Occurrence of virulent multidrug-resistant Enterococcus faecalis and Enterococcus faecium in the pigs, farmers and farm environments in Malaysia

Enterococci as a One Health indicator of antimicrobial resistance

The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.

Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium

Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.

Genomic Characterization and Phylogenetic Analysis of Linezolid-Resistant Enterococcus from the Nostrils of Healthy Hosts Identifies Zoonotic Transmission

Linezolid resistance in Enterococcus spp. is increasingly considered critically important and a public health threat which mandates the need to understand their genomic contents and dissemination patterns. Here, we used whole-genome sequencing to characterize the resistome, virulome and mobile genetic elements of nine linezolid-resistant (LZDR) enterococci (seven optrA-E. faecalis, one poxtA-E. faecium and one optrA-E. casseliflavus) previously obtained from the nares of healthy dogs, pigs, pig farmers and tracheal samples of nestling storks in Spain. Also, the relatedness of the isolates with publicly available genomes was accessed by core-genome single nucleotide polymorphism (SNP) analysis. The optrA gene of the E. faecalis and E. casseliflavus isolates was located downstream of the fexA gene. The optrA gene in the E. casseliflavus isolate was carried in a plasmid (pURX4962), while those in the seven E. faecalis isolates were chromosomally located. The OptrA proteins were mostly variants of wild type (DP-2: Y176D/T481P; RDK: I104R/Y176D/E256K; DD-3: Y176D/G393D; and EDD: K3E/Y176D/G393D), except two that were wild type (one E. faecalis and one E. casseliflavus). The poxtA gene in the E. faecium isolate was found alone within its contig. The cfrD was upstream of ermB gene in the E. casseliflavus isolate and flanked by ISNCY and IS1216. All the LZDR enterococci carried plasmid rep genes (2-3) containing tetracycline, chloramphenicol and aminoglycoside resistance genes. All isolates except E. casseliflavus carried at least one intact prophage, of which E. faecalis-ST330 (X4957) from a pig carried the highest (n = 5). Tn6260 was associated with lnuG in E. faecalis-ST330 while Tn554 was with fexA in E. feaecalis-ST59 isolates. All except E. casseliflavus (n = 0) carried at least two metal resistance genes (MRGs), of which poxtA-carrying E. faecium-ST1739 isolate contained the most (arsA, copA, fief, ziaA, znuA, zosA, zupT, and zur). SNP-based analyses identified closely related optrA-E. faecalis isolates from a pig and a pig farmer on the same farm (SNP = 4). Moreover, optrA- carrying E. faecalis-ST32, -ST59, and -ST474 isolates from pigs were related to those previously described from humans (sick and healthy) and cattle in Spain, Belgium, and Switzerland (SNP range 43-86). These findings strongly suggest the transmission of LZDR-E. faecalis between a pig and a pig farmer and potential inter-country dissemination. These highlight the need to strengthen molecular surveillance of LZDR enterococci in all ecological niches and body parts to direct appropriate control strategies.

Assessment of antibiotic resistance and biofilm formation of Enterococcus species isolated from different pig farm environments in Poland

BACKGROUND

Enteroccocus spp. are human opportunistic pathogens causing a variety of serious and life-threating infections in humans, including urinary tract infection, endocarditis, skin infection and bacteraemia. Farm animals and direct contact with them are important sources of Enterococcus faecalis (EFA) and Enterococcus faecium (EFM) infections among farmers, veterinarians and individuals working in breeding farms and abattoirs. The spread of antibiotic-resistant strains is one of the most serious public health concerns, as clinicians will be left without therapeutic options for the management of enterococcal infections. The aim of the study was to evaluate the occurrence and antimicrobial susceptibility of EFA and EFM strains isolated from a pig farm environment and to determine the biofilm formation ability of identified Enterococcus spp. strains.

