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

Abstract

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