Characteristics of High-Level Ciprofloxacin-Resistant Enterococcus faecalis and Enterococcus faecium from Retail Chicken Meat in Korea

Prevalence, Antimicrobial Resistance Patterns, and Emerging Carbapenemase-Producing Enterococcus Species from Different Sources in Lagos, Nigeria

Background: Enterococcus species present significant health risks due to their widespread presence in humans, animals, and the environment. This study examined the patterns of antimicrobial resistance (AMR) and the presence of carbapenemase-producing Enterococcus species from various sources. Methods: Between November 2023 and February 2024, 500 samples were collected in Lagos State, including 350 clinical human samples, 50 environmental samples, and 100 animal samples. The samples were processed, and Enterococcus isolates were identified and subjected to antimicrobial susceptibility tests (AST) by standard methods. Furthermore, carbapenemase (blaKPC and oxa-48) and virulence genes (gelE) were detected by real-time polymerase chain reaction (RT-PCR) methods using specific primers. Results: The overall prevalence of Enterococcus isolates was 4.6% (23/500), including 18 E. faecalis and 5 E. faecium. The source prevalence was 24% (12/50) from the environmental samples, 5% (5/100) from animal sources, and 1.7% (6/350) from the clinical samples. All Enterococcus isolates were 100% resistant to ciprofloxacin, erythromycin, imipenem, vancomycin, and ampicillin. However, 91% were susceptible to gentamicin. Six (6) distinct resistance profiles were observed, with the pattern AMP-ERY-TGC-CIP-TS-VA-CHL-AUG-MEM-IMI being the most frequent in 12 E. faecalis (4 isolates from humans, 2 from animals, and 6 from the environment). Notably, 39.1% (9/23) of multiple-drug resistant Enterococcus isolates harbored the gelE virulence gene, including seven E. faecalis (five environmental and two human) and two E. faecium from animal sources. The E. faecalis strains HB003 and HB050, from human bacteremia cases carrying gelE, were the first in Nigeria to produce blaKPC and oxa-48 carbapenemase genes. Conclusions: This study revealed the emergence of carbapenemase-producing Enterococcus species in our environment. A one-health approach and further molecular studies are essential to mitigate the spread and understand the transmission dynamics.

The Invisible Threat of Antibiotic Resistance in Food

The continued and improper use of antibiotics has resulted in the emergence of antibiotic resistance (AR). The dissemination of antibiotic-resistant microorganisms occurs via a multitude of pathways, including the food supply. The failure to comply with the regulatory withdrawal period associated with the treatment of domestic animals or the illicit use of antibiotics as growth promoters has contributed to the proliferation of antibiotic-resistant bacteria in meat and dairy products. It was demonstrated that not only do animal and human pathogens act as donors of antibiotic resistance genes, but also that lactic acid bacteria can serve as reservoirs of genes encoding for antibiotic resistance. Consequently, the consumption of fermented foods also presents a potential conduit for the dissemination of AR. This review provides an overview of the potential for the transmission of antibiotic resistance in a range of traditional and novel foods. The literature data reveal that foodborne microbes can be a significant factor in the dissemination of antibiotic resistance.

Characterisation of the CRISPR-Cas systems in Enterococcus faecalis from commercial broiler farm environments and its association with antimicrobial resistance

1. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) systems have been highlighted for their potential applications in controlling the spread of mobile genetic elements, including antimicrobial resistance (AMR) genes. This study investigated the characteristics of CRISPR-Cas systems in E. faecalis from commercial broiler farms and assessed the impact of these systems on AMR.2. All E. faecalis isolates contained CRISPR2, and CRISPR1-Cas and CRISPR3-Cas were identified in 84 (56.4%) and 144 (96.6%) isolates. A combination of CRISPR2 and CRISPR3-Cas and a combination of CRISPR1-Cas, CRISPR2 and CRISPR3-Cas were each identified in 27 (96.4%) farms.3. There were significant differences between CRISPR-Cas systems for phenotypic AMR: CRISPR1-Cas and CRISPR3-Cas. The E. faecalis isolates without CRISPR1-Cas showed higher resistance to most antimicrobials and had a higher prevalence of multidrug resistance (MDR) than those with CRISPR1-Cas. However, the resistance rate against most antimicrobials and the prevalence of MDR did not differ significantly depending on the presence or absence of CRISPR3-Cas.4. The E. faecalis isolates without CRISPR1-Cas harboured higher levels of all AMR genes, except for tetL, than those with CRISPR1-Cas. However, the E. faecalis isolates with CRISPR3-Cas showed a significant lower prevalence of tetL gene and a significantly higher prevalence of fexA and poxtA genes.5. In the distribution of rep families, the rep9 family was predominant, followed by rep1, rep7, rep2 and rep8 families. Only prevalence of the rep7 family was significantly higher in the E. faecalis isolates without CRISPR1-Cas (15.4%) than in those with CRISPR1-Cas (0%).6. This study is the first report on the characteristics of CRISPR-Cas systems in E. faecalis isolated from commercial broiler farm environments, and the results supported the hypothesis that the development of antimicrobial strategies requires an understanding of the distinctive capabilities between CRISPR1-Cas and CRISPR3-Cas and their underlying resistance mechanisms.

