Relationships between enterococcal virulence and antimicrobial resistance

Metal tolerance in enterococci isolated from seabirds in Abrolhos Archipelago, Brazil: Evaluating their role as bioindicators of marine pollution

Microbiota exposed to pollution provide insights into host physiology and ecosystem disruption. This study evaluated Enterococcus spp. tolerant to arsenic (As), copper (Cu), and mercury (Hg) from red-billed tropicbirds (Phaethon aethereus) and brown boobies (Sula leucogaster), which previously showed these metals in their blood and feathers, and their potential use as bioindicators of metal contamination. Enterococcus casseliflavus (47.9 %), E. faecalis (34.1 %), E. hirae (11.7 %), and E. faecium (5.3 %) were identified. Both seabird species had a high incidence of As-tolerant bacteria (84.0 %), with 40.4 % of these strains containing As efflux system genes (arsA_I and arsA_II). Cu efflux pump gene (tcrB) was detected in 30.9 % of strains, while Hg reductase genes (mer) were not found. As- and Cu-tolerance in enterococci observed in this study underlines their potential as bioindicators in metal-polluted marine environments. Further research may elucidate the role of these metal-tolerant enterococci in seabird gut and their adaptability to polluted environments.

Lipid discovery enabled by sequence statistics and machine learning

Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that Streptococcus agalactiae MprF synthesizes lysyl-phosphatidylglycerol (Lys-PG) from anionic PG, and a novel cationic lipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), from neutral glycolipid Glc-DAG. This unexpected result prompted us to investigate whether Lys-Glc-DAG occurs in other MprF-containing bacteria, and whether other novel MprF products exist. Here, we studied protein sequence features determining MprF substrate specificity. First, pairwise analyses identified several streptococ-cal MprFs synthesizing Lys-Glc-DAG. Second, a restricted Boltzmann machine-guided approach led us to discover an entirely new substrate for MprF in Enterococcus , diglucosyl-diacylglycerol (Glc 2 -DAG), and an expanded set of organisms that modify glycolipid substrates using MprF. Overall, we combined the wealth of available sequence data with machine learning to model evolutionary constraints on MprF sequences across the bacterial domain, thereby identifying a novel cationic lipid.

Development of a transcription factor decoy-nanocarrier system as a successful inhibitor of Enterococcus faecalis virulence in vitro and in vivo

Enterococcus faecalis is a troublesome nosocomial pathogen that acquired resistance to most available antimicrobial agents. Antivirulence agents represent an unconventional treatment approach. Here, transcription factor decoy (TFD)-loaded cationic liposomes (TLL) were developed as an inhibitor of the Fsr quorum-sensing system and its associated virulence traits, in E. faecalis. The consensus sequence of the FsrA binding site was found conserved among 651 E. faecalis annotated genomes. The TFD was synthesized as an 82 bp DNA duplex, containing the conserved binding sequence, and loaded onto cationic liposomes. The optimum loading capacity, mean particle size, and zeta potential of the TLL were characterized. The developed TLL lacked any effect on E. faecalis growth and significantly inhibited the in vitro production of the proteolytic enzymes controlled by the Fsr system; gelatinase and serine protease, in a concentration-dependent manner. This inhibition was accompanied by a significant reduction in the transcription levels of FsrA-regulated genes (fsrB, gelE, and sprE). The developed TLL were safe as evidenced by the nonhemolytic effect on human RBCs and the negligible cytotoxicity on human skin fibroblast cells. Moreover, in the larvae infection model, TLL displayed a significant abolish in the mortality rates of Galleria mellonella larvae infected with E. faecalis. In conclusion, the developed TLL offer a new safe strategy for combating E. faecalis infection through the inhibition of quorum-sensing-mediated virulence; providing a platform for the development of similar agents to combat many other pathogens.

Genome analysis of multidrug resistant Enterococcus faecium and Enterococcus faecalis circulating among hospitalized patients in uMgungundlovu District, KwaZulu-Natal, South Africa

BACKGROUND

Vancomycin-resistant enterococci (VRE) are important pathogens categorized as high-priority bacteria in the Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics published by the World Health Organization. The aim of this study was to determine the risk factors, resistance, virulence, mobilomes associated with multidrug-resistant and clonal lineages of Enterococcus faecium and faecalis circulating among hospitalized patients following the health system in South Africa, using whole genome sequencing (WGS).

METHODS

A cross-sectional study was conducted during a two-month periods among hospitalized patients in 2017. Rectal swabs were collected from patients admitted to medical and surgical wards in an urban tertiary hospital, and a rural district hospital in uMgungundlovu district, South Africa. Enterococci were screened for vancomycin resistance on bile esculin azide agar supplemented with 6 mg/L of vancomycin and confirmation of VRE was done using ROSCO kits. Conventional and real-time PCR methods were used to ascertain the presence of VanA, VanB, VanC-2/3 and VanC-1 genes. All six multidrug-resistant Enterococcus faecalis and faecium selected were identified using multiplexed paired-end libraries (2 × 300 bp) with the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA) and genome sequencing was done using Illumina MiSeq instrument with 100× coverage at the National Institute of Communicable Diseases Sequencing Core Facility, South Africa. Antibiotic resistance genes, virulence factors, plasmids, integrons and CRISPR were characterized using RAST, ResFinder, VirulenceFinder, PlasmidFinder, PHAST and ISFinder respectively.

RESULTS

Sequencing analysis revealed that these strains harbouring numerous resistance genes to glycopeptides (vanC[100%], vex3[100%], vex2[83,33%] and vanG[16,66%]), macrolides, lincosamides, sterptogramine B (ermB[33,32%], Isa[16,66%], emeA[16,66%]) and tetracyclines (tetM[33,32%]) in both district and tertiary hospitals. Multidrug efflux pumps including MATE, MFS and pmrA conferring resistance to several classes of antibiotics were also identified. The main transposable elements observed were in the Tn3 family, specifically Tn1546. Four single sequence types (STs) were identified among E. faecium in the district hospital, namely ST822, ST636, ST97 along with a novel ST assigned ST1386, while one lineage, ST29 was detected in the tertiary hospital.

CONCLUSION

The study reveals the genetic diversity and high pathogenicity of multidrug-resistant Enterococcus faecalis and faecium circulating among hospitalized patients. It underlines the necessity to implement routine screening of admitted patients coupled with infection control procedures, antimicrobial stewardship and awareness should be strengthened to prevent and/or contain the carriage and spread of multidrug resistant E. faecium and E. faecalis in hospitals and communities in South Africa.

Prevalence and Molecular Characteristics of Enterococci Isolated from Clinical Bovine Mastitis Cases in Ningxia

Purpose

This study aimed to investigate the prevalence and genetic characterization of enterococcal isolates (Enterococcus faecalis, Enterococcus faecium and Enterococcus hirae) isolated from clinical bovine mastitis cases in Ningxia, China.

Patients and Methods

The enterococci were identified by 16S rRNA amplification and sequencing. Antimicrobial resistance was determined by disc diffusion method. Virulence and antimicrobial resistance genes were detected by PCR assays.

Results

Overall, 198 enterococcal isolates were identified from 2897 mastitis samples, including 137 (4.7%) E. faecalis, 50 (1.7%) E. faecium and 11 (0.4%) E. hirae. E. faecalis, E. faecium and E. hirae isolates showed high resistance to tetracycline (92.7%, 68.0%, 90.9%), followed by erythromycin (86.9%, 76.0%, 72.7%). The multidrug-resistant strains of E. faecalis and E. faecium were 29 (21.2%) and 13 (26.0%), respectively. The resistance of E. faecalis, E. faecium and E. hirae isolates to tetracycline is mainly attributed to the presence of tetL (alone or combined with tetM and/or tetK), the erythromycin resistance to ermB (alone or combined with ermC and/or ermA). Moreover, cpd (94.2%), gelE (77.4%), efaAfs (93.4%), and esp (79.6%) were the most common virulence genes in E. faecalis. In E. faecium, except for the gene efaAfs (82.0%), other virulence genes are rarely found. Only two strains of E. hirae carrying asa1 gene were detected.

Conclusion

The results of this study can provide a reference for the prevention and treatment of bovine mastitis caused by enterococci.

