Antimicrobial resistance (AMR) is recognized as one of the major global health challenges of the 21st century. The interconnected microbiomes between humans, animals, and the environment contribute to the emergence, acquisition, and spread of AMR (Hiltunen et al., 2017). A One-health approach provides an in-depth knowledge of the evolution of AMR by focusing on those biological elements that influence the emergence of antimicrobial resistance genes (ARGs) within the microorganism and their dissemination among hosts (human and animals) and the environment (Hernando-Amado et al., 2019). Gram-positive enterococci are core members of the gastrointestinal microbiota of humans and animals and are frequently isolated from soil and water (Byappanahalli et al., 2012; Gilmore et al., 2014). Enterococci often carry ARGs as they compete within complex microbial communities and are exposed to antimicrobials in clinical settings and during livestock production (Murray, 1990; Moreno et al., 2006). Furthermore, depending on the species, enterococci exhibit intrinsic resistance to several antibiotics including cephalosporins, anti-staphylococcal penicillins, aztreonam, aminoglycosides, lincosamides, and streptogramins (Miller et al., 2014). Enterococci are typically commensals, but they can cause nosocomial infections in humans including septicemia, endocarditis, and urinary tract infections (Barnes et al., 2021). There are over 50 species of enterococci with E. faecalis and E. faecium most frequently linked to human infections. Occasionally, other species including E. hirae, E. avium, E. durans, E. gallinarum, E. casseliflavus, and E. raffinosus may also be associated with infections in people (Brayer et al., 2019; Pinkes et al., 2019; Winther et al., 2020). Due to their widespread occurrence and persistence in the environment, enterococci are considered indicators of fecal contamination (Byappanahalli and Fujioka, 2004; Yan et al., 2011) and also serve as key indicator bacteria for AMR surveillance systems in humans and animals (Harwood et al., 2000; Layton et al., 2010).

Studies have indicated that E. faecium and E. faecalis are more prevalent in human-associated environments, whereas E. hirae are prevalent in beef cattle production systems (Zaheer et al., 2020). E. hirae only accounts for 1% of enterococcal infections in humans (Heval Can et al., 2020) and is mainly linked to pyelonephritis (Chan et al., 2012; Pãosinho et al., 2016; Nakamura et al., 2021), endocarditis (Talarmin et al., 2011; Pinkes et al., 2019), and biliary tract infections (Tan et al., 2010; Bourafa et al., 2015). As with E. faecalis and E. faecium, E. hirae infections are typically treated with ampicillin, gentamicin, or vancomycin (Nakamura et al., 2021).

The focus of this study was to investigate the genomic relatedness of E. hirae across the environmental continuum and to identify the genetic nature of AMR in E. hirae. Furthermore, we applied a pan-genome analysis to identify genes that may account for the predominance of E. hirae within beef cattle production systems.

Enterococci are ubiquitous Gram-positive bacteria. They colonize gastrointestinal tracts of most multicellular eukaryotic organisms including humans, animals, and insects and aide in digestion and gut metabolic pathways (De Graef et al., 2003; Farrow and Collins, 1985; Devriese et al., 1990; Andrew and Mitchell, 1997; de Vaux et al., 1998; Muniesa et al., 1999; Fogarty et al., 2003; Law-Brown and Meyers, 2003; Maria da Gloria et al., 2006; Layton et al., 2010; Giraffa, 2014). In addition, they are also found in food, plant, and water ecosystems (Müller et al., 2001; Svec et al., 2001; Klein, 2003; Švec et al., 2006; Byappanahalli et al., 2012). Enterococci are remarkably resilient to broad pH ranges, temperature variation, and osmotic pressure, traits that contribute to their broad distribution in nature (Heim et al., 2002; Caretti and Lubello, 2003; Anderson et al., 2005). Resistant bacterial populations are selected by the exposure of commensal gut microorganisms such as enterococci to antimicrobials that are used for disease treatment and prevention (Francino, 2016). The ubiquitous nature of enterococci may facilitate the dissemination of antimicrobial resistance genes between different environments. For this reason, it is imperative to identify antimicrobial resistance determinants and their role in the spread of antimicrobial resistance (Cameron and McAllister, 2016). Here, we focused on E. hirae isolates recovered from a One-Health surveillance study (Zaheer et al., 2020). The genomic relatedness of E. hirae was examined across various sampling matrices of the continuum and AMR determinants that contribute to antimicrobial resistance were identified. Furthermore, we examined the genomic traits of E. hirae that may facilitate their growth in the cattle gut as compared with other human-associated Enterococcus species.