Antibiogram profile of Enterococcus faecalis and Enterococcus faecium in chicken meat from supermarkets in Sleman District, Indonesia

Background and Aim

Enterococci are commensal bacteria in the digestive tract of poultry and serve as indicators of fecal contamination. Their significance in veterinary and human medicine arises from their ability to acquire antibiotic-resistance genes, posing a potential public health risk. Poultry meat, a major protein source in Indonesia, can act as a reservoir for Enterococcus species, transferring antibiotic-resistant strains to humans through food handling. Despite rigorous hygiene standards in supermarket supply chains, limited studies have assessed contamination levels. This study aimed to identify Enterococcus species from supermarket chicken meat in Sleman District, Yogyakarta, Indonesia, and evaluate their antibiotic resistance profiles.

Materials and Methods

Chicken breast samples were randomly collected from three Supermarkets (A, B, and C). Bacterial isolation was performed using buffered peptone water and enterococcosel agar. Presumptive colonies were confirmed by polymerase chain reaction for genus and species identification. Antibiotic susceptibility was assessed using the Kirby-Bauer disk diffusion method against ampicillin (AMP), tetracycline (TET), erythromycin (ERY), and vancomycin (VAN).

Results

A total of 269 Enterococcus isolates were confirmed, including 163 Enterococcus faecium (EFM), 92 Enterococcus faecalis (EFS), and 14 other Enterococcus species. Resistance to AMP, TET, and ERY in EFM was 12.12%, 57.57%, and 66.67%, respectively, while resistance in EFS was 4.54%, 31.82%, and 63.63%. No isolates showed resistance to VAN. Multidrug resistance (MDR) was observed in 60.60% of EFM and 36.36% of EFS isolates.

Conclusion

Despite high susceptibility to AMP and VAN, resistance to TET and ERY was prevalent. The presence of MDR isolates underscores the need for continuous surveillance of antibiotic resistance in Enterococcus species within the food chain. This study highlights the necessity of further research with expanded sampling and antibiotic panels to assess the dissemination of antibiotic resistance genes and potential public health risks.

Virulence Factors and Susceptibility to Ciprofloxacin, Vancomycin, Triclosan, and Chlorhexidine among Enterococci from Clinical Specimens, Food, and Wastewater

Enterococcus faecalis and E. faecium are opportunistic pathogens commonly found in the microbiota of humans and other animals as well as in the environment. This article presents the results of antimicrobial susceptibility testing using phenotypic methods (broth microdilution and standardized disk diffusion) on selected clinical, food, and wastewater isolates of E. faecalis and E. faecium. The isolates were divided into subgroups based on their sensitivity to the following antibiotics: vancomycin (VAN) and ciprofloxacin (CIP), and biocides triclosan (TCL) and chlorhexidine (CHX). The study also investigated in vitro virulence factors, including biofilm formation ability, cell surface hydrophobicity (CSH) and β-hemolysis, to explore aspects of pathogenesis. In our study, regardless of the isolation source, VAN-resistant (VAN-R) and CIP-resistant (CIP-R) E. faecalis and E. faecium were detected. The highest proportion of CIP-R strains was found among clinical isolates of E. faecalis and E. faecium, with clinical E. faecium also showing the highest proportion of VAN-R strains. But the highest proportion of VAN-R E. faecalis strains was found in wastewater samples. The highest TCL MIC90 values for E. faecalis were found in wastewater isolates, while for E. faecium, the highest TCL MIC90 values were observed in food isolates. The highest CHX MIC90 values for both E. faecalis and E. faecium were identified in clinical specimens. The results obtained for E. faecalis did not indicate differences in TCL MIC and CHX MIC values with respect to sensitivity to VAN and CIP. Higher CHX MIC50 and CHX MIC90 values were obtained for CIP-R and VAN-R E. faecium. Among the tested isolates, 97.75% of the E. faecalis isolates produced biofilm, while 72.22% of the E. faecium isolates did so as well. In biofilm-forming strength categories III and IV, statistically significantly higher proportions of CIP-susceptible (CIP-S) and VAN-susceptible (VAN-S) E. faecalis were determined. In category III, there is no statistically significant difference in E. faecium CIP sensitivity. In category IV, we had a significantly higher proportion of CIP-R strains. On the other hand, the association between the moderate or strong category of biofilm formation and E. faecium VAN susceptibility was not significant. E. faecalis isolated from wastewater had a CSH index (HI) ≥ 50%, categorizing them as "moderate", while all the other strains were categorized as "low" based on the CSH index. Among the E. faecalis isolates, cell surface hydrophobicity indices differed significantly across isolation sources. In contrast, E. faecium isolates showed similar hydrophobicity indices across isolation sources, with no significant difference found. Moreover, no correlation was found between the enterococcal cell surface hydrophobicity and biofilm formation in vitro. After anaerobic incubation, β-hemolytic activity was confirmed in 19.10% of the E. faecalis and 3.33% of the E. faecium strains.