Identification and Safety Assessment of Enterococcus casseliflavus KB1733 Isolated from Traditional Japanese Pickle Based on Whole-Genome Sequencing Analysis and Preclinical Toxicity Studies

The present study involves the precise identification and safety evaluation of Enterococcus casseliflavus KB1733, previously identified using 16S rRNA analysis, through whole-genome sequencing, phenotypic analysis, and preclinical toxicity studies. Analyses based on the genome sequencing data confirm the identity of KB1733 as E. casseliflavus and show that the genes related to vancomycin resistance are only present on the chromosome, while no virulence factor genes are present on the chromosome or plasmid. Phenotypic analyses of antibiotic resistance and hemolytic activity also indicated no safety concerns. A bacterial reverse mutation test showed there was no increase in revertant colonies of heat-killed KB1733. An acute toxicity test employing heat-killed KB1733 at a dose of 2000 mg/kg body weight in rats resulted in no deaths and no weight gain or other abnormalities in the general condition of the animals, with renal depression foci and renal cysts only occurring at the same frequency as in the control. Taking the background data into consideration, the effects on the kidneys observed in the current study were not caused by KB1733. Our findings suggest that KB1733 is non-pathogenic to humans/animals, although further studies involving repeated oral toxicity tests and/or clinical tests are required.

In Vitro Interaction between Mycoplasma agalactiae and Small Ruminants' Endogenous Bacterial Strains of Enterococcus spp. and Coagulase-Negative Staphylococcus

Recently, an antimicrobial effect on Mycoplasma agalactiae (Ma), the main etiological agent of contagious agalactia (CA), was reported in vitro with strains of Enterococcus spp. from ovine and caprine milk. The aim of this work was to evaluate the interaction of Ma with the same Enterococcus spp. isolated from other anatomical locations (vagina) and other bacterial populations present in milk, such as coagulase-negative staphylococci (CNS). The vaginal Enterococcus strains and the raw milk CNS were isolated from sheep and goats. Experimental in vitro conditions were prepared to assess the growth of Ma with and without the presence of these strains. The selected vaginal strains were identified as Enterococcus (E.) hirae and E. mundtii, and the strains of CNS were identified as Staphylococcus petrasii. Different interactions of Ma with ovine and caprine wild vaginal strains of Enterococcus and dairy strains of CNS are described for the first time: Ma can grow exponentially during 15 h with the selected strains, although with certain strains, its optimal growth can be negatively affected (p < 0.05). The colonization and/or excretion of Ma could, therefore, be influenced by certain endogenous bacterial strains. Our results increase the knowledge about possible bacterial ecology dynamics surrounding CA.

The population structure of vancomycin-resistant and -susceptible Enterococcus faecium in a low-prevalence antimicrobial resistance setting is highly influenced by circulating global hospital-associated clones

Between 2010 and 2015 the incidence of vancomycin-resistant Enterococcus faecium (VREfm) in Norway increased dramatically. Hence, we selected (1) a random subset of vancomycin-resistant enterococci (VRE) from the Norwegian Surveillance System for Communicable Diseases (2010-15; n=239) and (2) Norwegian vancomycin-susceptible E. faecium (VSEfm) bacteraemia isolates from the national surveillance system for antimicrobial resistance in microbes (2008 and 2014; n=261) for further analysis. Whole-genome sequences were collected for population structure, van gene cluster, mobile genetic element and virulome analysis, as well as antimicrobial susceptibility testing. Comparative genomic and phylogeographical analyses were performed with complete genomes of global E. faecium strains from the National Center for Biotechnology Information (NCBI) (1946-2022; n=272). All Norwegian VREfm and most of the VSEfm clustered with global hospital-associated sequence types (STs) in the phylogenetic subclade A1. The vanB2 subtype carried by chromosomal Tn1549 integrative conjugative elements was the dominant van type. The major Norwegian VREfm cluster types (CTs) were in accordance with concurrent European CTs. The dominant vanB-type VREfm CTs, ST192-CT3/26 and ST117-CT24, were mostly linked to a single hospital in Norway where the clones spread after independent chromosomal acquisition of Tn1549. The less prevalent vanA VRE were associated with more diverse CTs and vanA carrying Inc18 or RepA_N plasmids with toxin-antitoxin systems. Only 5 % of the Norwegian VRE were Enterococcus faecalis, all of which contained vanB. The Norwegian VREfm and VSEfm isolates harboured CT-specific virulence factor (VF) profiles supporting biofilm formation and colonization. The dominant VREfm CTs in general hosted more virulence determinants than VSEfm. The phylogenetic clade B VSEfm isolates (n=21), recently classified as Enterococcus lactis, harboured fewer VFs than E. faecium in general, and particularly subclade A1 isolates. In conclusion, the population structure of Norwegian E. faecium isolates mirrors the globally prevalent clones and particularly concurrent European VREfm/VSEfm CTs. Novel chromosomal acquisition of vanB2 on Tn1549 from the gut microbiota, however, formed a single major hospital VREfm outbreak. Dominant VREfm CTs contained more VFs than VSEfm.

Distribution and association of antimicrobial resistance and virulence characteristics in Enterococcus spp. isolates from captive Asian elephants in China

Enterococcus spp., as an opportunistic pathogen, are widely distributed in the environment and the gastrointestinal tracts of both humans and animals. Captive Asian elephants, popular animals at tourist attractions, have frequent contact with humans. However, there is limited information on whether captive Asian elephants can serve as a reservoir of antimicrobial resistance (AMR). The aim of this study was to characterize AMR, antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), gelatinase activity, hemolysis activity, and biofilm formation of Enterococcus spp. isolated from captive Asian elephants, and to analyze the potential correlations among these factors. A total of 62 Enterococcus spp. strains were isolated from fecal samples of captive Asian elephants, comprising 17 Enterococcus hirae (27.4%), 12 Enterococcus faecalis (19.4%), 8 Enterococcus faecium (12.9%), 7 Enterococcus avium (11.3%), 7 Enterococcus mundtii (11.3%), and 11 other Enterococcus spp. (17.7%). Isolates exhibited high resistance to rifampin (51.6%) and streptomycin (37.1%). 50% of Enterococcus spp. isolates exhibited multidrug resistance (MDR), with all E. faecium strains demonstrating MDR. Additionally, nine ARGs were identified, with tet(M) (51.6%), erm(B) (24.2%), and cfr (21.0%) showing relatively higher detection rates. Biofilm formation, gelatinase activity, and α-hemolysin activity were observed in 79.0, 24.2, and 14.5% of the isolates, respectively. A total of 18 VAGs were detected, with gelE being the most prevalent (69.4%). Correlation analysis revealed 229 significant positive correlations and 12 significant negative correlations. The strongest intra-group correlations were observed among VAGs. Notably, we found that vancomycin resistance showed a significant positive correlation with ciprofloxacin resistance, cfr, and gelatinase activity, respectively. In conclusion, captive Asian elephants could serve as significant reservoirs for the dissemination of AMR to humans.

Sociodemographic distributions and molecular characterization of colonized Enterococcus faecium isolates from locality hospitals in Khartoum, Sudan

Background

Enterococcus faecium is an opportunistic pathogen of humans with diverse hosts, encompassing animals as well as human beings. In the past twenty years, there has been a rise in the instances of nosocomial infections that are linked to antibiotic-resistant Enterococcus faecium. The acquisition of diverse antimicrobial resistance factors has driven the global development of robust and convergent adaptive mechanisms within the healthcare environment. The presence of microorganisms in hospitalized and non-hospitalized patient populations has been significantly aided by the facilitation of various perturbations within their respective microbiomes.

Objective

This study aimed to determine the antimicrobial profile, demographic and clinical characteristics, along with the detection of virulence encoding genes, and to find out the clonal genetic relationship among colonized E. faecium strains.

Methodology

A hospital-based cross-sectional study was carried out between October 2018 and March 2020 at four Khartoum locality hospitals in Sudan. The study comprised a total of 108 strains of E. faecium isolated from patients admitted to four locality hospitals in Khartoum. A self-structured questionnaire was used to gather information on sociodemographic traits. Data were analyzed using chi-square test. In all cases, P value ≤ 0.05 with a corresponding 95% confidence interval was considered statistically significant. Moreover, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) was utilized to assess the prevalence of clonal relationships, and the gel was analyzed using CLIQS software.

