A novel putative enterococcal pathogenicity island linked to the esp virulence gene of Enterococcus faecium and associated with epidemicity

Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics

The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.

Pathogenic Potential and Antibiotic Susceptibility: A Comprehensive Study of Enterococci from Different Ecological Settings

The pathway and the lifestyle of known enterococcus species are too complicated. The aim of the present study is to trace the path of pathogenicity of enterococci isolated from seven habitats (Cornu aspersum intestine; Bulgarian yoghurt; goat and cow feta cheese-mature and young, respectively; Arabian street food-doner kebab; cow milk; and human breast milk) by comparing their pathogenic potential. In total, 72 enterococcal strains were isolated and identified by MALDI-TOF, sequencing, and PCR. Hemolytic and gelatinase activity were biochemically determined. PCR was carried out for detection of virulence factors (cylB, esp, gls24, nucl, psaA, agg, gelE, and ace) and antibiotic resistance (erm, ermB, blaZ, vanA, aphA, mefA, gyrA, catpIP501, and aac6'-aph2″). Phenotypic antibiotic resistance was assigned according to EUCAST. Eleven representatives of the genus Enterococcus were identified: E. mundtii, E. casseliflavus, E. gilvus, E. pseudoavium, E. pallens, E. malodoratus, E. devriesei, E. gallinarum, E. durans, E. faecium, and E. faecalis. Twenty-two strains expressed α-hemolysis. Thirteen strains had the cylB gene. Only two strains expressed α-hemolysis and possessed the cylB gene simultaneously. Positive amplification for gelE was found in 35% of the isolates, but phenotypic gelatinase activity was observed only in three strains. All isolates showed varying antibiotic resistance. Only E. faecalis BM15 showed multiple resistance (AMP-HLSR-RP). Correlation between genotypic and phenotypic macrolide resistance was revealed for two E. faecalis strains.

Safety evaluation of enterococci isolated from raw milk and artisanal cheeses made in Slovenia and Serbia

Enterococci represent a significant part of the non-starter LAB microbiota of artisanal cheeses produced mainly from raw milk. Common approaches to safety evaluation of enterococci isolates include assessment of antimicrobial resistance and virulence potential. Hence, a collection of 47 (n = 22, Serbia; n = 25, Slovenia) dairy enterococcal isolates, of which E. faecalis (n = 28), E. faecium (n = 11), E. durans (n = 5), E. casseliflavus (n = 2), and E. gallinarum (n = 1), was analyzed. The susceptibility to 12 antimicrobials was tested using a broth microdilution method, and the presence of the selected antimicrobial resistance and virulence genes was investigated using PCR. Isolates were resistant to tetracycline (TET) (25.5%), erythromycin (ERY) (17.0%), gentamycin and chloramphenicol (CHL) (∼6%). No resistance to ampicillin (AMP), ciprofloxacin (CIP), daptomycin (DAP), linezolid (LZD), teicoplanin (TEI), tigecycline (TGC) and vancomycin (VAN) was detected. Among all the resistance determinants analyzed, ermB gene was detected most frequently. All 10 virulence genes analyzed were detected with a distribution of cpd (72.3%), cob and ccf (70.2%), gelE (68.1%), hyl (59.6%), agg (53.2%) and esp (46.8%). The genes encoding cytolysin (cylA, cylM and cylB) were amplified to a lesser extent (21.3%, 21.3% and 12.8%, respectively). However, due to the limited number of enterococci isolates analyzed in the present study, further studies are still required in order to better document the safety status of dairy enterococci.

Strengthening of enterococcal biofilms by Esp

Multidrug-resistant (MDR) Enterococcus faecalis are major causes of hospital-acquired infections. Numerous clinical strains of E. faecalis harbor a large pathogenicity island that encodes enterococcal surface protein (Esp), which is suggested to promote biofilm production and virulence, but this remains controversial. To resolve this issue, we characterized the Esp N-terminal region, the portion implicated in biofilm production. Small angle X-ray scattering indicated that the N-terminal region had a globular head, which consisted of two DEv-Ig domains as visualized by X-ray crystallography, followed by an extended tail. The N-terminal region was not required for biofilm production but instead significantly strengthened biofilms against mechanical or degradative disruption, greatly increasing retention of Enterococcus within biofilms. Biofilm strengthening required low pH, which resulted in Esp unfolding, aggregating, and forming amyloid-like structures. The pH threshold for biofilm strengthening depended on protein stability. A truncated fragment of the first DEv-Ig domain, plausibly generated by a host protease, was the least stable and sufficient to strengthen biofilms at pH ≤ 5.0, while the entire N-terminal region and intact Esp on the enterococcal surface was more stable and required a pH ≤ 4.3. These results suggested a virulence role of Esp in strengthening enterococcal biofilms in acidic abiotic or host environments.

The bacterium Enterococcus faecalis is part of the normal microbiome but can also cause serious hospital-acquired infections. Enterococcus strains isolated from hospitals tend to have certain proteins not found in microbiome strains. Such proteins are therefore likely to be important in infection. We sought to understand the function of one such protein, Esp, through biochemical, biophysical, and microbiological techniques. We found that Esp, which is on the bacterial surface, formed amyloid-like fibrils that prevented removal of biofilms. Biofilms are bacterial communities enmeshed within a matrix, and form within the body or on inert objects like catheters. They promote infection by increasing resistance to antibiotics and interfering with clearance by the immune system. We observed that biofilms that lacked Esp could be disrupted much more easily than those that had Esp. We also found that Esp acted only at low pH (i.e., acidic conditions). Exactly how low a pH depended on whether Esp remained on the bacterial surface or was liberated from the surface by a protease, with a human intestinal protease being a likely cause of liberation. In summary, we found that Esp acts at acidic conditions and likely contributes to virulence by preventing the dispersal of biofilms.

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.

Molecular characterization and antimicrobial resistance of Enterococcus faecalis isolated from seafood samples

Background

Enterococcus faecalis is considered an opportunistic foodborne pathogen. The present study aimed to assess the prevalence, antimicrobial resistance, virulence characters, and molecular typing of E. faecalis strains isolated from seafood samples.

Methods

Two hundred and seventy‐six seafood samples were collected. E. faecalis was isolated from samples using bacterial culture. Furthermore, the disk diffusion assessed their antimicrobial resistance. Also, the distribution of virulence factors was determined using polymerase chain reaction (PCR) assay. Random amplified polymorphic DNA (RAPD) method was used for their molecular typing.

