A clonal lineage of VanA-type Enterococcus faecalis predominates in vancomycin-resistant Enterococci isolated in New Zealand

High Incidence of Multiple-Drug-Resistant Pheromone-Responsive Plasmids and Transmissions of VanA-Type Vancomycin-Resistant Enterococcus faecalis between Livestock and Humans in Taiwan

A total of seventy VanA-type vancomycin-resistant enterococci (VRE) isolates obtained in Taiwan in the early 2000s were retrospectively characterized. Forty isolates were obtained from human patients and thirty from livestock. Of these VRE isolates, twenty-three (57.5%) of the human VRE and thirty (100%) of the livestock VRE were Enterococcus faecalis, and the remaining seventeen (42.5%) of the human VRE were E. faecium. Of the 53 E. faecalis isolates, twenty-two (96%) of the human VRE and thirty (100%) of the livestock VRE exhibited a high level of resistance to vancomycin and sensitivity to teicoplanin. They also had three amino acid substitutions in the N-terminal region of the deduced VanS sequence. The vancomycin resistance of all of the 22 human isolates, and 20 of the 30 livestock isolates, transferred to E. faecalis FA2-2 at a frequency of 10-5 to 10-3 per donor cell in broth. Each of the transconjugants responded to E. faecalis pheromone (i.e., E. faecalis FA2-2 culture filtrate), indicating that the conjugative plasmids were pheromone-responsive plasmids. Three of the conjugative plasmids originated from human isolates, and five plasmids from livestock isolates were corresponded and classified as type A plasmid. Two plasmids originated from human isolates and six plasmids from livestock isolates were corresponded and classified as type B plasmid. E. faecalis FA2-2 containing either the type A or type B plasmid responded to the synthetic pheromone cAD1. The type A and type B plasmids transferred between E. faecalis FA2-2 and JH2SS at a frequency of about 10-2 per donor cell and conferred vancomycin, bacitracin, and erythromycin resistances. The complete DNA sequence of the representative type A plasmid pTW9 (85,068 bp) showed that the plasmid carried a Tn1546-like element encoding vanA-type resistance, erythromycin resistance (ermB), and bacitracin resistance (bcrABDR). The plasmid contained the regulatory region found in the pheromone-responsive plasmid and encoded the genes traA, traD and iad1, which are the key negative regulatory elements, and traE1, a key positive regulator of plasmid pAD1, indicating that plasmid pTW9 was pAD1-type pheromone-responsive plasmid. PFGE analysis of SmaI-digested chromosomal DNAs showed that several E. faecalis strains harboring an identical type A pheromone-responsive plasmid were indistinguishable, and that these were identified both in human and livestock isolates, indicating the transmissions of the VRE strains between livestock and humans. These data showed that the multiple-drug-resistant pheromone-responsive conjugative plasmids have been widely spread in both human and livestock VRE, and there was high potential for transfers of VRE from food animals to humans in Taiwan in the early 2000s.

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 streptococcal 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 (Glc2-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.

Enterococcus faecalis Strains with Compromised CRISPR-Cas Defense Emerge under Antibiotic Selection for a CRISPR-Targeted Plasmid

Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged that are replete with mobile genetic elements (MGEs). Non-MDR E. faecalis strains frequently possess CRISPR-Cas systems, which reduce the frequency of MGE acquisition. We demonstrated in previous studies that E. faecalis populations can transiently maintain both a functional CRISPR-Cas system and a CRISPR-Cas target. In this study, we used serial passage and deep sequencing to analyze these populations. In the presence of antibiotic selection for the plasmid, mutants with compromised CRISPR-Cas defense and enhanced ability to acquire a second antibiotic resistance plasmid emerged. Conversely, in the absence of selection, the plasmid was lost from wild-type E. faecalis populations but not E. faecalis populations that lacked the cas9 gene. Our results indicate that E. faecalis CRISPR-Cas can become compromised under antibiotic selection, generating populations with enhanced abilities to undergo horizontal gene transfer. IMPORTANCE Enterococcus faecalis is a leading cause of hospital-acquired infections and disseminator of antibiotic resistance plasmids among Gram-positive bacteria. We have previously shown that E. faecalis strains with an active CRISPR-Cas system can prevent plasmid acquisition and thus limit the transmission of antibiotic resistance determinants. However, CRISPR-Cas is not a perfect barrier. In this study, we observed populations of E. faecalis with transient coexistence of CRISPR-Cas and one of its plasmid targets. Our experimental data demonstrate that antibiotic selection results in compromised E. faecalis CRISPR-Cas function, thereby facilitating the acquisition of additional resistance plasmids by E. faecalis.

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

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

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis

The human microbiota harbors diverse bacterial and bacteriophage (phage) communities. Bacteria evolve to overcome phage infection, thereby driving phage evolution to counter bacterial resistance. Understanding how phages select for genetic alterations in medically relevant bacteria is important as phages become established biologics for the treatment of multidrug‐resistant (MDR) bacterial infections. Before phages can be widely used as standalone or combination antibacterial therapies, we must obtain a deep understanding of the molecular mechanisms of phage infection and how host bacteria alter their genomes to become resistant. We performed coevolution experiments using a single Enterococcus faecalis strain and two distantly related phages to determine how phage pressure impacts the evolution of the E. faecalis genome. Whole‐genome sequencing of E. faecalis following continuous exposure to these two phages revealed mutations previously demonstrated to be essential for phage infection. We also identified mutations in genes previously unreported to be associated with phage infection in E. faecalis. Intriguingly, there was only one shared mutation in the E. faecalis genome that was selected by both phages tested, demonstrating that infection by two genetically distinct phages selects for diverse variants. This knowledge serves as the basis for the continued study of E. faecalis genome evolution during phage infection and can be used to inform the design of future therapeutics, such as phage cocktails, intended to target MDR E. faecalis.

Environmental antibiotics and resistance genes as emerging contaminants: Methods of detection and bioremediation

In developing countries, the use of antibiotics has helped to reduce the mortality rate by minimizing the deaths caused by pathogenic infections, but the costs of antibiotic contamination remain a major concern. Antibiotics are released into the environment, creating a complicated environmental problem. Antibiotics are used in human, livestock and agriculture, contributing to its escalation in the environment. Environmental antibiotics pose a range of risks and have significant effects on human and animal health. Nevertheless, this is the result of the development of antibiotic-resistant and multi-drug-resistant bacteria. In the area of health care, animal husbandry and crop processing, the imprudent use of antibiotic drugs produces antibiotic-resistant bacteria. This threat is the deepest in the developing world, with an estimated 700,000 people suffering from antibiotic-resistant infections each year. The study explores how bacteria use a wide variety of antibiotic resistance mechanism and how these approaches have an impact on the environment and on our health. The paper focuses on the processes by which antibiotics degrade, the health effects of these emerging contaminants, and the tolerance of bacteria to antibiotics.

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.

