Critical genomic insights into vancomycin-resistant Enterococcus faecium in Lebanon

Abstract

Vancomycin-resistant Enterococcus faecium (VRE) poses a global public health threat, with particularly severe ramifications in low-resource settings. While E. faecium is commonly a commensal organism in the human gut, the acquisition of vancomycin resistance has contributed to the emergence of VRE as a major cause of hospital-acquired infections, especially in vulnerable populations. This study investigates the genetic characteristics of VRE isolated from hospitalized patients in Lebanon, focusing on antimicrobial resistance (AMR) phenotypes and the underlying resistome. We collected VRE isolates from patients at the time of admission or during routine screenings for multidrug-resistant pathogens. The isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and screened for antimicrobial susceptibility using the disk diffusion and E-test methods. Whole genome sequencing was conducted using Illumina technology, and bioinformatics analyses were carried out to identify the resistome, sequence types, plasmid types, and virulence genes. Additionally, we analyzed previously GenBank-deposited VRE genomes from Lebanon to assess genetic relationships. Our VRE isolates carried multiple acquired AMR genes and chromosomal mutations, exhibiting resistance to vancomycin, telavancin, ampicillin, erythromycin, norfloxacin, levofloxacin, and nitrofurantoin. The isolates belonged to three subtypes: ST203 (67%), ST612 (22%), and a novel ST2711 (11%), all of which belonged to CC17, a globally prevalent hospital-associated lineage known for high levels of AMR and hospital outbreaks. Core-genome single nucleotide variants (SNVs) phylogenetic analysis revealed that the ST203 isolates clustered with the previously GenBank-deposited ST203 Lebanese genomes. Taken together, these findings highlight the growing VRE burden in low-resource countries, emphasizing the need for enhanced surveillance and alternative treatment strategies.

Importance: The healthcare system in Lebanon faces substantial challenges due to ongoing economic instability and limited resources, creating a conducive environment for the spread of antimicrobial resistance. Vancomycin-resistant Enterococcus faecium (VRE) represents a growing public health threat, yet studies addressing its genetics in Lebanon are scarce. This study provided critical insights into the genomic features of VRE in clinical settings, highlighting the potential clonal dissemination of multidrug-resistant isolates carrying the vanHAX operon and belonging to CC17, a globally prevalent, hospital-associated lineage. Resistance to novel antimicrobials, such as telavancin, dalbavancin, and eravacycline, is alarming and necessitates immediate action to preserve these critical last-resort interventions. Notably, the identification of clonal spread and a novel sequence type (ST2711) within Lebanese hospitals, alongside resistance to last-resort antimicrobials, highlights the dynamic evolution of VRE and the urgent need to strengthen antimicrobial stewardship programs in Lebanon and beyond. Addressing this challenge requires integrated One Health strategies.

Keywords: CC17; One Health; antimicrobial resistance; genomic epidemiology; public health; surveillance; vancomycin-resistant Enterococcus faecium; whole genome sequencing.

Fig 1

Core-genome phylogenetic tree of our collected Enterococcus faecium isolates (n = 9) and all Lebanese E. faecium genomes available in GenBank Lebanon (n = 53). All isolates belong to clonal complex 17 (CC17). ST2711 is a novel subtype. The strips from left to right show the year of isolation, sequence type (ST), antimicrobial resistance genes, and the point mutations in gyrA, parC, and pbp5 genes detected in their whole-genome sequences. ¹pbp5 mutations are pbp5(V24A), pbp5(S27G), pbp5(R34Q), pbp5(G66E), pbp5(A68T), pbp5(E85D), pbp5(E100Q), pbp5(K144Q), pbp5(T172A), pbp5(L177I), pbp5(D204G), pbp5(A216S), pbp5(T324A), pbp5(M485A), pbp5(N496K), pbp5(A499T), pbp5(E525D), pbp5(E629V), and pbp5(P667S). AMG, aminoglycosides; MLD, macrolides; TET, tetracyclines; TMP, folate antagonist; GLY, glycopeptides; LIN, lincosamides; PHE, amphenicols; QUI, quinolones; B-LAC, β-lactams.