Introduction

Antimicrobial resistance (AMR) constitutes one of the major global health challenges that need a holistic “One Health” and “One World” approach to understand its emergence, evolution, and dissemination pattern [1]. Enterococci are very resilient as they can survive the effect of physicochemical agents for long periods [2]. Enterococcus is one of the suitable bacteria to study AMR across the “One Health” ecosystems, as certain species and genetic lineages could easily acquire or transfer critically important AMR to other species or genera in different hosts or niches via mobile genetic elements [3].

Linezolid (LZD) is one of the most important and “last resort” chemotherapeutic options for severe infections caused by vancomycin-resistant enterococci and multiresistant staphylococci [4]. Linezolid resistance (LZDR) is rare but represents a critically important public health problem that needs to be meticulously studied and reported at all levels. Linezolid is not used in animals but LZDR could be selected by the use of other antibiotics, as is the case of phenicols or lincomycin, among others [5].

Linezolid resistance is mediated either by the acquisition of transferable genes (optrA, poxtA, and cfr), or due to mutations in the V domain of the 23S rRNA or amino acid changes in the ribosomal proteins L3, L4 and/or L22 of the enterococci [6,7,8].

Concerning the transferable LZDR genes, optrA has been frequently reported [6]. At least 69 OptrA variants have been identified so far, with differences of 1–20 amino acid substitutions (i.e., of 97.1–99.8% amino acid identity) [8]. The optrA gene codes for an ATP-binding cassette F ribosomal protection protein that confers cross-resistance to chloramphenicol, linezolid and tedizolid [9]. The poxtA gene was identified and characterized in 2018 from a clinical MRSA in Italy [10]. This gene shares about 32% nucleotide homology with optrA and uses a similar mechanism to confer resistance to linezolid and exists in two variants, poxtA and poxtA2 [10, 11].

The cfr gene encodes a methyltransferase that modifies position A2503 of the 23S rRNA and confers cross-resistance to streptogramin A, lincosamides, pleuromutilins, phenicols and linezolid [8, 12]. There are four variants of the cfr gene, i.e., cfrB, cfrC, cfrD, and cfrE, of which cfrB and cfrD do not confer resistance on their own, except in combination with other linezolid resistance genes [13, 14]. Moreover, the cfrC and cfrE have not been reported in any Enterococcus spp. [6]. It appears that cfr-mediated LZDR is predominantly found in staphylococci whereas the cfr-like gene, cfrD, is common in enterococci [6].

The mutation-mediated LZDR enterococci emerged following linezolid chemotherapy in clinical practice with the predominant being the G2576T or G2505A in 23S rRNA [15]. However, other mutations leading to high-level linezolid resistance such as G2447U, G2576U, and G2504A, among others, have also been reported in enterococci [14]. It is important to remark that LZDR due to target mutations is not transferable as they are not bound to mobile genetic elements. However, the acquired LZDR genes are often carried by plasmids while in some instances, they are chromosomally located [6].

Linezolid-resistant enterococci and the mechanisms of resistance involved have been reported in Spain [7, 16,17,18,19,20,21,22]. However, few reports on their complete genomic characterization have been published [18, 23] and none on healthy human and animal populations. As the incidence of LZDR enterococci is gradually increasing all over the world, it is important to mount a genome-based surveillance system to track their dissemination patterns and relatedness with other reported cases from other countries. The present study characterized the genomic profile in a collection of enterococcal isolates belonging to three species (E. faecalis, E. faecium and E. casseliflavus) carrying LZDR genes previously identified from healthy animals and humans [7], to characterize their resistomes, virulomes, mobile genetic elements and to determine their phylogenetic relatedness with other publicly available strains with similar sequence types and AMR genes.