Molecular Characteristics of Enterococcus faecalis and Enterococcus faecium from Bulk Tank Milk in Korea

Simple Summary

Enterococci can be an opportunistic pathogen in milk, which can easily disseminate antimicrobial resistance and virulence genes. The purpose of this study was to characterize and compare the enterococci isolates from samples of bulk tank milk obtained from four dairy companies in Korea to prevent the spread of pathogenic and antimicrobial-resistant enterococci in dairy companies. The results demonstrated various degrees of antimicrobial resistance and virulence-factor distribution in enterococci from bulk tank milk in Korea and support the assessment that pathogens from bulk tank milk can also become a reservoir for dissemination of antimicrobial resistance and virulence factors through cross-contamination processes.

Abstract

Enterococci are considered to be environmental mastitis-causing pathogens that can easily spread antimicrobial resistance or virulence genes via horizontal transfer. In this study, the molecular characteristics of enterococci from bulk tank milk were investigated to assess the importance of dairy herd management. A total of 338 enterococci (305 Enterococcus faecalis and 33 Enterococcus faecium) were isolated from 1584 batches of bulk tank milk samples from 396 farms affiliated with four dairy companies in Korea, and significant differences (40.6–79.7%) (p < 0.05) in the prevalence of enterococci were observed in the samples from different companies. Enterococci showed the highest resistance to tetracycline (TET) (73.4%), followed by doxycycline (DOX) (49.7%) and erythromycin (ERY) (46.2%), while two enterococci isolates showed resistance to vancomycin (VAN). Among 146 tetracycline (TET) and ERY-resistant enterococci, each 50 (19.4%) enterococci carried combination-resistance and transposon gene types erm(B) + tet(M) + IntTn and erm(B) + tet(L) + tet(M) + IntTn, respectively. The virulence genes such as ace (99.0%), efaA (97.7%), cad1 (95.7%), and gelE (85.9%) were highly conserved in E. faecalis and significantly predominated over E. faecium (p < 0.001). Our results indicate that pathogens from bulk tank milk can also become a reservoir for the dissemination of antimicrobial resistance and virulence factors through cross-contamination processes.

Exploring Beneficial Properties of the Bacteriocinogenic Enterococcus faecium ST10Bz Strain Isolated from Boza, a Bulgarian Cereal-Based Beverage

The bacteriocin-producing strain Enterococcus faecium ST10Bz, isolated from boza, a Bulgarian cereal-based beverage, exhibited strong activity against Listeria strains, vancomycin-resistant and other Enterococcus strains, but not against most of the other lactic acid bacteria (LAB) strains included in the test panel. Bacteriocin ST10Bz was proven as a stable antimicrobial, even after exposure to various environmental conditions, including varying pH values, temperatures, and commonly used chemicals in industry and laboratory practice. Bacteriocin activity against L. monocytogenes ATCC^®15313™ was recorded at 25,600 AU/mL when the producer strain was cultured in MRS broth at 25 °C and 30 °C, and 19,200 AU/mL, when cultured at 37 °C. Additionally, bacteriocin ST10Bz exhibited bactericidal mode of action when added to actively growing cultures of L. monocytogenes ATCC^®15313™ and Enterococcus faecalis 200A. E. faecium ST10Bz was susceptible to the antibiotics kanamycin, gentamycin, ampicillin, streptomycin, tylosin, chloramphenicol, clindamycin, tetracycline, and vancomycin; with no evidence for vanA, B, C, D, E, or G genes. PCR analysis of DNA from strain ST10Bz generated positive results for presence of some bacterial adhesion genes, including map, mub and ef-tu, as well as the gamma aminobutyric acid (GABA) production-related gene, gad. Under simulated gastrointestinal conditions in single and co-culture with L. monocytogenes ATCC^®15313™ and E. faecalis 200A, E. faecium ST10Bz showed a high survival rate and the ability to reduce the viable numbers of the two test strains.

Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand

Historical antimicrobial use in NZ agriculture has driven the evolution of ST108, a VRE lineage carrying a range of clinically relevant antimicrobial resistances. The persistence of this lineage in NZ for over a decade indicates that coselection may be an important stabilizing mechanism for its persistence.

Enterococcus faecalis and Enterococcus faecium are human and animal gut commensals. Vancomycin-resistant enterococci (VRE) are important opportunistic pathogens with limited treatment options. Historically, the glycopeptide antibiotics vancomycin and avoparcin selected for the emergence of vancomycin resistance in human and animal isolates, respectively, resulting in global cessation of avoparcin use between 1997 and 2000. To better understand human- and animal-associated VRE strains in the postavoparcin era, we sequenced the genomes of 231 VRE isolates from New Zealand (NZ; 75 human clinical, 156 poultry) cultured between 1998 and 2009. E. faecium lineages and their antibiotic resistance carriage patterns strictly delineated between agricultural and human reservoirs, with bacitracin resistance ubiquitous in poultry but absent in clinical E. faecium strains. In contrast, one E. faecalis lineage (ST108) predominated in both poultry and human isolates in the 3 years following avoparcin discontinuation. Both phylogenetic and antimicrobial susceptibility (i.e., ubiquitous bacitracin resistance in both poultry and clinical ST108 isolates) analyses suggest an agricultural origin for the ST108 lineage. VRE isolate resistomes were carried on multiple, heterogeneous plasmids. In some isolate genomes, bacitracin, erythromycin, and vancomycin resistance elements were colocalized, indicating multiple potentially linked selection mechanisms.

IMPORTANCE Historical antimicrobial use in NZ agriculture has driven the evolution of ST108, a VRE lineage carrying a range of clinically relevant antimicrobial resistances. The persistence of this lineage in NZ for over a decade indicates that coselection may be an important stabilizing mechanism for its persistence.

Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Dairy Farm Environments: A New Zealand Perspective

Antimicrobial resistance (AMR) is a global issue for both human and animal health. Infections caused by antimicrobial-resistant bacteria present treatment option challenges and are often associated with heightened severity of infection. Antimicrobial use (AMU) in human and animal health is a main driver for the development of antimicrobial-resistant bacteria. Increasing levels of AMU and the development and spread of AMR in food-producing animals, especially in poultry and swine production, has been identified as a food safety risk, but dairy production systems have been less studied. A number of farm management practices may impact on animal disease and as a result can influence the use of antimicrobials and subsequently AMR prevalence. However, this relationship is multifactorial and complex. Several AMR transmission pathways between dairy cattle, the environment, and humans have been proposed, including contact with manure-contaminated pastures, direct contact, or through the food chain from contaminated animal-derived products. The World Health Organization has defined a priority list for selected bacterial pathogens of concern to human health according to 10 criteria relating to health and AMR. This list includes human pathogens such as the extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), which can be associated with dairy cattle, their environment, as well as animal-derived food products. ESBL-E represent a potential risk to human and animal health and an emerging food safety concern. This review addresses two areas; first, the current understanding of the role of dairy farming in the prevalence and spread of AMR is considered, highlighting research gaps using ESBL-E as an exemplar; and second, a New Zealand perspective is taken to examine how farm management practices may contribute to on-farm AMU and AMR in dairy cattle.

Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species

Clostridium difficile infection (CDI) is an urgent public health concern causing considerable clinical and economic burdens. CDI can be treated with antibiotics, but recurrence of the disease following successful treatment of the initial episode often occurs. Surotomycin is a rapidly bactericidal cyclic lipopeptide antibiotic that is in clinical trials for CDI treatment and that has demonstrated superiority over vancomycin in preventing CDI relapse. Surotomycin is a structural analogue of the membrane-active antibiotic daptomycin. Previously, we utilized in vitro serial passage experiments to derive C. difficile strains with reduced surotomycin susceptibilities. The parent strains used included ATCC 700057 and clinical isolates from the restriction endonuclease analysis (REA) groups BI and K. Serial passage experiments were also performed with vancomycin-resistant and vancomycin-susceptible Enterococcus faecium and Enterococcus faecalis. The goal of this study is to identify mutations associated with reduced surotomycin susceptibility in C. difficile and enterococci. Illumina sequence data generated for the parent strains and serial passage isolates were compared. We identified nonsynonymous mutations in genes coding for cardiolipin synthase in C. difficile ATCC 700057, enoyl-(acyl carrier protein) reductase II (FabK) and cell division protein FtsH2 in C. difficile REA type BI, and a PadR family transcriptional regulator in C. difficile REA type K. Among the 4 enterococcal strain pairs, 20 mutations were identified, and those mutations overlap those associated with daptomycin resistance. These data give insight into the mechanism of action of surotomycin against C. difficile, possible mechanisms for resistance emergence during clinical use, and the potential impacts of surotomycin therapy on intestinal enterococci.

Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing

Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing treatment options for these infections. MDR E. faecalis strains have large genomes containing mobile genetic elements (MGEs) that harbor genes for antibiotic resistance and virulence determinants. Bacteria commonly possess genome defense mechanisms to block MGE acquisition, and we hypothesize that these mechanisms have been compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the bacterial genome is methylated at cytosine (C) or adenine (A) residues by a methyltransferase (MTase), such that nonself DNA can be distinguished from self DNA. A cognate restriction endonuclease digests improperly modified nonself DNA. Little is known about R-M in E. faecalis. Here, we use genome resequencing to identify DNA modifications occurring in the oral isolate OG1RF. OG1RF has one of the smallest E. faecalis genomes sequenced to date and possesses few MGEs. Single-molecule real-time (SMRT) and bisulfite sequencing revealed that OG1RF has global 5-methylcytosine (m5C) methylation at 5'-GCWGC-3' motifs. A type II R-M system confers the m5C modification, and disruption of this system impacts OG1RF electrotransformability and conjugative transfer of an antibiotic resistance plasmid. A second DNA MTase was poorly expressed under laboratory conditions but conferred global N(4)-methylcytosine (m4C) methylation at 5'-CCGG-3' motifs when expressed in Escherichia coli. Based on our results, we conclude that R-M can act as a barrier to MGE acquisition and likely influences antibiotic resistance gene dissemination in the E. faecalis species.

IMPORTANCE

The horizontal transfer of antibiotic resistance genes among bacteria is a critical public health concern. Enterococcus faecalis is an opportunistic pathogen that causes life-threatening infections in humans. Multidrug resistance acquired by horizontal gene transfer limits treatment options for these infections. In this study, we used innovative DNA sequencing methodologies to investigate how a model strain of E. faecalis discriminates its own DNA from foreign DNA, i.e., self versus nonself discrimination. We also assess the role of an E. faecalis genome modification system in modulating conjugative transfer of an antibiotic resistance plasmid. These results are significant because they demonstrate that differential genome modification impacts horizontal gene transfer frequencies in E. faecalis.

The Resazurin Microplate Method for Rapid Detection of Vancomycin Resistance in Enterococci

Vancomycin-resistant enterococci (VRE) are a serious challenge for physicians because of the limited treatment options for infections caused by this organism. Prevention of VRE transmission in hospitals requires early detection of infected or colonized patients. Therefore rapid and correct detection of vancomycin resistance is essential. In this study, we use the resazurin microplate method (RMM), which is a modification of the NCCLS and BSAC broth microdilution methods to rapidly determine the susceptibilities of clinical enterococci isolates to vancomycin. The alteration in the RMM was relevant to the final bacterial count. In this method, inoculum that was 10-fold higher than standard methods was used. A total of 80 enterococci, including 11 VRE isolates and 6 vancomycin intermediate isolates, were screened with this modified colorimetric broth microdilution method. After 4 h of incubation 30 microl of 0.01% resazurin solution were added to each well and the plates were reincubated for color change for 5-10 min. The MICs were obtained at the 4th h. The results were in exact agreement with the NCCLS and the BSAC microdilution methods. Absolute and essential agreements were 100% and there were no minor, major or very major errors. In conclusion, this modified colorimetric broth microdilution method can be used as a reliable, easy, cheap and rapid method for early detection of VRE. Moreover, this method has the potential of being used to test the susceptibilities of different bacteria to other antibiotics.

Undecaprenyl pyrophosphate phosphatase confers low-level resistance to bacitracin in Enterococcus faecalis

OBJECTIVES

Undecaprenyl pyrophosphate phosphatases (UppPs) have been implicated in bacitracin resistance in some bacterial genera and the aim of this study was to determine the role of UppPs in mediating low-level bacitracin resistance in Enterococcus faecalis.

METHODS

The uppP gene was identified in the genomes of laboratory (JH2-2) and clinical (V583) strains of E. faecalis. Gene fusions (uppP-lacZ) and 5'-RACE were used to study uppP expression. The uppP gene in both strains was inactivated and mutants were studied for antimicrobial susceptibility and their susceptibilities to various stress agents.

RESULTS

The UppP protein from E. faecalis showed high sequence identity to the Escherichia coli BacA-type UppP and was predicted to be a hydrophobic protein with eight transmembrane helices. The expression of uppP-lacZ was constitutive and not affected by bacitracin or cell wall-active antimicrobials. E. faecalis uppP mutants showed no significant changes in growth rate, colony morphology and biofilm formation. The uppP mutants exhibited increased susceptibility to bacitracin (MICs=3-6 mg/L) relative to the isogenic wild-type (MICs=32-48 mg/L). When uppP was expressed in a wild-type background, the MIC of bacitracin increased to 128-≥256 mg/L. The MICs of cefoxitin, teicoplanin, vancomycin, gentamicin, enrofloxacin and d-cycloserine were unaltered in the uppP mutant relative to the wild-type, as were susceptibilities to other stress agents (glycine, lysozyme, NaCl, SDS, low and high pH, oxidative stress and ethanol).

CONCLUSIONS

The results demonstrate that low-level bacitracin resistance in E. faecalis is mediated by a BacA-type UppP.