RESULTS

A total numer of 160 enterococcal isolates were obtained from 475 samples collected in total (33.7%). Among them, 110 of genetically different strains were identified and classified into EFA (82; 74.5%) and EFM (28; 25.5%). Genetic similarity analysis revealed the presence of 7 and 1 clusters among the EFA and EFM strains, respectively. The highest percentage of EFA strains (16; 19.5%) was resistant to high concentrations of gentamicin. Among the EFM strains, the most frequent strains were resistant to ampicillin and high concentrations of gentamicin (5 each; 17.9%). Six (7.3%) EFA and 4 (14.3%) EFM strains showed vancomycin resistance (VRE - Vancomycin-Resistant Enterococcus). Linezolid resistance was found in 2 strains of each species. The multiplex PCR analysis was performed to identify the vancomycin resistant enterococci. vanB, vanA and vanD genotypes were detected in 4, 1 and 1 EFA strains, respectively. Four EFA VRE-strains in total, 2 with the vanA and 2 with the vanB genotypes, were identified. The biofilm analysis revealed that all vancomycin-resistant E. faecalis and E. faecium strains demonstrated a higher biofilm-forming capacity, as compared to the susceptible strains. The lowest cell count (5.31 log CFU / cm²) was reisolated from the biofilm produced by the vancomycin-sensitive strain EFM 2. The highest level of re-isolated cells was observed for VRE EFA 25 and VRE EFM 7 strains, for which the number was 7 log CFU / cm² and 6.75 log CFU / cm², respectively.

CONCLUSIONS

The irrational use of antibiotics in agriculture and veterinary practice is considered to be one of the key reasons for the rapid spread of antibiotic resistance among microorganisms. Owing to the fact that piggery environment can be a reservoir of antimicrobial resistance and transmission route of antimicrobial resistance genes from commensal zoonotic bacteria to clinical strains, it is of a great importance to public health to monitor trends in this biological phenomenon.

Multidrug-Resistant Gram-Negative Bacteria and Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae from the Poultry Farm Environment

The indiscriminate use and overuse of various antibiotics have caused the rapid emergence of antibiotic-resistant bacteria (ARB) in poultry products and the surrounding environment, giving rise to global public health issues. This study aimed to determine the prevalence of multidrug-resistant (MDR) Gram-negative bacteria (GNB) found in the environment of poultry farms and to evaluate the risk of contamination in these farms based on multiple antibiotic resistance (MAR) index values. Soil and effluent samples were collected from 13 poultry farms. The VITEK 2 system was used for bacterial identification and susceptibility testing of the isolates. The identified Gram-negative isolates were Acinetobacter spp., Aeromonas spp., Enterobacter spp., Klebsiella pneumoniae, Proteus spp., Providencia spp., Pseudomonas spp., and Sphingomonas paucimobilis. The results showed that Enterobacter spp., Aeromonas spp., and Providencia spp. exhibited the highest MDR rates and MAR indices; 14% of K. pneumoniae isolates (3/21 isolates) were resistant to 13 antibiotics and found to be extended-spectrum β-lactamase (ESBL)-producing bacteria. As for the tested antibiotics, 96.6% of the isolates (28/29 isolates) demonstrated resistance to ampicillin, followed by ampicillin-sulbactam (55.9% [33/59 isolates]) and cefazolin (54.8% [57/104 isolates]). The high percentage of MDR bacteria and the presence of ESBL-producing K. pneumoniae strains suggested the presence of MDR genes from the poultry farm environment, which poses an alarming threat to the effectiveness of the available antibiotic medicines to treat infectious diseases. Therefore, the use of antibiotics should be regulated and controlled, while studies addressing One Health issues are vital for combating and preventing the development and spread of ARB. IMPORTANCE The occurrence and spread of ARB due to high demand in poultry industries are of great public health concern. The widespread emergence of antibiotic resistance, particularly MDR among bacterial pathogens, poses challenges in clinical treatment. Some pathogens are now virtually untreatable with current antibiotics. However, those pathogens were rarely explored in the environment. In alignment with the concept of One Health, it is imperative to study the rate of resistance in the environment, because this domain plays an important role in the dissemination of bacteria to humans, animals, and other environmental areas. Reliable data on the prevalence of MDR bacteria are crucial to curb the spread of bacterial pathogens that can cause antimicrobial-resistant infections.

Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain

The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.

Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA

Enterococci are part of the commensal gut microbiota of mammals, with Enterococcus faecalis and Enterococcus faecium being the most clinically relevant species. This study assesses the prevalence and diversity of enterococcal species in cattle (n = 201) and pig (n = 249) cecal samples collected in 2017. Antimicrobial susceptibility profiles of E. faecium (n = 48) and E. faecalis (n = 84) were assessed by agar and microdilution methods. Resistance genes were screened through PCR and nine strains were analyzed by Whole Genome Sequencing. A wide range of enterococci species was found colonizing the intestines of pigs and cattle. Overall, the prevalence of resistance to critically important antibiotics was low (except for erythromycin), and no glycopeptide-resistant isolates were identified. Two daptomycin-resistant E. faecalis ST58 and ST93 were found. Linezolid-resistant strains of E. faecalis (n = 3) and E. faecium (n = 1) were detected. Moreover, oxazolidinone resistance determinants optrA (n = 8) and poxtA (n = 2) were found in E. faecalis (ST16, ST58, ST207, ST474, ST1178) and E. faecium (ST22, ST2138). Multiple variants of optrA were found in different genetic contexts, either in the chromosome or plasmids. We highlight the importance of animals as reservoirs of resistance genes to critically important antibiotics.

Effect of Intramuscularly Administered Oxytetracycline or Enrofloxacin on Vancomycin-Resistant Enterococci, Extended Spectrum Beta-Lactamase- and Carbapenemase-Producing Enterobacteriaceae in Pigs

Simple Summary

Nowadays, there is great concern about the prevalence of multidrug resistant bacteria in food-producing animals since they are potential sources of transmission to humans. The aim of this work was to evaluate the effect of two antibiotics (oxytetracycline and enrofloxacin) treatments in pigs on resistant bacteria that are considered a threat to public health. This study highlights that the use of oxytetracycline or enrofloxacin in food-producing animals could select resistant bacteria in pig faeces. Special care should be taken to avoid faecal contamination of carcasses during slaughter.

Abstract

Nowadays, there is a great concern about the prevalence of multidrug resistant Enterococcus spp. and Enterobacteriaceae in food-producing animals. The aim of this work was to evaluate the effect of oxytetracycline or enrofloxacin treatment on vancomycin-resistant enterococci (VRE), extended spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae in pigs. A total of 26 piglets were received and distributed in three groups. Group 1 was treated with enrofloxacin (N = 12), group 2 with oxytetracycline (N = 10) and group 3 did not receive any treatment (control group) (N = 4). A higher number of vancomycin-resistant E. faecium were recovered compared to E. faecalis. In the pigs treated with enrofloxacin, vancomycin resistant E. faecium was found in a higher percentage of animals than in the control group. ESBL-producing E. coli was not detected in rectal samples from control animals. However, it was detected in 17–20% of animals treated with oxytetracycline on days 6 to 17 and in 17–50% of the animals treated with enrofloxacin. Carbapenemase-producing E. coli was isolated in animals treated with oxytetracycline, but not in animals treated with enrofloxacin or in the control group. This study highlights that the use of oxytetracycline or enrofloxacin in food-producing animals could select ESBL and carbapenemase-producing E. coli. Further studies shall be needed to validate the results obtained, considering a more robust and extended experimental design.

Bacterial communities from Trichuris spp. A contribution to deciphering the role of parasitic nematodes as vector of pathogens