Materials and Methods

Nine LZDR enterococci were obtained in a previous study [7], and were included in the present work for complete genomic characterization. These isolates were all of nasal origin (except one of tracheal origin in stork), and belonged to three species: a) seven optrA-carrying E. faecalis isolates of pigs (n = 5), pig farmers (n = 1) and dogs (n = 1); b) one optrA/cfrD-carrying E. casseliflavus isolate from a pig; and c) one poxtA-carrying E. faecium isolate of a stork (Table 1). The E. faecalis isolates from the pig farms were selected based on their origins, sequence types (STs) and AMR genes. Details on the strategies of sample collection, processing, isolation, identification of bacteria, their antibiogram and AMR genotyping were presented in our previous study [7].

Table 1 Genomic characteristics of 9 linezolid-resistant Enterococcus spp. investigated in this study
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Whole Genome Sequencing, Assembly, and Phylogenetic Analyses

Whole genome sequencing of the selected LZDR enterococci was carried out on the NextSeq 550 platform (Illumina), while the E. casseliflavius isolate was further sequenced on the MinION platform (Oxford Nanopore Technologies (ONT), Oxford, United Kingdom) as described here. Single colonies were obtained from a fresh over-night blood agar plating and resuspended in enzymatic lysis buffer [Proteinase K (Roche); Lysozyme (Sigma)] and incubated at 37 °C (30 min) and 55 °C (1 h). The final buffer composition was as follows: 1× phosphate buffered Saline (pH 7.2 (ThermoFisher Scientific), 10× solution diluted to 1× in nuclease-free water), 20 mM Tris–HCl (pH 8; ThermoFisher Scientific), 2 mM EDTA (ThermoFisher Scientific), 1.2% Triton X-100 (Merck), 1.7 mg/ml Proteinase K (Roche), 20 mg/ml Lysozyme (Sigma).

The MagNA Pure 96 DNA and Viral NA Small Volume Multi-Sample Kit (Roche) was used to extract genomic DNA according to the manufacturer's instructions. DNA was quantified using the Quant-iT dsDNA BR and HS Assay Kits (Thermo Fisher Scientific, Scoresby, VIC, Australia) and fluorescence was measured on a FLUOstar Omega (BMG LabTech). For short-read sequencing on the Illumina platform, sequencing libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit (Illumina). The final libraries were analyzed on a TapeStation 4200 (Agilent) before sequencing on the NextSeq 550 platform (Illumina) using a 300-cycle kit to obtain paired-end 150 bp reads, as previously described [24]. For long-read sequencing on the MinION platform, the ONT rapid barcoding kit (SQK-RBK110.96) was used to generate the sequencing library. Four samples were multiplexed and sequenced on an R9.4.1 flow cell. Reads were demultiplexed and base-called with the base-calling model Guppy (v.6.1.5) at super-accurate setting and filtered on quality score > 10. All the genomes analyzed in this study were de novo assembled using SPAdes (v.3.15.5), performing the in silico typing with the settings of a minimum of 90% coverage and 80% identity. Core-genome single nucleotide polymorphisms (SNPs) were detected with the NASP pipeline v.1.0.0 [25]. GATK (v.4.2.2) was used to call SNPs and excluded positions featuring < 90% unambiguous variant calls and < 10 depth. IQ-TREE (v.2.1.2), was used to construct the phylogenetic trees using ModelFinder with 100 bootstraps. The graphical data were added to the phylogenies with iTOL v.6.6 [26].

Genome Annotation, Typing and In Silico Analysis

The STs were determined with MLST (v.2.16, https://cge.food.dtu.dk/services/MLST/). Virulence factors, plasmid replicons, and antimicrobial resistance genes were identified using ABRicate (v.0.9.0) [27], and the respective databases VFDB [28], Plasmidfinder [29], and Resfinder [30] from the Center for Genomic Epidemiology. Mutations associated with AMR were identified using ResFinder (v4.1) [30] and PointFinder [31]. Phaster was used to identify all prophage elements [32]. The genetic environments of optrA, poxtA and cfrD genes were illustrated using the reference strains [E. faecalis (GenBank accession ID KP399637), E. faecium plasmid pGZ8 (GenBank accession ID CP038162), E. faecium (GenBank accession ID MN831413) and E. faecalis (GenBank accession ID CP097040)] in EasyFig Software. The OptrA variants based on amino acid substitutions deduced from the optrA sequences, were analyzed according to a previously described nomenclature [8], using WP_063854496.1 as the wild-type reference.