Isolation and molecular characterization of vancomycin-resistant Enterococcus faecium from swine in Michigan, USA

In 2008, we identified vancomycin-resistant enterococci (VRE) in Michigan swine, which was the first report of VRE in livestock from North America. Continued sampling in 2009 and 2010 was conducted to determine whether VRE persisted in Michigan. In 2009, swine faecal and feed samples (n=56), county fair pig barn manure samples (n=9) and pooled Michigan State Fair pig barn manure samples (n=18) were screened for VRE. In 2010, swine faecal samples were collected from 26 county fairs (n=73) and nine commercial swine farms in six states (n=28). Recovered VRE isolates were molecularly evaluated by polymerase chain reaction, restriction fragment length polymorphism, pulsed-field gel electrophoresis (PFGE), S1 nuclease digestion and multilocus sequence typing (MLST). Six VRE isolates were identified in 2009 from the State Fair, and another six (8.2%) were recovered from the five county fairs in 2010. All 12 isolates were highly related to the first-reported VRE from Michigan swine: all were confirmed to be vancomycin-resistant Enterococcus faecium (VREf) carrying vanA gene on Tn1546 (Type D), were negative for IS1251, hyl and esp gene, carried a 150-160 kb megaplasmid, and have closely similar PFGE patterns with >80% similarity. Classified as ST5, ST6 or ST185 by MLST, all belong to the clonal complex 5, a strain recognized to be circulating among European pigs. This study reveals that VREf are widespread in Michigan swine and persist in the historical absence of the use of agricultural glycopeptides.

Large-scale screening of a targeted Enterococcus faecalis mutant library identifies envelope fitness factors

Spread of antibiotic resistance among bacteria responsible for nosocomial and community-acquired infections urges for novel therapeutic or prophylactic targets and for innovative pathogen-specific antibacterial compounds. Major challenges are posed by opportunistic pathogens belonging to the low GC% Gram-positive bacteria. Among those, Enterococcus faecalis is a leading cause of hospital-acquired infections associated with life-threatening issues and increased hospital costs. To better understand the molecular properties of enterococci that may be required for virulence, and that may explain the emergence of these bacteria in nosocomial infections, we performed the first large-scale functional analysis of E. faecalis V583, the first vancomycin-resistant isolate from a human bloodstream infection. E. faecalis V583 is within the high-risk clonal complex 2 group, which comprises mostly isolates derived from hospital infections worldwide. We conducted broad-range screenings of candidate genes likely involved in host adaptation (e.g., colonization and/or virulence). For this purpose, a library was constructed of targeted insertion mutations in 177 genes encoding putative surface or stress-response factors. Individual mutants were subsequently tested for their i) resistance to oxidative stress, ii) antibiotic resistance, iii) resistance to opsonophagocytosis, iv) adherence to the human colon carcinoma Caco-2 epithelial cells and v) virulence in a surrogate insect model. Our results identified a number of factors that are involved in the interaction between enterococci and their host environments. Their predicted functions highlight the importance of cell envelope glycopolymers in E. faecalis host adaptation. This study provides a valuable genetic database for understanding the steps leading E. faecalis to opportunistic virulence.

Genetic basis for daptomycin resistance in enterococci

The emergence of multidrug-resistant enterococci as a leading cause of hospital-acquired infection is an important public health concern. Little is known about the genetic mechanisms by which enterococci adapt to strong selective pressures, including the use of antibiotics. The lipopeptide antibiotic daptomycin is approved to treat Gram-positive bacterial infections, including those caused by enterococci. Since its introduction, resistance to daptomycin by strains of Enterococcus faecalis and Enterococcus faecium has been reported but is still rare. We evolved daptomycin-resistant strains of the multidrug-resistant E. faecalis strain V583. Based on the availability of a fully closed genome sequence for V583, we used whole-genome resequencing to identify the mutations that became fixed over short time scales (~2 weeks) upon serial passage in the presence of daptomycin. By comparison of the genome sequences of the three adapted strains to that of parental V583, we identified seven candidate daptomycin resistance genes and three different mutational paths to daptomycin resistance in E. faecalis. Mutations in one of the seven candidate genes (EF0631), encoding a putative cardiolipin synthase, were found in each of the adapted E. faecalis V583 strains as well as in daptomycin-resistant E. faecalis and E. faecium clinical isolates. Alleles of EF0631 from daptomycin-resistant strains are dominant in trans and confer daptomycin resistance upon a susceptible host. These results demonstrate a mechanism of enterococcal daptomycin resistance that is genetically distinct from that occurring in staphylococci and indicate that enterococci possessing alternate EF0631 alleles are selected for during daptomycin therapy. However, our analysis of E. faecalis clinical isolates indicates that resistance pathways independent from mutant forms of EF0631 also exist.

Antimicrobial-resistant enterococci in animals and meat: a human health hazard?

Enterococcus faecium and Enterococcus faecalis belong to the gastrointestinal flora of humans and animals. Although normally regarded harmless commensals, enterococci may cause a range of different infections in humans, including urinary tract infections, sepsis, and endocarditis. The use of avoparcin, gentamicin, and virginiamycin for growth promotion and therapy in food animals has lead to the emergence of vancomycin- and gentamicin-resistant enterococci and quinupristin/dalfopristin-resistant E. faecium in animals and meat. This implies a potential risk for transfer of resistance genes or resistant bacteria from food animals to humans. The genes encoding resistance to vancomycin, gentamicin, and quinupristin/dalfopristin have been found in E. faecium of human and animal origin; meanwhile, certain clones of E. faecium are found more frequently in samples from human patients, while other clones predominate in certain animal species. This may suggest that antimicrobial-resistant E. faecium from animals could be regarded less hazardous to humans; however, due to their excellent ability to acquire and transfer resistance genes, E. faecium of animal origin may act as donors of antimicrobial resistance genes for other more virulent enterococci. For E. faecalis, the situation appears different, as similar clones of, for example, vancomycin- and gentamicin-resistant E. faecalis have been obtained from animals and from human patients. Continuous surveillance of antimicrobial resistance in enterococci from humans and animals is essential to follow trends and detect emerging resistance.

Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance, and other traits

The Enterococcus faecalis pathogenicity island (PAI) encodes known virulence traits and >100 additional genes with unknown roles in enterococcal biology. Phage-related integration and excision genes, and direct repeats flanking the island, suggest it moves as an integrative conjugative element (ICE). However, transfer was observed not to require these genes. Transfer only occurred from donors possessing a pheromone responsive-type of conjugative plasmid, and was invariably accompanied by transfer of flanking donor chromosome sequences. Deletion of plasmid transfer functions, including the cis-acting origin of transfer (oriT), abolished movement. In addition to demonstrating PAI movement by a mechanism involving plasmid integration, we observed transfer of a selectable marker placed virtually anywhere on the chromosome. Transfer of this selectable marker was observed to be accompanied by chromosome-chromosome transfer of vancomycin resistance, MLST markers, and capsule genes as well. Plasmid mobilization therefore appears to be a major mechanism for horizontal gene transfer in the evolution of antibiotic resistant E. faecalis strains capable of causing human infection.