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.

Antimicrobial resistance of commensal Escherichia coli and Enterococcus faecalis isolated from clinically healthy captive wild animals in Seoul zoo

Despite the importance of antimicrobial resistance, only a few studies on the antimicrobial susceptibility on wild animals have been conducted owing to their population, accessibility, and characteristics. The objective of this study was to investigate the prevalence and characteristics of antimicrobial resistance pattern in Escherichia coli and Enterococcus faecalis isolated from the feces of captive wild animals in a zoo. A total of 61 captive wild animals were included in this study. E. coli was isolated from 58 of the 61 animals and E. faecalis was isolated from 29 animals. Among the isolated E. coli strains, ampicillin exhibited the highest resistance rate (27/29, 93.1%). Of these, 18 strains (18/29, 62%) showed multidrug resistance. The multilocus sequence typing (MLST) test showed that only ST155 was detected twice, while the other 16 strains showed different ST types. Among the E. faecalis strains, two were susceptible to all tested antimicrobials, whereas the remaining 27 strains showed resistance to one or more antimicrobials. Nine strains (9/27, 31%) showed multidrug resistance. Among the E. faecalis strains, resistance to quinupristin/dalfopristin was the highest at 96.3% (26/27), while the MLST of the nine MDR strains showed no predominant ST. Genetic association with human isolates or livestock products was observed in the isolated ST types. This indicates that antibiotic resistance in the zoo is responsible for the use of antibiotics and the partial horizontal transmission between humans and animals through feeding or contact.

Rapid Detection of Enterobacter cloacae With a Visualized Isothermal Recombinase Polymerase Amplification Assay

Enterobacter cloacae exhibits strong adhesion and invasion properties that contribute its ability to infect the host; it is considered an important opportunistic pathogen throughout the world. To control the spread of E. cloacae, simple, rapid, and accurate detection methods are required. Current methods suffer from various shortcomings and do not meet the demand for on-site quickly detection. Using recombinase polymerase amplification combined with lateral flow strip (RPA-LFS), an isothermal detection method was developed to target the outer membrane protein X (ompX) gene of E. cloacae. This reaction can be performed in 30 min at 37 °C. Limit of detection of 10 CFU/reaction was equivalent to that of the qPCR method. The detection accuracy of clinical samples was also equal to that of the qPCR method. In this study, we developed the RPA-LFS assay, which is simple, rapid, accurate, and does not require a laboratory facility. This assay may prove useful for detecting E. cloacae on-site.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

Situational analysis on fluoroquinolones use and characterization of high-level ciprofloxacin-resistant Enterococcus faecalis by integrated broiler operations in South Korea

Fluoroquinolones are classified as "critically important antimicrobials for human medicine"; however, their extensive use in livestock poses a significant health risk to humans as it leads to the rapid spread of antimicrobial resistance. This study confirmed that 40.0%-71.4% of the farms in three of the five integrated broiler operations were administered ciprofloxacin (CIP). Moreover, preventive purposes (60.9%), veterinarian prescriptions (82.6%), drinking water route (100%), and 1 to 3 days (82.6%) of age were significantly highest (P < 0.05). 194 high-level ciprofloxacin-resistant (HLCR) Enterococcus faecalis (E. faecalis) were found in 65 of 74 farms, and of which, the prevalence of qnrA (63.9%), tetM (60.3%), ermB (64.9%), blaz (38.7%), and catA (34.0%) was significantly highest (P < 0.05). 154 (79.4%) isolates showed MDR, and the distribution of MDR was significantly differences among the operations (P < 0.05). All HLCR E. faecalis possessed double mutations in gyrA and parC, and S83I/S80I (90.7%) mutations were most commonly identified. Interestingly, the distribution of isolates with MICs ≥ 512 for both CIP and moxifloxacin was significantly higher in CIP-administered farms (56.5%) than in non-CIP-administered farms (41.4%) (P < 0.05). Also, the prevalence of strong or moderate biofilm formers in HLCR E. faecalis was significantly higher than that of weak and no biofilm formers (P < 0.05). HLCR E. faecalis were heavily distributed in the broiler farms in Korea; therefore, it is necessary to minimize the prevalence of resistant bacteria via structural management regulations such as cleaning and disinfection of farm environments.