Phylogenetic Analysis by Core-Genome Single Nucleotide Polymorphism

The SNPs between the genomes of our seven optrA-E. faecalis isolates and those of 12 publicly available optrA-positive E. faecalis isolates was analyzed (GenBank accession numbers: SRR17662732, ERR2008110, ERR2008112, ERR1599987, ERR1599986, ERR2008113, ERR2008114, SRS7549315, SRS7549355, SRS7549357, SRS7549371, SRS7549400). These 12 genomes were selected because they carried the optrA gene and belonged to the same genetic lineages as the seven E. faecalis strains from this study.

Genome Availability

All the raw genome reads of the LZDR enterococci have been deposited at the European Nucleotide Archive under Study Accession number PRJEB62654. The optrA-associated plasmid in E. casseliflavus (pURX4962) was deposited in GenBank with the accession number OR069652.

Results

Genome Features

The genomes of the seven LZDR E. faecalis isolates had sizes in the range of 2.8–3.1 Mb and contigs range from 100 to 164 (Table 1). The LZDR E. faecium isolate had a genome size of 2.7 Mb and 136 contigs, whereas the LZDR E. casseliflavus isolate had a genome size of 3.7 Mb and 247 contigs (Table 1).

Antimicrobial and Metal Resistance

The minimum inhibition concentrations (MICs) of all enterococci to linezolid ranged from 2 to 14 μg/ml (Table 1). The in silico analysis of the optrA sequences of the eight E. faecalis/E.casseliflavus isolates revealed that two of them harbored the gene of the wild-type OptrA (E. faecalis and E. casseliflavus, both of pig origin), while the remaining six E. faecalis isolates carried the gene of four OptrA variants (DP-2: Y176D/T481P; RDK: I104R/Y176D/E256K; DD-3: Y176D/G393D; and EDD: K3E/Y176D/G393D) (Table 1). The OptrA variant DP-2 was detected in three E. faecalis isolates of pig, pig farmer and dog origin (ST330 and ST585), and the OptrA variants RDK, DD-3, and EDD in three E. faecalis isolates recovered from pigs (Table 1). Also, the LZDR-E. faecium isolate carried a poxtA type 1 gene (Table 1). In addition, all the optrA-positive enterococci co-carried the fexA gene; the fexB gene was co-carried by the poxtA-positive E. faecium isolate. Moreover, the E. casseliflavus co-carried the cfrD gene.

Beside the AMR genes presented in our previous studies [7], the following genes were detected: (a) E. casseliflavus isolate (X4962) carried the dfrG, vanC3, lnuB, aph3’ and lsaE genes; (b) E. faecalis-ST330 (X5386 and X5809) from pigs of farms B-D carried the ant4’, dfrG, lsaA, and aph3’genes; (c) E. faecalis-ST59 (X5799) carried the dfrG, lnuB, lsaE, and lsaA genes; (d) E. faecalis-ST32 (X5445) from a pig of farm B carried the lsaA, ant9’, dfrG, lnuG, and aph3’genes; (e) E. faecalis-ST330 (X5463) from a pig farmer of farm B carried the ant4’, dfrG, lsaA, and aph3’genes; (f) E. faecalis-ST585 (X6347) from a dog carried the lnuB and lsaA genes. There were no additional AMR genes detected in the E. faecium-ST1739 isolate (X3877) from a nesting of stork foraging in landfills (Table 1).

Aside from the AMR genes, chromosomal point mutations leading to ciprofloxacin resistance were detected in E. faecalis-ST330 isolates from pigs of farms B and D, associated with amino acid changes in ParC (S80I) and GyrA proteins (E87G). Moreover, only one amino acid change in ParC (S80I) was detected in the dog E. faecalis-ST475 isolate. In addition, 17 different amino acids substitutions were identified on the penicillin-binding protein 5 (S27G, A68T, A216S, T172A, V24A, 885D, K144Q, A499T, L177I, N496K, G66E, E100Q, D204G, P667S, E525D, T324A, R34Q) of the E. faecium isolate from stork nestling (poxtA-positive), some of them leading to penicillin resistance (Table 1).