Results

Fifty‐six of 276 (20.2%) seafood samples were contaminated with E. faecalis. Fish harboured the highest contamination rate (30.0%). Isolates harboured the highest resistance rate towards oxacillin (100%), tetracycline (100%), erythromycin (100%), cefoxitin (89.2%), cefazolin (87.5%), trimethoprim‐sulfamethoxazole (85.7%), rifampin (69.6%), clindamycin (69.6%), and gentamicin (64.2%) antimicrobials. Efa (100%), ebpA (89.2%), ebpB (58.9%), ebpC (53.5%), and esp (51.7%) were the most commonly detected virulence factors among E. faecalis isolates. RAPD–PCR analysis showed 11 different molecular clusters considering the closeness of more than 80%.

Conclusion

Seafood samples were considered reservoirs of virulence and resistant E. faecalis strains. Different molecular clusters of isolates may reflect their diverse sources of contamination.

Safety assessment and probiotic characteristics of Enterococcus lactis JDM1

OBJECTIVE

The aims of this study were to evaluate the safety and probiotic characteristics of the newly isolated Enterococcus lactis strain JDM1.

METHODS

Safety assessment of E. lactis JDM1 was accomplished by the combination of whole genome sequence information analysis and phenotypic assays, including antimicrobial susceptibility test, haemolysis assay, biogenic amine production assay, cytotoxicity assay. The bacteriostatic experiment and gastrointestinal tolerance experiment were also conducted to evaluate its applicability.

RESULTS

E. lactis JDM1 possesses good gastrointestinal tolerance and can inhibit the growth of the pathogenic bacteria Clostridioides difficile and Listeria monocytogenes. The chromosome size of JDM1 was 2,570,998 bp with a GC content of 38.46%, which contained a plasmid. One intact prophage, 13 genomic islands and 19 IS elements were predicted in the JDM1 chromosome. Five resistance-related genes and seven virulence-related genes were predicted in the genome. Most resistance genes were conserved, and virulence factors were not related to functional pathogenicity. Antimicrobial susceptibility tests showed that JDM1 was sensitive to tedizolid, ciprofloxacin, levofloxacin, penicillin, ampicillin, vancomycin, linezolid, tetracycline, high-level gentamicin and high-level streptomycin. Genes encoding putative enzymes responsible for adverse metabolites were not found and JDM1 was unable to produce the six main biogenic amines. Cytotoxicity test showed that the JDM1 supernatant had no toxic effect.

CONCLUSION

E. lactis JDM1 is expected to be developed as a probiotic, and its probiotic properties are worthy of further exploration.

The changing molecular epidemiology of Enterococcus faecium harbouring the van operon at a teaching hospital in Western Australia: A fifteen-year retrospective study

INTRODUCTION

Enterococcus faecium is an opportunistic pathogen that has become one of the leading causes of hospital acquired infection that are resistant to multiple critically important antimicrobials.

AIM

The objective of the study was to describe the molecular characteristics and relationship between major strains of E. faecium harbouring the van operon and to determine if the strains had increasing virulence and antimicrobial resistance determinants over time.

METHODS

E. faecium harbouring the van operon detected using PCR from surveillance rectal swabs of patients that were admitted to high-risk units at a Perth teaching hospital from 2001 to 2015 were retrospectively analysed using a whole genome sequencing and bioinformatics approach.

RESULTS

ST18, ST78, ST80, ST173, ST203 and ST555 were identified as the major STs accounting for 93.7% of E. faecium isolates. Except for ST173, major STs identified at Royal Perth Hospital (RPH) have been reported across Australia and internationally. Isolates from each ST formed independently branched phylogenetic clusters with each harbouring unique virulence and antimicrobial resistance profiles. Depending on the ST, different genes conferring resistance to similar antimicrobial classes were identified. Except for ST80 which harboured the vanA type operon, all major strains harboured the vanB operon conferring only vancomycin resistance.

CONCLUSION

Major strains of E. faecium isolated over 15-years showed unique virulome and resistome profiles with no indication of increasing virulence or antimicrobial resistance determinants. Strains were distantly related and the acquisition of different genes encoding similar antimicrobial resistances suggest the independent evolution of each strain.

DATA SUMMARY

The whole genome sequences of all isolates from this study are accessible from the NCBI-SRA database under project number PRJNA575940 and PRJNA524213. Published reference sequence Aus0004 was obtained from NCBI-SRA under project number PRJNA86649 DOI:10.1128/JB.00259-12.

Probiotic potential and safety assessment of bacteriocinogenic Enterococcus faecium strains with antibacterial activity against Listeria and vancomycin-resistant enterococci

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Bacteriocinogenic Enterococcus faecium strains were evaluated for their beneficial and safety properties.

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Safety of the strains were evaluated based on phenotypic and bio-molecular approaches.

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The beneficial properties of the strains were demonstrated.

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High survivability under simulated GIT conditions and inhibition of Listeria spp. were demonstrated.

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The strains were found to carry genes coding for GABA production.

Enterococcus spp., known for their wide ecological distribution, have been associated with various fermented food products of plant and animal origin. The strains used in this study, bacteriocinogenic Enterococcus faecium previously isolated from artisanal soybean paste, have shown strong activity against Listeria spp. and vancomycin-resistant enterococci. Although their antimicrobial activity is considered beneficial, the potential application of enterococci is still under debate due to concerns about their safety for human and other animal consumption. Therefore, this study not only focuses on the screening of potential virulence factors, but also the auxiliary beneficial properties of the strains Ent. faecium ST651ea, ST7119ea, and ST7319ea. Phenotypic screening for gelatinase, hemolysin, and biogenic amine production showed that the strains were all safe. Furthermore, the antibiogram profiling showed that all the strains were susceptible to the panel of antibiotics used in the assessment except for erythromycin. Yet, Ent. faecium ST7319ea was found to carry some of the virulence genes used in the molecular screening for safety including hyl, esp, and IS16. The probiotic potential and other beneficial properties of the strains were also studied, demonstrating high aggregation and co-aggregation levels compared to previously characterized strains, in addition to high survivability under simulated gastrointestinal conditions, and production of numerous desirable enzymes as evaluated by APIZym, indicating diverse possible biotechnological applications of these strains. Additionally, the strains were found to carry genes coding for γ-aminobutyric acid (GABA) production, an auxiliary characteristic for their probiotic potential. Although these tests showed relatively favorable characteristics, it should be considered that these assays were carried out in vitro and should therefore also be assessed under in vivo conditions.