A Tale of Two Pandemics: Antimicrobial Resistance Patterns of Enterococcus spp. in COVID-19 Era

Although the COVID-19 pandemic has held the spotlight over the past years, the antimicrobial resistance (AMR) phenomenon continues to develop in an alarming manner. The lack of strict antibiotic regulation added to the overuse of antimicrobials fueled the AMR pandemic. This paper aims to analyze and identify the impact of the COVID-19 pandemic on antibiotic resistance patterns of Enterococcus spp. The study was designed as a retrospective observational study. Enterococcus spp. infections data were collected from one academic hospital in Cluj-Napoca, Romania over 18 months. A statistical analysis was performed to compare antibiotic resistance phenotypes identified. We recorded an increase in the isolation rates of Enterococcus spp. strains, from 26 isolates (26.53%) during Period A (November 2020-April 2021) to 42 strains (42.85%) during Period C (November 2021-April 2022). The number of strains with resistance to vancomycin increased from 8 during Period A to 17 during Period C. Of the total 36 strains with resistance to vancomycin, 25 were identified as E. faecium. SARS-CoV-2 patients (n = 29) proved to be at risk to develop an E. faecium co-infection (n = 18). We observed that strains with resistance to ampicillin (n = 20) and vancomycin (n = 15) are more often isolated from these patients. All changes identified in our study are to be considered in the light of COVID-19 pandemic, highlighting the threatening AMR phenomenon in Romania. Further studies should be performed to quantify the worldwide effects of these pandemics.

Evaluation of the antibacterial activity of trans-anethole against Enterococcus cloacae and Enterococcus faecalis strains of food origin

The present study sought to evaluate the antibacterial activity of trans-anethole against food-borne strains of Enterobacter cloacae and Enterococcus faecalis. The study was performed using Minimum Inhibitory Concentration (MIC), and Minimum Bactericidal Concentration (MBC) methods, in addition, disc diffusion technique was used to evaluate the association of trans-anethole with synthetic antimicrobials. Minimum Inhibitory Concentration for Adherence (MICA) testing was also performed. The results revealed that trans-anethole presents no antibacterial activity at any of the concentrations used against the E. cloacae strains tested. However, trans-anethole presented antibacterial effect against five of the six E. faecalis bacterial strains tested, with MIC values ranging from 500 μg/mL to 1000 μg/mL. Further, when analyzing the MBC results against E. faecalis, it was observed that the compound presented values ranging from 500 μg/mL to 1000 μg/mL. As for the associations, it was observed that trans-anethole when combined with the antimicrobials ampicillin, gentamicin, ciprofloxacin, and ceftriaxone presented synergistic effect against most strains of E. faecalis. However, both trans-anethole and the control chlorhexidine (0.12%) presented no antibiofilm effects against strains of E. faecalis. In short, trans-anethole presented potential antibacterial against E. faecalis strains of food origin, and may upon further study, it may be used alone or in association with synthetic antimicrobials to combat infections caused by this bacterium.

Sensitive and Selective Detection of Enterococcus faecalis Using a New Turn-on Fluorogenic β-glucosidase Substrate Combined with a Modified Selective Broth

A new, simple-to-synthesize and sensitive turn-on fluorogenic substrate (CFMU-Glu) for β-glucosidase activity was developed. This probe was based on a 7-hydroxycoumarin derivative (CFMU) that could emit green fluorescence and had the low pK_a value of 5.61 ± 0.01. CFMU-Glu could be used for sensitive monitoring of the almond βGLU and Enterococcus faecalis (E. faecalis) at the optimal pHs of 6.50 and 7.00, respectively. Moreover, a new sensitive and selective fluorogenic broth (PBF-B) for E. faecalis, utilizing CFMU-Glu and polymyxin B, was also developed. Polymyxin B was discovered to can significantly improve the detection selectivity and signal intensity. The proposed 4-four method using PBF-B and a microcentrifuge tube could provide fluorogenic detection limits of 5.01 × 10⁴ and 1.0 × 10⁵  CFU mL^-1 by fluorescence microplate reader and naked eye, respectively; it could also provide a turn-on chromogenic detection limit of 1.0 × 10⁶  CFU mL^-1 by naked eye. The proposed method could detect 8 CFU mL^-1 of E. faecalis in drinking water, Liangcha (herbal tea) and milk samples within 10 h, without pre-enrichment.

Antibiotic Resistance of Enterococcus spp. Isolated from the Urine of Patients Hospitalized in the University Hospital in North-Central Poland, 2016-2021

