Detection and characterization of vancomycin-resistant enterococci in farm animals and raw meat products in Italy

Emergence of Virulent Extensively Drug-Resistant Vancomycin-Resistant Enterococci Among Diarrheic Pet Animals: A Possible Public Health Threat on the Move

Background: Vancomycin-resistant enterococci (VRE) have become an increasing public health concern in the past few decades, being associated with serious multidrug-resistant (MDR) infections. This study was conducted to investigate the role of diarrheic pet animals as potential reservoirs for virulent extensively drug-resistant (XDR) VRE and their threat on human health. Materials and Methods: Rectal swabs were collected from 153 diarrheic pet animals (80 dogs and 73 cats). The collected swabs were cultured on CHROMagarTMVRE for the isolation of vancomycin-resistant Enterococcus faecalis and Enterococcus faecium, and then suspected colonies were identified as enterococci after Gram staining, conventional biochemical tests, and molecular techniques. VRE were basically identified using the disk diffusion method; however, molecular identification of vanA and vanB genes was carried out among confirmed VRE isolates. Moreover, three virulence genes (cytolysin A, cylA; enterococcal surface protein, esp; and hyaluronidase, hyl) were investigated in VRE isolates. Thereafter, VRE strains that harbored virulence genes were tested for antimicrobial susceptibility. Results: Eighteen out of 153 animals (11.8%) were positive for VRE, which were obtained from 15% and 8.2% of the examined dogs and cats, respectively. None of the obtained isolates carried the vanA gene, whereas the vanB gene was detected in E. faecalis (4/10) with a prevalence rate (40%). Of the obtained VRE isolates, five possessed esp and/or cylA, while all strains were negative for the hyl gene. Furthermore, four virulent VRE isolates exhibited an XDR pattern, and one isolate was MDR. Conclusion: Diarrheic pet animals could represent a potential zoonotic reservoir for virulent XDR vancomycin-resistant E. faecalis, which may have serious public health implications.

Non-faecium non-faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance

SUMMARYEnterococci are a diverse group of Gram-positive bacteria that are typically found as commensals in humans, animals, and the environment. Occasionally, they may cause clinically relevant diseases such as endocarditis, septicemia, urinary tract infections, and wound infections. The majority of clinical infections in humans are caused by two species: Enterococcus faecium and Enterococcus faecalis. However, there is an increasing number of clinical infections caused by non-faecium non-faecalis (NFF) enterococci. Although NFF enterococcal species are often overlooked, studies have shown that they may harbor antimicrobial resistance (AMR) genes and virulence factors that are found in E. faecium and E. faecalis. In this review, we present an overview of the NFF enterococci with a particular focus on human clinical manifestations, epidemiology, virulence genes, and AMR genes.

Antibiotics in avian care and husbandry-status and alternative antimicrobials

Undoubtedly, the discovery of antibiotics was one of the greatest milestones in the treatment of human and animal diseases. Due to their over-use mainly as antibiotic growth promoters (AGP) in livestock farming, antimicrobial resistance has been reported with increasing intensity, especially in the last decades. In order to reduce the scale of this phenomenon, initially in the Scandinavian countries and then throughout the entire European Union, a total ban on the use of AGP was introduced, moreover, a significant limitation in the use of these feed additives is now observed almost all over the world. The withdrawal of AGP from widespread use has prompted investigators to search for alternative strategies to maintain and stabilize the composition of the gut microbiota. These strategies include substances that are used in an attempt to stimulate the growth and activity of symbiotic bacteria living in the digestive tract of animals, as well as living microorganisms capable of colonizing the host’s gastrointestinal tract, which can positively affect the composition of the intestinal microbiota by exerting a number of pro-health effects, i.e., prebiotics and probiotics, respectively. In this review we also focused on plants/herbs derived products that are collectively known as phytobiotic.