Enterococci from Raw-Milk Cheeses: Current Knowledge on Safety, Technological, and Probiotic Concerns

The present study is focused on the safety, technological characteristics, and probiotic evaluation of Enterococcus species from different artisanal raw milk dairy products, mainly cheeses with ripening. Apart from proteolytic and lipolytic activities, most enterococci show the ability to metabolize citrate and convert it to various aromatic compounds. Long-ripened cheeses therefore have a specific flavor that makes them different from cheeses produced from thermally treated milk with commercial starter cultures. In addition, enterococci are producers of bacteriocins effective against spoilage and pathogenic bacteria, so they can be used as food preservatives. However, the use of enterococci in the dairy industry should be approached with caution. Although originating from food, enterococci strains may carry various virulence factors and antibiotic-resistance genes and can have many adverse effects on human health. Still, despite their controversial status, the use of enterococci in the food industry is not strictly regulated since the existence of these so-called desirable and undesirable traits in enterococci is a strain-dependent characteristic. To be specific, the results of many studies showed that there are some enterococci strains that are safe for use as starter cultures or as probiotics since they do not carry virulence factors and antibiotic-resistance genes. These strains even exhibit strong health-promoting effects such as stimulation of the immune response, anti-inflammatory activity, hypocholesterolemic action, and usefulness in prevention/treatment of some diseases.

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.

Functional characterization of a gene cluster responsible for inositol catabolism associated with hospital-adapted isolates of Enterococcus faecium

Enterococcus faecium is a nosocomial, multidrug-resistant pathogen. Whole genome sequence studies revealed that hospital-associated E. faecium isolates are clustered in a separate clade A1. Here, we investigated the distribution, integration site and function of a putative iol gene cluster that encodes for myo-inositol (MI) catabolism. This iol gene cluster was found as part of an ~20 kbp genetic element (iol element), integrated in ICEEfm1 close to its integrase gene in E. faecium isolate E1679. Among 1644 E. faecium isolates, ICEEfm1 was found in 789/1227 (64.3 %) clade A1 and 3/417 (0.7 %) non-clade A1 isolates. The iol element was present at a similar integration site in 180/792 (22.7 %) ICEEfm1-containing isolates. Examination of the phylogenetic tree revealed genetically closely related isolates that differed in presence/absence of ICEEfm1 and/or iol element, suggesting either independent acquisition or loss of both elements. E. faecium iol gene cluster containing isolates E1679 and E1504 were able to grow in minimal medium with only myo-inositol as carbon source, while the iolD-deficient mutant in E1504 (E1504∆iolD) lost this ability and an iol gene cluster negative recipient strain gained this ability after acquisition of ICEEfm1 by conjugation from donor strain E1679. Gene expression profiling revealed that the iol gene cluster is only expressed in the absence of other carbon sources. In an intestinal colonization mouse model the colonization ability of E1504∆iolD mutant was not affected relative to the wild-type E1504 strain. In conclusion, we describe and functionally characterise a gene cluster involved in MI catabolism that is associated with the ICEEfm1 island in hospital-associated E. faecium isolates. We were unable to show that this gene cluster provides a competitive advantage during gut colonisation in a mouse model. Therefore, to what extent this gene cluster contributes to the spread and ecological specialisation of ICEEfm1-carrying hospital-associated isolates remains to be investigated.

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.

Molecular characterization of vancomycin-resistant Enterococcus faecium isolates from two German hospitals

Introduction: Vancomycin-resistant Enterococcusfaecium accounts for around 10–23% of nosocomial enterococcal infections and constitutes a relevant therapeutic problem due to its limited susceptibility to antibiotics. The resistance towards glycopeptide antibiotics is mediated by the so-called van genes. Currently, the most common resistance type in Germany is the vanB-type. Little data are available on the molecular epidemiology in Germany. Therefore, an epidemiological typing of Enterococcusfaecium isolates with vanB-type resistance from two German hospitals in Essen and Nuremberg was performed. Two outbreaks and 104 sporadic cases were investigated.

Methods: All 128 isolates with vanB-type resistance were collected between 2011–2012 and 2017–2018. They were characterized using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE).

Results: ST 117 was the most common sequence type (ST) in both hospitals, especially since 2017. PFGE divided the isolates of this study into 68 PFGE types and showed a broad genetic diversity. Two epidemiologically assumed in-hospital outbreaks were genetically confirmed. Apart from that, in-hospital transmissions were rare events.

Conclusion: The results obtained by MLST confirmed the previously described allocation of STs in Germany. PFGE showed a broad genetic diversity of vanB VRE between the two hospitals and also within each hospital. In-hospital transmissions were rare, but outbreaks did occur. Our data supports the strategy to screen and isolate patients in transmission events in order to detect monoclonality indicating a common source or hygiene mismanagement.

Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium

Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.

Thirty years of VRE in Germany - "expect the unexpected": The view from the National Reference Centre for Staphylococci and Enterococci

Enterococci are commensals of the intestinal tract of many animals and humans. Of the various known and still unnamed new enterococcal species, only isolates of Enterococcus faecium and Enterococcus faecalis have received increased medical and public health attention. According to textbook knowledge, the majority of infections are caused by E. faecalis. In recent decades, the number of enterococcal infections has increased, with the increase being exclusively associated with a rising number of nosocomial E. faecium infections. This increase has been accompanied by the dissemination of certain hospital-acquired strain variants and an alarming progress in the development of antibiotic resistance namely vancomycin resistance. With this review we focus on a description of the specific situation of vancomycin resistance among clinical E. faecium isolates in Germany over the past 30 years. The present review describes three VRE episodes in Germany, each of which is framed by the beginning and end of the respective decade. The first episode is specified by the first appearance of VRE in 1990 and a country-wide spread of specific vanA-type VRE strains (ST117/CT24) until the late 1990s. The second decade was initially marked by regional clusters and VRE outbreaks in hospitals in South-Western Germany in 2004 and 2005, mainly caused by vanA-type VRE of ST203. Against the background of a certain "basic level" of VRE prevalence throughout Germany, an early shift from the vanA genotype to the vanB genotype in clinical isolates already occurred at the end of the 2000s without much notice. With the beginning of the third decade in 2010, VRE rates in Germany have permanently increased, first in some federal states and soon after country-wide. Besides an increase in VRE prevalence, this decade was marked by a sharp increase in vanB-type resistance and a dominance of a few, novel strain variants like ST192 and later on ST117 (CT71, CT469) and ST80 (CT1065). The largest VRE outbreak, which involved about 2,900 patients and lasted over three years, was caused by a novel and until that time, unknown strain type of ST80/CT1013 (vanB). Across all periods, VRE outbreaks were mainly oligoclonal and strain types varied over space (hospital wards) and time. The spread of VRE strains obviously respects political borders; for instance, both vancomycin-variable enterococci which were highly prevalent in Denmark and ST796 VRE which successfully disseminated in Australia and Switzerland, were still completely absent among German hospital patients, until to date.