Evidence for the clustering of antibacterial resistance phenotypes of enterococci within integrated poultry companies

From July to December 2006, a panel of 401 enterococci was isolated from carcass rinse samples collected in five poultry processing plants in New Zealand. Agar diffusion assays for nine antibacterial drugs were used to obtain a resistance phenotype for each isolate. Hierarchical clustering techniques and diversity indices showed a high diversity of resistance phenotypes within each plant, with populations of Enterococcus faecalis showing greater heterogeneity than Enterococcus faecium. Bayesian modelling identified three clusters of phenotype patterns within the panel: the E. faecium isolates showed a high probability of containing two distinct clusters, whilst the E. faecalis isolates all grouped together to form the third cluster. The validity of these three clusters was examined using pairwise fixation indices and analysis of variance. Comparing the three clusters to the structure of the participating companies showed that resistance phenotypes for E. faecium isolated from processing plants that were geographically separated but were operated by the same integrated poultry company were more similar than E. faecium isolated from unconnected companies. Company-level management factors, such as the routine use of antibacterial drugs and the genetic line of birds reared, mirrored the structure of these clusters, thus indicating that company-level factors were the dominant selective pressures upon resistance phenotypes across all operating units within these integrated poultry companies.

Identification of tetracycline- and erythromycin-resistant Gram-positive cocci within the fermenting microflora of an Italian dairy food product

AIMS

Microbiological and molecular analysis of antibiotic resistance in Gram-positive cocci derived from the Italian PDO (Protected Designation of Origin) dairy food product Mozzarella di Bufala Campana.

METHODS AND RESULTS

One hundred and seven coccal colonies were assigned to Enterococcus faecalis, Lactococcus lactis and Streptococcus bovis genera by ARDRA analysis (amplified ribosomal DNA restriction analysis). Among them, 16 Ent. faecalis, 26 L. lactis and 39 Strep. bovis displayed high minimum inhibitory concentration (MIC) values for tetracycline, while 17 L. lactis showed high MIC values for both tetracycline and erythromycin. Strain typing and molecular analysis of the phenotypically resistant isolates demonstrated the presence of the tet(M) gene in the tetracycline-resistant strains and of tet(S) and erm(B) in the double-resistant strains. Southern blot analysis revealed plasmid localization of L. lactis tet(M), as well as of the erm(B) and tet(S) genes. Genetic linkage of erm(B) and tet(S) was also demonstrated by PCR amplification. Conjugation experiments demonstrated horizontal transfer to Ent. faecalis strain JH2-2 only for the plasmid-borne L. lactis tet(M) gene.

CONCLUSIONS

We characterized tetracycline-and erythromycin-resistance genes in coccal species, representing the fermenting microflora of a typical Italian dairy product.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results are of particular relevance from the food safety viewpoint, especially in the light of the potential risk of horizontal transfer of antibiotic-resistance genes among foodborne commensal bacteria.

Clonal expansion within clonal complex 2 and spread of vancomycin-resistant plasmids among different genetic lineages of Enterococcus faecalis from Portugal

OBJECTIVES

The aim of this study was to assess the diversity of Enterococcus faecalis populations recovered in different regions of Portugal during the last decade (1996-2007) and to analyse their genetic elements associated with vancomycin resistance.

METHODS

Forty E. faecalis isolates (22 vancomycin-susceptible and 18 vancomycin-resistant) representing disseminated and/or multiresistant strains from different sources (humans, animals and the environment) were characterized by PFGE and multilocus sequence typing. Genes encoding putative virulence markers and the backbone of Tn1546 were investigated by PCR. Plasmid analysis included determination of size, content (S1 hybridization) and comparison of restriction fragment length polymorphism patterns.

RESULTS

The 40 E. faecalis isolates (22 PFGE types) mostly clustered within the worldwide-spread clonal complexes (CCs) CC2 (13 ST6 mostly corresponding to an epidemic strain, where ST stands for sequence type), CC21 (3 ST21, 1 ST22 and 1 ST224) and ST16 (n = 7), but also comprised ST159, ST35, ST19, ST26, ST30, ST41, ST55, ST59, ST117, ST160 and ST200. CC2 and CC21 were isolated from both hospital and community settings. Similar Tn1546-like elements encoding VanA were found on related plasmids within strains belonging to different clonal lineages and recovered in distinct hospitals over several years.

CONCLUSIONS

The predominance of E. faecalis CC2 is mainly due to the dissemination of a particular clone persistently recovered for 11 years. The presence in the community of specific strains belonging to major clonal lineages highlights the role of community-associated hosts as possible reservoirs of putative human pathogenic enterococci. Both clonal expansion and dissemination of epidemic conjugative VanA plasmids seem to join forces in the establishment of pathogenic E. faecalis strains.

Relation of Enterococcus faecalis and Enterococcus faecium isolates from foods and clinical specimens

Clinical Enterococcus faecalis (n=65) and Enterococcus faecium (n=12) blood isolates from three Swiss hospitals were characterized with testing for resistance to antimicrobial agents, pulsed-field gel electrophoresis (PFGE), and the occurrence of virulence factors. Phenotypic determination of resistance to antimicrobial agents resulted in 20% of E. faecalis isolates showing a triple resistance against chloramphenicol, tetracycline, erythromycin, and seven isolates (two E. faecalis and five E. faecium) exhibiting a multiresistance against five or more antimicrobials. One isolate each of E. faecalis and E. faecium showed vancomycin resistance. All isolates contained at least two of the nine tested virulence genes (agg, gelE, cyl, esp, efaAfs, efaAfm, cpd, cob, and ccf). Phylogenetic analysis of the PFGE profiles identified several small clusters within E. faecalis isolates, one of which included isolates of all three hospitals. Fifty-six (73%) isolates occurred as unique, patient-specific clones. Several PFGE types were associated with shared features in their resistance patterns, indicating spread between and within wards. Finally, enterococci from this study and previous isolates from cheeses were examined by PFGE typing. The comparison of PFGE profiles from human and food isolates resulted in clusters of genetically strong related strains, which suggests high similarities of the enterococcal community composition of these two environments. A possible spread of the enterococcal isolates through the food supply cannot be excluded.

Antibiotic resistance among indicator bacteria isolated from healthy pigs in New Zealand

AIM

To determine the resistance to antibiotics among the indictor bacteria, Escherichia coli and Enterococcus spp, isolated from the faeces of healthy pigs on three conventional pig farms and one organic farm in the North Island of New Zealand.

METHODS

Faecal samples, collected at intervals between March and October 2001, were plated onto MacConkey agar and Slanetz-Bartley agar and examined after 1-3 days incubation for colonies resembling E. coli and Enterococcus spp, respectively. Typical colonies were subcultured for further identification and storage. The isolates were tested for antibiotic resistance, using disc diffusion, to ampicillin, gentamicin, streptomycin, and tetracycline. Escherichia coli isolates were also tested for resistance to ciprofloxacin, cotrimoxazole and neomycin. Enterococcus spp isolates were also tested for resistance to vancomycin, erythromycin and virginiamycin.

