspoet R, Auclair E, Gancel F, Kempf I, Drider D. Benefits and inputs from lactic acid bacteria and their bacteriocins as alternatives to antibiotic growth promoters during food-animal production. Front Microbiol. 2019; 10: 1-17.
doi: 10.3389/fmicb.2019.00057
Sharma P, Tomar SK, Goswami P, Sangwan V, Singh R. Antibiotic resistance among commercially available probiotics. Food Res Int. 2014; 57: 176-195.
doi: 10.1016/j.foodres.2014.01.025
Landers TF, Cohen B, Wittum TE, Larson EL. A review of antibiotic use in food animals: Perspective, policy and potential. Public Health Rep. 2012; 127(1): 4-22.
doi: 10.1177/003335491212700103
Manyi-Loh C, Mamphweli S, Meyer E, Okoh A. Antibiotic use in agriculture and its consequential resistance in environmental sources: Potential public health implications. Molecules 2018; 23(4): 1-48.
doi: 10.3390/molecules23040795
Li T, Teng D, Mao R, Hao Y, Wang X, Wang J. A critical review of antibiotic resistance in probiotic bacteria. Food Res Int. 2020; 136:1-16
doi: 10.1016/j.foodres.2020.109571
Abriouel H, Casado Munoz M del C, Lavilla Lerma L, Perez Montoro B, Bockelmann W, Pichner R, Kabisch J, Cho GS, Franz CMAP, Galvez A, Benomar N. New insights in antibiotic resistance of Lactobacillus species from fermented foods. Food Res Int. 2015; 78: 465-481.
doi: 10.1016/j.foodres.2015.09.016
Campedelli I, Mathur H, Salvetti E, Clarke S, Rea MC, Torriani S, Ross RP, Hill C, O’Toole PW. Genus-wide assessment of antibiotic resistance in Lactobacillus spp. Appl Environ Microbiol. 2019; 85(1): 1-21.
doi: 10.1128/AEM.01738-18
EFSA Panel on additives and products or substances used in Animal Feed (FEEDAP); guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance. Eur Food Saf Authority J. 2012; 10(6): 1-10.
doi:10.2903/j.efsa.2012.2740
Rahayu ES. Lactic acid bacteria in fermented foods of origin. Agritech. 2003; 23(2): 75-84.
doi: 10.22146/agritech.13515
Purwandhani SN, Rahayu ES. Isolation and selection of Lactobacillus as potential probiotics agents (in Indonesian). Agritech. 2003; 23(2): 67-74.
doi: 10.22146/agritech.13514
Rahayu ES, Yogeswara A, Mariyatun, Windiarti L, Utami T, Watanabe K. Molecular characteristics of indigenous probiotic strains from Indonesia. Int J Probiotics Prebiotics. 2015; 11(2): 109-116.
Rahayu ES, Purwandhani SN. Supplementation of Lactobacillus acidophilus SNP-2 on fermented cassava (tape) and its effect to the volunteer (in Indonesian). J Teknol dan Industri Pangan. 2004; 15(2): 129-134.
Rahayu ES, Rusdan IH, Athennia A, Kamil RZ, Pramesi PC, Marsono Y, Utami T, Widada J. Safety assessment of indigenous probiotic strain Lactobacillus plantarum dad-13 isolated from dadih using sprague dawley rats as a model. Am J Pharmacol. 2019; 14: 38-47.
doi:10.3844/ajptsp.2019.38.47
Ikhsani AY, Riftyan E, Safitri RA, Marsono Y, Utami T, Widada J, Rahayu ES. Safety assessment of indigenous probiotic strain Lactobacillus plantarum mut-7 using sprague dawley rats as a model. Am J Pharmacol. 2020; 15: 7-16.
doi: 10.3844/ajptsp.2020.7.16
Balouiri M, Sadiki M, Ibnsouda SK. Methods for in evaluating antimicrobial activity: A review. J Pharm Anal. 2016; 6: 71-79.
doi: 10.1016/j.jpha.2015.11.005
Sharma P, Tomar SK, Sangwan V, Goswami P, Singh R. Antibiotic resistance of Lactobacillus sp. Isolated from commercial probiotic preparations. J Food Saf. 2016; 36(1): 38-51.
doi: 10.1111/jfs.12211
Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen ALV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG. CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020; 48: D517-D525.
doi: 10.1093/nar/gkz935
Anisimova EA, Yarullina DR. Antibiotic resistance of Lactobacillus strains. Curr Microbiol. 2019; 76(12): 1407-1416.
doi: 10.1007/s00284-019-01769-7
Gueimonde M, Sanchez B, de los Reyes-Gavilan CG, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol. 2013; 4: 1-6.