Results

In this study, the isolation rate of colonized E. faecium strains was 108/170 (63.5%). The colonization of E. faecium and its association with various sociodemographic and clinical features was examined. 73 (67.6%) of patients had multidrug-resistant (MDR), and 22 (20.4%) had extensively drug-resistant (XDR), 73 (67.6%) of patients engaged in self-medication practices. Eighty patients (74.1%) were non-adherence to prescribed antibiotics, while 70 (64.8%) patients reported recent antibiotic usage within the 3 months. The present study suggests that demographic factors may not be significantly associated with the incidence of E. faecium infection except for patients who had a prior history of antibiotic use (P ≤ 0.005). The analysis of virulence genes showed a high prevalence of asa1 gene (22.2%) among strains. In ERIC-PCR the genetic relatedness of E. faecium showed seven identical clusters (A-G) with 100% genetic similarity. This implies clonal propagation in hospitals and communities.

Conclusion

This study found that the incidence of E. faecium isolated from locality hospitals in Khartoum was likely due to the spread of E. faecium clones, thereby highlighting the need for intensifying infection control measures to prevent the spreading of nosocomial infection.

Genome Characterization of Enterococcus faecalis Bacteriophage EFKL

We characterized the complete genome of the lytic Enterococcus faecalis phage EFKL, which was isolated from a sewage treatment plant in Kuala Lumpur, Malaysia. The phage, which was classified in the genus Saphexavirus, has a 58,343-bp double-stranded DNA genome containing 97 protein-encoding genes and shares 80.60% nucleotide similarity with Enterococcus phage EF653P5 and Enterococcus phage EF653P3.

Toxin-linked mobile genetic elements in major enteric bacterial pathogens

One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.

Persistence Infection of TGEV Promotes Enterococcus faecalis Infection on IPEC-J2 Cells

Transmissible gastroenteritis virus (TGEV) is a coronavirus causing diarrhea with high incidence in swine herds. Its persistent infection might lead to epithelial-mesenchymal transition (EMT) of swine intestinal epithelial cells, followed by subsequent infections of other pathogens. Enterococcus faecalis (E. faecalis) is a member of the enteric microorganisms and an opportunistic pathogen. There is no report of secondary E. faecalis infection to TGEV, even though they both target to the intestinal tracts. To investigate the interactions between TGEV and E. faecalis, we set up an in vitro infection model by the swine IPEC-J2 cells. Dynamic changes of cell traits, including EMT and cell motility, were evaluated through qPCR, Western blot, electronic microscopy, scratch test, Transwell migration test and invasion test, respectively. The adhesion and invasion tests of E. faecalis were taken to verify the impact of the preceding TGEV infection. The cell morphology and molecular marker evaluation results showed that the TGEV persistent infection induced EMT on IPEC-J2 cells; increased cellular motility and invasion potential were also observed. Spontaneously, the expression levels of fibronectin (FN) and the membrane protein integrin-α5, which are dominant bacterial receptors on IPEC-J2 cells, were upgraded. It indicated that the bacteria E. faecalis adhered to IPEC-J2 cells through the FN receptor, and then invaded the cells by binding with the integrin-α5, suggesting that both molecules were critical for the adhesion and invasion of E. faecalis to IPEC-J2 cells. Additionally, it appeared that E. faecalis alone might trigger certain EMT phenomena, implying a vicious circle might occur. Generally, bacterial and viral co-infections are frustrating yet common in both human and veterinary medicines, and our observations on enteric TGEV and E. faecalis interactions, especially the diversity of bacterial invasion strategies, might provide new insights into the mechanisms of E. faecalis pathogenicity.

Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens

Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA-protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA-protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA-protein complexes such as the 6S RNA-RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).

Comparative metabolite profiling of four polyphenol rich Morus leaves extracts in relation to their antibiofilm activity against Enterococcus faecalis

Enterococci are a common cause of urinary tract infections. The severity of enterococcal infections is associated with their ability to form biofilms. Morus leaves are known as a natural antibacterial, however, their antibiofilm activity against Enterococcus remains unveiled. This study aimed to evaluate the ability of four polyphenol-rich Morus leaves extracts (Morus nigra, M. rubra, M. macroura, and M. alba) to inhibit biofilm formed by enterococcal clinical isolates in relation to their metabolic profiling. Results revealed that 48% of the isolates formed strong biofilm, 28% formed moderate biofilm, 20% formed weak biofilm, and only 4% did not form a biofilm. The strong biofilm-forming isolates were E. faecalis, and hence were chosen for this study. The antibiofilm activity of the four polyphenol-rich Morus leaves extracts revealed that the M. nigra extract exhibited the highest percentage of biofilm inhibition followed by M. rubra then M. macroura and the least inhibition was detected in M. alba, and these results were in accordance with the phenolic and flavonoid contents of each extract. UPLC-ESI-MS/MS identified 61 polyphenolic compounds in the four extracts. Further, multivariate analysis confirmed clear segregation of M. nigra from the other species suggesting disparity in its metabolome, with accumulation of flavonoids, anthocyanidins, phenolic acids and coumarin derivatives. Quercetin and kaempferol glycosides were found to be positively and significantly correlated to the antibiofilm activity. In conclusion, M. nigra ethanolic extracts showed the highest phenolic content and antibiofilm activity and they could be developed as a complementary treatment for the development of antimicrobial agents.

Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors and MGEs were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical and associated habitats. Neither lineages of E. faecium, type A and B, nor MGEs are constrained by geographic proximity, but our results show evidence of a strong association of many profiled genes and MGEs with habitat. Many features were associated with a group of clinical and municipal wastewater genomes that are likely forming a new human-associated ecotype within type A. The evolutionary dynamics of E. faecium make it a highly versatile emerging pathogen, and its ability to acquire, transmit and lose features presents a high risk for the emergence of new pathogenic variants and novel resistance combinations. This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.

Analysis of virulence genes, drug resistance detection, and pathogenicity in Enterococcus from farm animals

This study aimed to investigate the presence of eight virulence genes (ace, asa1, esp, efaA, gelE, cylA, agg, fsr) in Enterococcus from a variety of animals and to explore the drug resistance and pathogenicity. This could provide a theoretical basis for clinical treatment of Enterococcus infections. Anal swabs from pigs, chickens, cattle, and dogs in farms and pet hospitals were collected for Enterococcus isolation and identification. Eight virulence genes were detected (PCR method), and drug resistance was assessed (drug-sensitive paper method). The strains containing different virulence genes were then divided into EV1, EV2, and EV3 groups. The LD₅₀ and pathogenicity was examined by intra-peritoneal injection to infect mice. Differences were found in the detection rates of virulence genes in Enterococcus from the different animals. The highest overall detection rate was for the esp gene (78.0%), and the lowest for the cylA gene (15.5%). Eight genes were detected most frequently in Enterococcus from dogs and least frequently from cattle. Among the Enterococcus strains from four variety of animals, drug resistance was highest against sulfamethoxazole (100%), cefotaxime (>97%), and cefotaxitin (>93%). Drug resistance was lowest against vancomycin (0%), levofloxacin (<12%) and ciprofloxacin (<13%). The LD₅₀ for each of the three groups was EV1_LD50=8.71×10⁹CFU， EV2_LD50=2.34×10¹⁰CFU，and EV3_LD50=9.33×10¹⁰CFU. The Enterococcus12LD₅₀ dose group caused significant clinical symptoms in mice, with pathological effects on the heart, liver, lungs, and kidneys, and particularly on the urinary system. The abundance of Enterococcus virulence genes, drug resistance, and pathogenicity vary among different animal origins, and the pathology caused by Enterococcus requires effective treatment protocols based on species and regional characteristics.

