{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:54:53Z","timestamp":1792788893573,"version":"4.5.0"},"reference-count":100,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T00:00:00Z","timestamp":1634774400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ITM Hungary","award":["TKP 2020-4.1.1.-TKP2020"],"award-info":[{"award-number":["TKP 2020-4.1.1.-TKP2020"]}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["874735 (VEO)"],"award-info":[{"award-number":["874735 (VEO)"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003825","name":"Hungarian Academy of Sciences","doi-asserted-by":"publisher","award":["Lend\u00fclet-Programme  (LP2020-5\/2020)"],"award-info":[{"award-number":["Lend\u00fclet-Programme  (LP2020-5\/2020)"]}],"id":[{"id":"10.13039\/501100003825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W\/N\/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.<\/jats:p>","DOI":"10.3390\/antibiotics10111287","type":"journal-article","created":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T14:37:48Z","timestamp":1634827068000},"page":"1287","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":80,"title":["Mobile Antimicrobial Resistance Genes in Probiotics"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9291-9759","authenticated-orcid":false,"given":"Adrienn Gr\u00e9ta","family":"T\u00f3th","sequence":"first","affiliation":[{"name":"Health Services Management Training Centre, Semmelweis University, 1125 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9232-9898","authenticated-orcid":false,"given":"Istv\u00e1n","family":"Csabai","sequence":"additional","affiliation":[{"name":"Department of Phyisics of Complex Systems, E\u00f6tv\u00f6s Lor\u00e1nd University, 1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maura Fiona","family":"Judge","sequence":"additional","affiliation":[{"name":"Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3705-0461","authenticated-orcid":false,"given":"Gergely","family":"Mar\u00f3ti","sequence":"additional","affiliation":[{"name":"Institute of Plant Biology, Biological Research Center, 6726 Szeged, Hungary"},{"name":"Faculty of Water Sciences, University of Public Service, 6500 Baja, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8567-9216","authenticated-orcid":false,"given":"\u00c1gnes","family":"Becsei","sequence":"additional","affiliation":[{"name":"Department of Phyisics of Complex Systems, E\u00f6tv\u00f6s Lor\u00e1nd University, 1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7834-4642","authenticated-orcid":false,"given":"S\u00e1ndor","family":"Spis\u00e1k","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1783-2041","authenticated-orcid":false,"given":"Norbert","family":"Solymosi","sequence":"additional","affiliation":[{"name":"Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,10,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1111\/nbu.12334","article-title":"Probiotics for human use","volume":"43","author":"Sanders","year":"2018","journal-title":"Nutr. Bull."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1016\/j.cell.2018.08.041","article-title":"Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features","volume":"174","author":"Zmora","year":"2018","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1126\/science.aan4236","article-title":"Gut microbiome modulates response to anti\u2013PD-1 immunotherapy in melanoma patients","volume":"359","author":"Gopalakrishnan","year":"2018","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"908","DOI":"10.3389\/fmicb.2017.00908","article-title":"Assessing the risk of probiotic dietary supplements in the context of antibiotic resistance","volume":"8","author":"Zheng","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13104-020-05114-1","article-title":"Evaluation of commercial veterinary probiotics containing enterococci for transferrable vancomycin resistance genes","volume":"13","author":"Berreta","year":"2020","journal-title":"BMC Res. Notes"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"108388","DOI":"10.1016\/j.ijfoodmicro.2019.108388","article-title":"Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data","volume":"314","author":"Rozman","year":"2020","journal-title":"Int. J. Food Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.jgar.2020.02.007","article-title":"Revealing antibiotic resistance in therapeutic and dietary probiotic supplements","volume":"22","author":"Selvin","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP), Rychen, G., Aquilina, G., Azimonti, G., Bampidis, V., Bastos, M.d.L., Bories, G., Chesson, A., Cocconcelli, P.S., and