Microbiome taxa associated with parasitic nematodes is unknown. These invertebrate parasites could act not only as reservoirs and vectors for horizontally transferred virulence factors, but could also provide a potential pool of future emerging pathogens. Trichuris trichiura and Trichuris suis are geohelminths parasitizing the caecum of primates, including humans, and pigs, respectively. The present work is a preliminary study to evaluate the bacterial communities associated with T. trichiura and T. suis, using High Throughput Sequencing and checking the possible presence of pathogens in these nematodes, to determine whether parasitic helminths act as vectors for bacterial pathogens in human and animal hosts. Five T. trichiura adult specimens were obtained from the caecum of macaque (Macaca sylvanus) and two T. suis adults were collected from the caecum of swine (Sus scrofa domestica). The 16S rRNA gene HTS approach was employed to investigate the composition and diversity of bacterial communities in Trichuris spp., with special emphasis at its intestinal level. All samples showed a rich colonization by bacteria, included, preferently, in the phyla Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia. A total of 36 phyla and more than 200 families were identified in the samples. Potential pathogen bacteria were detected in these helminths related to the genera Bartonella, Mycobacterium, Rickettsia, Salmonella, Escherichia/Shigella, Aeromonas and Clostridium. The presence of pathogenic bacteria in Trichuris spp. would position these species as a new threat to humans since these nematodes could spread new diseases. This study will also contribute to the understanding of the host-microbiota relation.

Occurrence of multidrug-resistant Enterococcus faecium isolated from environmental samples

Enterococcus species are present in the microbiota of humans and animals and have also been described in the environment. Among the species, Enterococcus faecium is one of the main pathogens associated with nosocomial infections worldwide. Enterococcus faecium isolates resistant to different classes of antimicrobials have been increasingly reported, including multidrug-resistant (MDR) isolates in environmental sources, which is worrying. Therefore, this study aimed to characterize E. faecium isolates obtained from soil and water samples regarding antimicrobial resistance and virulence determinants. A total 40 E. faecium isolates were recovered from 171 environmental samples. All isolates were classified as MDR, highlighting the resistance to the fluoroquinolones class, linezolid and vancomycin. Furthermore, high-level aminoglycoside resistance and high-level ciprofloxacin resistance were detected in some isolates. Several clinically relevant antimicrobial resistance genes were found, including vanC1, ermB, ermC, mefAE, tetM, tetL, ant(6')-Ia, ant(4')-Ia, aph(3')-IIIa and aac(6')-Ie-aph(2″)-Ia. Three virulence genes were detected among the MDR E. faecium isolates, such as esp, gelE and ace. The results of this study contribute to a better understanding of MDR E. faecium isolates carrying antimicrobial resistance and virulence genes in environmental sources and report for the first time in the world the presence of vanC1-producing E. faecium isolated from soil.

From the Farms to the Dining Table: The Distribution and Molecular Characteristics of Antibiotic-Resistant Enterococcus spp. in Intensive Pig Farming in South Africa

Foodborne pathogens, including antibiotic-resistant species, constitute a severe menace to food safety globally, especially food animals. Identifying points of concern that need immediate mitigation measures to prevent these bacteria from reaching households requires a broad understanding of these pathogens’ spread along the food production chain. We investigated the distribution, antibiotic susceptibility, molecular characterization and clonality of Enterococcus spp. in an intensive pig production continuum in South Africa, using the farm-to-fork approach. Enterococcus spp. were isolated from 452 samples obtained along the pig farm-to-fork continuum (farm, transport, abattoir, and retail meat) using the IDEXX Enterolert^®/Quanti-Tray^® 2000 system. Pure colonies were obtained on selective media and confirmed by real-time PCR, targeting genus- and species-specific genes. The susceptibility to antibiotics was determined by the Kirby–Bauer disk diffusion method against 16 antibiotics recommended by the WHO-AGISAR using EUCAST guidelines. Selected antibiotic resistance and virulence genes were detected by real-time PCR. Clonal relatedness between isolates across the continuum was evaluated by REP-PCR. A total of 284 isolates, consisting of 79.2% E. faecalis, 6.7% E. faecium, 2.5% E. casseliflavus, 0.4% E. gallinarum, and 11.2% other Enterococcus spp., were collected along the farm-to-fork continuum. The isolates were most resistant to sulfamethoxazole-trimethoprim (78.8%) and least resistant to levofloxacin (5.6%). No resistance was observed to vancomycin, teicoplanin, tigecycline and linezolid. E. faecium displayed 44.4% resistance to quinupristin-dalfopristin. Also, 78% of the isolates were multidrug-resistant. Phenotypic resistance to tetracycline, aminoglycosides, and macrolides was corroborated by the presence of the tetM, aph(3′)-IIIa, and ermB genes in 99.1%, 96.1%, and 88.3% of the isolates, respectively. The most detected virulence gene was gelE. Clonality revealed that E. faecalis isolates belonged to diverse clones along the continuum with major REP-types, mainly isolates from the same sampling source but different sampling rounds (on the farm). E. faecium isolates revealed a less diverse profile. The results suggest that intensive pig farming could serve as a reservoir of antibiotic-resistant bacteria that could be transmitted to occupationally exposed workers via direct contact with animals or consumers through animal products/food. This highlights the need for more robust guidelines for antibiotic use in intensive farming practices and the necessity of including Enterococcus spp. as an indicator in antibiotic resistance surveillance systems in food animals.