Antimicrobial resistance and genetic diversity of Enterococcus faecalis from yolk sac infections in broiler chicks

Despite restrictions on the use of antibiotics in poultry, the percentage of multidrug resistant bacteria, isolated from both adult birds and chicks, remains high. These bacteria can spread between countries via hatching eggs or chicks. Antibiotic resistant bacteria can also pose a threat to hatchery and farm workers or to consumers of poultry. The aim of the study was to perform a phenotypic and genotypic analysis of the drug resistance of E. faecalis isolates from yolk sac infections in broiler chicks from Poland and the Netherlands and to determine their genetic diversity. The tests revealed resistance to antibiotics from category D, that is, tetracycline (69.7%); category C – lincomycin (98.7%), erythromycin (51.3%), aminoglycosides (high-level streptomycin and kanamycin resistance – 10.5% and 3.95%, respectively), and chloramphenicol (7.9%); and category B – ciprofloxacin (25% with resistance or intermediate resistance). No resistance to penicillin, ampicillin, high-level gentamicin, tigecycline, or linezolid was noted. Various combinations of the erm(B), tet(M), tet(L), tet(O), ant(6)-Ia, aph(3′)-IIIa, ant(4′)-Ia, cat, and msr(A/B) genes were detected in all isolates (irrespective of the drug-resistance phenotype). Among isolates that carried the tet(M) and/or the tet(L) gene, 28% also had the Int-Tn gene, in contrast with isolates possessing tet(O). There were 28 sequence types and 43 PFGE restriction patterns. About 60% of isolates were of sequences types ST59, ST16, ST116, ST282, ST36, and ST82. Nine new sequence types were shown (ST836-ST844). In conclusion, broiler chicks can be a source of drug-resistant sequence types of E. faecalis that are potentially hazardous for people and animals. Restrictive programs for antibiotic use in broiler breeding flocks should be developed to decrease drug resistance in day-old chicks and reduce economic losses during rearing.

Prevalence of antimicrobial resistance genes and its association with restricted antimicrobial use in food-producing animals: a systematic review and meta-analysis

BACKGROUND

There is ongoing debate regarding potential associations between restrictions of antimicrobial use and prevalence of antimicrobial resistance (AMR) in bacteria.

OBJECTIVES

To summarize the effects of interventions reducing antimicrobial use in food-producing animals on the prevalence of AMR genes (ARGs) in bacteria from animals and humans.

METHODS

We published a full systematic review of restrictions of antimicrobials in food-producing animals and their associations with AMR in bacteria. Herein, we focus on studies reporting on the association between restricted antimicrobial use and prevalence of ARGs. We used multilevel mixed-effects models and a semi-quantitative approach based on forest plots to summarize findings from studies.

RESULTS

A positive effect of intervention [reduction in prevalence or number of ARGs in group(s) with restricted antimicrobial use] was reported from 29 studies for at least one ARG. We detected significant associations between a ban on avoparcin and diminished presence of the vanA gene in samples from animals and humans, whereas for the mecA gene, studies agreed on a positive effect of intervention in samples only from animals. Comparisons involving mcr-1, blaCTX-M, aadA2, vat(E), sul2, dfrA5, dfrA13, tet(E) and tet(P) indicated a reduced prevalence of genes in intervention groups. Conversely, no effects were detected for β-lactamases other than blaCTX-M and the remaining tet genes.

CONCLUSIONS

The available body of scientific evidence supported that restricted use of antimicrobials in food animals was associated with an either lower or equal presence of ARGs in bacteria, with effects dependent on ARG, host species and restricted drug.

Global Prevalence of Vancomycin-Resistant Enterococci in Food of Animal Origin: A Meta-Analysis

Vancomycin-resistant enterococci (VRE) are a leading cause of nosocomial infections in patients worldwide. VRE contamination in food of animal origin may create a risk for human health. This study was conducted to estimate the pooled prevalence of VRE in food of animal origin worldwide, to assess the result heterogeneity, and to determine cumulative evidence and the trend of the prevalence over time. Relevant studies were retrieved from PubMed, Scopus, and Web of Science. A random-effects model was used to calculate the pooled prevalence of VRE in food of animal origin. Subgroup meta-analysis was used to assess the heterogeneity of the results. A cumulative meta-analysis and meta-regression were conducted to determine cumulative evidence and the trend of the prevalence of VRE in food of animal origin over time, respectively. Of the 1352 retrieved studies, 50 articles were included. The pooled prevalence of VRE in food of animal origin was 11.7% (95% confidence interval [95% CI] = 8.4 to 16.0). Subgroup meta-analyses showed a significant difference in the prevalence of VRE for two characteristics. First, for the source of food, the prevalence of VRE was highest in aquatic food (43.4% [95% CI = 28.4 to 59.7]) and lowest in dairy food (4.1% [95% CI = 1.7 to 9.8]). Second, for continents, the prevalence of VRE was highest in Africa (18.5% [95% CI = 12.8 to 26.1]) and lowest in North America (0.3% [95% CI = 0.1 to 1.1]). Cumulative evidence showed two distinct features in two different periods. The pooled prevalence of VRE rapidly decreased from 79.3% in 1998 to 13.1% in 2003; it has slightly fluctuated between 10.5% and 20.5% since 2004. The results of the meta-regression indicated that the prevalence gradually decreased over time. In conclusion, the estimate of overall VRE prevalence worldwide in food of animal origin was ∼12%, indicating the burden of VRE contamination in food of animal origin.