All LZDR isolates except E. casseliflavus X4962 carried at least two metal resistance genes (MRGs), of which E. faecium-ST1739 carried most of them (arsA, copA, fief, ziaA, znuA, zosA, zupT, zur) (Table 1). Moreover, E. faecalis X5386 carried only two of the MRGs (cutC and znuA).

Virulence Determinants

Many virulence genes that have been associated with surface adherence, biofilm formation, and cytolysis were detected in the optrA-carrying E. faecalis isolates, most frequently being the ebpA, tpx, elrA, hylA, srtA, gelE, fsrB, ace, cOB1, cCF10, dad, agg, camE, efaAfs, hylB, and cylA genes. In the E. faecium X3877 isolate, only acm and efaAfm genes were found. However, none of these genes were identified in the E. casseliflavus X4962 isolate (Table 1).

Mobile Genetic Elements

All the enterococci carried at least one plasmid replicon gene (1–5 rep genes), however, only some of the plasmid replicons (2–3 per isolate) were associated with AMR genes. The three optrA-positive E. faecalis-ST330 isolates carried different number of plasmid replicons (Table 1). The repUS52 in strain X5386 was found co-located with the aminoglycoside resistance ant4’ gene. Three resistance genes (tet(L), tet(M), and cat) were bound on plasmid rep9a and repUS43 of all E. faecalis isolates from the pigs and pig farmers (Table 1). The aminoglycoside resistance gene, str was found on plasmid rep7 in the E. faecalis isolate from a dog (X6347). Moreover, the agg virulence gene was also co-located on the rep9a contig of E. faecalis-ST330 (X5463) and E. faecalis-ST32 (X5445). Three replicons were identified in the poxtA-carrying E. faecium isolate (rep29, rep1, repUS15) and none was co-located with any other AMR genes. Moreover, five replicons (rep14b, repUS41, repUS1, rep1, and rep40) were identified in the optrA-positive E. casseliflavus X4962 isolate, of which repUS40 was associated with the optrA-fexA genes (Fig. 1), and was 99.83% identical with plasmid pE3954 of E. faecalis (GenBank accession no: KP399637).

Fig. 1
figure 1

Genetic environment of the optrA gene in the eight E. faecalis and E. casseliflavus isolates from healthy pigs, pig farmer, and a dog. Shown in the figure are AMR genes located in the same contigs and frames with their corresponding mobile genetic elements. The percentage of identity and scale bar legends are presented on the right side of the image. The comparison was made with a reference E. faecalis strain E349 (GenBank Accession number: KP399637) (colour figure online)

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Two different transposons were identified, viz: Tn6260 and Tn554 associated with lnuG and fexA genes of E. faecalis-ST330 and -ST59 isolates, respectively. Also, the Tn6260 identified in three of our optrA-positive E. faecalis isolates have previously been shown associated with lnuG.

Different insertion sequences were detected among our LZDR isolates: E. faecalis-ST59 (ISS1N and ISEnfa4), E. faecalis-ST330 (ISEnfa1), E. faecium (ISSsu5) and E. casseliflavus (ISEnfa1) (Table 1). The optrA gene was chromosomally located in all our E. faecalis isolates. Nevertheless, the optrA gene of E. casseliflavus strain X4962 was located in a plasmid (37.9 kb, pURX4962) (Fig. 2), that showed 99.98% similarity with the one of an E. faecalis strain from China (GenBank Accession number: KP399637.1). All our LZDR E. faecalis and E. faecium isolates carried at least one prophage, of which E. faecalis -ST330 (X4957) from a pig carried the highest variety (n = 5), viz: phiEf11, phiFL4A, phiFL2A, EFC_1 and LP_101 (Table 1).