Urinary Tract Infections (UTIs) are common outpatient and inpatient infections, often treated with empirical therapy. Enterococcus spp. is responsible for about 10% of UTIs. This study aimed to determine the necessity of changing the empirical treatment of UTIs caused by Enterococcus spp. The evaluation was performed for 542 Enterococcus strains isolated from urine samples in the years 2016-2021. We identified three Enterococcus species that were found: E. faecalis (389, 71.8%), E. faecium (151, 27.8%) and E. gallinarum (2, 0.4%). E. faecalis was the dominant species every year. Among E. faecalis, the most prevalent was resistance to norfloxacin (51.4%). Almost all E. faecium strains (150, 99.3%) were resistant to beta-lactams and norfloxacin. Eighty-three strains (55.0%) were resistant to vancomycin and 72 (47.7%) to teicoplanin. E. faecium strains showed a significantly higher percentage of resistance mechanisms GRE (Glicopeptide-Resistant Enterococcus) (72, 48.7%) and VRE (Vancomycin-Resistant Enterococcus) (11, 7.3%), while only five strains of E. feacalis showed a VRE mechanism (1.3%). In the therapy of E. faecalis UTIs, ampicillin and imipenem still remain effective. However, the above-mentioned antibiotics, as well as fluoroquinolones, are not recommended in the treatment of UTIs of E. faecium etiology.

Longitudinal Analysis of Antimicrobial Resistance among Enterococcus Species Isolated from Australian Beef Cattle Faeces at Feedlot Entry and Exit

Enterococcus faecium are commensal bacteria inhabiting the gastrointestinal tract of animals and humans and an important cause of drug-resistant nosocomial infections. This longitudinal study aimed to determine whether changes in the antimicrobial resistance (AMR) phenotype and genotype occurred among Enterococcus spp. isolated from cattle rectal samples obtained at the entry to and exit from an Australian feedlot. The samples obtained at the feedlot induction yielded enterococci (104/150; 69.3%), speciated as E. hirae (90/104; 86.5%), E. faecium (9/104; 8.7%), E. mundtii (3/104; 2.9%), E. durans, and E. casseliflavus (1/104; 1.0% each). AMR was observed to lincomycin (63/104; 60.6%), daptomycin (26/104; 25.0%), nitrofurantoin (9/104; 8.7%), ciprofloxacin (7/104; 6.7%), tetracycline (5/104; 4.8%), tigecycline (4/104; 3.9%), and quinupristin/dalfopristin (3/104; 2.9%). From the rectal swab samples collected at the abattoir from the same animals (i.e., the feedlot exit), the enterococci recovery was significantly higher (144/150; 96.0%), with a marked shift in species distribution dominated by E. faecium (117/144; 81.3%). However, the prevalence of AMR to individual antimicrobials remained largely static between the entry and exit except for the increased resistance to nitrofurantoin (77/144; 53.5%) and quinupristin/dalfopristin (26/144; 18.1%). Overall, 13 AMR genes were observed among the 62 E. faecium isolates. These included aac(6')Ii, aac(6')-Iid, and ant(6)-Ia (aminoglycosides); eatAv, lnu(G), vat(E), msr(C), and erm(B) (macrolides, lincosamides, and streptogramins); efmA (fluoroquinolones); and tet(45), tet(L), tet(M), and tet(S) (tetracyclines). The results confirm the presence of fluoroquinolone- and streptogramin-resistant enterococci in cattle faeces at the feedlot entry in the absence of antimicrobial selection pressure. E. faecium, exhibiting increased nitrofurantoin resistance, became the dominant Enterococcus spp. during the feeding period.

Rapid and specific detection of Enterococcus faecalis with a visualized isothermal amplification method

Enterococcus faecalis is a serious problem for hospitals and can spread from patient to patient. Most of the current detection methods are associated with limitations associated with the need for trained personnel; they are also time-consuming. Thus, it is necessary to develop rapid and accurate detection methods to control the spread of E. faecalis. In this study, we developed a rapid and accurate detection method for E. faecalis using recombinase polymerase amplification (RPA) combined with a lateral flow strip (LFS). This method could be completed in approximately 35 min at 37°C. The limit of detection was 10 CFU/µL, irrespective of whether the templates were pure or complex. This method also showed good specificity and compatibility. In total, 278 clinical samples were tested using the RPA-LFS method; the detection accuracy was equal to that of the conventional qPCR method. This visualized isothermal amplification method could be useful for the future on-site detection of E. faecalis.

Enterococcus Virulence and Resistant Traits Associated with Its Permanence in the Hospital Environment

Enterococcus are opportunistic pathogens that have been gaining importance in the clinical setting, especially in terms of hospital-acquired infections. This problem has mainly been associated with the fact that these bacteria are able to present intrinsic and extrinsic resistance to different classes of antibiotics, with a great deal of importance being attributed to vancomycin-resistant enterococci. However, other aspects, such as the expression of different virulence factors including biofilm-forming ability, and its capacity of trading genetic information, makes this bacterial genus more capable of surviving harsh environmental conditions. All these characteristics, associated with some reports of decreased susceptibility to some biocides, all described in this literary review, allow enterococci to present a longer survival ability in the hospital environment, consequently giving them more opportunities to disseminate in these settings and be responsible for difficult-to-treat infections.

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.