A multiplex PCR kit for the detection of three major virulent genes in Enterococcus faecalis

A multiplex PCR kit that detects three major virulence genes, gelE, hyl and asaI, in Enterococcus faecalis was developed. Analyses of the available sequences of three major virulence genes and designed primers allowed us to develop the three-gene, multiplex PCR protocol that maintained the specificity of each primer pair. The resulting three amplicon bands for gelE, hyl and asaI were even and distinct with product sizes of 213, 273 and 713 bp, respectively. The multiplex PCR procedure was validated with a total of 243 E. faecalis strains that included 02 ATCC strains, 109 isolates from marine samples (sediment, water and sea foods), 22 isolates from cattle fodder, 79 isolates fresh water samples and 31 isolates from nosocomial samples. Specificity of the kit was indicated by amplification of only three major virulent genes gelE, hyl and asaI without any nonspecific bands. Tests for the limit of detection revealed that amplified genes from the sample with a minimum of 10⁴ CFU/g or CFU/mL (10 cells/reaction) of E. faecalis and lower cell load samples, after a 3 h enrichment in NIOT-E. faecalis enrichment medium at 37 °C, a sensitivity level of 10 CFU/g or CFU/mL was achieved.

Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control

The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P < 0.05). The metabonome of farmers and human controls were highly similar. Notably, higher trimethylamine N-oxide (TMAO) and butyrate were detected in human control and swine, respectively. The relative abundance of TMAO was positively correlated with Prevotella copri. Overall, we compared and established the relationship between the metabolites and microbiota composition of swine, farmers and human control. Based on the data obtained, we deduced that long term occupational exposure to swine and farm environment had affected the gut bacterial composition of farmers. Nonetheless, the effect was less prominent in the metabolite profiles, suggesting the gut bacteria expressed high functional plasticity and are therefore resilience to the level of community shift detected.

Assessment of Susceptibility to Five Common Antibiotics and Their Resistance Pattern in Clinical Enterococcus Isolates

Background & Objective:

Enterococcus Species are the common cause of nosocomial infections, which are highly resistant to different antibiotics. Therefore, determination of their antibiotic susceptibility patterns and simultaneous resistance to antibiotics is important for better treatment strategies.

Methods:

400 clinical Enterococcus isolates were collected from different hospitals in Tehran, Iran. Standard phenotypic-biochemical tests and PCR were used to identify the Enterococcus species. The antimicrobial susceptibility patterns and simultaneous resistance to selected antibiotics were determined by disk diffusion method according to the CLSI guidelines. All data analysis was performed using Python packages Scipy and Stats models.

Results:

According to the biochemical and PCR analyses, among 400 Enterococcus species, 72% of samples were Enterococcus faecalis, 10.75% Enterococcus faecium, and 17.25% other Enterococcus species. The results determined antimicrobial resistances of these strains against gentamicin, vancomycin, fosfomycin trometamol, teicoplanin, and quinupristin/dalfopristin. Results confirmed a significant correlation between resistance to vancomycin and resistance to teicoplanin. This correlation remains significant when including only E. faecium or E. faecalis species. We also found a negative correlation between resistance to teicoplanin and quinupristin/dalfopristin. Additionally, Quinupristin/dalfopristin was the least effective antibiotic while vancomycin and teicoplanin were the most effective ones.