Prevalence and Epidemiology of Multidrug-Resistant Pathogens in the Food Chain and the Urban Environment in Northwestern Germany

The surveillance of antimicrobial resistance among humans and food-producing animals is important to monitor the zoonotic transmission of multidrug-resistant bacteria (MDRB). We assessed the prevalence of four MDRB within the meat production chain, including extended-spectrum β-lactamase (ESBL)-producing, carbapenemase-producing Enterobacterales (CPE) and colistin-resistant Enterobacterales (Col-E), as well as vancomycin-resistant enterococci (VRE). In total, 505 samples from four stages of meat production, i.e., slaughterhouses, meat-processing plants, fresh food products and the urban environment, were collected in northwestern Germany in 2018/2019 and screened for the presence of MDRB using both culture-based and PCR-based techniques. We detected genes encoding for carbapenemases in 9–56% (bla_OXA-48, bla_KPC, bla_NDM, bla_VIM) and colistin resistance-encoding mcr genes in 9–26% of the samples from all stages. Culture-based analysis found CPE and VRE only in environmental samples (11% and 7%, respectively), but Col-E and ESBL-producers in 1–7% and 12–46% of samples from all stages, respectively. Overall, our results showed that ESBL-producers and mcr-carrying Col-E were common in food-producing animals at slaughterhouses, in meat-processing plants and in food items at retail, while CPE and VRE were only found in the environment. The discrepancy between detected carbapenemase genes and isolated CPE emphasizes the need for more sensitive detection methods for CPE monitoring.

Detection of vancomycin-resistant enterococci in samples from broiler flocks and houses in Turkey

Vancomycin-resistant enterococcus (VRE) is a global threat to public health. Knowledge about the occurrence of vanA-carrying enterococci in broiler and environmental samples is important as antibiotic resistance can be transferred to human bacteria. The aim of this study was to investigate the presence of VRE in broiler cloacal and environmental (house) samples and to genotype the isolates. In this study, 350 swabs were collected from broiler farms. All samples were plated onto enterococcus selective agar containing 6 mg/L vancomycin and 64 mg/L ceftazidime. Minimum inhibitory concentration (MIC) values were determined for vancomycin and teicoplanin. Vancomycin-resistant Enterococcus faecium (VREfm) was isolated from 6 out of 300 (2%) broiler cloacal samples and 13 out of 50 (26%) house samples. All E. faecium isolates had vanA genes. All VREfm isolates (19 isolates) were confirmed to be 95% similar to each other. In conclusion, although 20 years have passed since the ban on avoparcin in Turkey, the present study shows that VREfm isolates are still present in broiler production and especially in broiler houses, and most importantly, a major VREfm clone was isolated from broiler cloacal and house samples.

Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)

Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of Enterococcus spp. that originated from processed meat, through phenotypic and genotypic techniques, as well as to detect putative antibiotic resistance biomarkers. The 19 VRE identified had high resistance to teicoplanin (89%), tetracycline (94%), and erythromycin (84%) and a low resistance to kanamycin (11%), gentamicin (11%), and streptomycin (5%). Based on a Next-Generation Sequencing NGS technique, most isolates were vanA-positive. The most prevalent resistance genes detected were erm(B) and aac(6')-Ii, conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the Enterococcus genus at m/z (mass-to-charge-ratio) 4428 ± 3, and a peak at m/z 6048 ± 1 allowed us to distinguish Enterococcus faecium from the other species. Several statistically significant protein masses associated with resistance were detected, such as peaks at m/z 6358.27 and m/z 13237.3 in ciprofloxacin resistance isolates. These results reinforce the relevance of the combined and complementary NGS and MALDI-TOF MS techniques for bacterial characterization.