Flachowsky, G. (2018). Guidance on the characterisation of microorganisms used as feed additives or as production organisms. EFSA J., 16, e05206.","DOI":"10.2903\/j.efsa.2018.5206"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (2021). EFSA statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain. EFSA J., 19, e06506.","DOI":"10.2903\/j.efsa.2021.6506"},{"key":"ref_10","first-page":"81","article-title":"Towards an integrated model of bacterial conjugation","volume":"39","author":"Arechaga","year":"2015","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Goh, S. (2016). Phage transduction. Clostridium Difficile, Humana Press.","DOI":"10.1007\/978-1-4939-6361-4_13"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2751","DOI":"10.1128\/AEM.02459-06","article-title":"Tetracycline resistance mediated by tet (W), tet (M), and tet (O) genes of Bifidobacterium isolates from humans","volume":"73","author":"Aires","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_13","first-page":"6","article-title":"Molecular characterization of intrinsic and acquired antibiotic resistance in lactic acid bacteria and bifidobacteria","volume":"14","author":"Ammor","year":"2008","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1128\/AEM.02493-10","article-title":"Screening for antimicrobial resistance genes and virulence factors via genome sequencing","volume":"77","author":"Bennedsen","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"202","DOI":"10.3389\/fmicb.2013.00202","article-title":"Antibiotic resistance in probiotic bacteria","volume":"4","author":"Gueimonde","year":"2013","journal-title":"Front. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Mancino, W., Lugli, G.A., van Sinderen, D., Ventura, M., and Turroni, F. (2019). Mobilome and resistome reconstruction from genomes belonging to members of the Bifidobacterium genus. Microorganisms, 7.","DOI":"10.3390\/microorganisms7120638"},{"key":"ref_17","unstructured":"FAO\/WHO (2001). Health and Nutritional Properties of Probiotics in Food Including Powder Milk with Live Lactic Acid Bacteria, FAO. Food and Agriculture Organization of the United Nations and World Health Organization Expert Consultation Report."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"ref_19","unstructured":"R Core Team (2021). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"McMurdie, P.J., and Holmes, S. (2013). Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0061217"},{"key":"ref_21","unstructured":"Lahti, L., and Shetty, S. (2021, March 22). Microbiome R package, 2012\u20132019. Available online: http:\/\/microbiome.github.io."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Hyatt, D., Chen, G.L., LoCascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-119"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e35","DOI":"10.1093\/nar\/gkx1321","article-title":"PlasFlow: Predicting plasmid sequences in metagenomic data using genome signatures","volume":"46","author":"Krawczyk","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-020-00990-y","article-title":"VirSorter2: A multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses","volume":"9","author":"Guo","year":"2021","journal-title":"Microbiome"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1128\/AEM.70.4.2161-2171.2004","article-title":"Characterization of Bacillus probiotics available for human use","volume":"70","author":"Duc","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1007\/s12602-016-9235-9","article-title":"Effect of potential probiotic Lactococcus lactis subsp. lactis on growth performance, intestinal microbiota, digestive enzyme activities, and disease resistance of Litopenaeus vannamei","volume":"9","author":"Adel","year":"2017","journal-title":"Probiotics Antimicrob. Proteins"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"881","DOI":"10.3389\/fmicb.2019.00881","article-title":"Probiotic potential and safety evaluation of Enterococcus faecalis OB14 and OB15, isolated from traditional tunisian testouri cheese and rigouta, using physiological and genomic analysis","volume":"10","author":"Baccouri","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"123","DOI":"10.4103\/JCD.JCD_505_18","article-title":"Probiotic Streptococcus strains in caries prevention: A systematic review","volume":"22","author":"Poorni","year":"2019","journal-title":"J. Conserv. Dent. JCD"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Bozkurt, H.S., and Quigley, E.M. (2020). The probiotic