AUTHOR=Lu Jingda , Shen Tingting , Zhang Yixin , Ma Xinwei , Xu Sheng , Awad Sameh , Du Muying , Zhong Zhi 

TITLE=Safety assessment of Enterococcus lactis based on comparative genomics and phenotypic analysis

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1196558

DOI=10.3389/fmicb.2023.1196558

ISSN=1664-302X

ABSTRACT=<p><italic>Enterococcus faecium</italic> is sometimes used in food production; however, its acquisition of antibiotic resistance has become an alarming health concern. The <italic>E. lactis</italic> species is closely related to <italic>E. faecium</italic> and has good probiotic potential. This study aimed to investigate the antibiotic resistance of <italic>E. lactis.</italic> We analyzed the antibiotic resistance phenotype and whole-genome sequences of 60 <italic>E. lactis</italic> 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 <italic>E. lactis</italic> genomes carried only a subset of commonly reported antibiotic resistance genes (ARGs) in <italic>E. faecium</italic>. Five ARGs were detected across the investigated <italic>E. lactis</italic>, including two universally present genes (<italic>msrC</italic> and <italic>AAC(6′)-Ii</italic>) and three rarely detected ARGs (<italic>tet(L)</italic>, <italic>tetM</italic>, and <italic>efmA</italic>). 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 <italic>E. lactis</italic>. The fact that the lower number of ARGs present in <italic>E. lactis</italic> supports that it may be an alternative to <italic>E. faecalis</italic> for use in the food industry. Data generated in this work is of interest to the dairy industry.</p>