A three-year whole genome sequencing perspective of Enterococcus faecium sepsis in Australia

Background

Over the last three decades, hospital adapted clonal complex (CC) 17 strains of Enterococcus faecium have acquired and exchanged antimicrobial resistance genes leading to the widespread resistance to clinically important antimicrobials globally. In Australia, a high prevalence of vancomycin resistance has been reported in E. faecium in the last decade.

Methods

In this study, we determined the phylogenetic relationship and genetic characteristics of E. faecium collected from hospitalized patients with blood stream infections throughout Australia from 2015 to 2017 using high throughput molecular techniques.

Results

Using single nucleotide polymorphism based phylogenetic inference, three distinct clusters of isolates were observed with additional sub-clustering. One cluster harboured mostly non-CC17 isolates while two clusters were dominant for the vanA and vanB operons.

Conclusion

The gradual increase in dominance of the respective van operon was observed in both the vanA and vanB dominant clusters suggesting a strain-van operon affinity. The high prevalence of the van operon within isolates of a particular sub-cluster was linked to an increased number of isolates and 30-day all-cause mortality. Different dominant sub-clusters were observed in each region of Australia. Findings from this study can be used to put future surveillance data into a broader perspective including the detection of novel E. faecium strains in Australia as well as the dissemination and evolution of each strain.

Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic

Industrial farms are unique, human-created ecosystems that provide the perfect setting for the development and dissemination of antibiotic resistance. Agricultural antibiotic use amplifies naturally occurring resistance mechanisms from soil ecologies, promoting their spread and sharing with other bacteria, including those poised to become endemic within hospital environments. To better understand the role of enterococci in the movement of antibiotic resistance from farm to table to clinic, we characterized over 300 isolates of Enterococcus cultured from raw chicken meat purchased at U.S. supermarkets by the Consumers Union in 2013. Enterococcus faecalis and Enterococcus faecium were the predominant species found, and antimicrobial susceptibility testing uncovered striking levels of resistance to medically important antibiotic classes, particularly from classes approved by the FDA for use in animal production. While nearly all isolates were resistant to at least one drug, bacteria from meat labeled as raised without antibiotics had fewer resistances, particularly for E. faecium Whole-genome sequencing of 92 isolates revealed that both commensal- and clinical-isolate-like enterococcal strains were associated with chicken meat, including isolates bearing important resistance-conferring elements and virulence factors. The ability of enterococci to persist in the food system positions them as vehicles to move resistance genes from the industrial farm ecosystem into more human-proximal ecologies.IMPORTANCE Bacteria that contaminate food can serve as a conduit for moving drug resistance genes from farm to table to clinic. Our results show that chicken meat-associated isolates of Enterococcus are often multidrug resistant, closely related to pathogenic lineages, and harbor worrisome virulence factors. These drug-resistant agricultural isolates could thus represent important stepping stones in the evolution of enterococci into drug-resistant human pathogens. Although significant efforts have been made over the past few years to reduce the agricultural use of antibiotics, continued assessment of agricultural practices, including the roles of processing plants, shared breeding flocks, and probiotics as sources for resistance spread, is needed in order to slow the evolution of antibiotic resistance. Because antibiotic resistance is a global problem, global policies are needed to address this threat. Additional measures must be taken to mitigate the development and spread of antibiotic resistance elements from farms to clinics throughout the world.

The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study

Background

Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Australia, there has been a recent concerning increase in bacteraemia associated with the vanA genotype, prompting investigation into the genomic epidemiology of VREfm.

Methods

A population-level study of VREfm (10 November-9 December 2015) was conducted. A total of 321 VREfm isolates (from 286 patients) across Victoria State were collected and sequenced with Illumina NextSeq. SNPs were used to assess relatedness. STs and genes associated with resistance and virulence were identified. The vanA-harbouring plasmid from an isolate from each ST was assembled using long-read data. Illumina reads from remaining isolates were then mapped to these assemblies to identify their probable vanA-harbouring plasmid.

Results

vanA-VREfm comprised 17.8% of isolates. ST203, ST80 and a pstS(-) clade, ST1421, predominated (30.5%, 30.5% and 37.2%, respectively). Most vanB-VREfm were ST796 (77.7%). vanA-VREfm were more closely related within hospitals versus between them [core SNPs 10 (IQR 1-357) versus 356 (179-416), respectively], suggesting discrete introductions of vanA-VREfm, with subsequent intra-hospital transmission. In contrast, vanB-VREfm had similar core SNP distributions within versus between hospitals, due to widespread dissemination of ST796. Different vanA-harbouring plasmids were found across STs. With the exception of ST78 and ST796, Tn1546 transposons also varied. Phylogenetic analysis revealed Australian strains were often interspersed with those from other countries, suggesting ongoing cross-continental transmission.

Conclusions

Emerging vanA-VREfm in Australia is polyclonal, indicating repeat introductions of vanA-VREfm into hospitals and subsequent dissemination. The close relationship to global strains reinforces the need for ongoing screening and control of VREfm in Australia and abroad.

High Phenotypic and Genotypic Diversity of Enterococcus faecium from Clinical and Commensal Isolates in Third Level Hospital

Background: The use of antimicrobials and myeloablative chemotherapy regimens has promoted multiresistant microorganisms to emerge as nosocomial pathogens, such as vancomycin-resistant Enterococcus faecium (VREfm). We described a polyclonal outbreak of bloodstream infection caused by Efm in a hemato-oncological ward in Mexico. Our aim was to describe the clonal complex (CC) of the Efm strains isolated in the outbreak in comparison with commensal and environmental isolates. Methodology: Sixty Efm clinical, environmental, and commensal strains were included. We constructed a cladogram and a phylogenetic tree using Vitek and Multilocus sequence typing data, respectively. Results: We reported 20 new sequence types (ST), among which 17/43 clinical isolates belonged to CC17. The predominant ST in the clinical strains were ST757, ST1304, ST412, and ST770. Neither environmental nor commensal isolates belonged to CC17. The phylogeny of our collection shows that the majority of the clinical isolates were different from the environmental and commensal isolates, and only a small group of clinical isolates was closely related with environmental and commensal isolates. The cladogram revealed a similar segregation to that of the phylogeny. Conclusions: We found a high diversity among clinical, environmental, and commensal strains in a group of samples in a single hospital. Highest diversity was found between commensal and environmental isolates.