Bifidobacterium in the management of Coronavirus: A theoretical basis. Int. J. Immunopathol. Pharmacol., 34.","DOI":"10.1177\/2058738420961304"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Drago, L., Meroni, G., Chiaretti, A., Laforgia, N., Cucchiara, S., and Baldassarre, M.E. (2020). Effect of Limosilactobacillus reuteri LRE02\u2013Lacticaseibacillus rhamnosus LR04 Combination on Antibiotic-Associated Diarrhea in a Pediatric Population: A National Survey. J. Clin. Med., 9.","DOI":"10.3390\/jcm9103080"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2207","DOI":"10.1080\/10408398.2020.1774496","article-title":"Bio-functional properties of probiotic Lactobacillus: Current applications and research perspectives","volume":"61","author":"Minj","year":"2020","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Dec, M., St\u0119pie\u0144-Py\u015bniak, D., Puchalski, A., Hauschild, T., Pietras-O\u017cga, D., Ignaciuk, S., and Urban-Chmiel, R. (2021). Biodiversity of Ligilactobacillus salivarius Strains from Poultry and Domestic Pigeons. Animals, 11.","DOI":"10.3390\/ani11040972"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Garcia-Gonzalez, N., Battista, N., Prete, R., and Corsetti, A. (2021). Health-Promoting Role of Lactiplantibacillus plantarum Isolated from Fermented Foods. Microorganisms, 9.","DOI":"10.3390\/microorganisms9020349"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Hussain, N., Li, R., Takala, T.M., Tariq, M., Zaidi, A.H., and Saris, P.E. (2021). Generation of Lactose-and Protease-Positive Probiotic Lacticaseibacillus rhamnosus GG by Conjugation with Lactococcus lactis NCDO 712. Appl. Environ. Microbiol., 87.","DOI":"10.1128\/AEM.02957-20"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"613","DOI":"10.5897\/AJB2016.15212","article-title":"Characterization of potential probiotic bacteria isolated from sorghum and pearl millet of the semi-arid tropics","volume":"15","author":"Kunchala","year":"2016","journal-title":"Afr. J. Biotechnol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3282","DOI":"10.3389\/fmicb.2018.03282","article-title":"High-throughput sequence analyses of bacterial communities and multi-mycotoxin profiling during processing of different formulations of Kunu, a traditional fermented beverage","volume":"9","author":"Ezekiel","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"5753","DOI":"10.1099\/ijsem.0.004475","article-title":"Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: Description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species","volume":"70","author":"Gupta","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"103643","DOI":"10.1016\/j.jff.2019.103643","article-title":"Probiotic characteristics of Bacillus coagulans and associated implications for human health and diseases","volume":"64","author":"Cao","year":"2020","journal-title":"J. Funct. Foods"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/0378-1119(89)90241-2","article-title":"Nucleotide sequence of the chromosomal gene coding for the aminoglycoside 6-adenylyltransferase from Bacillus subtilis Marburg 168","volume":"78","author":"Keiichi","year":"1989","journal-title":"Gene"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2189","DOI":"10.1128\/jb.179.7.2189-2193.1997","article-title":"Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr","volume":"179","author":"Klyachko","year":"1997","journal-title":"J. Bacteriol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"2311","DOI":"10.1128\/JB.182.8.2311-2313.2000","article-title":"A broad-specificity multidrug efflux pump requiring a pair of homologous SMR-type proteins","volume":"182","author":"Jack","year":"2000","journal-title":"J. Bacteriol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"5640","DOI":"10.1128\/JB.186.17.5640-5648.2004","article-title":"Bacillus subtilis LmrA is a repressor of the lmrAB and yxaGH operons: Identification of its binding site and functional analysis of lmrB and yxaGH","volume":"186","author":"Yoshida","year":"2004","journal-title":"J. Bacteriol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"4326","DOI":"10.1128\/AAC.01819-10","article-title":"Reduction in membrane phosphatidylglycerol content leads to daptomycin resistance in Bacillus subtilis","volume":"55","author":"Hachmann","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"8978","DOI":"10.1073\/pnas.1808535115","article-title":"Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR","volume":"115","author":"Graf","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-017-02680-0","article-title":"The