Fig. 2
figure 2

Genetic representation of the optrA-carrying plasmid pURX4962. Colors and arrows indicate the represented genes and their orientation (color figure online)

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Genetic Environment of the Linezolid Resistance Genes

Five different genetic environments of the optrA gene were detected among the eight isolates that carried this gene: (a) E. casseliflavus X4962 (OptrA wild type); (b) E. faecalis X4957, X5386, and X5463 (OptrA—variants RDK and DP-2); (c) E. faecalis X5445 and X5809 (OptrA -variants DD-3 and EDD); (d) E. faecalis X5799 (OptrA- wild type); and (e) E. faecalis X6347 (OptrA variant DP-2). The fexA gene, which confers resistance to phenicols, was detected upstream of the optrA gene in all the eight E. faecalis and E. casselifavus isolates (Fig. 1). Moreover, an ermA-like gene was detected in the seven optrA-carrying E. faecalis isolates. Of these, the ermA-like gene was found in the environment of the optrA gene in four of isolates (Fig. 1). This ermA-like gene was identical to that detected in Streptococcus suis (GenBank accession number: EU348758). Regarding the cfrD gene, we could identify the presence of a guaA gene encoding a glutamine-hydrolyzing guanosine monophosphate synthase in the downstream region. Upstream of the cfrD gene, we detected the ermB gene flanked by IS1216 and ISNCY (Fig. 3). The genetic environment of the cfrD gene (1074 bp) revealed 100% nucleotide similarity with that of an E. faecium isolate in France (GenBank accession number: NG_067192).

Fig. 3
figure 3

Schematic comparison between the environment of the cfrD gene in the E. casseliflavus isolate X4962 with E. faecalis (GenBank Accession number: CP097040) and E. faecium (GenBank Accession number: MN831413) (color figure online)

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Sequence analysis revealed that E. faecium-X3877 harbored the wild-type poxtA gene with 100% nucleotide sequence identity to that of E. faecium plasmid pGZ8 (GenBank accession number: CP038162) (Fig. 4).

Fig. 4
figure 4

Genetic environment of the poxtA gene in the E. faecium isolate X3877 in comparison with the previously described plasmid-bound poxtA gene in the E. faecium strain pGZ8 (GenBank Accession number: CP038162) (color figure online)

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Relatedness of the E. faecalis Isolates

First, SNP analyses identified high relatedness (SNP = 4) of a pig isolate (X5386) with that of a pig farmer (X5463) from the same farm in our study (Supplementary Table S1). Both isolates carried the gene associated with the same OptrA variant (DP-2) and the same optrA-genetic environment and were E. faecalis of the lineage ST330.

Then, analyses with other publicly available genomes revealed relatedness of E. faecalis-ST32 (X5445) that was closely related to an isolate from a healthy human (SNP = 86) in Switzerland (SRR17662732). Moreover, the pig isolate (X5799) was related to two isolates from cattle origin (SNP = 44 and 48) in Belgium (id2205 and id2235) (Fig. 5 and Supplementary Table S1). Furthermore, the pig isolate (X5809) was closely related (< 50 SNP) to two isolates previously described from hospitalized patients in Spain (ERR2008113 and ERR2008114).

Fig. 5
figure 5

Phylogenetic tree based on core-genome SNPs analysis of seven optrA-carrying E. faecalis isolates from healthy hosts in this study with twelve publicly available E. faecalis genomes with similar STs and linezolid resistance genes. Colors (in circles) of the AMR genes are as follows: dark purple for optrA while and light purple for fexA and cat (color figure online)

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Discussion

Here we present a genomic investigation of nine LZDR enterococci from four different healthy host types (humans, pigs, dogs, and storks). To the best of our knowledge, this is the first genomic comparative study on LZDR enterococci in healthy human and animal populations in Spain.