As described previously, E. hirae is highly prevalent in cattle and thus can be readily isolated from bovine feces, bovine manure, and feedlot catch-basin water samples (Jackson et al., 2011; Zaheer et al., 2013, 2020; Beukers et al., 2015). The number of E. hirae isolates recovered from urban wastewater was low (3%) and most of the Enterococcus spp. from this source were identified as either E. faecalis or E. faecium. Similarly, only E. faecalis or E. faecium was identified among human clinical isolates, confirming that E. hirae is generally not associated with human infections. However, E. hirae have occasionally been isolated from human cases of septicemia (Gilad et al., 1998), endocarditis (Poyart et al., 2002; Talarmin et al., 2011), urinary tract infections (Chan et al., 2012; Bourafa et al., 2015), spondylodiscitis (Canalejo et al., 2008), and acute pancreatitis (Dicpinigaitis et al., 2015). The rarity of this species among clinical enterococci isolates suggests that this species may not be as virulent as E. faecalis and E. faecium. This finding is also evident from our comparative genomic analysis where virulence genes were frequently identified in E. faecalis and E. faecium, but not in E. hirae.

The phenotypic resistance profiles of 1,319 E. hirae isolates showed that antimicrobial use and resistance phenotype were linked within a particular environment. For example, macrolides and tetracyclines are commonly used in beef cattle production systems for disease treatment and prevention including prophylaxis/metaphylaxis (Hurd and Malladi, 2008; Cameron and McAllister, 2016; Vikram et al., 2017). Isolates recovered from bovine feces, feedlot catch basin, stockpiled bovine manure, and natural surface water in the vicinity of the feedlots showed high occurrence of resistance to these antibiotics. Although only nine E. hirae isolates were recovered from urban wastewater, their resistance profiles indicated linkage with drugs commonly used to treat human infections including nitrofurantoin, tigecycline, and linezolid.

Genotypic resistance profiles of E. hirae corroborated to their phenotypic profiles, where tetracycline and macrolide resistance genes were predominantly present in isolates recovered from the beef cattle production system and natural water sources. This is consistent with previous studies where tetracycline and macrolide resistance genotypes were prevalent in beef production systems (Zaheer et al., 2013, 2019; Rovira et al., 2019). Tetracycline resistance was associated with the presence of tetL, M, and O. Two mosaic tetracycline genes tetS/M and tetO/32/O were also identified. tetL confers resistance via an efflux mechanism, while tetM, tetS/M, O, and O/32/O encode for ribosomal protection proteins (Safferling et al., 2003; Kazimierczak et al., 2008; Barile et al., 2012; Crespo et al., 2012; Dönhöfer et al., 2012). These genes are mostly found on transposable elements that are often linked with chloramphenicol and macrolide resistance determinants (Opal and Pop-Vicas, 2015). Macrolide resistance was associated with the presence of erm(B), which confers resistance against macrolide-lincosamide-streptogramin antibiotics (Okitsu et al., 2005). Others have also found erm(B) in E. hirae (Portillo et al., 2000; Chajęcka-Wierzchowska et al., 2016), as well as in E. faecalis and E. faecium isolated from chickens (Kim et al., 2019, 2021), turkies (Tremblay et al., 2011; Demirgül and Tuncer, 2017), pigs (Aarestrup, 2000), fermented food (Sanchez Valenzuela., 2013), and clinical settings (Schmitz et al., 2000; Chen et al., 2010; Wang et al., 2021). The macrolide resistance gene and tetracycline resistance genes in E. hirae appear to be identical to those in E. faecalis and E. faecium (Beukers et al., 2017; Zaheer et al., 2020). Considering that all of these species carry similar AMR determinants, the possibility of horizontal gene transfer across species seems probable (Palmer et al., 2010). Studies have identified the presence of pheromone responsive plasmids in E. faecium and E. faecium that either encode vancomycin resistance or facilitate the transfer of plasmids carrying vancomycin ARGs into recipient cells (Flannagan and Clewell, 2002; Johnson et al., 2021). These plasmids can also transfer between Enterococcus species, as the pMG1 plasmid has been shown to transfer between E. faecium and E. faecalis, and from E. faecium to E. hirae (Costa et al., 1993).