Antibiotic Susceptibility and Virulence Genes in Enterococcus Isolates from Wild Mammals Living in Tuscany, Italy

Drug resistance is of great importance to human and animal health, but wild environments are still poorly understood in terms of their function as reservoirs of dangerous microbes and resistance determinants. The aim of the study was to determine the antibiotic susceptibility and virulence factors of Enterococcus bacteria from wildlife in Tuscany, Italy. Of the 36 mammalian fecal samples, 52 isolates were derived and classified as Enterococcus faecium (46% of isolates), Enterococcus hirae (19%), Enterococcus faecalis (13%), Enterococcus gallinarum (8%), Enterococcus casseliflavus (6%), Enterococcus durans (4%), Enterococcus mundtii (2%), and Enterococcus canintestini (2%) using both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and methods based on analysis of genetic material. The isolates tested showed the most frequent resistance to tetracycline (36.5% isolates), ciprofloxacin (36.5%), and erythromycin (25%). Three isolates showed high level of resistance (minimal inhibitory concentration ≥1,024 μg/mL) to vancomycin and teicoplanin, and 15% of the isolates demonstrated multidrug resistance. No isolate resistant to ampicillin, linezolid, or streptomycin was found. Among resistance genes, aac(6)-Ii (50% isolates), msrA/B (48%), msrC (42%), and tetM (31%) were identified most frequently. All E. faecium and E. faecalis isolates were positive for the efaAfm and efaAfs genes, respectively. Other virulence-associated genes, that is, gelE, cylA, asa1, esp, ace, orf1481, ptsD, and sgrA, were found in the majority of E. faecalis and several E. faecium isolates. Multilocus sequence typing analysis performed for selected isolates revealed three new sequence types. The results obtained indicate that wild mammals might act as reservoirs of resistance and virulence determinants that could be transferred between different ecosystems.

Comparison of different approaches to antibiotic restriction in food-producing animals: stratified results from a systematic review and meta-analysis

BACKGROUND

We have previously reported, in a systematic review of 181 studies, that restriction of antibiotic use in food-producing animals is associated with a reduction in antibiotic-resistant bacterial isolates. While informative, that report did not concretely specify whether different types of restriction are associated with differential effectiveness in reducing resistance. We undertook a sub-analysis of the systematic review to address this question.

METHODS

We created a classification scheme of different approaches to antibiotic restriction: (1) complete restriction; (2) single antibiotic-class restriction; (3) single antibiotic restriction; (4) all non-therapeutic use restriction; (5) growth promoter and prophylaxis restriction; (6) growth promoter restriction and (7) other/undetermined. All studies in the original systematic review that were amenable to meta-analysis were included into this substudy and coded by intervention type. Meta-analyses were conducted using random effects models, stratified by intervention type.

RESULTS

A total of 127 studies were included. The most frequently studied intervention type was complete restriction (n=51), followed by restriction of non-therapeutic (n=33) and growth promoter (n=19) indications. None examined growth promoter and prophylaxis restrictions together. Three and seven studies examined single antibiotic-class and single antibiotic restrictions, respectively; these two intervention types were not significantly associated with reductions in antibiotic resistance. Though complete restrictions were associated with a 15% reduction in antibiotic resistance, less prohibitive approaches also demonstrated reduction in antibiotic resistance of 9%-30%.

CONCLUSION

Broad interventions that restrict global antibiotic use appear to be more effective in reducing antibiotic resistance compared with restrictions that narrowly target one specific antibiotic or antibiotic class. Importantly, interventions that allow for therapeutic antibiotic use appear similarly effective compared with those that restrict all uses of antibiotics, suggesting that complete bans are not necessary. These findings directly inform the creation of specific policies to restrict antibiotic use in food-producing animals.

Antimicrobial Resistance in Enterococcus spp. of animal origin

Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover, Enterococcus is an important opportunistic pathogen, especially the species E. faecalis and E. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such as optrA and cfr, is highlighted. The molecular epidemiology and the population structure of E. faecalis and E. faecium isolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.

Molecular and phenotypic characterization of enterococci isolated from broiler flocks in Turkey