Since the first detection of LZDR enterococci in 2003 in Spain, two years after the approval of linezolid for clinical use [22], the detection rate of LZDR has risen significantly, especially during and after the post-COVID-19 era [32]. In our previous study [7], LZDR genes were detected after the selective inclusion of chloramphenicol resistance phenotype and characteristic green colonies on CHROMagar LIN by the three Enterococcus species (E. faecalis, E. faecium and E. casseliflavus). This was not expected as the animals and human hosts were healthy and were not on any antibiotic chemotherapy for at least six months before their enrolment into the study. This suggests that LZDR could persist for a long period in enterococci, considering that the bacterial genus is very tolerant to environmental factors such as sunlight and temperature [2].

In a recent study conducted by our research group and others in Spain, LZDR genes were detected from hospital settings with a high frequency of the optrA/poxtA genes among E. faecalis and E. faecium [17, 18]. This partly corroborated our finding as all the E. faecalis carried the optrA gene, but not poxtA, as in the case of Ruiz-Ripa et al. [18].

Worth mentioning is that most of the optrA genes carried by the E. faecalis strains from this current study (6/7) corresponded to variants of the OptrA wild-type (DP-2, RDK, DD-3, and EDD). The OptrA variants may affect the level of MIC value for linezolid [8, 33, 34], in which some strains show low MICs while others are within the breakpoint classified as resistance. In a study that showed a correlation between linezolid MIC and OptrA variants, it was detected that the EDM variant was associated with linezolid MICs ≤ 4 μg/ml, while the variant RDK (also found among our enterococci) with MIC values ≥ 8 μg/ml [34]. In the present study, all the LZDR enterococci had MICs of ≥ 8 µg/ml, except one isolate carrying a wild-type OptrA (X5799) with an MIC of 2 μg/ml. Nevertheless, this unique finding implies that LZDR may go unnoticed by phenotypic assays unless nucleic acid amplification tests are performed. As indicated in our previous study [7], chloramphenicol resistance could be considered as a marker to screen for linezolid resistance genes. Nevertheless, genes that mediate multidrug resistance (MDR) phenotypes identified from our isolates are frequent findings in LZDR enterococci from previous studies [16,17,18,19,20]. Interestingly, none of the isolates was resistant to other last-resort antibiotics such as vancomycin, which could serve as an alternative for the LZDR enterococci in clinical practice.

It is important to remark that the classification of optrA variants and their nomenclature is not uniform. In this regard, two types of classifications are available; one is based on amino acid changes in the wild-type OptrA protein (the one used in this study) while the other is based on numerical classification of the variants as a result of mutations in the nucleotides of the optrA gene [8, 35].

Enterococcus faecium showing ampicillin resistance is an additional problem in the clinical chemotherapy of enterococci [36]. Chromosomal point mutations putatively conferring resistance to linezolid (in 23S rRNA and ribosomal proteins L3/L4/L22) were not detected in our isolates. However, E. faecalis-ST330 from healthy pigs and pig farmer presented ParC (S80I) and GyrA (E87G) anino acid changes associated with fluoroquinolone resistance, which are commonly identified in samples obtained from livestock, foodstuffs, and from human infections [37, 38].

Several MRGs were identified in most of the isolates from this study. Specifically, cutC and znuA encode for copper homeostasis protein and high-affinity zinc uptake binding protein ZnuA, respectively [39]. Other LZDR isolates carried three MRGs, cutC, tcrB, and znuA. It is important to highlight that metal resistance is a matter of public health concern due to its potential hazards in the food chain and co-selection of other AMRs [40]. Specifically, MRGs are common in enterococci strains due to the frequent use of some metals, such as zinc micronutrients in livestock feed supplements [41]. It is important to emphasize that the feed-relate source of these metals could have been deposited in the environment which caused the bacteria to develop resistance to these metals.

More worrisome is that E. faecium isolate X3877 carried diverse MRGs including those that represent higher environmental health challenges such as arsenic (arsA). For this reason, there is great debate in the EU about the banning of metals in the feed of pig farming to avoid these processes of co-selection to clinically relevant antibiotics [42]. The presence of these MGRs in X3877 of a nestling of a parent stork that forages in a landfill is an indication that metal pollution in the environment is linked to high anthropogenic activities [42, 43].

