Molecular Typing Reveals Environmental Dispersion of Antibiotic-Resistant Enterococci under Anthropogenic Pressure

Abstract

As a consequence of global demographic challenges, both the artificial and the natural environment are increasingly impacted by contaminants of emerging concern, such as bacterial pathogens and their antibiotic resistance genes (ARGs). The aim of this study was to determine the extent to which anthropogenic contamination contributes to the spread of antibiotic resistant enterococci in aquatic compartments and to explore genetic relationships among Enterococcus strains. Antimicrobial susceptibility testing (ampicillin, imipenem, norfloxacin, gentamycin, vancomycin, erythromycin, tetracycline, trimethoprim-sulfamethoxazole) of 574 isolates showed different rates of phenotypic resistance in bacteria from wastewaters (91.9–94.4%), hospital effluents (73.9%), surface waters (8.2–55.3%) and groundwater (35.1–59.1%). The level of multidrug resistance reached 44.6% in enterococci from hospital effluents. In all samples, except for hospital sewage, the predominant species were E. faecium and E. faecalis. In addition, E. avium, E. durans, E. gallinarum, E. aquimarinus and E. casseliflavus were identified. Enterococcus faecium strains carried the greatest variety of ARGs (blaTEM-1, aac(6′)-Ie-aph(2″), aac(6′)-Im, vanA, vanB, ermB, mefA, tetB, tetC, tetL, tetM, sul1), while E. avium displayed the highest ARG frequency. Molecular typing using the ERIC2 primer revealed substantial genetic heterogeneity, but also clusters of enterococci from different aquatic compartments. Enterococcal migration under anthropogenic pressure leads to the dispersion of clinically relevant strains into the natural environment and water resources. In conclusion, ERIC-PCR fingerprinting in conjunction with ARG profiling is a useful tool for the molecular typing of clinical and environmental Enterococcus species. These results underline the need of safeguarding water quality as a strategy to limit the expansion and progression of the impending antibiotic-resistance crisis.

Comparing antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa from environmental and clinical settings

“…In contrast to the current study, Farkas et al [ 92 ] observed that E. faecium isolates from aquatic matrices exhibited the same or similar ERIC-PCR fingerprints to that of hospital-derived variants as they clustered within the same clade. This is significant as E. faecium has been associated with HA infections, however the bacteria are rarely observed amongst healthy individuals [ 92 ]. The results of the current study are however, comparable to observations made by Serrano et al [ 93 ], as the P. aeruginosa REP-PCR demonstrated that a wide genetic diversity was observed across the P. aeruginosa ( n = 16) clinical and environmental isolates.…”

“…While limited literature is available on the extensive epidemiological survey of E. faecium , K. pneumoniae , and P. aeruginosa in environmental reservoirs, REP-PCR has previously been implemented in the medical, agricultural and food industries for the identification of contamination sources, cross-transmission routes, and the recognition of virulent strains [ 91 , 92 ]. For example, Farkas et al [ 92 ] investigated the extent to which anthropogenic contamination contributes to the spread of antibiotic resistant enterococci in aquatic environments and additionally explored the genetic relationships (REP-PCR with ERIC primers) amongst Enterococcus strains (i.e., E. avium, E. faecalis and E. faecium ). In contrast to the current study, Farkas et al [ 92 ] observed that E. faecium isolates from aquatic matrices exhibited the same or similar ERIC-PCR fingerprints to that of hospital-derived variants as they clustered within the same clade.…”

“…For example, Farkas et al [ 92 ] investigated the extent to which anthropogenic contamination contributes to the spread of antibiotic resistant enterococci in aquatic environments and additionally explored the genetic relationships (REP-PCR with ERIC primers) amongst Enterococcus strains (i.e., E. avium, E. faecalis and E. faecium ). In contrast to the current study, Farkas et al [ 92 ] observed that E. faecium isolates from aquatic matrices exhibited the same or similar ERIC-PCR fingerprints to that of hospital-derived variants as they clustered within the same clade. This is significant as E. faecium has been associated with HA infections, however the bacteria are rarely observed amongst healthy individuals [ 92 ].…”

Detection of an Enterococcus faecium Carrying a Double Copy of the PoxtA Gene from Freshwater River, Italy

“…Enterococcus species have frequently been described as carriers of antibiotic resistance across the One Health continuum. Hospital effluents, untreated sewage, and raw manure have been identified as the main hotspots for antibiotic-resistant enterococci and as sources for their environmental spread [ 37 ].…”

Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains

“…Enterococci are Gram-positive facultative anaerobic cocci that constitute normal commensal microbiota of the human gastrointestinal tract ( Attallah et al, 2022 ). In recent years, enterococci have become one of the leading causes of hospital-acquired infections and are common pathogens in various wound and surgical site infections ( Farkas et al, 2022 ). The isolation rate of clinical strains Enterococcus is high among which Enterococcus faecalis ( E. faecalis ) and Enterococcus faecium ( E. faecium ) were the most prominent ( Zhang et al, 2017 ).…”