The aim of this study was to determine the antimicrobial resistance, resistance mechanisms implicated, and virulence genes (asa1, gelE, cylA, esp, and hyl) of Enterococcus spp. isolated from broiler flocks in Turkey. In addition, clonality of ampicillin and vancomycin-resistant enterococci was also investigated using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Out of 430 cloacal swab samples investigated, 336 (78.1%) Enterococcus spp. was isolated. The most frequently identified species were E. faecalis (87.8%), E. faecium (8.3%), E. durans (2.4%), E. casseliflavus (0.9%), and E. hirae (0.6%). The most common resistance was against tetracycline (81.3%), erythromycin (77.1%), ciprofloxacin (56.8%), and chloramphenicol (46.4%). Fifty (14.9%) isolates showed high-level gentamicin resistance (HLGL) phenotype. Ampicillin and vancomycin resistance were observed in 3.3% and 1.5% of the isolates, respectively. Two hundred eighty-three isolates were positive for the presence of virulence genes. Among the virulence genes tested, only gelE, asa1, esp, and cylA genes were detected. The most prevalent virulence gene was gelE (234, 69.6%), followed by asa1 (160, 47.6%), esp (37, 11%), and cylA (2, 0.6%). In conclusion, this study revealed that commensal enterococci from broiler flocks showed high rate of resistance to antimicrobials including clinically important antimicrobials for humans. The main underlying reason for high resistance could be attributed to the inappropriate and widespread use of antimicrobials. Therefore, there is an urgent need to develop control strategies to prevent the emergence and spread of antimicrobial resistance.

Vancomycin-Resistant Enterococci: A Review of Antimicrobial Resistance Mechanisms and Perspectives of Human and Animal Health

Vancomycin-resistant enterococci (VRE) are both of medical and public health importance associated with serious multidrug-resistant infections and persistent colonization. Enterococci are opportunistic environmental inhabitants with a remarkable adaptive capacity to evolve and transmit antimicrobial-resistant determinants. The VRE gene operons show distinct genetic variability and apparently continued evolution leading to a variety of antimicrobial resistance phenotypes and various environmental and livestock reservoirs for the most common van genes. Such complex diversity renders a number of important therapeutic options including "last resort antibiotics" ineffective and poses a particular challenge for clinical management. Enterococci resistance to glycopeptides and multidrug resistance warrants attention and continuous monitoring.

Characterization of antimicrobial resistance and virulence genes in Enterococcus spp. isolated from retail meats in Alberta, Canada

The objective of this study was to characterize antimicrobial resistance (AMR) and virulence genotypes of Enterococcus spp. particularly Enterococcus faecalis isolated from retail meats purchased (2007-2008) in Alberta, Canada. Unconditional statistical associations between AMR pheno- and genotypes and virulence genotypes were determined. A total of 532 enterococci comprising one isolate from each positive sample were analyzed for antimicrobial susceptibility. A customized enterococcal microarray was used for species identification and the detection of AMR and virulence genes. E. faecalis was found in >94% of poultry samples and in about 73% of beef and 86% of pork samples. Enterococcus faecium was not found in turkey meat and its prevalence was 2% in beef and pork and 4% in chicken samples. None of the enterococci isolates were resistant to the clinically important drugs ciprofloxacin, daptomycin, linezolid and vancomycin. Multiresistance (≥3 antimicrobials) was more common in E. faecalis (91%) isolated from chicken and turkey (91%) than those isolated from beef (14%) or pork (45%). Resistance to aminoglycosides was also noted at varying degrees. The most common resistance genes found in E. faecalis were aminoglycosides (aac, aphA3, aadE, sat4, aadA), macrolides (ermB, ermA), tetracyclines (tetM, tetL, tetO), streptogramin (vatE), bacitracin (bcrR) and lincosamide (linB). Virulence genes expressing aggregation substances (agg) and cytolysin (cylA, cylB, cylL, cylM) were found more frequently in poultry E. faecalis and were unconditionally associated with tetM, linB and bcrR resistance genes. Other virulence genes coding for adhesion (ace, efaAfs), gelatinase (gelE) were also found in the majority of E. faecalis. Significant statistical associations were found between resistance and virulence genotypes, suggesting their possible physical link on a common genetic element. This study underscores the importance of E. faecalis as a reservoir of resistance and virulence genes and their potential transfer to humans through consumption of contaminated undercooked meat.

Detection of genetic elements carrying glycopeptide resistance clusters in Enterococcus by DNA microarrays

Glycopeptide resistance in enterococci is conferred by discrete genetic elements, which can carry mutations, deletions, and partial disruptions. We developed a custom DNA microarray as a tool for typing glycopeptide resistant enterococci. Oligonucleotide DNA microarrays were produced targeting the genes of enterococcal glycopeptide resistance gene clusters. A total of 105 probes selective for 42 genes were designed. The microarrays were validated on DNA extracted from reference strains and used to type 24 enterococcal strains belonging to various species and with different resistance phenotype, detecting all the genes of the resistance clusters which were actually present in each control and study strain. Moreover, this technique was capable of identifying the presence of additional resistant elements masked by a higher or similar resistance phenotype, and also of correcting an erroneous assignment made on the basis of phenotype alone. The use of our microarrays provided additional and complementary information compared to the phenotype alone. Our screening technique compares favourably, in aggregate terms of turnaround time, costs and convenience with other molecular biology techniques such as amplification and sequencing when applied to the study of complex genetic elements composed of several genes, such as glycopeptide resistance elements in enterococci.