Virulence factors are very relevant in the pathogenesis of enterococci. Many of these genes such as the ebpA seem to be related to clinical enterococcal strains [18, 44]. Other virulence genes that contribute to the colonization and persistence of enterococcal infections were also identified in most of the isolates [45, 46]. Also, the optrA-carrying E. faecalis isolates recovered from dog, pigs and pig farmers carried ace, gelE and agg genes, previously described in hospital-associated E. faecalis isolates [35, 47].

Regarding virulence factors of the poxtA-positive E. faecium X3877 isolate, it carried the acm and efaA genes that encode collagen-binding, although it seems the efaA is widely distributed in most E. faecium isolates, regardless of whether they are clinical or commensal strains [13].

Generally, the E. faecalis isolates analyzed carried plasmids belonging to many of the known replicon families in enterococci [35, 48]. The variability of plasmid content found illustrates the diverse nature of MGE in enterococci and their potential to facilitate the dissemination of some critical AMR genes, such as the optrA, as in the case of the E. casseliflavus isolate. Importantly, four plasmid replicons were found bound to genes that mediate resistance to tetracyclines, aminoglycosides and chloramphenicol. This could explain the reason why these AMR genes (tet(M), tet(L), cat and ant4’) persist in the enterococci and other related bacteria (such as staphylococci) from pigs and pig farmers and the farm environments [35, 49].

Oftentimes, the fexA gene is associated with Tn554, as previously reported in LZDR-E. faecalis [35, 50]. However, only one E. faecalis isolate carried this transposon in our study. The lnuG gene identified confers resistance to lincomycin through nucleotidylation in enterococci [51, 52]. The detection of lnuG in the LZDR E. faecalis-ST330 isolates from two pigs could lead to increased dissemination of lincosamide resistance in the food chain through Tn6260 [52].

Concerning phages in enterococci, when detected, most intact prophage-associated sequences are found in clinical enterococci in humans and in animal populations [53], but their distribution and involvement in the pathogenesis of enterococcal infection are poorly characterized [47]. Nonetheless, it is important to mention that the therapeutic potential of some of the identified intact prophages has previously been evaluated [54, 55].

Contrary to most other poxtA-carrying E. faecium isolates, the fexB gene in our isolate was in entirely a different contig of the genome, which is often downstream of poxtA [23, 56]. Perhaps, the termination of the contig carrying the poxtA in our E. faecium isolate precludes the co-location of the fexB on the same contig.

The phylogenomic analyses from this study strongly suggests the zoonotic transmission of LZDR-E. faecalis isolates and highlight the impact of pigs’ gut bacteria (such as multidrug-resistant E. faecalis) contaminating the farm environment and finding its way to the farmer’s nostrils and other body parts [57, 58]. This is a situation of occupational biohazard on the side of the pig farmer [57, 58]. Moreover, the SNP-based phylogeny illustrates the potential flow and transfer of LZDR-E. faecalis isolates from multiple sources and countries.

Conclusions

The data presented in this study comprise one of the few available comprehensive genomic datasets of LZDR enterococci in healthy hosts, including key AMR genes, virulence, prophages, and the plasmidome. The phylogenetic relatedness of our optrA-positive E. faecalis with those of publicly available genomes from discrete lineages but varied sources and geographical locations revealed close relatedness with most strains from Spain, and other European, and American countries. Additionally, our study detected an interesting variability of optrA in some E. faecalis isolates of the same lineage (ST330). Findings from this study demonstrated the transmission of LZDR-E. faecalis between a pig and a pig farmer (zoonosis) and highlight the need to strengthen molecular surveillance of LZDR enterococci in all ecological niches to direct appropriate control strategies. A larger number of isolates could have provided more credence to the findings obtained. However, as linezolid resistance is a rare trait in healthy humans and animals, the data from this study enhances our comprehension of the molecular epidemiology of this critical resistance in healthy hosts.