Table_3_Safety assessment of Enterococcus lactis based on comparative genomics and phenotypic analysis.xlsx

Enterococcus faecium is sometimes used in food production; however, its acquisition of antibiotic resistance has become an alarming health concern. The E. lactis species is closely related to E. faecium and has good probiotic potential. This study aimed to investigate the antibiotic resistance of E. lactis. We analyzed the antibiotic resistance phenotype and whole-genome sequences of 60 E. lactis isolates (23, 29, and 8 isolates from dairy products, Rice wine Koji, and human feces, respectively). These isolates showed varying degree of resistance to 13 antibiotics, and were sensitive to ampicillin and linezolid. The E. lactis genomes carried only a subset of commonly reported antibiotic resistance genes (ARGs) in E. faecium. Five ARGs were detected across the investigated E. lactis, including two universally present genes (msrC and AAC(6′)-Ii) and three rarely detected ARGs (tet(L), tetM, and efmA). To identify other undescribed antibiotic resistance-encoding genes, a genome-wide association study was performed, returning 160 potential resistance genes that were associated with six antibiotics, namely chloramphenicol, vancomycin, clindamycin, erythromycin, quinupristin-dalfopristin, and rifampicin. Only around one-third of these genes encode known biological functions, including cellular metabolism, membrane transport, and DNA synthesis. This work identified interesting targets for future study of antibiotic resistance in E. lactis. The fact that the lower number of ARGs present in E. lactis supports that it may be an alternative to E. faecalis for use in the food industry. Data generated in this work is of interest to the dairy industry.

屎肠球菌（Enterococcus faecium）有时应用于食品生产，但其获得抗生素耐药性已成为令人担忧的公共卫生问题。乳酸肠球菌（E. lactis）与屎肠球菌亲缘关系密切，且具备良好的益生菌潜力。本研究旨在探究乳酸肠球菌的抗生素耐药性。我们对60株乳酸肠球菌分离株的抗生素耐药表型与全基因组序列进行了分析，其中23株分离自乳制品、29株分离自米酒曲（Rice wine Koji）、8株分离自人粪便。上述分离株对13种抗生素表现出程度不一的耐药性，且对氨苄西林与利奈唑胺敏感。乳酸肠球菌基因组仅携带屎肠球菌中常见抗生素耐药基因（ARGs）的一个子集。在所研究的乳酸肠球菌中共检测到5种抗生素耐药基因，包括2种普遍存在的基因（msrC与AAC(6′)-Ii），以及3种罕见的耐药基因（tet(L)、tetM与efmA）。为鉴定其他尚未被描述的抗生素耐药编码基因，本研究开展了全基因组关联分析，共筛选出与6种抗生素——氯霉素、万古霉素、克林霉素、红霉素、奎奴普丁-达福普汀、利福平——相关的160个潜在耐药基因。其中仅约三分之一的基因编码已知生物学功能，涵盖细胞代谢、膜转运与DNA合成等过程。本研究明确了未来探究乳酸肠球菌抗生素耐药性的潜在研究靶点。乳酸肠球菌所携带的抗生素耐药基因数量更少，这支持其可作为粪肠球菌（E. faecalis）在食品工业中的替代菌株。本研究产生的数据对乳制品行业具有参考价值。