Biofilm formation capacity and presence of virulence factors among commensal Enterococcus spp. from wild birds

Enterococci are opportunistic pathogens that can form biofilms during infections and many virulence determinants are involved in this process. Although the virulence factors are often analysed in Enterococcus spp. from humans and food animals, little is known about gut enterococcal isolates from wild birds. Therefore, the determination of virulence factors among enterococci isolated from wild birds may provide new information about a possible source of infection for humans and animals or vice versa via the environment. We analysed different phenotypic and genotypic traits in enterococci from wild birds related to potential virulence in humans and animals and to evaluate biofilm formation and its relationship to virulence genes. The E. faecalis isolates were characterised by greater frequency of biofilm formation in BHI than E. faecium. There was a correlation between hydrophobicity and biofilm formation in BHI broth in E. faecalis. None of the isolates was haemolytic. The presence of some adhesion and gelatinase genes was detected in biofilm-positive isolates. The enterococcal pathogenic factors (esp, hyl, and cyl operon genes) did not seem to be necessary or sufficient for production of biofilm by analysed bacteria. Enterococcus species isolated from wild birds should be considered as a possible source of some virulence determinants.

Pathogenicity of Enterococci

Enterococci are unusually well adapted for survival and persistence in a variety of adverse environments, including on inanimate surfaces in the hospital environment and at sites of infection. This intrinsic ruggedness undoubtedly played a role in providing opportunities for enterococci to interact with other overtly drug-resistant microbes and acquire additional resistances on mobile elements. The rapid rise of antimicrobial resistance among hospital-adapted enterococci has rendered hospital-acquired infections a leading therapeutic challenge. With about a quarter of a genome of additional DNA conveyed by mobile elements, there are undoubtedly many more properties that have been acquired that help enterococci persist and spread in the hospital setting and cause diseases that have yet to be defined. Much remains to be learned about these ancient and rugged microbes, particularly in the area of pathogenic mechanisms involved with human diseases.

Antimicrobial Resistance, Virulence Determinants, and Biofilm Formation of Enterococcus Species From Ready-to-Eat Seafood

Enterococcus species form an important population of commensal bacteria and have been reported to possess numerous virulence factors considered significantly important in exacerbating diseases caused by them. The present study was designed to characterize antibiotic-resistant and virulent enterococci from ready-to-eat (RTE) seafood. A total of 720 RTE shrimp samples comprising sauced shrimp (n = 288), boiled shrimp (n = 216), and smoked shrimp (n = 216) obtained from open markets in Delta State, Nigeria, were assessed. Standard classical methods and polymerase chain reaction (PCR) were used in identifying the Enterococcus species. Potential virulence factors (β-hemolysis, gelatinase activity, S-layer, and biofilm formation) were assessed using standard procedures. The antibiotic susceptibility profile of the identified enterococci isolates was assayed using the Kirby–Bauer disc diffusion method. PCR was further used to screen selected antibiotic resistance and virulence genes. Prevalence of Enterococcus species from shrimp varieties is as follows: sauced, 26 (9.03%); boiled, 6 (2.78%); and smoked, 27 (12.50%), with an overall prevalence of 59 (8.19%) based on the occurrence of black hallow colonies after incubation. Enterococcus species detected include E. faecalis, 17 (28.8%); E. faecium, 29 (49.2%); E. gallinarum, 6 (10.2%); E. casseliflavus, 2 (3.4%); E. hirae, 3 (5.1%); and E. durans, 2 (3.4%). Biofilm occurrence among the shrimp varieties is as follows: 19/26 (73.1%) for sauced shrimps, 5/6 (83.3%) for boiled shrimps, and 16/27 (59.3%) for smoked shrimps. The phenotypic expression of the enterococci virulence revealed the following: S-layer, 59 (100%); gelatinase production, 19 (32.2%); and β-hemolysis, 21 (35.6%). An average of 3–11 virulence genes were detected in the Enterococcus species. The resistance profile of Enterococcus species is as follows: erythromycin, 29 (49.2%); vancomycin, 22 (37.3%); and tetracycline, 27 (45.8%). The frequency of occurrence of antibiotic resistance genes from the phenotypic resistant enterococci isolates to the macrolide, glycopeptide, and tetracycline antibiotics is as follows: ermA, 13/29 (44.8%); vanA, 14/22 (63.6%); tetA, 14/27 (51.9%); tetM, 15/27 (55.6%); ermB, 4/29 (13.8%); and vanB, 5/22 (22.7%). Findings from this study reveal the antibiotic resistance of enterococci strains of such species as E. durans, E. casseliflavus, E. gallinarum, and E. hirae. This study further revealed that RTE food products are reservoirs of potential virulent enterococci with antibiotic-resistant capabilities. This provides useful data for risk assessment and indicates that these foods may present a potential public health risk to consumers.

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of healthcare-associated infection. Reservoirs of VREfm are largely assumed to be nosocomial although there is a paucity of data on alternative sources. Here, we describe an integrated epidemiological and genomic analysis of E. faecium associated with bloodstream infection and isolated from wastewater. Treated and untreated wastewater from 20 municipal treatment plants in the East of England, United Kingdom was obtained and cultured to isolate E. faecium, ampicillin-resistant E. faecium (AREfm), and VREfm. VREfm was isolated from all 20 treatment plants and was released into the environment by 17/20 plants, the exceptions using terminal ultraviolet light disinfection. Median log₁₀ counts of AREfm and VREfm in untreated wastewater from 10 plants in direct receipt of hospital sewage were significantly higher than 10 plants that were not. We sequenced and compared the genomes of 423 isolates from wastewater with 187 isolates associated with bloodstream infection at five hospitals in the East of England. Among 481 E. faecium isolates belonging to the hospital-adapted clade, we observed genetic intermixing between wastewater and bloodstream infection, with highly related isolates shared between a major teaching hospital in the East of England and 9/20 plants. We detected 28 antibiotic resistance genes in the hospital-adapted clade, of which 23 were represented in bloodstream, hospital sewage, and municipal wastewater isolates. We conclude that our findings are consistent with widespread distribution of hospital-adapted VREfm beyond acute healthcare settings with extensive release of VREfm into the environment in the East of England.

Antimicrobial-resistant CC17 Enterococcus faecium: The past, the present and the future

Enterococcus faecium is a robust opportunistic pathogen that is most commonly found as a commensal of the human and animal gut but can also survive in the environment. Since the introduction and use of antimicrobials, E. faecium has been found to rapidly acquire resistance genes that, when expressed, can effectively circumvent the effects of most antimicrobials. The rapid acquisition of multiple antimicrobial resistances has led to the adaptation of specific E. faecium clones in the hospital environment, collectively known as clonal complex 17 (CC17). CC17 E. faecium are responsible for a significant proportion of hospital-associated infections, which can cause severe morbidity and mortality. Here we review the history of E. faecium from commensal to a significant hospital-associated pathogen, its robust phenotypic characteristics, commonly used laboratory typing schemes, and antimicrobial resistances with a focus on vancomycin and its associated mechanism of resistance. Finally, we review the global epidemiology of vancomycin-resistant E. faecium and potential solutions to problems faced in public health.