RESULTS

A total of 296 E. coli and 273 Enterococcus spp isolates were obtained from the three conventional farms, and 79 E. coli and 80 Enterococcus spp isolates were obtained from the organic farm. All the E. coli isolates from both the conventional and organic pig farms were susceptible to ciprofloxacin, and all the Enterococcus spp isolates were susceptible to ampicillin, gentamicin and vancomycin. Isolates of E. coli from conventional pig farms were resistant to gentamicin (0.7%), neomycin (0.7%), ampicillin (2.7%), cotrimoxazole (11%), streptomycin (25%) and tetracycline (60%). Enterococcus spp isolates from the same farms were resistant to erythromycin (68%), tetracycline (66%), streptomycin (54%) and virginiamycin (49%). By contrast, for the organic pig farm <or=5% of either the E. coli or the Enterococcus spp isolates were resistant to any of the antibiotics tested.

CONCLUSIONS

On commercial pig farms which used antimicrobial agents, there was a higher level of antimicrobial resistance in the E. coli and Enterococcus spp cultured from the faeces of pigs compared with an organic farm which used no antibiotics. Overall levels of antibiotic resistance in the indicator bacteria isolated from conventional pig farms in this study were similar to those reported for indicator bacteria from pigs in Europe.

Isolation of quinupristin/dalfopristin-resistant Streptococcus agalactiae from asymptomatic Korean women

Seven Streptococcus agalactiae isolates were obtained from the vagina of 80 asymptomatic women. Three of these isolates showed multi-drug resistant (MDR) phenotypes: two isolates were resistant to clarithromycin, clindamycin, erythromycin, and tetracycline; and one isolate was resistant to clarithromycin, clindamycin, erythromycin, tetracycline, and quinupristin/dalfopristin. There was no clonal relationship among the MDR isolates. This is the first report of quinupristin/dalfopristin-resistant S. agalactiae.

Molecular analysis of BcrR, a membrane-bound bacitracin sensor and DNA-binding protein from Enterococcus faecalis

BcrR has been identified as a novel regulatory protein of high level bacitracin resistance encoded by the bcrABD operon in Enterococcus faecalis. The N-terminal domain of BcrR has similarity to the helix-turn-helix motif of DNA-binding proteins, and topological modeling predicts that the C-terminal domain contains four transmembrane alpha-helices. These data have led to the hypothesis that BcrR functions as both a membrane-bound sensor and transducer of bacitracin availability to regulate bcrABD expression. To characterize the bcrABD promoter and identify the promoter elements to which BcrR binds, a series of bcrA-lacZ fusions were constructed. A 69-bp region was identified that was essential for bacitracin-dependent bcrA-lacZ expression. Mutations that targeted this region were used to identify two inverted repeat sequences, each with the sequence 5'-GACA(N)(7)TGTC-3', on the bcrABD promoter that were required for bcrA-lacZ expression. To study BcrR binding to this region, we over-produced BcrR with a C-terminal hexa-histidine tag in Escherichia coli membranes, extracted the protein with n-dodecyl-beta-d-maltoside, and subsequently purified it via Ni(2+)-nitrilotriacetic acid and gel filtration chromatography to apparent homogeneity. Purified BcrR was reconstituted into liposomes, and BcrR binding to bcrABD promoter DNA was analyzed using electrophoretic mobility shift assays. Both inverted repeat sequences were required for BcrR binding, both in the presence and absence of bacitracin. These data demonstrate that membrane-bound BcrR binds specifically to the bcrABD promoter, irrespective of bacitracin concentration. We therefore propose that bacitracin-dependent induction of bcrABD expression by BcrR occurs after DNA binding.

Characterization of monolaurin resistance in Enterococcus faecalis

There is increasing concern regarding the presence of vancomycin-resistant enterococci in domestically farmed animals, which may act as reservoirs and vehicles of transmission for drug-resistant enterococci to humans, resulting in serious infections. In order to assess the potential for the use of monolaurin as a food preservative, it is important to understand both its target and potential mechanisms of resistance. A Tn917 mutant library of Enterococcus faecalis AR01/DGVS was screened for resistance (MIC, >100 microg/ml) to monolaurin. Three mutants were identified as resistant to monolaurin and were designated DGRM2, DGRM5, and DGRM12. The gene interrupted in all three mutants was identified as traB, which encodes an E. faecalis pheromone shutdown protein and whose complementation in trans restored monolaurin sensitivity in all three mutants. DGRM2 was selected for further characterization. E. faecalis DGRM2 showed increased resistance to gentamicin and chloramphenicol (inhibitors of protein synthesis), while no difference in the MIC was observed with the cell wall-active antibiotics penicillin and vancomycin. E. faecalis AR01/DGVS and DGRM2 were shown to have similar rates (30% cell lysis after 4 h) of cell autolytic activity when activated by monolaurin. Differences in cell surface hydrophobicity were observed between the wild type and the mutant, with the cell surface of the parent strain being significantly more hydrophobic. Analysis of the cell wall structure of DGRM2 by transmission electron microscopy revealed an increase in the apparent cell wall thickness and contraction of its cytoplasm. Taken together, these results suggest that the increased resistance of DGRM2 was due to a change in cell surface hydrophobicity, consequently limiting the diffusion of monolaurin to a potential target in the cytoplasmic membrane and/or cytoplasm of E. faecalis.

Genetic diversity among Enterococcus faecalis

Enterococcus faecalis, a ubiquitous member of mammalian gastrointestinal flora, is a leading cause of nosocomial infections and a growing public health concern. The enterococci responsible for these infections are often resistant to multiple antibiotics and have become notorious for their ability to acquire and disseminate antibiotic resistances. In the current study, we examined genetic relationships among 106 strains of E. faecalis isolated over the past 100 years, including strains identified for their diversity and used historically for serotyping, strains that have been adapted for laboratory use, and isolates from previously described E. faecalis infection outbreaks. This collection also includes isolates first characterized as having novel plasmids, virulence traits, antibiotic resistances, and pathogenicity island (PAI) components. We evaluated variation in factors contributing to pathogenicity, including toxin production, antibiotic resistance, polymorphism in the capsule (cps) operon, pathogenicity island (PAI) gene content, and other accessory factors. This information was correlated with multi-locus sequence typing (MLST) data, which was used to define genetic lineages. Our findings show that virulence and antibiotic resistance traits can be found within many diverse lineages of E. faecalis. However, lineages have emerged that have caused infection outbreaks globally, in which several new antibiotic resistances have entered the species, and in which virulence traits have converged. Comparing genomic hybridization profiles, using a microarray, of strains identified by MLST as spanning the diversity of the species, allowed us to identify the core E. faecalis genome as consisting of an estimated 2057 unique genes.

Transposon characterization of vancomycin-resistant Enterococcus faecium (VREF) and dissemination of resistance associated with transferable plasmids

OBJECTIVES

VanA glycopeptide resistance has persisted on broiler farms in the UK despite the absence of the antimicrobial selective pressure, avoparcin. This study aimed to investigate the contribution of horizontal gene transfer of Tn1546 versus clonal spread in the dissemination of the resistance.