Isolation of Enterococcus faecalis pathogenic genes isolated from oral infection by the effect of ionic liquids based on amino acid and its expression by real-time PCR

Enterococcus faecalis is an important factor in nosocomial infections. The aim of this study was the isolation of the pathogenic genes of Enterococcus faecalis in mouth infection and the study of the expression of these genes by real-time PCR. In this study, 60 isolates of E. faecalis were isolated from oral infections. The presence and frequency of cyl, hyl, and esp genes and their expression by ionic liquid were evaluated using real-time PCR. MIC was determined by broth dilution method and biofilm production was measured, then biofilm inhibition ability and cytotoxicity test were performed by MTT method. The esp, cyl, and hyl genes were observed in 10, 11, and 2 isolates, respectively. cyl gene with the highest frequency of expression in the treated group was reduced by 1.14% under the influence of ionic liquid with methionine base. The results of MIC and Sub MIC concentrations were obtained with the effect of ionic liquid including 125 and 225 µg/mL, respectively. Amino-acid-based ionic liquids can also reduce biofilm production at sub-MIC concentrations (P < 0.05), and changes in cytotoxicity at different concentrations and over time are significant (P-value < 0.001). E. faecalis strains are genetically diverse and this indicates the polyclonal prevalence of strains in clinical specimens. Combination treatment of ionic liquid with common antimicrobial drugs has good antibacterial effects against Enterococcus species, and ionic liquid with a minimum dose can be a good alternative to single-drug treatment of Enterococcus infections.

Antibacterial Effects of Recombinant Endolysins in Disinfecting Medical Equipment: A Pilot Study

Nosocomial infections caused by multidrug-resistant (MDR) bacteria are severe life-threatening factors. Endolysins (lysins) degrade the bacterial cell wall peptidoglycan and may help control pathogens, especially MDR bacteria prevalent in hospital settings. This study was conducted to verify the potential of lysin as disinfectant to kill bacteria contaminating medical devices that cause hospital infections. Eight catheters removed from hospitalized patients were collected and tested for their ability to kill bacteria contaminating the catheters using two lysins, LysSS and CHAP-161. Catheter-contaminating bacterial species were isolated and identified by 16s rRNA sequencing. From the eight catheters, bacteria were cultured from seven catheters, and five bacterial species (Bacillus megaterium, Bacillus muralis, Corynebacterium striatum, Enterococcus faecium, and Staphylococcus epidermidis) were identified. LysSS could inhibit catheter-contaminating bacteria, including C. striatum and S. epidermidis, compared with untreated controls but could not inhibit the growth of E. faecium. CHAP-161 showed more bactericidal effects than LysSS, but could not inhibit the growth of S. epidermidis. This study showed the potential of lysin as an alternative disinfectant for hazardous chemical disinfectants used in hospitals.

Antibiotic Stewardship Related to Delayed Diagnosis and Poor Prognosis of Critically Ill Patients with Vancomycin-Resistant Enterococcal Bacteremia: A Retrospective Cohort Study

Purpose

Patients with septicemia caused by vancomycin-resistant Enterococcus (VRE) bacteremia have higher mortality rates than patients infected by VSE. Vancomycin or teicoplanin is selected as the antibiotic stewardship intervention to cover methicillin-resistant Staphylococcus aureus infections before blood culture reveals VRE bacteremia in critically ill patients with Gram-positive cocci (GPC) bacteremia; this may require linezolid or daptomycin treatment instead. We thus evaluated antibiotic stewardship practices, such as appropriate timing of antibiotic use in GPC bacteremia, and clinical outcomes of critically ill patients with VRE infection.

Patients and Methods

This retrospective study enrolled 191 critically ill patients with enterococcal bacteremia at the Taipei Tzu Chi Hospital during January 1, 2019–December 31, 2020. Demographic and clinical characteristics, as well as disease outcomes and appropriate antibiotic use after GPC bacteremia diagnosis, were compared between the VRE and VSE groups.

Results

Of 191 patients, 55 had VRE bacteremia (case group) and 136 had VSE bacteremia (control group). The rate of antibiotic change after initial antibiotic use for GPC bacteremia was higher in the VRE bacteremia group (100% vs 10.3%; p<0.001). The time to appropriate antibiotic administration after GPC bacteremia diagnosis was longer in the VRE bacteremia group (3.3±2.1 vs 1.5±1.8 days; p<0.001). Patients with VRE bacteremia had higher 28-day mortality rates (relative risk, 1.997; 95% confidence interval [CI], 1.041–3.83). Multivariate Cox regression analysis showed that delayed appropriate antibiotic administration of >3 days after GPC bacteremia diagnosis increased the risks of 28-day all-cause mortality (adjusted hazard ratio, 2.045; 95% CI, 1.089–3.84; p=0.026) in patients with VRE infection.

Conclusion

Patients with VRE bacteremia with delayed appropriate antibiotic administration of >3 days after GPC bacteremia diagnosis had increased 28-day mortality risks. New strategies for early VRE detection in GPC bacteremia may shorten the time to administer appropriate antibiotics and lower mortality rates.

Comparative characteristics of sequence types, genotypes and virulence of multidrug-resistant E. faecium isolated from various hosts in eastern Poland. Spread of clonal complex 17 in humans and animals

The aim of the study was to carry out a comparative analysis of the occurrence of sequence types, genotypes, and virulence genes of multidrug-resistant E. faecium isolated from humans, domestic animals, and wildlife from eastern Poland. The genetic correlation of strains was determined using multilocus sequence typing, and the method of Amplification of DNA fragments Surrounding Rare Restriction Sites. The presence of 49 different STs (including 12 not reported previously) was shown. All human isolates, 56% of E. faecium isolated from poultry and 40% isolated from wildlife, belonged to the hospital-adapted CC17. E. faecium CC17 were characterized by statistically higher resistance to aminoglycosides and penicillin, the presence of the aac(6')-Ie-aph(2")-Ia and hyl gene and mutations in gyrA and parC, compared to other strains (p > 0.05). E. faecium were classified into 73 genotypes grouped into clusters including isolates from the same host species. The present study showed that the virulence, resistance, and genotype profiles of E. faecium were correlated with the individual host but not with the sequence type. The occurrence of E. faecium CC17 in both humans and animals proves the large circulation of the complex among various hosts.

Enterococcus spp.: Is It a Bad Choice for a Good Use-A Conundrum to Solve?

Since antiquity, the ubiquitous lactic acid bacteria (LAB) Enterococci, which are just as predominant in both human and animal intestinal commensal flora, have been used (and still are) as probiotics in food and feed production. Their qualities encounter several hurdles, particularly in terms of the array of virulence determinants, reflecting a notorious reputation that nearly prevents their use as probiotics. Additionally, representatives of the Enterococcus spp. genus showed intrinsic resistance to several antimicrobial agents, and flexibility to acquire resistance determinants encoded on a broad array of conjugative plasmids, transposons, and bacteriophages. The presence of such pathogenic aspects among some species represents a critical barrier compromising their use as probiotics in food. Thus, the genus neither has Generally Recognized as Safe (GRAS) status nor has it been included in the Qualified Presumption of Safety (QPS) list implying drastic legislation towards these microorganisms. To date, the knowledge of the virulence factors and the genetic structure of foodborne enterococcal strains is rather limited. Although enterococcal infections originating from food have never been reported, the consumption of food carrying virulence enterococci seems to be a risky path of transfer, and hence, it renders them poor choices as probiotics. Auspiciously, enterococcal virulence factors seem to be strain specific suggesting that clinical isolates carry much more determinants that food isolates. The latter remain widely susceptible to clinically relevant antibiotics and subsequently, have a lower potential for pathogenicity. In terms of the ideal enterococcal candidate, selected strains deemed for use in foods should not possess any virulence genes and should be susceptible to clinically relevant antibiotics. Overall, implementation of an appropriate risk/benefit analysis, in addition to the case-by-case assessment, the establishment of a strain's innocuity, and consideration for relevant guidelines, legislation, and regulatory aspects surrounding functional food development seem to be the crucial elements for industries, health-staff and consumers to accept enterococci, like other LAB, as important candidates for useful and beneficial applications in food industry and food biotechnology. The present review aims at shedding light on the world of hurdles and limitations that hampers the Enterococcus spp. genus and its representatives from being used or proposed for use as probiotics. The future of enterococci use as probiotics and legislation in this field are also discussed.