Characterization of Clinical Vancomycin-Resistant Enterococcus faecium Isolated in Eastern Hungary

OBJECTIVES

The aim of our study was to characterize and elicit the genetic relatedness of emerging vancomycin-resistant enterococci (VRE) isolated between 2012 and 2015 at a teaching hospital in Debrecen, Hungary.

RESULTS

Altogether 43 nonduplicate vancomycin-resistant Enterococcus faecium (VREfm) clinical isolates were obtained. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used for species identification. Isolates showed 100% resistance to ampicillin and ciprofloxacin while 81.4% were resistant to gentamicin. PCR analysis revealed the presence of VanB in 40 and VanA in 3 isolates. Among ace, agg, and esp virulence genes only esp was found in seven cases. Modified microtiter-plate test showed 13 weak and 4 moderate biofilm producer isolates. Pulsed-field gel electrophoresis revealed nine pulsotypes. According to multilocus sequence typing all of the tested isolates belonged to clonal complex 17 (CC17).

CONCLUSIONS

We report on the alarming emergence of multidrug-resistant VREfm belonging to CC17 at a tertiary hospital in Eastern Hungary. This is the first report of sequence types 412 and 364 from this region. Although outbreak did not occur the increasing prevalence of VREfm is of concern and dissemination must be prevented with proper infection control measures and regular VRE screening.

The Alpha-Like Surface Proteins: An Example of an Expanding Family of Adhesins

The Alpha-like protein (Alp) family, repeat-containing surface proteins once thought to be important adhesion factors confined to pathogenic streptococci and enterococci, is broader than previously known. Analysis of the annotated microbial genomes has identified new potential members of the Alp family not only in other Gram- positive opportunistic pathogens but also in commensal microflora of the human gut and the skin. This finding has highlighted the importance of genome sequencing projects for unraveling in greater detail lateral gene transfer events involving virulence factors between pathogens and commensals. These should receive constant attention not only as part of infectious disease prevention programs, but also in the food and biotechnology industries. (Int J Artif Organs 2008; 31: 834–40)

Small RNAs in vancomycin-resistant Enterococcus faecium involved in daptomycin response and resistance

Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and outbreaks. Regulatory RNAs (sRNAs) are major players in adaptive responses, including antibiotic resistance. They were extensively studied in gram-negative bacteria, but less information is available for gram-positive pathogens. No sRNAs are described in E. faecium. We sought to identify a set of sRNAs expressed in vancomycin-resistant E. faecium Aus0004 strain to assess their roles in daptomycin response and resistance. Genomic and transcriptomic analyses revealed a set of 61 sRNA candidates, including 10 that were further tested and validated by Northern and qPCR. RNA-seq was performed with and without subinhibitory concentrations (SICs) of daptomycin, an antibiotic used to treat enterococcal infections. After daptomycin SIC exposure, the expression of 260 coding and srna genes was altered, with 80 upregulated and 180 downregulated, including 51% involved in carbohydrate and transport metabolisms. Daptomycin SIC exposure significantly affected the expression of seven sRNAs, including one experimentally confirmed, sRNA_0160. We studied sRNA expression in isogenic mutants with increasing levels of daptomycin resistance and observed that expression of several sRNAs, including sRNA_0160, was modified in the stepwise mutants. This first genome-wide sRNA identification in E. faecium suggests that some sRNAs are linked to antibiotic stress response and resistance.

Virulence and Antibiotic Resistance of Enterococci Isolated from Healthy Breastfed Infants

Pathogenic ability has been extensively studied in clinical enterococci, but to a lesser extent in community-derived ones. Most studies to date in enterococci from healthy infants have been focused on Enterococcus faecalis, despite the growing concern about nosocomial infections caused by E. faecium. In this work, we studied the antibiotic resistance and virulence determinants of 26 E. faecalis and 15 E. faecium intestinal isolates from Spanish healthy breastfed infants. Overall, commensal enterococci studied contained antibiotic resistance and virulence genes, although their patterns were not according to those described for antibiotic-resistant hospital-associated enterococci. None of the isolates was resistant to vancomycin, although the majority showed resistance to some antibiotics. E. faecalis isolates harbored considerably more virulence determinants than E. faecium isolates, but some genes linked to colonization were abundant in both species. Hemolysin activity was not detected in any of the isolates; and the gelatinase gene, when present, was silent in E. faecium, whereas gelatinase activity occurred in half of the E. faecalis isolates studied. These results suggest an ambivalent role of some virulence determinants as elements of pathogenesis.

Molecular characterization of vancomycin-resistant Enterococcus faecium isolates from Bermuda

Molecular characteristics of vancomycin resistant enterococci isolates from Bermuda Island is currently unknown. This study was conducted to investigate phenotypic and genotypic characteristics of VRE isolates from Bermuda Island using the chromogenic agar, E-tests, polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Eighteen E. faecium isolates were completely analyzed and were all resistant to vancomycin, susceptible to linezolid and quinupristin/dalfopristin, positive for vanA and esp genes. The MLST analysis confirmed most isolates were of the sequence types linked to clonal complex 17 (CC17) that is widely associated with outbreaks in hospitals. Infection control measures, antibiotic stewardship, and surveillance activities will continue to be a priority in hospital on the Island.

Draft Genome Sequence of an Attenuated Streptococcus agalactiae Strain Isolated from the Gut of a Nile Tilapia (Oreochromis niloticus)

Streptococcus agalactiae is a pathogen that causes severe anthropozoonosis within a broad range of hosts from aquatic animals to mammals, including human beings. Here, we describe the draft genome of S. agalactiae HZAUSC001, a low-virulent strain isolated from the gut of a moribund tilapia (Oreochromis niloticus) in China.

Molecular Characterization of Vancomycin-Resistant Enterococci from Clinical and Surveillance Specimens

Objective:

To compare the molecular characteristics of infection-derived (ID) isolates and intestinal colonization–derived (ICD) isolates of vancomycin-resistant enterococci (VRE) recovered from hospitalized patients.

Design.

A 12-month prospective cohort study.

Setting.

A 1,000-bed teaching facility.

Methods.