Antimicrobial Resistance and Virulence Factor Gene Profiles of Enterococcus spp. Isolated from Giant Panda Oral Cavities

Introduction

The objective of this study was to determine the prevalence and characteristics of antimicrobial-resistant Enterococcus faecalis and E. faecium isolated from the oral cavities of captive giant pandas in China.

Material and Methods

The virulence-associated determinant and antimicrobial resistance genes were detected and antimicrobial susceptibility tests were performed on 54 strains of each bacterium.

Results

All isolates showed 100% multidrug resistance. E. faecalis isolates showed a higher percentage of strains resistant to gentamicin (48.1%), vancomycin (55.6%), linezolid (100%), and streptomycin (33.3%) than E. faecium isolates. The resistance genes of Enterococcus spp. were present to highly varying extents according to antibiotic type, their presence breaking down for E. faecalis and E. faecium respectively as aac(6')/aph(2″) 5.56% and 5.56%; aph(3')-Ⅲ 0% and 14.81%; ant(6)-I 0% and 3.7%; ant(4')-Ia 0% and 64.81%; tetL 20.37% and 100%; vanA 92.59% and 46.3%; vanB 0% and 0%; cfr 0% and 90.74%; optrA 96.3% and 3.7%; blaZ 0% and 1.85%; blaTEM 0% and 0%; tetA 20.37% and 0%; tetC 24.07% and 100%; tetM 0% and 0%; ermA 12.96% and 100%; ermB 5.56% and 3.7%; and ermC 0% and 1.85%.Virulence-associated determinants were detected in this research, which typically include efaA, gelE, asa1, ace, cylA, esp and hyl; however, the latter three were not detected. High proportions of the isolates carried the efaA, gelE, asa1, and ace genes. Respectively for E. faecalis and E. faecium their detection was efaA 98.1% and 85.2%; gelE 98.1% and 87%; asa1 92.6% and 87%; and ace 87% and 85.2%.

Conclusion

This is the first study on the potential disease risk and antimicrobial-resistant characteristics of E. faecalis and E. faecium isolates in giant panda oral cavities. The results of this study show that the antimicrobial resistance rate of Enterococcus spp. isolated from the oral cavity of captive pandas is very high, and thus needs to be monitored.

Molecular characteristics of optrA-carrying Enterococcus faecalis from chicken meat in South Korea

The purpose of this study was to identify the genetic environment of optrA gene in linezolid (LZD)-resistant Enterococcus faecalis from chicken meat and to describe the probable mechanism of dissemination of the optrA gene through plasmid or chromosomal integration. Whole genome sequencing and analysis revealed that all 3 E. faecalis isolates confirmed as LZD- and chloramphenicol-resistant carried fexA adjacent to the optrA gene as well as a variety of resistance genes for macrolides, tetracyclines, and aminoglycosides, simultaneously. But, the other genes conferring LZD resistance, cfr and poxtA, were not detected in those strains. Two isolates harboring the optrA gene in their chromosomal DNA showed >99% similarity in arrangement to the transposon Tn6674 and the transposase genes, tnpA, tnpB, and tnpC and were located in the first open reading frame for transposase. One isolate harboring an optrA-carrying plasmid also showed >99% similarity with the previously reported pE439 plasmid but had 2 amino acid changes (Thr96Lys and Tyr160Asp) and a higher minimum inhibitory concentration against LZD of 16 mg/L than that of pE439 (8 mg/L). Mobile genetic elements such as transposons or plasmids flanking the optrA gene conduct a crucial role in the dissemination of antimicrobial resistance genes. Further investigations are required to identify the way by which optrA is integrated into chromosomal DNA and plasmids.

Characteristics of linezolid-resistant Enterococcus faecalis isolates from broiler breeder farms

Linezolid is an oxazolidinone class antibiotic used for treatment infections caused by various multidrug-resistant gram-positive pathogens including enterococci. However, recently, linezolid-resistant isolates in animals are considered as a human health hazard. In a broiler operation system, antimicrobial resistance can be transferred to the environment and commercial broiler via the fecal-oral route. Therefore, this study was conducted to investigate the prevalence and characteristics of linezolid-resistant Enterococcus faecalis (E. faecalis) from broiler parent stock in a broiler operation system. Among 297 E. faecalis isolates from 85 flocks in 8 broiler breeder farms, the prevalence of chloramphenicol- and linezolid-resistant isolates was 0 to 12.1% and 0 to 8.0%, respectively; however, there were no significant differences between farms. Therefore, a total of 14 (4.7%) chloramphenicol- and/or linezolid-resistant E. faecalis showed resistance to 7 or more antimicrobial classes. The drug-resistance gene optrA, which can confer resistance to linezolid, tedizolid, and phenicols, was found in 8 (2.69%) isolates, and 7 (2.36%) of the 8 optrA-positive isolates co-carried the phenicol exporter gene fexA. However, E. faecalis isolates from 3 of 8 broiler breeder farms only carried the optrA and/or fexA genes. As linezolid is one of the last antimicrobial treatments of choice for multidrug-resistant gram-positive pathogens including E. faecalis, the presence of antibiotic-resistant E. faecalis in broiler breeder farms should be monitored to prevent the introduction of linezolid-resistant strains to the food chain.