Aminoglycoside gene acc(6′)-lid is known to be intrinsic in E. hirae (Costa et al., 1993) and was detected in all but two genomes, likely as a result of gene coverage and assemblage issues. It is not surprising that vancomycin resistance genes were not identified in E. hirae, as this drug is not approved for veterinary use in North American cattle. Our result is consistent with a previous study where vancomycin resistance genes were not identified in Enterococcus spp. isolated from bovine feces (Beukers et al., 2017). The virulence genes identified in E. hirae were mostly associated with biofilm formation and polysaccharide biosynthesis, as described by others (Hashem et al., 2017). The 10 virulence genes that were identified in E. hirae were similar to those in E. faecalis and E. faecium, but many more (i.e., 49) virulence genes were found in E. faecium and E. faecalis (Zaheer et al., 2020).

Pan-genome analysis is an important comparative analysis tool that allows linkages between genetic changes and specific phenotypes as it describes core- and accessory genomes as well as species-specific genes (Vernikos, 2020). The core genome constituted only 64% of the total genome in E. hirae. Both horizontal and vertical transfer of genes, including those that confer antimicrobial resistance, play a significant role in shaping the pan-genome of a bacterial species (Ding et al., 2018). The pan-genome of E. hirae was considered “open” as there was no sign of saturation and it would be expected to expand with the addition of new genomes as illustrated by the pan-genome curve (Figure 4B). The high presence of cloud genes reflects the heterogeneity of the pan-genome of E. hirae. The existence of E. hirae in diverse environments may increase the chance of gene acquisition, in contrast to other Enterococcus species that may live in more specific environments that require less genomic variation for survival (Costa et al., 2020).

Gram-positive bacteria have sophisticated cell wall structures that ensure bacterial structural integrity and cellular viability and are also a major component of the host defense system (Koch, 2003; Silhavy et al., 2010). For this reason, numerous studies have been conducted to explore components of cell wall synthesis pathways as potential targets for drug therapy. Genes involved in cell wall synthesis were identified as discriminatory genomic signatures between E. faecalis and E. hirae. Identification of these different signatures [peptidoglycan synthesis genes (Mur E, F, and Y), penicillin-binding protein (pbpE and pbpX), teichoic acid synthesis genes (tag H, G, and U), and enterococcal polysaccharide antigen (eps E, D, M, and N)] may identify targets that offer more specific drug development against E. faecalis and E. faecium (Parisien et al., 2008).

Members of gut microflora compete with each other for nutrient availability. Therefore, the ability of one bacterial species to utilize multiple nutrients for energy generation provides an advantage over other species. We found genes involved in the synthesis of cobalamin (vitamin B12), pyridoxine (vitamin B6), riboflavin (vitamin B2), biotin (vitamin B7), and folic acid exclusive to the E. hirae species compared with other enterococci analyzed in this study. With vitamins being undeniably important for both bacteria and the mammalian host, gut bacteria associated with their production directly contribute to the development and welfare of the host and thus may have a specific function within the microbiome of the digestive tract of cattle. In E. hirae genomes, multiple phosphotransferase systems (PTS) for fructose, galactitol, mannose, sorbose, glucose, N-acetyl glucosamine, and cellobiose were identified. The presence of these PTS promotes colonization of these bacterial populations (Jeckelmann and Erni, 2020). In addition, compared to E. faecalis and E. faecium, E. hirae harbored genes that were predicted to contribute to the synthesis of bacterial cellulose. These findings indicate that cellular metabolism genes identified in E. hirae may contribute to fitness within the cattle gut, accounting for its high prevalence in beef cattle.

Analysis of the annotated genomes indicated that E. hirae possessed genes coding for the production of antimicrobial agents like bacilysin, subtilosin, and narbonolide. Bacilysin is a dipeptide antimicrobial with antifungal and antibacterial activity (Özcengiz and Öğülür, 2015). Subtilosin belongs to the lantibiotics class of bacteriocins and has anti-biofilm activity (Babasaki et al., 1985; Algburi et al., 2017). These bacteria are also capable of producing gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter. GABA may increase feed intake in cattle and reduce anxiety and pain (Sarasa et al., 2020; Mamuad and Lee, 2021). These findings suggest that E. hirae may have probiotic properties that could benefit the gastrointestinal environment of cattle (Ben Braïek and Smaoui, 2019). Previously, E. hirae has been employed as a probiotic bacteria in freshwater fish (Adnan et al., 2017). Recent studies have also demonstrated that E. hirae may confer probiotic properties within the intestinal tract of cattle (Arokiyaraj et al., 2014; Daillère et al., 2016).