evolution of substrate discrimination in macrolide antibiotic resistance enzymes","volume":"9","author":"Pawlowski","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"2697","DOI":"10.1099\/ijs.0.020339-0","article-title":"Differentiation of Bifidobacterium species using partial RNA polymerase \u03b2-subunit (rpoB) gene sequences","volume":"60","author":"Kim","year":"2010","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-30429-2","article-title":"Bifidobacterium adolescentis is intrinsically resistant to antitubercular drugs","volume":"8","author":"Lokesh","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"39","DOI":"10.12938\/bmfh.17-017","article-title":"Investigating the transmissibility of tet (W) in bifidobacteria exposed to acid and bile stress","volume":"37","author":"Polit","year":"2018","journal-title":"Biosci. Microbiota Food Health"},{"key":"ref_55","first-page":"1","article-title":"A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt","volume":"10","author":"Csabai","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3141","DOI":"10.1128\/AEM.02540-10","article-title":"Insights into physiological and genetic mupirocin susceptibility in bifidobacteria","volume":"77","author":"Serafini","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1128\/AAC.43.1.141","article-title":"Characterization of Dihydrofolate Reductase Genes from Trimethoprim-Susceptible and Trimethoprim-Resistant Strains ofEnterococcus faecalis","volume":"43","author":"Coque","year":"1999","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"G\u00f3mez-Sanz, E., Haro-Moreno, J.M., Jensen, S.O., Roda-Garcia, J.J., and Lopez-Perez, M. (2020). Staphylococcus sciuri C2865 from a distinct subspecies cluster as reservoir of the novel transferable trimethoprim resistance gene, dfrE, and adaptation driving mobile elements. bioRxiv.","DOI":"10.1101\/2020.09.30.320143"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1248\/bpb.26.266","article-title":"Functional cloning and expression of emeA, and characterization of EmeA, a multidrug efflux pump from Enterococcus faecalis","volume":"26","author":"Lee","year":"2003","journal-title":"Biol. Pharm. Bull."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.fm.2014.06.009","article-title":"Role of EfrAB efflux pump in biocide tolerance and antibiotic resistance of Enterococcus faecalis and Enterococcus faecium isolated from traditional fermented foods and the effect of EDTA as EfrAB inhibitor","volume":"44","author":"Lerma","year":"2014","journal-title":"Food Microbiol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1128\/AAC.46.6.1845-1850.2002","article-title":"An Enterococcus faecalis ABC homologue (Lsa) is required for the resistance of this species to clindamycin and quinupristin-dalfopristin","volume":"46","author":"Singh","year":"2002","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1007\/s00248-009-9533-9","article-title":"Horizontal transfer of the tetracycline resistance gene tetM mediated by pCF10 among Enterococcus faecalis in the house fly (Musca domestica L.) alimentary canal","volume":"58","author":"Akhtar","year":"2009","journal-title":"Microb. Ecol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1128\/AAC.01068-10","article-title":"Cross-resistance to lincosamides, streptogramins A, and pleuromutilins due to the lsa (C) gene in Streptococcus agalactiae UCN70","volume":"55","author":"Malbruny","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/j.foodres.2018.02.062","article-title":"Food isolate Listeria monocytogenes harboring tetM gene plasmid-mediated exchangeable to Enterococcus faecalis on the surface of processed cheese","volume":"107","author":"Haubert","year":"2018","journal-title":"Food Res. Int."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/s00284-019-01817-2","article-title":"Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated bla CTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial Pathogens","volume":"77","author":"Gabashvili","year":"2020","journal-title":"Curr. Microbiol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1896","DOI":"10.1128\/AAC.37.9.1896","article-title":"Characterization of the chromosomal aac (6\u2019)-Ii gene specific for Enterococcus faecium","volume":"37","author":"Costa","year":"1993","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"4463","DOI":"10.1128\/AAC.01030-13","article-title":"Genetic basis for in vitro and in vivo resistance to lincosamides, streptogramins A, and pleuromutilins (LSAP phenotype) in Enterococcus