Department of Biotechnology, University of Verona, Verona, Italy.
APC Microbiome Ireland, University College Cork, Cork, Ireland.
Appl Environ Microbiol. 2018 Dec 13;85(1). doi: 10.1128/AEM.01738-18. Print 2019 Jan 1.
species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of species and their carriage of antibiotic resistance (AR) genes is under continuing review. To comprehensively update the identification of AR in the genus , we determined the antibiotic susceptibility patterns of 182 type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes and , involved in resistance to aminoglycosides and clindamycin, respectively, were found in spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in , , and , flanked in the genome by mobile genetic elements with potential for horizontal transfer. species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening.
物种被广泛用作益生菌和起始培养物，用于各种食品，这得益于其长期安全使用的历史。尽管超过 35 个物种符合欧洲食品安全局（EFSA）的合格安全状态推定标准，但对物种及其携带抗生素耐药性（AR）基因的安全性仍在持续审查中。为了全面更新属内抗生素耐药性的鉴定，我们确定了 182 个模式株的抗生素药敏模式，并根据 AR 基因的全基因组注释将这些表型与基因型进行了比较。对甲氧苄啶、万古霉素和卡那霉素的耐药性是最常见的表型。基于同源性筛选和手动注释相结合的方法，确定了编码对氨基糖苷类（20 个序列）、四环素（18 个）、红霉素（6 个）、克林霉素（60 个）和氯霉素（42 个）耐药性的基因。特别是，分别参与对氨基糖苷类和克林霉素耐药性的基因和在 spp.中发现。在 spp.中检测到预测编码四环素和红霉素耐药性的获得性决定簇，这些决定簇被移动遗传元件包围，这些元件具有水平转移的潜力。通常认为属内的物种是非致病性的，用于人类和动物的各种食品和产品。然而，本研究中检查的许多物种的抗生素耐药水平超过了 EFSA 推荐的水平，这表明应根据这里讨论的耐药遗传基础重新审查这些截止值。我们的数据为合理修订进入食物链的作为起始培养物、食品防腐剂或益生菌的乳杆菌的安全性评估监管指南提供了证据，并将有助于基于全基因分型对菌株进行全面的安全性筛选。
