Genome-based studies indicate that the Enterococcus faecium Clade B strains belong to Enterococcus lactis species and lack of the hospital infection associated markers

Abstract

Enterococcus lactis and the heterotypic synonym Enterococcus xinjiangensis from dairy origin have recently been identified as a novel species based on 16S rRNA gene sequence analysis. Enterococcus faecium type strain NCTC 7171T was used as the reference genome for determining E. lactis and E. faecium to be separate species. However, this taxonomic classification did not consider the diverse lineages of E. faecium , and the double nature of hospital-associated (clade A) and community-associated (clade B) isolates. Here, we investigated the taxonomic relationship among isolates of E. faecium of different origins and E. lactis , using a genome-based approach. Additional to 16S rRNA gene sequence analysis, we estimated the relatedness among strains and species using phylogenomics based on the core pangenome, multilocus sequence typing, the average nucleotide identity and digital DNA–DNA hybridization. Moreover, following the available safety assessment schemes, we evaluated the virulence profile and the ampicillin resistance of E. lactis and E. faecium clade B strains. Our results confirmed the genetic and evolutionary differences between clade A and the intertwined clade B and E. lactis group. We also confirmed the absence in these strains of virulence gene markers IS16, hylEfm and esp and the lack of the PBP5 allelic profile associated with ampicillin resistance. Taken together, our findings support the reassignment of the strains of E. faecium clade B as E. lactis .

Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 15: suitability of taxonomic units notified to EFSA until September 2021

“…Body of knowledge E. lactis was isolated from traditional chickpea liquid starter and dough samples for bakeries in Turkey (Gunduz et al, 2020), from traditional (raw) milk cheeses (Morandi et al, 2012;Mangia et al, 2016), artisanal animal rennet pastes (Cruciata et al, 2014) and a traditional cereal based Indian product (idli batter) (Thumu and Halami, 2012). Recent evidence supports the presence of E. lactis, which was previously identified as E. faecium clade B, in the human and animal gut (Belloso Daza et al, 2021).…”

“…The species Enterococcus xinjiangensis (Ren et al, 2016;Oren and Garrity, 2020) was accepted as a heterotypic synonym of E. lactis (Li and Gu, 2021). Belloso Daza et al (2021) reassigned the strains of Enterococcus faecium clade B to E. lactis.…”

Identification of Leuconostoc species based on novel marker genes identified using real-time PCR via computational pangenome analysis

“…Recently, PCR methods targeting specific genes were developed from comparative genomics to accurately identify closely related species within genera. Pangenome analysis helps in finding more DNA markers for identifying closely related species (Belloso Daza et al, 2021). Highly specific genes identified via pangenome analysis are useful alternative genetic markers for differentiating closely related species.…”

Safety and efficacy of a feed additive consisting of Bacillus subtilis FERM BP‐07462, Enterococcus lactis FERM BP‐10867 and Clostridium butyricum FERM BP‐10866 (BIO‐THREE®) for chickens for fattening, chickens reared for laying, turkeys for fattening, turkeys reared for breeding, all avian species for rearing/fattening to slaughter and all avian species reared for laying or breeding to point of lay (TOA BIOPHARMA Co., Ltd.)

“…According to the FEEDAP guidance (EFSA FEEDAP Panel, 2018a ), the E. faecium safety should be assessed demonstrating the absence of genetic markers typical of the clinical isolates E. faecium clade A (IS 16 , esp , hyl ) and the susceptibility to ampicillin. Taking into consideration the allocation of clade B strains to E. lactis species (Belloso Daza et al, 2021 ), the FEEDAP Panel considers these criteria applicable also to E. lactis strains. E. lactis FERM BP‐10867 proved to be susceptible to ampicillin.…”