METHODS AND RESULTS

One hundred and one vancomycin-resistant Enterococcus faecium isolated from 19 unrelated farms have been investigated. Tn1546 characterization by long PCR and ClaI-digestions of amplicons showed a very low diversity of Tn types (n=4) in comparison to the high genotypic diversity demonstrated by PFGE (n=62). Conjugation experiments were carried out to assess the transfer of vancomycin resistance. Co-transfer of vanA together with erm(B) positioned on the same conjugative plasmid containing a replicon similar to pRE25 was demonstrated and also the presence of different plasmid replicons, associated with antimicrobial resistance on several unrelated farms.

CONCLUSIONS

Horizontal transfer of vancomycin resistance may play a more important role in the persistence of antimicrobial resistance than clonal spread. The presence of different plasmid replicons, associated with antimicrobial resistance on several unrelated farms, illustrates the ability of these enterococci to acquire and disseminate mobile genetic elements within integrated livestock systems.

Vancomycin-susceptible dairy and clinical enterococcal isolates carry vanA and vanB genes

A total of 109 enterococcal isolates from dairy food products and from human and dog infections, isolated in Portugal, and 26 type and reference strains of the genus Enterococcus were screened for vancomycin resistance. MIC values, both for vancomycin and teicoplanin, were determined. The genetic relatedness of isolates carrying either vanA and/or vanB was determined using Pulsed Field Gel Electrophoresis. For vanA carrying isolates, transposon Tn1546 was partially mapped using PCR. None of the 59 dairy isolates was resistant to vancomycin. Among the 50 clinical isolates, only one, carrying vanB, behaved as resistant, with a MIC value of 256 microg/mL. The type and reference strains used were susceptible both to vancomycin and teicoplanin. vanA was found in 37% of the dairy isolates and 40% of the clinical isolates. vanB was only detected in 18% of the clinical, both human and dog, isolates. PCR partial mapping of Tn1546 revealed 23 different patterns among 42 isolates. Some patterns were shared between dairy and clinical isolates. Using Pulsed Field Gel Electrophoresis six groups of isolates were found to be genetically undistinguishable and grouping was found to be geographically and location specific/related. No genetic relatedness was found between isolates from dairy, human and veterinary sources. These results show that an incomplete and/or unfunctional Tn1546 element may explain the absence of resistant behaviour in the studied isolates, even when vanA gene is present. Moreover, the work reported shows that both clinical (human and animal) and dairy isolates have been in contact with VanA genotype of resistance and suggest that dissemination of vanA gene has been through transposable elements, like Tn1546, and not by clonal dissemination of a resistant strain. Therefore, a national strategy should be implemented to survey both vancomycin resistance and its genetic dissemination.

Evaluation of clonality in enterococci isolated in Brazil carrying Tn1546-like elements associated with vanA plasmids

Fifty-one vancomycin-resistant enterococci samples isolated from different geographic regions in Brazil were studied. All the isolates harboured the vanA gene as demonstrated by PCR analysis, and in a majority of strains the gene was associated with a transferable plasmid of 70 kb. A single variant of the prototype Tn1546 associated with common transferable vanA-containing plasmids has spread among the enterococcal strains circulating in Brazil. The VanA element integrity in these enterococci strains and the different pulsed-field gel electrophoresis patterns suggest horizontal transmission of the vancomycin resistance transposon in Brazilian strains.

Comparative study ofvanAgene transfer fromEnterococcus faeciumtoEnterococcus faecalisand toEnterococcus faeciumin the intestine of mice

Vancomycin-resistant enterococci represent a large reservoir in animals because of the use of avoparcin as a growth promoter in Europe. These strains of animal origin enter the food chain and can either colonize the human gut or transfer their resistance genes to the human microbiota. In this study, we compared the transfer of vancomycin resistance from resistant animal Enterococcus faecium to sensitive human Enterococcus faecalis and E. faecium. We analysed these transfers in dibiotic mice and human faecal flora-associated mice. VanA transfer from animal E. faecium to human E. faecalis occurred in dibiotic mice. The transconjugants appeared rapidly and persisted at levels between 3.0 and 4.0 log10 colony-forming units g(-1) of faeces. In human faecal flora-associated mice, vanA gene transfer was not detected towards E. faecalis but was possible between E. faecium strains. Our experiments revealed the possibility of vanA transfer from animal E. faecium to human E. faecalis in vitro and in vivo in the intestine of dibiotic mice. However, intraspecies transfer of vanA gene seems more common than interspecies transfer among enterococci.

Vancomycin-resistant enterococci: consequences for therapy and infection control

Vancomycin-resistant enterococci (VRE) have emerged as important nosocomial pathogens, initially in the USA, but now also in Europe, where hospital outbreaks are being reported with increasing frequency, although the incidence of VRE infections remains extremely low in most European countries. The recently demonstrated in-human transmission of vancomycin resistance from VRE to methicillin-resistant Staphylococcus aureus (MRSA) in two American patients underscores the potential danger of a coexisting reservoir of both pathogens. As MRSA is already endemic in many European hospital settings, prevention of endemicity with VRE seems relevant, but should be balanced against the costs associated with the implementation of effective strategies. The presence of a large community reservoir of VRE in Europe could hamper the feasibility of infection control strategies. Although the prevalence of colonisation amongst healthy subjects has apparently decreased after the ban on avoparcin use in the agricultural industry, a large proportion of admitted patients are still potential sources of VRE transmission. With no risk profile available to identify these carriers, effective screening, followed by barrier precautions for carriers, seems to be impossible. Recent studies, however, have suggested that hospital outbreaks are almost exclusively caused by specific genogroups of VRE that can be characterised phenotypically and genotypically (e.g., co-resistance to ampicillin and the presence of the variant esp gene). Based on our own experience, we propose that VRE infection control programmes should be restricted to patients colonised with these VRE strains. If such a strain is cultured from a clinical sample, surveillance amongst contact patients is recommended and barrier precautions should be implemented in the case of documented spread.

Combined antimicrobial resistance in Enterococcus faecium isolated from chickens

Nineteen E. faecium strains isolated from chicken caecum samples, collected in slaughterhouses and highly resistant to vancomycin or gentamicin, were coresistant to erythromycin, and/or tetracyclines, and/or streptogramins, and/or avilamycin. Multiple antibiotic resistance was related to the presence in various combinations of aac(6')-aph(2"), erm(B), emtA, mef(A), tet(L), tet(M), and vanA genes.

