Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum

Abstract

Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.

Molecular characterization of probiotic Enterococcus hirae from fermenting acalypha wilkesiana (Irish Petticoat) and Talinum triangulare (Water Leaf) medicinal plants

“…The probiotic potential of E. hirae observed in this work was in line with the finding of Arokiyaraj et al (2014), Kamni and Ramesh (2020), de Castro Santos Melo et al (2021), and Rajput et al (2022. Its antibiotic susceptibility contradicts the findings of Zaidi et al (2022) who reported that antimicrobial susceptibility profiling of E. hirae isolates originating from beef production systems showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multidrug resistance while it was in conformity with the work of Kamni and Ramesh (2020) who isolated E hirae from indigenous raw goat milk and reported that it was susceptible to amikacin, carbenicillin kanamycin, ciprofloxacin, co-trimazine, nitrofurantoin, streptomycin, and tetracycline.…”

Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression

“…1 and Table 3 , 4 , 5 and S1). Studies on E. faecium, E. faecalis , and E. hirae have shown that, even at the species level, virulence-associated elements, such as biofilm formation and cell adhesion, and carbohydrate metabolism are highly niche-dependent (Zaidi et al 2022 ). Additionally, food-related enterococcal strains tend to have multiple copies of those genes required to use specific carbohydrates, such as lactose, and of certain proteolytic genes due to the selective pressure of the medium (Olvera-García et al 2018 ).…”

Chagas disease is related to structural changes of the gut microbiota in adults with chronic infection (TRIPOBIOME Study)

“…faecalis are more prevalent in human-associated environments, E . hirae is a common coloniser of animal species, especially cattle, and can be easily isolated from cattle manure and water samples from feeding basins [ 67 , 68 ]. E .…”

“…are rarely implicated as pathogens, consumption of these bacteria can lead to their establishment in the gastrointestinal tract [66]. While E. faecium and E. faecalis are more prevalent in humanassociated environments, E. hirae is a common coloniser of animal species, especially cattle, and can be easily isolated from cattle manure and water samples from feeding basins [67,68]. E. hirae was the predominant species recovered from cattle production systems including both bovine feces (92%), and feedlot catch basins (60%), it was not isolated in any of the 1849 human clinical samples it was sampled [68].…”

“…While E. faecium and E. faecalis are more prevalent in humanassociated environments, E. hirae is a common coloniser of animal species, especially cattle, and can be easily isolated from cattle manure and water samples from feeding basins [67,68]. E. hirae was the predominant species recovered from cattle production systems including both bovine feces (92%), and feedlot catch basins (60%), it was not isolated in any of the 1849 human clinical samples it was sampled [68]. E. hirae has also been described in psittacine birds and chickens [69] and in rats and cats [70].…”