One of the goals of this study was to identify the niche-specific genes in E. faecalis and E. faecium that may contribute to virulence and infection. Several virulence factors that contribute to the pathogenesis of E. faecalis and E. faecium have been reported (Ali et al., 2017; Zhou et al., 2020). Several virulence genes were unique to E. faecium and/or E. faecalis and were not found in E. hirae. Members of the SlyA/ MarA family of proteins are associated with virulence gene regulation, promote biofilm formation, and act as cell adhesions. The presence of genomic signatures corresponding to these genes may in part account for the higher prevalence of E. faecalis and E. faecium infections than E. hirae infections in humans (Mäkinen et al., 1989; Michaux et al., 2011; Yang et al., 2015). Lipoproteins facilitate intake of nutrients and are often associated with ABC transporters that are linked to pathogenesis. This supports our findings as genes encoding lipoproteins mapped with ABC transport systems for manganese, arabinose, and methionine (Zhang et al., 1998; Hutchings et al., 2009). Furthermore, in E. faecalis and E. faecium, we also identified an arginine-ornithine antiporter which could contribute to cell fitness by facilitating arginine uptake. A study conducted to investigate the role of arginine-ornithine antiporter in Streptococcus suis reported that intercellular survival of this pathogen within epithelial cells was compromised in the absence of the antiporter (Fulde et al., 2014).

The potential of E. hirae as an opportunistic pathogen cannot be ignored, as it is occasionally recovered from both human and animal clinical samples (Nicklas et al., 2010; Dicpinigaitis et al., 2015; Ebeling and Romito, 2019; Pinkes et al., 2019; Bilek et al., 2020). Despite a higher prevalence of virulence genes in E. faecium and E. faecalis, some virulence genes were also identified in E. hirae, like genes associated with the ESX (or Type VII) secretion system, bicyclomycin resistance, capsule biogenesis, quorum sensing system, and an ABC transporter for iron import (Stauff et al., 2008; Rutherford and Bassler, 2012; Borst et al., 2015; Hatosy and Martiny, 2015; Poweleit et al., 2019). In addition, a lipoprotein gene associated with the iron transport system has been identified and is thought to play a role in E. hirae establishing opportunistic infections (Hutchings et al., 2009).

In conclusion, E. hirae has a tremendous ability for survival and adaptation. It has acquired resistance to the most common antimicrobials used in beef production systems. In addition, cellular metabolism genes involved in vitamin biosynthesis, multiple ABC and PTS transport systems, chitin degradation, and cellulose synthesis provide selective advantage and facilitate intestinal colonization of the cattle gut. As E. hirae appears to be uniquely adapted to cattle hosts, this likely limits the extent to which it transfers genes to bacteria that are important in human health. Regardless, the absence of resistance to critical antimicrobials in E. hirae gives credibility to limiting use of these drugs in feedlots and suggests that prudent management of antimicrobials in feedlot settings is an important practice.

The datasets presented in this study can be found in BioProject PRJNA604849 and in online repositories. The names of the repositories and accession number(s) can be found in the article/supplementary material.

The animal study was reviewed and approved by the Lethbridge Research Centre Animal Care and Use Committee and was conducted according to the Canadian Council of Animal Care Guidelines. Sampling procedures were conducted according to the protocol approved by the Animal Care Committee, University of Calgary (Protocol ID: AC14 -0029). Written informed consent was obtained from the owners for the participation of their animals in this study.

RZ and TM designed the study. SH and CB arranged for collection of feedlot samples, metadata, and antimicrobial use data. RB, SC, and RZ isolated and characterized enterococci. RB performed AST. S-e-ZZ, generated figures, analyzed overall data/results, and wrote first draft of the manuscript. GD provided and managed the bioinformatics cluster facility and bioinformatics tools. S-e-ZZ and RZ analyzed sequence data. TM and AZ provided funding and supervision. All authors participated in editing and reviewing the manuscript and approved the final manuscript.

Authors are grateful to the Major Innovation Fund of the Government of Alberta in conjunction with the University of Calgary AMR One Health Consortium, the Beef Cattle Research Council (BCRC) Project FOS 10.13, and Genomics Research and Development Initiative of the Government of Canada for financial support.

CB is part owner and managing partner of Feedlot Health Management Services.

The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.