Wildlife symbiotic bacteria are indicators of the health status of the host and its ecosystem

Lactic acid bacteria (LAB) are gut symbionts that can be used as a model to understand the host-microbiota crosstalk under unpredictable environmental conditions such as wildlife ecosystems. The aim of this study was to determine whether viable LAB can be informative of the health status of wild boar populations. We monitored the genotype and phenotype of LAB based on markers that included safety and phylogenetic origin, antibacterial activity and immunomodulatory properties. A LAB profile dominated by lactobacilli appears to stimulate protective immune responses and relates to strains widely used as probiotics, resulting in a potentially healthy wildlife population whereas microbiota overpopulated by enterococci was observed in a hostile environment. These enterococci were closely related to pathogenic strains that have developed mechanisms to evade innate immune system, posing a potential risk for the host health. Furthermore, our LAB isolates displayed antibacterial properties in a species-dependent manner. Nearly all of them were able to inhibit bacterial pathogens, raising the possibility of using them as a la carte antibiotic alternative in the unexplored field of wildlife disease mitigation. Our study highlights that microbiological characterization of LAB is a useful indicator of wildlife health status and the ecological origin from which they derive. Significance Statement The wildlife symbiotic microbiota is an important component to the greater for greater diversity and functionality of their bacterial populations, influencing the host health and adaptability to its ecosystem. Although many microbes are partly responsible for the development of multiple physiological processes, only certain bacterial groups such as lactic acid bacteria (LAB) have the capacity to overpopulate the gut, promoting health (or disease) when specific genetic and environmental conditions are present. LAB have been exploited in many ways due to their probiotic properties, in particular lactobacilli, however their relationship with wildlife gut-associated microbiota hosts remains to be elucidated. On the other hand, it is unclear whether LAB such as enterococci, which have been associated with detrimental health effects, could lead to disease. These important questions have not been properly addressed in the field of wildlife, and therefore, should be clearly attained.

The Many Faces of Enterococcus spp.-Commensal, Probiotic and Opportunistic Pathogen

Enterococcus spp. are Gram-positive, facultative, anaerobic cocci, which are found in the intestinal flora and, less frequently, in the vagina or mouth. Enterococcus faecalis and Enterococcus faecium are the most common species found in humans. As commensals, enterococci colonize the digestive system and participate in the modulation of the immune system in humans and animals. For many years reference enterococcal strains have been used as probiotic food additives or have been recommended as supplements for the treatment of intestinal dysbiosis and other conditions. The use of Enterococcus strains as probiotics has recently become controversial due to the ease of acquiring different virulence factors and resistance to various classes of antibiotics. Enterococci are also seen as opportunistic pathogens. This problem is especially relevant in hospital environments, where enterococcal outbreaks often occur. Their ability to translocate from the gastro-intestinal tract to various tissues and organs as well as their virulence and antibiotic resistance are risk factors that hinder eradication. Due to numerous reports on the plasticity of the enterococcal genome and the acquisition of pathogenic microbial features, we ask ourselves, how far is this commensal genus from acquiring pathogenicity? This paper discusses both the beneficial properties of these microorganisms and the risk factors related to their evolution towards pathogenicity.

Antimicrobial Resistance of Enterococcus sp. Isolated from Sheep and Goat Cheeses

This study aimed to calculate the proportion of antibiotic resistance profiles of Enterococcus faecium, E. faecalis, and E. durans isolated from traditional sheep and goat cheeses obtained from a selected border area of Slovakia with Hungary (region Slanské vrchy). A total of 110 Enterococcus sp. were isolated from cheese samples, of which 52 strains (E. faecium (12), E. faecalis (28), E. durans (12)) were represented. After isolation and identification by polymerase chain reaction and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, the enterococci (E. faecium, E. faecalis, and E. durans) were submitted to susceptibility tests against nine antimicrobial agents. In general, strains of E. faecalis were more resistant than E. durans and E. faecium. A high percentage of resistance was noted in E. faecalis to rifampicin (100%), vancomycin (85.7%), teicoplanin (71.4%), erythromycin (71.4%), minocycline (57.1%), nitrofurantoin (57.1%), ciprofloxacin (14.3%), and levofloxacin (14.3%). E. durans showed resistance to rifampicin (100%), teicoplanin (100%), vancomycin (66.7%), erythromycin (66.7%), nitrofurantoin (66.7%), and minocycline (33.3%), and E. faecium showed resistance to vancomycin, teicoplanin, and erythromycin (100%). Multidrug-resistant strains were confirmed in 80% of the 52 strains in this study. Continuous identification of Enterococcus sp. and monitoring of their incidence and emerging antibiotic resistance is important in order to prevent a potential risk to public health caused by the contamination of milk and other dairy products, such as cheeses, made on farm level.

Cloning and sequencing of lsaE efflux pump gene from MDR Enterococci and its role in erythromycin resistance

Enterococci are opportunistic members of intestinal microbiota with notable ability to transmit antimicrobial resistance genes. Among the different resistance mechanisms, multidrug efflux is evolving as a huge problem in conferring multidrug resistance to bacterial cells because these pumps extrude a broad range of antimicrobials. Therefore, the aim of this work was to evaluate role of efflux pumps in the development of multi-drug resistance in Enterococci through studying the antimicrobial resistance profiles of Enterococci isolates, phenotypically and genotypically investigating the role of active efflux pumps in development of resistance, in addition to characterizing the most common efflux pump genes. The study involved the recovery of 149 Enterococci isolates from specimens of patients suffering infections in some hospitals in Egypt. Antimicrobial resistance profiles of isolates showed that only 1.3% of the isolates were resistant to each of linezolid, daptomycin, and fosfomycin. The highest resistance was to ampicillin (60.4%) while 47 of the isolates (31.54%) were found to be multidrug-resistant. Efflux pumps have shown to have a significant role in erythromycin resistance in 11 isolates (23.4% of MDR isolates) as indicated by an 8 or more fold decrease in minimum inhibitory concentration in the presence of the efflux pump inhibitor, carbonyl cyanide m- chlorophenylhydrazone (CCCP). End point PCR was used to detect efflux pump genes lsaE, msrC, and mefA in the 11 isolates at which efflux pumps were found to play a significant role in resistance. Nine out of the 11 isolates (81.8%) were found to carry lsaE gene. This gene was inserted into pUC21 vector and cloned into DH5α E. coli resulting in successful transformation and expression of erythromycin resistance in this host. Finally, sequencing of the lsaE gene was carried out. To the best of our knowledge, this is the first report on the cloning of lsaE gene from MDR Enterococcus isolates.

Identification and safety assessment of Enterococcus thailandicus TC1 isolated from healthy pigs

Enterococci have the dual characteristics of being opportunistic pathogens and promising probiotics. The isolation from patients of CDC PNS-E2, a newly described Enterococcus species Enterococcus sanguinicola, may pose potential hazards. Enterococcus thailandicus from fermented sausage is a senior subjective synonym of E. sanguinicola. In this study, Enterococcus thailandicus TC1 was first isolated in healthy pigs in Tongcheng, China and identified by phenotypic analysis and 16S rRNA-based techniques. To evaluate the strain safety, an approach including virulence factors, antibiotic resistance, and animal experiments was adopted. The results show that cylA, gelE, esp, agg, ace, efaAfm, efaAfs, ptsD genes were undetected, and that the strain was sensitive or poorly resistant to some clinically relevant antibiotics. However, the isolated strain demonstrated β-hemolytic activity in rabbit blood agar plates. Analysis of animal experiments revealed that the isolated strain had no adverse effect on translocation and the internal organ indices, though significant differences in histology (villi height, crypts height) of ileum were observed. The data acquired suggest that E. thailandicus TC1 may be associated with a potential health risk.