faecium","volume":"57","author":"Isnard","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1128\/AAC.45.1.263-266.2001","article-title":"Disruption of an Enterococcus faecium species-specific gene, a homologue of acquired macrolide resistance genes of staphylococci, is associated with an increase in macrolide susceptibility","volume":"45","author":"Singh","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/jac\/dki378","article-title":"Resistance to telithromycin is conferred by msr (A), msrC and msr (D) in Staphylococcus aureus","volume":"56","author":"Reynolds","year":"2005","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/j.1574-6968.2006.00371.x","article-title":"Ubiquity and diversity of multidrug resistance genes in Lactococcus lactis strains isolated between 1936 and 1995","volume":"263","author":"Wind","year":"2006","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1128\/JCM.00150-17","article-title":"Bifidobacterium bacteremia: Clinical characteristics and a genomic approach to assess pathogenicity","volume":"55","author":"Esaiassen","year":"2017","journal-title":"J. Clin. Microbiol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.1574-6941.2002.tb01019.x","article-title":"Gentamicin resistance genes in environmental bacteria: Prevalence and transfer","volume":"42","author":"Heuer","year":"2002","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1016\/j.rvsc.2009.05.006","article-title":"Resistance patterns and detection of aac (3)-IV gene in apramycin-resistant Escherichia coli isolated from farm animals and farm workers in northeastern of China","volume":"87","author":"Zhang","year":"2009","journal-title":"Res. Vet. Sci."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1128\/CMR.18.4.657-686.2005","article-title":"Extended-spectrum \u03b2-lactamases: A clinical update","volume":"18","author":"Paterson","year":"2005","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"263","DOI":"10.4103\/0974-777X.68531","article-title":"Extended-spectrum \u03b2-lactamases in Gram Negative Bacteria","volume":"2","author":"Rawat","year":"2010","journal-title":"J. Glob. Infect. Dis."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2902","DOI":"10.1128\/JCM.42.7.2902-2906.2004","article-title":"Molecular characterization of extended-spectrum beta-lactamases produced by clinical isolates of Klebsiella pneumoniae and Escherichia coli from a Korean nationwide survey","volume":"42","author":"Jeong","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"258","DOI":"10.4103\/0255-0857.83909","article-title":"First detection of TEM-116 extended-spectrum \u03b2-lactamase in a Providencia stuartii isolate from a Tunisian hospital","volume":"29","author":"Lahlaoui","year":"2011","journal-title":"Indian J. Med Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1089\/mdr.2006.12.12","article-title":"Extended-spectrum \u03b2-lactamase genes of Klebsiella pneumoniae strains in Taiwan: Recharacterization of shv-27, shv-41, and tem-116","volume":"12","author":"Lin","year":"2006","journal-title":"Microb. Drug Resist."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/0378-1119(82)90015-4","article-title":"The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers","volume":"19","author":"Vieira","year":"1982","journal-title":"Gene"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1093\/jac\/dkm239","article-title":"Learning from mistakes: Taq polymerase contaminated with \u03b2-lactamase sequences results in false emergence of Streptococcus pneumoniae containing TEM","volume":"60","author":"Koncan","year":"2007","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nrmicro3399","article-title":"What is a resistance gene? Ranking risk in resistomes","volume":"13","author":"Coque","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_82","unstructured":"CDC (2018). Outpatient Antibiotic Prescriptions."},{"key":"ref_83","unstructured":"WHO (2019). WHO Report on Surveillance of Antibiotic Consumption: 2016\u20132018 Early Implementation, WHO."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1128\/JB.186.5.1423-1429.2004","article-title":"Role of histone-like protein H-NS in multidrug resistance of Escherichia coli","volume":"186","author":"Nishino","year":"2004","journal-title":"J. Bacteriol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"98","DOI":"10.7196\/SAMJ.2021.v111i2.15454","article-title":"Enterococcus faecalis ST21 harbouring Tn6009 isolated from a carriage sample in South Africa","volume":"111","author":"Founou","year":"2021","journal-title":"S. Afr. Med J."