VanA-type enterococci from humans, animals, and food: species distribution, population structure, Tn1546 typing and location, and virulence determinants

VanA-type human (n=69), animal (n=49), and food (n=36) glycopeptide-resistant enterococci (GRE) from different geographic areas were investigated to study their possible reservoirs and transmission routes. Pulsed-field gel electrophoresis (PFGE) revealed two small genetically related clusters, M39 (n=4) and M49 (n=13), representing Enterococcus faecium isolates from animal and human feces and from clinical and fecal human samples. Multilocus sequence typing showed that both belonged to the epidemic lineage of CC17. purK allele analysis of 28 selected isolates revealed that type 1 was prevalent in human strains (8/11) and types 6 and 3 (14/15) were prevalent in poultry (animals and meat). One hundred and five of the 154 VanA GRE isolates, encompassing different species, origins, and PFGE types, were examined for Tn1546 type and location (plasmid or chromosome) and the incidence of virulence determinants. Hybridization of S1- and I-CeuI-digested total DNA revealed a plasmid location in 98% of the isolates. Human intestinal and animal E. faecium isolates bore large (>150 kb) vanA plasmids. Results of PCR-restriction fragment length polymorphism and sequencing showed the presence of prototype Tn1546 in 80% of strains and the G-to-T mutation at position 8234 in three human intestinal and two pork E. faecium isolates. There were no significant associations (P>0.5) between Tn1546 type and GRE source or enterococcal species. Virulence determinants were detected in all reservoirs but were significantly more frequent (P<0.02) among clinical strains. Multiple determinants were found in clinical and meat Enterococcus faecalis isolates. The presence of indistinguishable vanA elements (mostly plasmid borne) and virulence determinants in different species and PFGE-diverse populations in the presence of host-specific purK housekeeping genes suggested that all GRE might be potential reservoirs of resistance determinants and virulence traits transferable to human-adapted clusters.

Direct detection of antibiotic resistance genes in specimens of chicken and pork meat

Antibiotic resistance (AR) in bacteria, a major threat to human health, has emerged in the last few decades as a consequence of the selective pressure exerted by the widespread use of antibiotics in medicine, agriculture and veterinary practice and as growth promoters in animal husbandry. The frequency of 11 genes [tet(M), tet(O), tet(K), erm(A), erm(B), erm(C), vanA, vanB, aac (6')-Ie aph (2'')-Ia, mecA, blaZ] encoding resistance to some antibiotics widely used in clinical practice was analysed in raw pork and chicken meat and in fermented sausages as well as in faecal samples from the relevant farm animals using a molecular approach based on PCR amplification of bacterial DNA directly extracted from specimens. Some of the 11 AR genes were highly prevalent, the largest number being detected in chicken meat and pig faeces. The genes found most frequently in meat were tet(K) and erm(B); vanB and mecA were the least represented. All 11 determinants were detected in faecal samples except mecA, which was found only in chicken faeces. erm(B) and erm(C) were detected in all faecal samples. The frequency of AR genes was not appreciably different in meat compared to faecal specimens of the relevant animal except for vanB, which was more prevalent in faeces. Our findings suggest that AR genes are highly prevalent in food-associated bacteria and that AR contamination is likely related to breeding rather than processing techniques. Finally, the cultivation-independent molecular method used in this work to determine the prevalence of AR genes in foods proved to be a rapid and reliable alternative to traditional tools.