Development and Characterization of High-Throughput Caenorhabditis elegans - Enterococcus faecium Infection Model

The genus Enterococcus includes two Gram-positive pathogens of particular clinical relevance: E. faecalis and E. faecium. Infections with each of these pathogens are becoming more frequent, particularly in the case of hospital-acquired infections. Like most other bacterial species of clinical importance, antimicrobial resistance (and, specifically, multi-drug resistance) is an increasing threat, with both species considered to be of particular importance by the World Health Organization and the US Centers for Disease Control. The threat of antimicrobial resistance is exacerbated by the staggering difference in the speeds of development for the discovery and development of the antimicrobials versus resistance mechanisms. In the search for alternative strategies, modulation of host-pathogen interactions in general, and virulence inhibition in particular, have drawn substantial attention. Unfortunately, these approaches require a fairly comprehensive understanding of virulence determinants. This requirement is complicated by the fact that enterococcal infection models generally require vertebrates, making them slow, expensive, and ethically problematic, particularly when considering the thousands of animals that would be needed for the early stages of experimentation. To address this problem, we developed the first high-throughput C. elegans-E. faecium infection model involving host death. Importantly, this model recapitulates many key aspects of murine peritonitis models, including utilizing similar virulence determinants. Additionally, host death is independent of peroxide production, unlike other E. faecium-C. elegans virulence models, which allows the assessment of other virulence factors. Using this system, we analyzed a panel of lab strains with deletions of targeted virulence factors. Although removal of certain virulence factors (e.g., Δfms15) was sufficient to affect virulence, multiple deletions were generally required to affect pathogenesis, suggesting that host-pathogen interactions are multifactorial. These data were corroborated by genomic analysis of selected isolates with high and low levels of virulence. We anticipate that this platform will be useful for identifying new treatments for E. faecium infection.

Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles

As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, and rheological properties, thus contributing to the development of its typical sensorial properties. Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autolysis of other lactic acid bacteria (LAB), control pathogens and deterioration microorganisms, and may offer beneficial effects to the health of their hosts. They could in principle be employed as adjunct/protective/probiotic cultures; however, due to their propensity to acquire genetic determinants of virulence and antibiotic resistance, together with the opportunistic character of some of its members, this genus does not possess Qualified Presumption of Safety (QPS) status. It is, however, noteworthy that some putative virulence factors described in foodborne enterococci may simply reflect adaptation to the food environment and to the human host as commensal. Further research is needed to help distinguish friend from foe among enterococci, eventually enabling exploitation of the beneficial aspects of specific cheese-associated strains. This review aims at discussing both beneficial and deleterious roles played by enterococci in artisanal cheeses, while highlighting the need for further research on such a remarkably hardy genus.

In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci

Vancomycin-resistant enterococci (VRE) are a serious public health threat and a leading cause of healthcare-associated infections. Bacterial resistance to antibiotics recommended for the treatment of enterococcal infections complicates the management of these infections. Hence, there is a critical need for the discovery of new anti-VRE agents. We previously reported carbonic anhydrase inhibitors (CAIs) as new potent VRE inhibitors. In the present study, the activity of the CAI, dorzolamide was evaluated against VRE both in vitro and in vivo. Dorzolamide exhibited potent activity against a panel of clinical VRE isolates, with minimum inhibitory concentration (MIC) values ranging from 1 µg/mL to 8 µg/mL. A killing kinetics experiment determined that dorzolamide exhibited a bacteriostatic effect against VRE, which was similar to the drug of choice (linezolid). Dorzolamide interacted synergistically with gentamicin against four strains of VRE, and exhibited an additive interaction with gentamicin against six VRE strains, reducing gentamicin’s MIC by several folds. Moreover, dorzolamide outperformed linezolid in an in vivo VRE colonization reduction mouse model. Dorzolamide significantly reduced the VRE burden in fecal samples of mice by 2.9-log₁₀ (99.9%) and 3.86-log₁₀ (99.99%) after 3 and 5 days of treatment, respectively. Furthermore, dorzolamide reduced the VRE count in the cecal (1.74-log₁₀ (98.2%) reduction) and ileal contents (1.5-log₁₀ (96.3%)) of mice, which was superior to linezolid. Collectively, these results indicate that dorzolamide represents a promising treatment option that warrants consideration as a supplement to current therapeutics used for VRE infections.

In Vivo Antibacterial Activity of Acetazolamide

Vancomycin-resistant enterococci (VRE) represent a major public health threat that requires the development of new therapeutics. In the present study, acetazolamide (AZM) was evaluated against enterococci. It inhibited different enterococcal strains tested at clinically achievable concentrations. Moreover, AZM outperformed linezolid, the drug of choice for VRE infections, in two in vivo VRE mouse models-murine colonization-reduction and VRE septicemia. Collectively, these results indicate that AZM warrants consideration as a promising treatment option for VRE infections.

First characterization of Tn1546-like structures of vancomycin-resistant Enterococcus faecium Thai isolates

INTRODUCTION

Vancomycin-resistant Enterococcus faecium (VREfm) carrying vanA was first isolated from patient at Siriraj Hospital, Thailand in 2004. Since then, VREfm isolates have been detected increasingly in this 2500-bed university hospital. To understand the epidemiology of vanA VREfm in this setting, the isolates collected during 2004-2013 were characterized.

METHODS

A total of 49 vanA VREfm isolates previously confirmed by multiplex PCR were characterized by determining resistance phenotypes to vancomycin, teicoplanin, ampicillin and ciprofloxacin by broth microdilution method. Multilocus sequence typing (MLST) and virulence genes of those isolates were investigated. The Tn1546 structure diversity was studied by long-range overlapping PCR and primer walking sequencing.

RESULTS

Of all isolates studied, 9 sequence types (ST17, ST80, ST78, ST730, ST203, ST18, ST280, ST64, ST323) in clonal complex 17 and a novel ST1051 were revealed. The esp-positive isolates were 73.5%. Of all vanA operons characterized, at least 9 types of Tn1546-like structures were detected. All of vanA determinants contained 5'-end different from the Tn1546 prototype. Approximately 47% of them also carried the insertion sequence IS1251 at the intergenic region between vanS and vanH. Interestingly, another IS (ISEfa4) was found to be inside the sequence of IS1251 in ST17 isolate.

CONCLUSION

Heterogeneity of vanA VREfm was observed. Nearly all of isolates studied belonged to CC17. One novel ST1051 strain was detected. Isolates in the initial period carried vanA operon similar to the prototype. The diversity of vanA determinants has been increased in the recent isolates. A novel vanA operon structure was detected.

A systematic review and meta-analysis on the prevalence of vancomycin-resistant enterococci (VRE) among Nigerians

BACKGROUND

Enterococci are opportunistic pathogens and are one of the most important bacteria in hospital-acquired infections. Their resistance to antibiotics such as vancomycin has led to life-threatening and difficult-to-treat nosocomial infections. The true prevalence in clinical settings in Nigeria is not well known due to the lack of a comprehensive antibiotic surveillance system. This study aims to estimate the prevalence of vancomycin-resistant enterococci (VRE) in clinical infections in Nigeria.

METHODS

Databases (PubMed, African Journal Online, and Google scholar) were searched following the Preferred Reporting Items for Systematic review and meta-analysis protocols (PRISMA-P) 2015 statements for articles reporting VRE prevalence, and were published before August 5, 2020. Data from the studies were extracted and analyzed using Microsoft Excel and Comprehensive Meta-Analysis (CMA 3.0), respectively. The pooled prevalence of VRE was estimated with the random-effects model and the 95% confidence interval (CI). The heterogeneity level was assessed using Cochran Q and I 2 tests.

RESULTS

A total of 35 articles were scanned for eligibility, among which 7 were included in the study after fulfilling the eligibility criteria. The studies analyzed a total of 832 enterococci isolates and 90 VRE strains. The prevalence of Enterococcus faecium and E faecalis in this study are 361 (59.3%) and 248 (40.7%), respectively, among which 41 (63.1%) of the E faecium and 24 (36.9%) of the E faecalis were vancomycin resistant. The pooled prevalence of VRE was estimated at (95% CI; 10.0-53.9%; I 2 = 93.50%; P < .001). The highest prevalence of VRE was reported from western Nigeria, 14.6% (95% CI; I 2 = 97.27; P < .001).

CONCLUSION

The prevalence of VRE in Nigeria according to the reports from this study is relatively high. The report of this study should help policymakers to put in place measures that will help curb the spread of VRE and associated resistant genes to other important clinical pathogens like Staphylococcus aureus.