From January through December 2004, a total of 30 pairs ofvanA-containing enterococcal isolates were collected from patients admitted to a teaching hospital in South Korea. Each pair comprised an ID and an ICD VRE isolate from the same patient. All VRE isolates were investigated on the basis ofSmaI-restricted pulsed-field gel electrophoresis (PFGE) pattern, Tn1546type, and presence of theespgene, including A and C repeat number variation.

Results.

Members of 19 pairs (63%) of VRE isolates were genetically indistinguishable from each other. The 11 patients for whom the molecular characteristics of the ID isolates differed from those of the ICD isolates had longer durations of hospitalization and intensive care unit (ICU) stay, compared with the other 19 patients.

Conclusions.

These findings suggest the longer durations of hospitalization and ICU stay may be possible risk factors for colonization with multiple clones of VRE.

Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?

Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis.

Virulence determinants and production of extracellular enzymes in Enterococcus spp. from surface water sources

Virulence factors in Enterococcus may be indicative of potential pathogenicity. The aim of this study was to determine the relationship between the presence of clinically relevant virulence genes, in Enterococcus spp. from environmental water, and their in vitro expression. One hundred and twenty-four Enterococcus isolates (seven species), from five surface water systems in the North West Province, South Africa, were screened for the presence of asa1, cylA, esp, gelE and hyl using polymerase chain reaction. The expression of cylA, hyl and gelE was determined by phenotypic assessments. Sixty-five percent of the isolates were positive for one virulence gene and 13% for two or more. Most frequently detected genes were gelE (32%) and cylA (28%). Enterococcal surface protein was absent in all isolates screened. The presence of virulence genes was correlated with their extracellular enzyme production. The results show that a large percentage of these environmental Enterococcus spp. possess virulence factors that could be expressed in vitro. This is a cause for concern and could have implications for individuals using this water for recreational and cultural purposes. Further investigation is required into the sources of these potential pathogenic Enterococcus isolates and measures to minimize their presence in water sources.

Molecular Analysis of Vancomycin-Resistant Enterococci Isolated from Regional Hospitals in Trinidad and Tobago

Geographic spread of vancomycin-resistant enterococci (VRE) clones in cities, countries, or even continents has been identified by molecular techniques. This study aimed at characterizing virulent genes and determining genetic relatedness of 45 VRE isolates from Trinidad and Tobago using molecular tools, including polymerase chain reaction, pulsed-field gel electrophoresis (PFGE), and Random Amplification Polymorphic DNA (RAPD). The majority (84%) of the isolates were Enterococcus faecium possessing vanA gene while the rest (16%) were Enterococcus faecalis possessing vanB. The esp gene was found in all 45 VRE isolates while hyl genes were found only in E. faecium species. The E. faecium species expressed five distinct PFGE patterns. The predominant clones with similar or common patterns belonged to clones one and three, and each had 11 (29%) of the VRE isolates. Plasmid content was identified in representative isolates from each clonal group. By contrast, the E. faecalis species had one PFGE pattern suggesting the presence of an occult and limited clonal spread. The emergence of VRE in the country seems to be related to intra/interhospital dissemination of an epidemic clone carrying the vanA element. Therefore, infection control measures will be warranted to prevent any potential outbreak and spread of VRE in the country.

Surface protein Esp enhances pro-inflammatory cytokine expression through NF-κB activation during enterococcal infection

Enterococcal surface protein (Esp) is encoded on a pathogenicity island in Enterococcus faecalis and E. faecium and is involved in biofilm formation and binding to epithelial cells. In this study, using Esp-expressing E. faecalis MMH594 and its isogenic Esp-deficient strain, as well as purified Esp, we show that Esp is sufficient for activation of NF-κB and the subsequent production of pro-inflammatory cytokines IL-1β and TNF-α in macrophages in vitro. In a mouse peritonitis model, we also show that mice infected with Esp-expressing E. faecalis showed comparatively higher levels of cytokines TNF-α, IL-1β and IL-6 in peritoneal fluid, and IL-6 in serum. Moreover, neutrophil infiltration and tissue damage in the liver was higher in the mice infected with the Esp-expressing strain compared with mice infected with the Esp-deficient mutant. These results add Esp to the growing list of enterococcal virulence factors that can modulate inflammation during infection and has implications for enterococcal pathogenesis.

A multicentre hospital outbreak in Sweden caused by introduction of a vanB2 transposon into a stably maintained pRUM-plasmid in an Enterococcus faecium ST192 clone

The clonal dissemination of VanB-type vancomycin-resistant Enterococcus faecium (VREfm) strains in three Swedish hospitals between 2007 and 2011 prompted further analysis to reveal the possible origin and molecular characteristics of the outbreak strain. A representative subset of VREfm isolates (n = 18) and vancomycin-susceptible E. faecium (VSEfm, n = 2) reflecting the spread in time and location was approached by an array of methods including: selective whole genome sequencing (WGS; n = 3), multi locus sequence typing (MLST), antimicrobial susceptibility testing, virulence gene profiling, identification of mobile genetic elements conferring glycopeptide resistance and their ability to support glycopeptide resistance transfer. In addition, a single VREfm strain with an unrelated PFGE pattern collected prior to the outbreak was examined by WGS. MLST revealed a predominance of ST192, belonging to a hospital adapted high-risk lineage harbouring several known virulence determinants (n≥10). The VREfm outbreak strain was resistant to ampicillin, gentamicin, ciprofloxacin and vancomycin, and susceptible to teicoplanin. Consistently, a vanB2-subtype as part of Tn1549/Tn5382 with a unique genetic signature was identified in the VREfm outbreak strains. Moreover, Southern blot hybridisation analyses of PFGE separated S1 nuclease-restricted total DNAs and filter mating experiments showed that vanB2-Tn1549/Tn5382 was located in a 70-kb sized rep17/pRUM plasmid readily transferable between E. faecium. This plasmid contained an axe-txe toxin-antitoxin module associated with stable maintenance. The two clonally related VSEfm harboured a 40 kb rep17/pRUM plasmid absent of the 30 kb vanB2-Tn1549/Tn5382 gene complex. Otherwise, these two isolates were similar to the VREfm outbreak strain in virulence- and resistance profile. In conclusion, our observations support that the origin of the multicentre outbreak was caused by an introduction of vanB2-Tn1549/Tn5382 into a rep17/pRUM plasmid harboured in a pre-existing high-risk E. faecium ST192 clone. The subsequent dissemination of VREfm to other centres was primarily caused by clonal spread rather than plasmid transfer to pre-existing high-risk clones.