Vancomycin-resistant enterococci (VRE) in meat and environmental samples

We investigated the spread of vancomycin-resistant enterococci (VRE) in strains from meat and environmental samples and the location of glycopeptide-resistance determinants in VanA isolates. VRE and VSE (vancomycin-sensitive enterococci) resistance patterns to six antimicrobials were also evaluated. A total of 59 meat isolates (35%) and 119 environmental isolates (26.5%) were glycopeptide resistant enterococci. In particular, 10.7% meat isolates belonged to the VanA, 8.3% to VanB and 16% to VanC phenotypes. Environmental samples presented 0.7% VanA, 14.5% VanB, and 11.4% VanC strains. Evident differences were not observed among the resistance patterns of VRE and VSE isolates. Neither an important difference was observed comparing the resistance patterns in enterococci from meat and environment. In particular a low incidence of beta-lactamic resistant strains was found, whereas high rates of resistance were observed for streptomycin (85.7% and 92.8%), kanamycin (79.7% and 96%) and gentamycin (85.1% and 91.7%). An intermediate rate of resistant bacteria emerged for erythromycin (35.1% and 10.5%). All VanA isolates independent of origin had more plasmids with different molecular weights. PCR amplification of the 732 bp fragment in plasmids from the VanA strains confirmed affiliation to the vanA gene cluster and the extrachromosomal location of the glycopeptide-resistance determinants. Our study suggests that food and environment play a potential role as reservoirs of resistance determinants, prompting the need to undertake epidemiological and molecular studies to evaluate the mobility of these genes.

Occurrence and relatedness of vancomycin-resistant enterococci in animals, humans, and the environment in different European regions

Vancomycin-resistant enterococci (VRE) in Europe are thought to have emerged partly due to the use of the glycopeptide avoparcin in animal husbandry. We compared the occurrence of VRE in geographical regions of Europe in which until 1997 large amounts of avoparcin were used (Spain, United Kingdom, and Denmark) with the occurrence of VRE in Sweden, where avoparcin was banned in 1986. We also studied the relatedness between VRE strains from different regions and habitats. In total, 2,580 samples were collected from humans, animals, and the environment (soil, sewage, recipient water). VRE resistant to 20 microg/ml vancomycin were identified in 8.2% of the samples and were found most frequently in raw and treated urban sewage samples (means, 71% and 36% of the samples, respectively), pig manure (17%), and hospital sewage (16%). The proportions of VRE-positive sewage samples were similar in Sweden, Spain, and the United Kingdom, whereas pig feces and manure were more often positive in Spain than in Sweden (30% versus 1%). Most VRE were Enterococcus faecium carrying vanA, and computerized biochemical phenotyping of the isolates of different ecological origins showed a high degree of polyclonality. In conclusion, it seems that animal-associated VRE probably reflect the former use of avoparcin in animal production, whereas VRE in human-associated samples may be a result of antibiotic use in hospitals. Since there seems to be a reservoir of the resistance genes in all countries studied, precautions must be taken to limit the use of antibiotics and antibiotic-like feed additives.

Clonal spread of a vancomycin-resistant Enterococcus faecium strain among bloodstream-infecting isolates in Italy

Recent data indicated that the rate of vancomycin resistance in bloodstream-infecting enterococcal isolates in Italy is one of the highest in Europe. The aims of this study were to characterize bloodstream-infecting vancomycin-resistant enterococci (VRE) obtained from various Italian hospitals and to establish whether the isolates were clonally related. During the years 2001 to 2003, a total of 39 VRE isolates were obtained from 19 hospital laboratories in various areas of Italy. Species identification and resistance genotypes of the isolates were obtained by multiplex PCR. Further characterization included antibiotic susceptibility testing, pulsed-field gel electrophoresis (PFGE) of SmaI-digested genomic DNA, detection of virulence genes (esp and hyl), and multilocus sequence typing (MLST) of selected isolates. VRE were identified as 31 Enterococcus faecium (VREfm) isolates and 8 E. faecalis isolates. All but one isolate carried the vanA gene; one VREfm isolate carried the vanB gene. Analysis of the PFGE profiles showed that 28 VREfm isolates shared a similar electrophoretic profile, designed type 1, and were clonally related. All type 1 isolates were resistant to ampicillin, streptomycin, gentamicin, and rifampin and were positive for the esp gene. MLST identified an allelic profile (ST78) comprising purK allele 1, belonging to the C1 clonal lineage, characteristic of human infection and hospital outbreak isolates. The vanB-carrying VREfm isolate, of PFGE type 2, was shown to be a single-locus variant of ST78. Our data indicate that the recent increase in the number of bloodstream infections caused by VRE in Italy is due to the spread of a hospital-adapted, multidrug-resistant VREfm clone belonging to an internationally disseminated lineage.