Conclusion:

Based on the results and association between simultaneous resistance to some antibiotics such as vancomycin and teicoplanin, in the case of antibiotic resistance, the choice of a second antibiotic can be very important which can lead to good or bad effects.

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.

A significant number of multi-drug resistant Enterococcus faecalis in wildlife animals; long-term consequences and new or known reservoirs of resistance?

As the last link in the food chain in a complex ecosystem covering at least three different environmental spheres, species of wildlife carnivorous mammals constitute a group accumulating potential pathogens and factors resulting from human activity, including the emergence of drug resistance. Therefore, the aim of this study was to evaluate the level and range of resistance in commensal E. faecalis isolated from wildlife carnivorous mammals and genetic relationships in terms of the source of these strains as well as resistance and virulence genes. Differentiation between strains was performed based on ADSRRS-fingerprinting method. The results showed that almost half of the tested animals (48%) were carriers of at least one multidrug resistant E. faecalis strain. Moreover, 44% of MDR-positive animals showed two or three strains differing in both the genotype and the resistance phenotype. A significant percentage of strains were resistant to high-level aminoglycosides (from 20% to even 57.5%). The resistance and virulence gene profiles showed a rich panel of genes closely related to isolates from nosocomial infection and from livestock animals. The presence of the same genotypes in different hosts reflects not only a possible transfer of genes between E. faecalis strains but also exchange of strains between animals. The obtained results reflect a very high level of contamination of animals that are not subjected to targeted antibiotic therapy, which may suggest the degree of pollution of the environment. Wildlife animals and their environment can be a link closing the circulation cycle of genes and even epidemiologically important strains; therefore, there is a high risk that this pool will never run out and will be maintained at a high level.

Molecular epidemiology of antibiotic-resistant Enterococcus spp. from the farm-to-fork continuum in intensive poultry production in KwaZulu-Natal, South Africa

The poultry industry is among the main protein suppliers worldwide. Thus, this study determined the antibiotic resistance and virulence profiles of Enterococcus spp. along the farm-to-fork production chain of an intensive poultry system in the uMgungundlovu District, Kwazulu-Natal, South Africa. Overall, 162 samples along the continuum (growth phase, transport and post-slaughter) were evaluated for the presence of Enterococcus spp. using selective media, biochemical tests and polymerase chain reaction (PCR). Resistance profiles were assessed by Kirby-Bauer disk diffusion method following the WHO-AGISAR recommended antibiotics panel for Enterococcus spp. Antibiotic resistance and virulence genes were detected using real-time PCR. Clonal relatedness was evaluated by REP-PCR. Overall, 131 isolates were recovered across the continuum, (34% E. faecalis, 32% E. faecium, 2% E. gallinarum and 32% other Enterococcus spp.). Resistance to tetracycline (79%), erythromycin (70%), nitrofurantoin (18%), ampicillin (15%), streptomycin (15%), chloramphenicol (10%), ciprofloxacin (4%), tigecycline (4%), gentamicin (4%), teicoplanin (3%) was observed among all Enterococcus spp.; no vancomycin resistance (0%) was recorded. Also, 24% of E. faecium were resistant to quinupristin-dalfopristin. Twenty-four multidrug resistance (MDR) antibiograms were observed across all species; E. faecium (43%) showed the highest frequency of MDR. The most frequently observed antibiotic resistomes were tetM (76%) and ermB (66%) while smaller percentages were noted for aph(3')-IIIa (12%) and vanC1 (1%). Virulence genes efaAFs (100%), cpd (96%) and gelE (80%) were more prevalent in E. faecalis. Clonality revealed that isolates along the continuum were highly diverse with major REP-types consisting of isolates from the same sampling point. This study highlights the diversity of MDR Enterococcus in the food chain with isolates harbouring resistance and virulence genes. These could be reservoirs for the potential transfer of pathogenic enterococci carrying these genes from poultry to humans through the food chain continuum, thus, underscoring the need for routine antibiotic resistance surveillance in food animals.