Environmental and animal-associated enterococci

Enterococci are generally commensal bacteria inhabiting the gastrointestinal tract of humans and animals. They have, however, been implicated as the etiological agent of a variety of illnesses and nosocomial infections. In addition to pathogenic potential, there is growing concern regarding the incidence of antibiotic resistance and genetic exchange among Enterococcus spp. within and among a variety of animal hosts. While primarily considered an enteric group, extra-enteric habitats in which enterococci persist and potentially grow have been studied for decades. Although many biotic (e.g., predation) and abiotic (e.g., sunlight, nutrients, and salinity) stressors have been thought to limit the success of enterococci in these secondary habitats, a growing body of evidence suggests that certain strains may become naturalized to environmental habitats. Enterococci have also been used for decades as indicators of fecal contamination in recreational waters where increased concentrations of this group have been linked to the incidence of illness in humans following recreational use of these waters. Persistence of enterococci in secondary habitats, however, suggests that their presence in ambient waters may prove to be a poor indicator of actual risks to public health. In this chapter, we provide a review of the existing body of literature concerning animal host associations, genetic exchange is reviewed, and emphasis is placed on the growing body of evidence for the persistence and growth of enterococci in secondary habitats.

Friend turned foe: evolution of enterococcal virulence and antibiotic resistance

The enterococci are an ancient genus that evolved along with the tree of life. These intrinsically rugged bacteria are highly adapted members of the intestinal consortia of a range of hosts that spans the animal kingdom. Enterococci are also leading opportunistic hospital pathogens, causing infections that are often resistant to treatment with most antibiotics. Despite the importance of enterococci as hospital pathogens, the vast majority live outside of humans, and nearly all of their evolutionary history took place before the appearance of modern humans. Because hospital infections represent evolutionary end points, traits that exacerbate human infection are unlikely to have evolved for that purpose. However, clusters of traits have converged in specific lineages that are well adapted to colonize the antibiotic-perturbed gastrointestinal tracts of patients and that thrive in the hospital environment. Here we discuss these traits in an evolutionary context, as well as how comparative genomics is providing new insights into the evolution of the enterococci.

Biofilm formation, gel and esp gene carriage among recreational beach Enterococci

Biofilm production, gel and esp gene carriage was enumerated among forty six vancomycin resistant enterococci (VRE) and vancomycin susceptible enterococci (VSE) beach isolates. A higher proportion (61.54%) of biofilm producers was observed among beach sand as compared to beach water enterococci isolates (30%) indicating that enterococci within the sand column may be more dependent on biofilm production for survival than their beach water counterparts. Correlation analysis revealed strongly negative correlation (r=-0.535, p=0.015) between vancomycin resistance and biofilm formation. Given the observation of high prevalence of biofilm production among beach sand and the concomitant absence of esp gene carriage in any of the isolate, esp gene carriage may not be necessary for the production of biofilms among beach sand isolates. On the whole beach sand and water isolates demonstrated clearly different prevalence levels of vancomycin resistance, biofilm formation, esp and gel gene carriage. Application of these differences may be found useful in beach microbial source tracking studies. Tested starved cells still produced biofilm albeit at lower efficiencies. Non-dividing enterococci in beach sand can survive extended periods of environmental hardship and can resume growth or biofilm production in appropriate conditions thus making them infectious agents with potential health risk to recreational beach users.

The cell wall architecture of Enterococcus faecium: from resistance to pathogenesis

The cell wall of Gram-positive bacteria functions as a surface organelle that continuously interacts with its environment through a plethora of cell wall-associated molecules. Enterococcus faecium is a normal inhabitant of the GI tract of mammals, but has recently become an important etiological agent of hospital-acquired infections in debilitated patients. Insights into the assembly and function of enterococcal cell wall components and their interactions with the host during colonization and infection are essential to explain the worldwide emergence of E. faecium as an important multiantibiotic-resistant nosocomial pathogen. Understanding the biochemistry of cell wall biogenesis and principles of antibiotic resistance at the molecular level may open up new frontiers in research on enterococci, particularly for the development of novel antimicrobial strategies. In this article, we outline the current knowledge on the most important antimicrobial resistance mechanisms that involve peptidoglycan synthesis and the role of cell wall constituents, including lipoteichoic acid, wall teichoic acid, capsular polysaccharides, LPxTG cell wall-anchored surface proteins, WxL-type surface proteins and pili, in the pathogenesis of E. faecium.

Molecular analysis and distribution of multidrug-resistant Enterococcus faecium isolates belonging to clonal complex 17 in a tertiary care center in Mexico City

Background

Enterococcus faecium has recently emerged as a multidrug-resistant nosocomial pathogen involved in outbreaks worldwide. A high rate of resistance to different antibiotics has been associated with virulent clonal complex 17 isolates carrying the esp and hyl genes and the purK1 allele.

Results

Twelve clinical vancomycin-resistant Enterococcus faecium (VREF) isolates were obtained from pediatric patients at the Hospital Infantil de México Federico Gómez (HIMFG). Among these VREF isolates, 58.3% (7/12) were recovered from urine, while 41.7% (5/12) were recovered from the bloodstream. The VREF isolates showed a 100% rate of resistance to ampicillin, amoxicillin-clavulanate, ciprofloxacin, clindamycin, chloramphenicol, streptomycin, gentamicin, rifampicin, erythromycin and teicoplanin. In addition, 16.7% (2/12) of the isolates were resistant to linezolid, and 66.7% (8/12) were resistant to tetracycline and doxycycline. PCR analysis revealed the presence of the vanA gene in all 12 VREF isolates, esp in 83.3% (10/12) of the isolates and hyl in 50% (6/12) of the isolates. Phylogenetic analysis via molecular typing was performed using pulsed-field gel electrophoresis (PFGE) and demonstrated 44% similarity among the VREF isolates. MLST analysis identified four different sequence types (ST412, ST757, ST203 and ST612).

Conclusion

This study provides the first report of multidrug-resistant VREF isolates belonging to clonal complex 17 from a tertiary care center in Mexico City. Multidrug resistance and genetic determinants of virulence confer advantages among VREF in the colonization of their host. Therefore, the prevention and control of the spread of nosocomial infections caused by VREF is crucial for identifying new emergent subclones that could be challenging to treat in subsequent years.

Nonclinical and clinical Enterococcus faecium strains, but not Enterococcus faecalis strains, have distinct structural and functional genomic features

Certain strains of Enterococcus faecium and Enterococcus faecalis contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31 E. faecium and 38 E. faecalis strains. Hierarchical clustering of 7,017 orthologs found in the E. faecium pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC E. faecium genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes. E. faecium ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CL-enriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL E. faecium genomes. In contrast, differences were not observed between NC and CL E. faecalis genomes despite their having larger genomes than E. faecium. Our findings show that unlike E. faecalis, NC and CL E. faecium strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments.