Literature-Based Phenotype Survey and In Silico Genotype Investigation of Antibiotic Resistance in the Genus Bifidobacte
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Literature‑Based Phenotype Survey and In Silico Genotype Investigation of Antibiotic Resistance in the Genus Bifidobacterium Linyan Cao1 · Huahai Chen1 · Qinghao Wang1 · Baiyuan Li1 · Yunfei Hu1 · Changhui Zhao1 · Yongfei Hu2 · Yeshi Yin1 Received: 31 March 2020 / Accepted: 29 September 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Bifidobacteria are typical commensals inhabiting the human intestine and are beneficial to the host because of their probiotic properties. One of the risks concerning probiotics is the potential of introducing antibiotic resistance genes (ARGs) to the host gut pathogens. This study was aimed to depict the general antibiotic resistance characteristics of the genus Bifidobacterium by combining the reported phenotype dataset and in silico genotype prediction. Bifidobacteria were mostly reported to be sensitive to beta-lactams, glycopeptides, chloramphenicol, and rifampicin, but resistant to aminoglycosides, polypeptides, quinolones, and mupirocin. Generally, the resistance phenotypes to erythromycin, tetracycline, fusidic acid, metronidazole, clindamycin, and trimethoprim were variable. Besides cmX and tetQ, characterized in bifidobacterial resident plasmids, 3520 putative ARGs were identified from 831 bifidobacterial genomes through BLASTP search. The identified ARGs matched thirty-eight reference ARGs, four of which seemed to be mutant housekeeping genes. The two high-abundant ARGs, tetW and ermX, were found to have different distribution traits. The predicted ARGs reasonably explained most of the corresponding resistant phenotypes in the published literature.
Introduction Bifidobacteria are typical commensals that mainly inhabit the gastrointestinal tract of mammals and other animals [1]. Strains of the genus Bifidobacterium are increasingly used in the food and feed products because of their potential health benefits [2, 3]. The species Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve, and Bifidobacterium longum were Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00284-020-02230-w) contains supplementary material, which is available to authorized users. * Yongfei Hu [email protected] * Yeshi Yin [email protected] 1
Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, Hunan, China
State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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recommended for Qualified Presumption of Safety (QPS) status by the European Food Safety Authority (EFSA) [4]. The Bifidobacterium strains that have given the Recognized as Safe (GRAS) status notices from the US Food and Drug Administration (FDA) also belong to the QPS species (https://www.cfsanappsexternal.fda.gov/scripts/fdcc/ index.cfm?set=GRASNotices). However, for
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