Persistence of vancomycin-resistant enterococci in New Zealand broilers after discontinuation of avoparcin use

Large amounts of tylosin, zinc-bacitracin, and avilamycin are currently used as prophylactics in New Zealand broiler production. Avoparcin was also used from 1977 to 2000. A total of 382 enterococci were isolated from 213 fecal samples (147 individual poultry farms) using enrichment broths plated on m-Enterococcus agar lacking antimicrobials. These isolates were then examined to determine the prevalence of antimicrobial resistance. Of the 382 isolates, 5.8% (22 isolates) were resistant to vancomycin, and 64.7% were resistant to erythromycin. The bacitracin MIC was > or =256 microg/ml for 98.7% of isolates, and the avilamycin MIC was > or =8 microg/ml for 14.9% of isolates. No resistance to ampicillin or gentamicin was detected. Of the 22 vancomycin-resistant enterococci (VRE) isolates, 18 (81.8%) were Enterococcus faecalis, 3 were Enterococcus faecium, and 1 was Enterococcus durans. However, when the 213 fecal enrichment broths were plated on m-Enterococcus agar containing vancomycin, 86 VRE were recovered; 66% of these isolates were E. faecium and the remainder were E. faecalis. Vancomycin-resistant E. faecium isolates were found to have heterogenous pulsed-field gel electrophoresis (PFGE) patterns of SmaI-digested DNA, whereas the PFGE patterns of vancomycin-resistant E. faecalis isolates were identical or closely related, suggesting that this VRE clone is widespread throughout New Zealand. These data demonstrate that vancomycin-resistant E. faecalis persists in the absence and presence of vancomycin-selective pressure, thus explaining the dominance of this VRE clone even in the absence of avoparcin.

Acquired bacitracin resistance in Enterococcus faecalis is mediated by an ABC transporter and a novel regulatory protein, BcrR

Bacitracin resistance (bacitracin MIC, >/=256 microg ml(-1)) has been reported in Enterococcus faecalis, and in the present study we report on the genetic basis for this resistance. Mutagenesis was carried out with transposon Tn917 to select for E. faecalis mutants with decreased resistance to bacitracin. Two bacitracin-sensitive mutants (MICs, 32 microg ml(-1)) were obtained and Tn917 insertions were mapped to genes designated bcrA and bcrB. The amino acid sequences of BcrA (ATP-binding domain) and BrcB (membrane-spanning domain) are predicted to constitute a homodimeric ATP-binding cassette (ABC) transporter, the function of which is essential for bacitracin resistance in E. faecalis. The bcrA and bcrB genes were organized in an operon with a third gene, bcrD, that had homology to undecaprenol kinases. Northern analysis demonstrated that bcrA, bcrB, and bcrD were transcribed as a polycistronic message that was induced by increasing concentrations of bacitracin but not by other cell wall-active antimicrobials (e.g., vancomycin). Upstream of the bcrABD operon was a putative regulatory gene, bcrR. The bcrR gene was expressed constitutively, and deletion of bcrR resulted in a bacitracin-sensitive phenotype. No bcrABD expression was observed in a bcrR mutant, suggesting that BcrR is an activator of genes essential for bacitracin resistance (i.e., bcrABD). The bacitracin resistance genes were found to be located on a plasmid that transferred at a high frequency to E. faecalis strain JH2-2. This report represents the first description of genes that are essential for acquired bacitracin resistance in E. faecalis.

Characterization of high-level aminoglycoside-resistant enterococci in Kuwait hospitals

This study investigated the distribution of genes for aminoglycoside-modifying enzymes (AME) and the genetic relatedness of high-level aminoglycoside-resistant enterococci isolated in Kuwait hospitals. A total of 117 enterococci, consisting of 109 Enterococcus faecalis, seven Enterococcus faecium, and one Enterococcus casseliflavus were studied. The MICs of gentamicin, kanamycin, amikacin, tobramycin, and streptomycin were determined by agar dilution and the genes encoding the AAC(6')- APH(2"), ANT(4'), APH(3'), APH (2")-Ib, APH (2")-Ic, APH (2")-Id, and ANT(6) enzymes were amplified by PCR. They were typed by pulsed-field gel electrophoresis (PFGE). Filter mating was used to transfer gentamicin resistance determinants. They were all resistant to kanamycin (MIC 2000 mg/L). Fifty-five isolates were resistant to gentamicin (MIC 500 mg/L), 72 were resistant to tobramycin (MIC 64 mg/L), 115 were resistant to amikacin (MIC 64 mg/L), and 97 were resistant to streptomycin (MIC 1000 mg/L). The aac(6')-Ie-aph(2")-Ia was detected in all isolates with gentamicin MIC 500 mg/L and in 15 isolates with gentamicin MIC 256 mg/L. The aph(3')-IIIa gene was detected in 101 isolates, whereas the ant(6')-Ia gene was detected in 85 of the 97 streptomycin-resistant isolates with MIC 1000 mg/L. The aac(6')-Ii gene was detected only in the seven E. faecium isolates. None of them contained ant(4')-Ia, aph(2")-Ib, aph(2")-Ic and aph(2")-Id. PFGE revealed heterogeneous patterns with no dominant clone. The results demonstrated that AME are common in aminoglycoside-resistant enterococci isolated in Kuwait. However, the absence of a dominant clone suggests that they acquired high-level aminoglycoside independently.

Antimicrobial resistance gene delivery in animal feeds

Avoparcin, a glycopeptide antimicrobial agent related to vancomycin, has been used extensively as a growth promoter in animal feeds for more than 2 decades, and evidence has shown that such use contributed to the development of vancomycin-resistant enterococci. A cluster that includes three genes, vanH, vanA, and vanX, is required for high-level resistance to glycopeptides. In the vancomycin producer Amycolatopsis orientalis C329.2, homologs of these genes are present, suggesting an origin for the cluster. We found substantial bacterial DNA contamination in animal-feed-grade avoparcin. Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans.

Antibiotics in animal feed and their role in resistance development

Animals and humans constitute overlapping reservoirs of resistance, and consequently use of antimicrobials in animals can impact on public health. For example, the occurrence of vancomycin-resistant enterococci in food-animals is associated with the use of avoparcin, a glycopeptide antibiotic used as a feed additive for the growth promotion of animals. Vancomycin-resistant enterococci and vancomycin resistance determinants can therefore spread from animals to humans. The bans on avoparcin and other antibiotics as growth promoters in the EU have provided scientists with a unique opportunity to investigate the effects of the withdrawal of a major antimicrobial selective pressure on the occurrence and spread of antimicrobial resistance. The data shows that although the levels of resistance in animals and food, and consequently in humans, has been markedly reduced after the termination of use, the effects on animal health and productivity have been very minor.

Characterization of a vancomycin-resistant Enterococcus faecalis (VREF) isolate from a dog with mastitis: further evidence of a clonal lineage of VREF in New Zealand

We report here on the characterization of a vancomycin-resistant Enterococcus faecalis (VREF) isolated from a dog with mastitis. The isolate was positive for the vanA, ermB, and tet(M) genes, with vanA and ermB carried on the same transferable plasmid. Comparison of this isolate with VREF from poultry and human sources in New Zealand demonstrated identical SmaI macrorestriction patterns and Tn1546-like elements. This is further evidence of a clonal lineage of VREF in New Zealand.