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1093\/jac\/dkn280","article-title":"Analysis of tetracycline resistance tet (W) genes and their flanking sequences in intestinal Bifidobacterium species","volume":"62","author":"Ammor","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Duranti, S., Lugli, G.A., Mancabelli, L., Turroni, F., Milani, C., Mangifesta, M., Ferrario, C., Anzalone, R., Viappiani, A., and van Sinderen, D. (2017). Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria. Appl. Environ. Microbiol., 83.","DOI":"10.1128\/AEM.02894-16"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1128\/AAC.01587-05","article-title":"Comparative analysis of sequences flanking tet (W) resistance genes in multiple species of gut bacteria","volume":"50","author":"Kazimierczak","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Ramirez, M.S., and Tolmasky, M.E. (2017). Amikacin: Uses, resistance, and prospects for inhibition. Molecules, 22.","DOI":"10.3390\/molecules22122267"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"3672","DOI":"10.1128\/AAC.45.12.3672-3673.2001","article-title":"The newly described msrC gene is not equally distributed among all isolates of Enterococcus faecium","volume":"45","author":"Werner","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.3201\/eid1707.110209","article-title":"Extended-spectrum \u03b2-lactamase genes of Escherichia coli in chicken meat and humans, The Netherlands","volume":"17","author":"Overdevest","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Kamaruzzaman, E.A., Abdul Aziz, S., Bitrus, A.A., Zakaria, Z., and Hassan, L. (2020). Occurrence and Characteristics of Extended-Spectrum \u03b2-Lactamase-Producing Escherichia coli from Dairy Cattle, Milk, and Farm Environments in Peninsular Malaysia. Pathogens, 9.","DOI":"10.20944\/preprints202009.0485.v1"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"137497","DOI":"10.1016\/j.scitotenv.2020.137497","article-title":"A clinically important, plasmid-borne antibiotic resistance gene (\u03b2-lactamase TEM-116) present in desert soils","volume":"719","author":"Naidoo","year":"2020","journal-title":"Sci. Total. Environ."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-017-01405-7","article-title":"The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity","volume":"8","author":"Sharma","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1016\/j.ygeno.2021.03.021","article-title":"Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium","volume":"113","author":"Panthee","year":"2021","journal-title":"Genomics"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1128\/AAC.47.4.1343-1346.2003","article-title":"Chromosomal aadD2 encodes an aminoglycoside nucleotidyltransferase in Bacillus clausii","volume":"47","author":"Bozdogan","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"S261","DOI":"10.1016\/S1590-8658(07)60006-1","article-title":"Antibiotic resistance: The pros and cons of probiotics","volume":"38","author":"Courvalin","year":"2006","journal-title":"Dig. Liver Dis."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"590325","DOI":"10.3389\/fmicb.2020.590325","article-title":"A cross-sectional study of dairy cattle metagenomes reveals increased antimicrobial resistance in animals farmed in a heavy metal contaminated environment","volume":"11","author":"Gaeta","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1021\/acs.est.0c05698","article-title":"Will a Non-antibiotic Metalloid Enhance the Spread of Antibiotic Resistance Genes: The Selenate Story","volume":"55","author":"Shi","year":"2020","journal-title":"Environ. Sci. Technol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.3389\/fmicb.2019.01683","article-title":"Accurate and strict identification of probiotic species based on coverage of whole-metagenome shotgun sequencing data","volume":"10","author":"Seol","year":"2019","journal-title":"Front. Microbiol."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/11\/1287\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:20:31Z","timestamp":1760167231000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/11\/1287"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,21]]},"references-count":100,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2021,11]]}},"alternative-id":["antibiotics10111287"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics10111287","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.05.04.442546","asserted-by":"object"}]},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,21]]}}}