Identification of drug-resistant phenotypes and resistance genes in Enterococcus faecalis isolates from animal feces originating in Xinjiang, People’s Republic of China

This study examined the presence and the antibiotic resistance patterns of Enterococcus faecalis isolated from the feces of 285 animals. Polymerase chain reaction tests verified the presence of E. faecalis from 49 pigs, 20 cows, 174 sheep, 17 horses, 21 chickens, and four dung beetles. Bacterial strains from different animals showed differences in susceptibility and resistance to the tested antimicrobials. The isolates exhibited resistance to ampicillin (6.32%), ciprofloxacin (40.00%), nitrofurantoin (1.40%), erythromycin (54.04%), streptomycin (82.11%), tetracycline (45.26%), amoxicillin (64.91%), penicillin (92.28%), and vancomycin (0.35%). The resistant strains also possessed varying complements of resistance genes including tem (77.89%), tetM (33.68%), gyrA (37.54%), parC (34.74%), aph(3′)-III (22.46%), aac(6′)/aph2″ (10.88%), and ant(6′)-I (8.42%). Genes for vancomycin resistance (vanB and vanC) and erythromycin resistance (mefA) were not detected. These results indicate high levels of antibiotic resistance among the isolates, although no positive correlation was observed between resistance genes and antibiotic resistance spectrum.

Prevalence, antibiotic resistance and virulence of Enterococcus spp. from wastewater treatment plant effluent and receiving waters in South Africa

Poorly operating wastewater treatment plants (WWTPs) result in faecal pollution of receiving waters, posing a health risk to humans and animals. The aim of this study was to determine the antimicrobial resistance patterns and presence of virulent genes in Enterococcus spp. isolated from three WWTPs' final effluent and receiving waters in the North West Province, South Africa. Sixty-three Enterococcus spp. were identified and their antimicrobial susceptibility, as well as the presence of five virulence genes, determined. The antibiotic inhibition zone diameter data were subject to cluster analysis. Sixty-eight percent of the screened Enterococcus spp. were resistant to three or more antibiotics and harboured plasmids. Five virulence genes were detected and six multi-virulence profiles observed. Cluster analysis indicated groupings of isolates from all three effluent points downstream together, and between plants 1 and 2 together. The findings of this study have demonstrated that Enterococcus spp. harbouring virulence factors and plasmids that mediate multiple antibiotic resistance are present in effluent and receiving water systems that support various social needs. This is a cause for concern and it is recommended that Enterococcus be used as an additional faecal indicator when microbiological quality of water is assessed.

Dissemination of Linezolid Resistance Through Sex Pheromone Plasmid Transfer in Enterococcus faecalis

Despite recent recognition of the ATP-binding cassette protein OptrA as an important mediator of linezolid resistance in Enterococcus faecalis worldwide, the mechanisms of optrA gene acquisition and transfer remain poorly understood. In this study, we performed comprehensive molecular and phenotypic profiling of 44 optrA-carrying E. faecalis clinical isolates with linezolid resistance. Pulse-field gel electrophoresis and DNA hybridization revealed the presence of optrA in the plasmid in 26 (59%) isolates and in the chromosome in 18 (41%) isolates. Conjugation experiments showed a successful transfer of optrA in 88.5% (23/26) of isolates carrying optrA in plasmids while no transfer occurred in any isolates carrying optrA in the chromosome (0/18). All 23 transconjugants exhibited in vitro resistance to linezolid and several other antibiotics and were confirmed to contain optrA and other resistance genes. Plasmid typing demonstrated a predominance (18/23,78%) of rep ₉-type plasmids (pCF10 prototype) known to be the best studied sex pheromone responsive plasmids. Full plasmid genome sequencing of one isolate revealed the presence of drug resistance genes (optrA and fexA) and multiple sex pheromone response genes in the same plasmid, which represents the first sex pheromone responsive plasmid carrying optrA from a clinical isolate. PCR-based genotyping revealed the presence of three key sex pheromone response genes (prgA, prgB, and prgC) in 23 optrA-carrying isolates. Finally, functional studies of these isolates by clumping induction assay detected different degrees of clumping in 17 isolates. Our analysis suggests that optrA-mediated linezolid resistance can be widely disseminated through sex pheromone plasmid transfer.

Linezolid-resistant Enterococcus faecium strains isolated from one hospital in Poland -commensals or hospital-adapted pathogens?

One of the most pressing problems of enterococci infections is occurring resistance to linezolid, which is an antibiotic used in the treatment of infections caused by vancomycin-resistant strains (VRE). The main objective of our research was to investigate the relationship of 19 linezolid-resistant E. faecium isolates from 18 patients hospitalized at Clinical Hospital in Gdansk (Poland). One of the LZDREF was isolated in 2003 (K2003), and another 18 were collected from 2013 to 2017. Genotyping with PCR MP method indicated 14 main unrelated genetic profiles and no association with K2003 strain. Two isolates with the same genotype and genetically closely related two sub-types (2 isolates for each sub-type) were hospital-derived colonizations of patients. The other unrelated genotypes were discussed in the context of colonization, nosocomial infections, and commensal origin, taking into account prior exposure to linezolid. We determined the presence of a point mutation G2576T in six loci of 23S rDNA. There was also a significant correlation (p<0.0015) between the presence of MIC>32 value and the presence of G2576T point mutation on the sixth rrn. We also detected 5 virulence genes for all isolates: gelE, cylA, asa1, hyl, esp. Correlation (p≤0.0001) was observed between the presence of gelE gene encoding gelatinase and two other genes: cylA and asa1 encoding cytolysin and collagen binding protein responsible for aggregation of bacterial cells, respectively. Significant correlation was also observed between asa1 and cfr genes encoding 23S rRNA rybonuclease responsible for resistance to PhLOPSA antibiotics (p = 0.0004). The multidimensional analysis has also shown the correlation between cfr gene and GI-tract (p = 0, 0491), which suggests horizontal gene transfer inside the gut microbiota and the risk of colonization with linezolid-resistant strains without previously being treated with the antibiotic. The patient could have been colonized with LZDRVREF strains which in the absence of competitive microbiota quickly settle in ecological niches favourable for them and pose a risk for the patient.

A new use of Lactobacillus rhamnosus GG administration in the NICU: colonized vancomycin-resistant enterococcus eradication in the gastrointestinal system

Introduction: Enterococci are microbiota microorganisms that normally have low virulence; however, under some conditions they may cause community-acquired urinary tract and even hospital-acquired serious infections. Vancomycin-resistant enterococci (VRE) can cause aggressive infections in immunosuppressive patients; especially in newborns in intensive care units. Asymptomatic gastrointestinal system carriers are important sources of VRE. Asymptomatic patients colonized by VRE can infect both other patients and the environment. Prevention of gastrointestinal colonization of VRE is an important issue to prevent VRE infection, and for rational use of hospital source.Method: This study was carried out at Hacettepe University, Faculty of Medicine in Newborn Intensive Care Unit between November 2015 and March 2017. The newborn infants who were find as colonized by VRE during weekly surveillance VRE rectal stool culture screening were taken into the study. A single dose of one million colonies of Lactobacillus rhamnosus GG (LGG®) was given to the study group daily. The probiotic supplement continued until consecutive three negative cultures were detected or maximum 6 months. Control group received conventional treatment.Results: In the study group, VRE eradication was successful in 21 patients out of 22 within 6 months and 1 patient was still VRE positive at 6 months. In the control group, VRE was eradicated in 12 patients out of 23 and 11 patients continued to be colonized by VRE at 6 months. There was a statistically significant difference between the groups (p <.05).Conclusion: Lactobacillus rhamnosus GG use is associated with early clearance of vancomycin-resistant enterococcus in newborn patients.

A clinical approach to multidrug-resistant urinary tract infection and subclinical bacteriuria in dogs and cats

Multidrug-resistant bacteria are increasingly isolated from the urinary tract of pets, particularly those that suffer from concurrent conditions, have been hospitalised, or were treated with antimicrobials in the recent past. Many of the multidrug-resistant bacteria encountered are resistant to all commonly used oral antibiotics. This poses both a therapeutic dilemma in the individual pet and a threat to public health. This article begins with an overview of multidrug resistance in organisms that are commonly isolated from the urinary tract of pets. This is followed by a proposed clinical approach to managing multidrug-resistant urinary bacteria, which summarises current knowledge regarding appropriate sampling and analysis, reviews the current guidelines regarding appropriate antimicrobial use and discusses treatment options that might be considered. The article highlights several shortcomings of the current knowledge to be considered when planning future clinical research and developing policies.