doi: 10.3389/fmicb.2013.00202
Wang K, Zhang H, Feng J, Ma L, Fuente-Nunez C de la, Wang S, Lu X. Antibiotic resistance of lactic acid bacteria isolated from dairy products in Tianjin, China. J Agric Food Res. 2019; 1: 1-5.
doi: 10.1016/j.jafr.2019.100006
Kirtzalidou E, Pramateftaki P, Kotsou M, Kyriacou A. Screening for lactobacilli with probiotic properties in the infant gut microbiota. Anaerobe. 2011; 17(6): 440-443.
doi: 10.1016/j.anaerobe.2011.05.007
Grossman TH. Tetracycline antibiotics and resistance. Cold Spring Harb Perspect Med. 2016; 6(4): 1-25.
doi: 10.1101/cshperspect.a025387
Wilson DN, Hauryliuk V, Atkinson GC, O’Neill AJ. Target protection as a key antibiotic resistance mechanism. Nat Rev Microbiol. 2020; 18(11): 637-648.
doi: 10.1038/s41579-020-0386-z
Schedlbauer A, Kaminishi T, Ochoa-Lizarralde B, Dhimole N, Zhou S, Lopez-Alonso JP, Connell SR, Fucini P. Structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome. Antimicrob Agents Chemother. 2015; 59(5): 2849-2854.
doi: 10.1128/AAC.04895-14
Li W, Lu C, Chan K, Atkinson GC, Thakor NS, Tenson T, Schulten K, Wilson KS, Hauryliuk V, Frank J. Mechanism of tetracycline resistance by ribosomal protection protein Tet(O). Nat Commun. 2013; 4: 1-8
doi: 10.1038/ncomms2470
Redgrave LS, Sutton SB, Webber MA, Piddock LJ. Fluoroquinolone resistance: mechanisms, impact on bacteria and role in evolutionary success. Trends Microbiol. 2014; 22(8): 438-445.
doi: 10.1016/j.tim.2014.04.007
Mac Aogain M, Kilkenny S, Walsh C, Lindsay S, Moloney G, Morris T, Jones S, Rogers TR. Identification of a novel mutation at the primary dimer interface of GyrA conferring fluoroquinolone resistance in Clostridium difficile. J Global Antimicrobial Resistance. 2015; 3(4): 295-299.
doi: 10.1016/j.jgar.2015.09.007
Sanfilippo CM, Hesje CK, Haas W, Morris TW. Topoisomerase mutations that are associated with high-level resistance to earlier fluoroquinolones in staphylococcus aureus have less effect on the antibacterial activity of besifloxacin. Chemotherapy 2011; 57: 363-371.
doi: 10.1159/000330858.
Li S, Li Z, Wei W, Ma C, Song X, Li S, He W, Tian J, Huo X. Association of mutation patterns in GyrA and ParC genes with quinolone resistance levels in lactic acid bacteria. J Antibiotics. 2015; 68(2): 81-87. doi:10.1038/ja.2014.113
Bush K. The ABCD’s of -lactamase nomenclature. J Infect Chemother. 2013; 19(4): 549-559.
doi: 10.1007/s10156-013-0640-7.
Kwon S, Yoo W, Kim OK, Kim Y, Kim KK TD. Molecular characterization of a novel family VIII esterase with -lactamase activity (PsEstA) from Paenibacillus sp. Biomol. 2019; 9(12): 1-15.
doi:10.3390/biom9120786
Blanco P, Hernando-Amado S, Reales-Calderon JA, Corona F, Lira F, Alcalde-Rico M, Bernardini A, Sanchez MB, Martinez JL. Bacterial multidrug efflux pumps: Much more than antibiotic resistance determinants. Microorganisms. 2016; 4(1): 1-14.
doi:10.3390/microorganisms4010014.
Pasqua M, Grossi M, Zennaro A, Fanelli G, Micheli G, Barras F, Colonna B, Prosseda G. The varied role of efflux pumps of the mfs family in the interplay of bacteria with animal and plant cells. Microorganisms 2019; 7: 285.
doi:10.3390/microorganisms70902850/
Alcalde-Rico M, Hernando-Amado S, Blanco P, Martinez J L. Multidrug efflux pumps at the crossroad between antibiotic resistance and bacterial virulence. front microbiol. 2016; 7: 1-14.
doi: 10.3389/fmicb.2016.01483.
Sirichoat A, Florez AB, Vazquez L, Buppasiri P, Panya M, Lulitanond V, Mayo B. Antibiotic susceptibility profiles of lactic acid bacteria from the human vagina and genetic basis of acquired resistances. Int J Mol Sci. 2020; 21(7): 2594: 1-14
doi: 10.3390/ijms21072594
Marshall BM, Levy SB. Food animals and antimicrobials: Impacts on human health. Clin Microbiol Rev. 2011; 24(4): 718-733doi: 10.1128/CMR.00002-11
- Abstract Viewed: 855 times
- pdf Downloaded: 713 times