Novel insights into healthy humans’ faecal carriage of enterococci: Enterococcus lactis is as a dominant highly bacteriocinogenic species

• Author(s): Almeida-Santos, A. C. ; Duarte, B. ; Teixeira, M. J. ; Tedim, A. P. ; Novais, C. ; Peixe, L. ; Freitas, A. R.
• Date: 2023
• Origin: Scientific Letters
• Subject(s): Selected Oral Communication
• Document Type: Journal article
• Language: English

Description

Background: Enterococcus lactis (Elts) [former Enterococcus faecium (Efm) clade-B] has been greatly associated with human colonization, but its epidemiology is unknown since this reclassification [1]. We aimed to assess the contemporary faecal carriage of enterococci species among healthy-humans (HH) in Portugal and get novel insights about Efm/Elts differences. Methods: Fifty-one faecal samples (29-women/22-men;18-85/~45-years) from HH in Northern Portugal (February-July 2022) were processed by enrichment/selection steps with/without ampicillin, vancomycin or linezolid. Efm, Elts and other species were identified by PCR [2, 3] and antibiotic-susceptibility by disk-diffusion/broth-microdilution (EUCAST/CLSI). Representatives/sample (n=40) were characterized by Whole-Genome-Sequencing/CGE-tools, including a homemade bacteriocins(bac) database. Qualitative bacteriocin production/sensitivity was performed in sequenced Efm/Elts and selected clinical VREfm (vancomycin-resistant-Efm) and Elts (all-against-all) using the soft-agar-overlay technique. Results: All samples carried Enterococcus (n=337), with most containing Elts-73% (p<0.05) and/or E.faecalis (Efs)-61% and variable occurrence for Efm-45%, E.hirae-16%, and/or other species (<2%). Samples (24% multidrug-resistant) included isolates resistant to erythromycin [73%;erm(B)/msr(C)], tetracycline [63%;tet(M)/tet(L)], high-level-streptomycin (22%;ant(6)-Ia/str), chloramphenicol (12%;cat/fexA/fexB/optrA/poxtA), quinupristin-dalfopristin (12%), high-level-gentamycin [4%;aac(6’)-Ie-aph(2’’)-Ia] and linezolid (4%-optrA/poxtA;MIC50/MIC90 4-mg/L). Acquired linezolid-resistance genes were detected in two samples: optrA (one E. thailandicus; MIC=8-mg/L) and optrA+poxtA (ST128-Efm; MIC=8-16-mg/L). Typical bacteriocins and plasmids from clinical Efm/Efs were scarce. Elts (2-5 bac; 100%-bac-genes+) and Efm (0-9; 71%-bac+) shared bacteriocins (e.g.,entP/entQ) contrasting with others exclusive of Efs (0-2;22%-bac+). No isolate could inhibit all or be inhibited by all, but the ones with more bacteriocins were less inhibited. Most Efm/Elts showed no activity against each other but ~30%/each inhibited most strains tested, including VREfm. Conclusions: Elts is one predominant enterococci gut species that would be misidentified as Efm without an accurate Efm/Elts distinction. Elts co-exist with Efm in the intestine, but specific Efm/Elts inhibiting most strains tested may contribute to microbiota restoration after antibiotic treatments. Linezolid-resistance genes finding is worrisome, suggesting an environmental/food-chain role in this acquisition since they were not described in enterococci from Portuguese hospitals before.