High prevalence of the recently identified clonal lineage ST1299/CT3109 vanA among vancomycin-resistant Enterococcus faecium strains isolated from municipal wastewater

• Published in: mSphere Vol. 9; no. 9; p. e0039624
• Main Authors: Valenza, Giuseppe, Eisenberger, David, Esse, Jan, Held, Jürgen, Lehner-Reindl, Verena, Plaumann, Peter-Louis, Ziegler, Tobias, Knauer, Max, Bogdan, Christian, Dudler, Patrick
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 25.09.2024
• Subjects: Anti-Bacterial Agents - pharmacology; Bacterial Proteins - genetics; Carbon-Oxygen Ligases - genetics; Clinical Microbiology; core genome multilocus sequence typing; Cross Infection - epidemiology; Cross Infection - microbiology; Enterococcus faecium; Enterococcus faecium - classification; Enterococcus faecium - drug effects; Enterococcus faecium - genetics; Enterococcus faecium - isolation & purification; Germany - epidemiology; Gram-Positive Bacterial Infections - epidemiology; Gram-Positive Bacterial Infections - microbiology; Humans; Microbial Sensitivity Tests; Multilocus Sequence Typing; Observation; Polymorphism, Single Nucleotide; Prevalence; single nucleotide polymorphisms; ST1299/CT3109; Vancomycin Resistance - genetics; vancomycin-resistance; Vancomycin-Resistant Enterococci - classification; Vancomycin-Resistant Enterococci - drug effects; Vancomycin-Resistant Enterococci - genetics; Vancomycin-Resistant Enterococci - isolation & purification; wastewater; Wastewater - microbiology; Germany; Enterococcus faecium; ST1299/CT3109; wastewater; vancomycin-resistance; ST117/CT71; single nucleotide polymorphisms; core genome multilocus sequence typing
• ISSN: 2379-5042; 2379-5042
• DOI: 10.1128/msphere.00396-24

Previously, we demonstrated that the majority of vancomycin-resistant (VREfm) strains from in-patients of the University Hospital Erlangen, Germany, belonged to only three clonal lineages, namely ST117/CT71 and two novel ST1299 lineages classified as CT3109 and CT1903. The goal of the current study was (i) to investigate whether VREfm is also detectable in wastewater of the city of Erlangen, (ii) to identify their molecular features, and (iii) to clarify whether VREfm could arise from the community of the city of Erlangen or can be (directly) connected to nosocomial infections in the hospital setting. From April to May 2023, a total of 244 VREfm strains from raw wastewater of the city of Erlangen were analyzed by core genome multilocus sequence typing (cgMLST). Moreover, 20 of them were further investigated for single nucleotide polymorphisms (SNPs). The molecular characterization of the wastewater VREfm strains revealed a high prevalence (27.9%) of the recently identified clonal lineage ST1299/CT3109 which is mainly characterized by the presence of the tetracycline-resistance determinant ) and the virulence genes and . The SNPs analysis revealed the presence of two major clusters, namely cluster I (≤65 SNPs), which included well-known hospital-adapted clonal lineages such as ST117/CT71 and ST80/CT1065 and cluster II (≤70 SNPs), which were mainly characterized by the lineage ST1299/CT3109 . Based on the concomitant resistance to vancomycin and tetracycline, we propose that ST1299/CT3109 primarily originated and spread outside of hospital settings.IMPORTANCEThis study provides a detailed genomic analysis of vancomycin-resistant (VREfm) strains isolated from municipal wastewater with a particular focus on clonal lineages, antimicrobial resistance, and the presence of virulence genes. The high wastewater prevalence of the recently identified clonal lineage ST1299/CT3109 , which has been previously detected in hospitals, suggests an enormous potential for future spread in Germany.