Occurrence, Antimicrobial Resistance and Molecular Diversity of Enterococcus faecium in Processed Pork Meat Products in Korea

Because Enterococcus faecium is an important nosocomial pathogen and sentinel organism for tracking antimicrobial resistance, information on the contamination and antimicrobial resistance patterns of E. faecium in food are essential to public health and food safety. We analyzed the occurrence of E. faecium in retail pork meat products (n = 124), and antimicrobial resistance of 30 E. faecium isolates were examined against 14 antimicrobials using the broth dilution test and disc diffusion test. Rep-PCR-based molecular diversity was also analyzed using Deviersilab. The highest contamination of enterococci was observed for minced pork meat but most of the E. faecium was isolated from meatball-type frozen pork meat products (FP). Incidences of antimicrobial-resistant E. faecium against erythromycin, clindamycin and nitrofurantoin were 80%, 50% and 20%, respectively. No vancomycin-resistant enterococci were analyzed. Rep-PCR showed distinctive clusters with a similarity ≥ 98%, consisting of 18 E. faecium isolates from FP manufactured in seven companies. The analyzed data on the contamination and antimicrobial resistance patterns combined with molecular typing can be useful to derive risk management of antimicrobial-resistant enterococci in food.

Biofilm formation and transfer of a streptomycin resistance gene in enterococci from fermented pork

OBJECTIVES

Multidrug-resistant (MDR) enterococci are found extensively in food samples. This study characterized the phenotypic virulence factors and the ability of horizontal gene transfer of a streptomycin resistance gene among enterococci isolated from fermented pork.

METHODS

Thirty-six MDR enterococci were subjected to screening of gelatinase, biofilm formation at various temperatures (4 °C, 25 °C and 37 °C), clumping ability and conjugation.

RESULTS

All gelatinase-positive and clumping-positive strains were Enterococcus faecalis (41.7% and 38.9%, respectively). None of Enterococcus faecium and Enterococcus hirae demonstrated both phenotypes. Moderate and strong biofilm formations were found mostly at optimal temperatures in all the three species tested. However, moderate and weak biofilm formations could be found in 52.8% at 4 °C. No association was observed between biofilm formation and asa1, efaA, gelE and esp genes. Surprisingly, our data revealed evidence of the streptomycin resistance gene (aadE) being transferred among meat E. faecalis isolates as characterized by the pheromone-clumping response.

CONCLUSIONS

Here we report the co-existence of some virulence factors and MDR enterococci from fermented pork. Our data demonstrated for the first time that the aadE gene could be transferred via conjugation among enterococci isolated from meat, contributing to streptomycin resistance. This study highlights the importance of horizontal gene transfer within the food chain reservoir and that transfer to humans might be possible, causing harm or untreatable diseases.

Characterization of a Lytic Bacteriophage vB_EfaS_PHB08 Harboring Endolysin Lys08 Against Enterococcus faecalis Biofilms

Enterococcus faecalis is an opportunistic pathogen that causes illnesses ranging from urinary tract infections to sepsis in humans and animals. However, the overuse of antibiotics has increased rates of drug resistance among E. faecalis isolates. Bacteriophages and their derivatives have recently been identified as good candidates for the treatment of drug-resistant bacterial infections. Here, we isolated a virulent E. faecalis phage, PHB08, using the double-layer plate method. The bioactivity of the phage was determined via one-step growth curve testing and bacterial killing assays, and whole-genome sequencing was performed using the Illumina HiSeq platform. In addition, protein expression and antibiofilm assays were performed to investigate the activity of the phage lysin. Results showed that PHB08 has a 55,244-bp linear double-stranded DNA genome encoding 91 putative coding sequences. PHB08 inhibited the growth of host strain EF3964 at 37 °C in tryptic soy broth (TSB) medium, while in vegetable models, PHB08 caused a 4.69-log decrease in viable E. faecalis cells after 24 h. Both PHB08 and its endolysin lys08 showed antibiofilm activity against E. faecalis biofilms, which was enhanced by Mn²⁺ ions. Thus, virulent phage PHB08 and endolysin lys08 may be good candidates for reducing and/or eradicating E. faecalis infections.