Antivirulence activity of auranofin against vancomycin-resistant enterococci: in vitro and in vivo studies

INTRODUCTION

Vancomycin-resistant enterococci (VRE) are a leading cause of nosocomial infections because of the limited number of effective therapeutic options. In an effort to repurpose FDA-approved drugs against antibiotic-resistant bacteria, auranofin has been identified as a potent drug against VRE.

METHODS AND RESULTS

The present study determined that auranofin's antibacterial activity was not affected when evaluated against a higher inoculum size of VRE (~10⁷ CFU/mL), and auranofin successfully reduced the burden of stationary phase VRE cells via a time-kill assay. In addition, auranofin reduced VRE production of key virulence factors, including proteases, lipase and haemagglutinin. The promising features of auranofin prompted evaluation of its in vivo efficacy in a lethal mouse model of VRE septicaemia. All mice receiving auranofin at 0.125 mg/kg orally, 0.125 mg/kg subcutaneously (SC) or 0.0625 mg/kg (SC) survived the lethal VRE challenge. Additionally, auranofin was superior to linezolid, the current drug of choice, in reducing VRE burden in the liver, kidneys and spleen of mice. Remarkably, auranofin successfully reduced VRE below the limit of detection in murine internal organs after 4 days of oral or subcutaneous treatment.

CONCLUSION

These results indicate that auranofin warrants further investigation as a new treatment for systemic VRE infections.

Emerging resistance of van genotype in enterococci: A potential menace for therapeutic failure

Objectives:

Emerging cases of vancomycin-resistant enterococci (VRE) are detrimental for the patients. The current study aimed to ascertain the occurrence of VRE, their antibiogram and the van genotype responsible for vancomycin resistance.

Methods:

A total number of 2,958 clinical specimens were processed at Microbiology Department of the Alrazi Health Care, Lahore during the one year (2016-2017) using microbiological culture media, biochemical and serology. Antibiogram of enterococcal strains was performed using disc diffusion and E-test. ATCC Enterococcus faecalis 29212 was used as a quality control strain. The detection of van genotypes was accomplished by multiplex PCR assay.

Results:

Out of the 147 enterococci, 139 (94.6%) were E. faecalis, and 8 (5.4%) were E. faecium. Statistically significant associations of urine (p < 0.001), pus (p < 0.001) and wound swabs (p = 0.001) were observed with E. faecalis. A significant correlation of enterococcal infections (p = 0.05) was seen with female patients. Four (2.9%) strains of E. faecalis found to be VRE with vanB (75%) and vanA (25%) genotypes.

Conclusion:

The emerging strains of VRE (vanB and vanA genotype) in the current study are a potential menace for therapeutic failure, which left the physicians with only linezolid as a therapeutic option.

Study of vancomycin and high-level aminoglycoside-resistant Enterococcus species and evaluation of a rapid spot test for enterococci from Central Referral Hospital, Sikkim, India

BACKGROUND:

Enterococcus is an important pathogen, and with its emergence of resistance to multiple antimicrobials, the management of infection is becoming increasingly difficult.

AIM:

The aim of the study is to determine the prevalence, antibiotic resistance, and risk factors associated with enterococcal infection or colonization.

MATERIALS AND METHODS:

In this prospective study, samples from inpatients were screened for resistant enterococci. Antibiotic susceptibility testing was performed using the disc diffusion method and minimum inhibitory concentration by the agar dilution method. A modification of a test tube method of sodium chloride-esculin hydrolysis to a spot test was evaluated for its rapidity and reliability in the presumptive diagnosis of enterococci.

STATISTICAL ANALYSIS USED:

Fisher's exact test was used for continuous (Student's t-test) and categorical variables. Multivariate analysis was performed with logistic regression using IBM SPSS 20.0 software (Armonk, NY, USA).

RESULTS:

Enterococcus species were isolated from 182 samples: Enterococcus faecalis (68.7%), Enterococcus faecium (20.9%), Enterococcus gallinarum (6%), and Enterococcus durans (4.4%). Maximum resistance was to ciprofloxacin (59.3%) and least to linezolid (0.5%). The isolation rate of vancomycin-resistant enterococci (VRE) was 13.7%; 30.2% and 20.9% were of high-level gentamicin and streptomycin, respectively. All 182 Enterococcus species gave positive results within 30–60 min by the rapid spot test.

CONCLUSIONS:

Overall, high-level aminoglycoside resistance (HLAR) was observed more than glycopeptide resistance. Surveillance strategies need to be upgraded and implemented in order to prevent the emergence and further spread of not only VRE but also HLAR enterococci in the hospital. The spot test gave reliable and rapid results in presumptive identification of enterococci.

Multiplex PCR analysis of virulence genes and their influence on antibiotic resistance in Enterococcus spp. isolated from broiler chicken

Enterococcus spp. are opportunistic pathogens that cause lameness in broiler chickens, resulting in serious economic losses worldwide. Virulence of Enterococcus spp. is associated with several putative virulence genes including fsr, efm, esp, cylA, cad1, ace, gelE, and asa1. In this study, multiplex polymerase chain reaction (PCR) for the simultaneous detection of these virulence genes in Enterococcus spp. was developed, and detection limits for E. faecium, E. faecalis, and E. hirae were 64.0 pg/µL, 320.0 pg/µL, and 1.6 ng/µL DNA, respectively. Among 80 Enterococcus isolates tested, efm and cad1 were detected in all 26 E. faecium samples, and only cad1 was observed in E. hirae. Additionally, the presence of virulence genes in 25 E. faecalis isolates were 100% for cad1, 88.0% for gelE, 64.0% for fsr, 44.0% for asa1, 16.0% for cylA, and 4.0% for esp. No virulence genes were found in E. gallinarum isolates. A total of 49 isolates were resistant to tigecycline and to at least 2 different classes of antibiotics. The most prevalent resistance was to ciprofloxacin (73.5%), quinupristin/dalfopristin (55.1%), and tetracycline (49.0%). No strains were resistant to vancomycin or linezolid. This is the first multiplex PCR assay to simultaneously detect eight virulence genes in Enterococcus spp., and the method provides diagnostic value for accurate, rapid, and convenient detection of virulence genes. Additionally, we report the prevalence of virulence genes and antimicrobial resistance in Enterococcus isolates from commercial broiler chickens suffering lameness.

High-level aminoglycoside resistance and distribution of aminoglycoside resistance genes among Enterococcus spp. clinical isolates in Tehran, Iran

OBJECTIVES

Enterococci have gained attention during the past decade as important nosocomial pathogens. Their increasing prevalence has been paralleled by the occurrence of multidrug-resistant and high-level aminoglycoside-resistant strains. This study isolated Enterococcus spp. from hospital samples and determined their antibiotic resistance profile, focusing on aminoglycosides, and associated resistance mechanisms.

METHODS

A total of 195 enterococci from hospital samples in Tehran were studied. Isolates were identified by biochemical reactions. Antimicrobial resistance was determined by disk diffusion. The vancomycin MIC for vancomycin-resistant isolates was determined by agar dilution. Detection of aminoglycoside resistance genes and intI1 and intI2 gene was performed by PCR.

RESULTS

The majority of isolates were Enterococcus faecalis (65.1%), followed by Enterococcus faecium (31.8%), Enterococcus gallinarum (2.6%) and Enterococcus solitarius (0.5%). According to antibiogram results, 42.1% of isolates were high-level gentamicin-resistant (HLGR) and 40.5% were high-level streptomycin-resistant (HLSR). There was a high prevalence of aac(6')-Ie-aph(2")-Ia (96.3%) among HLGR isolates. ant(6)-Ia and aadA were identified in 93.7% and 64.6% of HLSR isolates, respectively. aph(2'')-Ic was detected in 7 isolates (3.6%) and aph(2'')-Ib in only 4 isolates (2.1%); no isolates harboured aph(2'')-Id, intI1 or intI2.

CONCLUSION

Multidrug resistance was higher among HLGR and HLSR isolates compared with non-HLGR and non-HLSR isolates, which may result in limited treatment options. More than 50% of isolates were susceptible to aminoglycosides, thus correct identification in clinical laboratories and administration of these antibiotics can result in decreased used of antibiotics such as vancomycin and linezolid and help to reduce the emergence of resistance to these drugs.