Antimicrobial resistance monitoring of commensal Enterococcus faecalis in broiler breeders

Enterococcus faecalis (E. faecalis) has rapidly acquired resistance to multiple antimicrobials, and the antimicrobial resistance of E. faecalis from broiler breeders has been implicated in its vertical transmission to their offspring. The objective of this study was to investigate the antimicrobial resistance and genetic diversity of commensal E. faecalis isolated from the broiler breeder farms. Among a total of 229 E. faecalis isolates from 9 broiler breeder farms, the highest resistance rate was observed in tetracycline (78.2%), followed by doxycycline (58.1%) and erythromycin (43.7%), and the prevalence of antimicrobial resistance showed significant differences among the 9 broiler breeder farms (P < 0.05). The tetM gene (77.1%) and ermB gene (85.0%) were detected at the highest levels in 179 TE-and 100 E-resistant isolates, respectively. Twenty-four high-level gentamicin-resistant isolates carried aac(6″)Ie-aph(2″)-la gene, and 9 high-level ciprofloxacin-resistant isolates showed point mutations in both gyrA and parC genes. All high-level gentamicin-resistant or high-level ciprofloxacin-resistant isolates showed one of the two different virulence gene patterns, ace-asa1-efaA-gelE complex or ace-efaA-gelE complex. These results indicate that constant epidemiological monitoring at the breeder level is required to prevent the pyramidal transmission of antimicrobial-resistant E. faecalis.

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.

Molecular characterization of antimicrobial-resistant Enterococcus faecalis and Enterococcus faecium isolated from layer parent stock

Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium) are ubiquitous intestinal bacteria in humans and animals that can easily acquire antimicrobial resistance, which allows them to have roles as antimicrobial resistance indicators. In addition, layer parent stock produces thousands of eggs for the production of commercial laying hens and can transfer a variety of viral and bacterial agents to chicks. The objective of this study was to determine the prevalence and characteristics of antimicrobial-resistant E. faecalis and E. faecium isolated in the layer parent stock level of the egg-layer operating system in South Korea. A total of 129 E. faecalis and 166 E. faecium isolates from 74 flocks of 30 layer parent stock were tested for resistance in this study. The prevalence of doxycycline- (51.9%), erythromycin- (53.5%), high-level gentamicin- (13.2%), high-level kanamycin- (31.0%), high-level streptomycin- (30.2%), and tetracycline- (64.3%) resistant E. faecalis isolates were higher than those for E. faecium isolates (P < 0.05). The ermB gene was detected in 66 (95.7%) erythromycin-resistant E. faecalis isolates, which was higher than that of 32 (71.7%) erythromycin-resistant E. faecium isolates. Twenty-one high-level gentamicin-resistant Enterococcus spp. (17 E. faecalis and 4 E. faecium) carried at least one aminoglycoside-modifying enzyme gene, aac(6')Ie-aph(2')-Ia or ant(6)-Ia. Fourteen isolates that harbored both aac(6')Ie-aph(2')-Ia and ant(6)-Ia exhibited pattern A with IS256 at both ends. Ten high-level ciprofloxacin-resistant Enterococcus spp. (8 E. faecalis and 2 E. faecium) showed amino acid changes from serine to isoleucine at codons 83 in gyrA, and 80 in parC. Also, the virulence genes ace, asa1, efaA, and gelE were detected in this study. To the best of our knowledge, this is the first study to examine the prevalence and characteristics of antimicrobial-resistant E. faecalis and E. faecium isolates in the layer parent stock. Our findings support the need for a surveillance program to monitor the emergence of antimicrobial-resistant E. faecalis and E. faecium in layer operating system.

Genetic characterization of high-level aminoglycoside-resistant Enterococcus faecalis and Enterococcus faecium isolated from retail chicken meat

Retail chicken meat can play a role in the transfer of drug resistance to humans through the handling or ingestion of improperly cooked meat contaminated with resistant enterococci. In fact, high-level aminoglycoside-resistance (HLAR) in enterococci identified in human cases. Therefore, the prevalence and genetic characterization of HLAR in enterococci in retail chicken meat were investigated in this study. Of the 345 enterococci strains, 29 (8.7%) showed HLAR. All HLAR in enterococci carried at least 1 of 2 aminoglycoside-modifying enzyme genes, aac(6')Ie-aph(2″)-Ia and ant(6)-Ia. Among the 13 isolates that carried aac(6')Ie-aph(2″)-Ia, 3 had pattern A, with IS256 at both ends, and the other 10 had pattern D, without IS256 at both ends. All HLAR in enterococci also showed multidrug resistance. Among the 24 erythromycin-resistant enterococci, 19 (79.2%) harbored the ermB gene, and one (4.2%) harbored both the ermB and ermA genes. A total of 21 enterococci were tetracycline-resistant and harbored one or more of the following tetracycline resistance genes tet(M), tet(L), and tet(O). The Int-Tn gene was detected in one isolate (3.4%) carrying the tet(M) and ermB genes. All 4 chloramphenicol-resistant isolates carried either the phenicol resistance gene cfr alone (one isolate), both cfr and fexA (one isolate), or both fexA and optrA (2 isolates). Four efflux pump genes, efr(A), efr(B), emeA, and lsa, were detected in all HLAR in Enterococcus faecalis isolates. These results improve our understanding of the transmission dynamics of HLAR in enterococci from non-hospital sources to humans.