Contribution of enterococci to the spread of antibiotic resistance in the production chain of swine meat commodities

Thirty-six samples, including fecal specimens, dry feedstuffs, raw and processed pork meat products, and dry fermented sausages, were collected from two production chains of swine meat commodities and analyzed for the presence of 11 antibiotic resistance (AR) genes. Specific PCR assays carried out on DNA extracted directly from the samples revealed a high incidence of the genes tet(K) (80.5%), ermB (66.7%), and tet(M) (66.7%). Feces and feedstuffs gave the largest number of positive amplifications. To elucidate the contribution of enterococci to the occurrence and spread of AR, 146 resistant enterococci were isolated, and their identity, genetic fingerprints, and AR gene profiles were determined by means of molecular techniques. Enterococcus faecalis and Enterococcus faecium were the predominant isolated species (43.8 and 38.4%, respectively); Other Enterococcus species identified were E. durans (8.9%), E. hirae (2.7%), E. gallinarum (2.1%), E. mundtii (2.1%), and E. casseliflavus (2.1%). A number of isolates displayed a complex AR gene profile comprising up to four different resistance determinants. The genes tet(M) and ermB were highly diffused, being present in 86.9 and 84.9%, respectively, of the isolates. The application of amplified fragment length polymorphism fingerprinting was particularly valuable to monitor the resistant enterococcal isolates along the production chain and to individuate steps in which contamination might occur. In fact, isolates of E. faecalis and E. faecium showing the same amplified fragment length polymorphism profile and AR gene pattern were detected in samples taken at different steps of the food chain suggesting three cases of bacterial clonal spread.

Veterinary Drug Usage and Antimicrobial Resistance in Bacteria of Animal Origin

In the production of food animals, large amounts of antimicrobial agents are used for therapy and prophylaxis of bacterial infections and in feed to promote growth. There are large variations in the amounts of antimicrobial agents used to produce the same amount of meat among the different European countries, which leaves room for considerable reductions in some countries. The emergence of resistant bacteria and resistance genes due to the use of antimicrobial agents are well documented. In Denmark it has been possible to reduce the usage of antimicrobial agents for food animals significantly and in general decreases in resistance have followed. Guidelines for prudent use of antimicrobial agents may help to slow down the selection for resistance and should be based on knowledge regarding the normal susceptibility patterns of the causative agents and take into account the potential problems for human health. Current knowledge regarding the occurrence of antimicrobial resistance in food animals, the quantitative impact of the use of different antimicrobial agents on selection of resistance and the most appropriate treatment regimes to limit the development of resistance is incomplete. Programmes monitoring the occurrence and development of resistance and consumption of antimicrobial agents are strongly desirable, as is research into the most appropriate ways to use antimicrobial agents in veterinary medicine.

Prevalence of Vancomycin Resistant Enterococci on Poultry Farms Established After the Ban of Avoparcin

Fecal samples from poultry on farms established after the ban of avoparcin (study farms) and from poultry on farms previously exposed to avoparcin (control farms) were examined for the presence of vancomycin-resistant enterococci (VRE). The samples were collected during the autumn and winter of 2001-2002. One isolate from each positive sample was selected, identified to species level, and examined for the presence of the vanA gene. The concentration of VRE and generic enterococci in the samples were also determined. In addition, the susceptibility to the ionophoric coccidiostat narasin was examined in a number of enterococcal isolates from poultry and in some enterococci of porcine origin that had not been exposed to narasin. VanA-type VRE was detected in samples from 64% of the study farms and 96% of the control farms. However, the concentration of VRE in the control samples was about six times larger than in the samples from the study farms. The minimum inhibitory concentration values for narasin differed between the poultry (1-4 mg/liter) and the porcine (0.25-0.5 mg/liter) isolates, indicating a decreased susceptibility towards narasin among enterococci from poultry.

Antimicrobial susceptibility of vancomycin-susceptible and -resistant enterococci isolated in Italy from raw meat products, farm animals, and human infections

The susceptibility of vancomycin-resistant (VRE) and vancomycin-susceptible (VSE) enterococci to 10 antimicrobial agents was evaluated. The strains, belonging to different species, were isolated in Italy from raw meat products, farm animals, and human clinical infections in the years 1997-2000. High frequency of resistance to tetracycline and erythromycin was observed in all the groups of strains. On the contrary, chloramphenicol was the only drug that showed a relatively low rate of resistance in all the groups examined. In general, the resistance rates observed for VSE did not differ from those observed for VRE of the same species and origin. Some differences could be noticed among the different enterococcal species, with Enterococcus faecium strains being usually more resistant to beta-lactams, and Enterococcus faecalis strains more resistant to gentamicin. However, the strongest differences were observed when the strains were compared according to their source, the human isolates being usually more resistant than the isolates of animal origin. No significant difference was observed between isolates of swine and poultry origin. Among VRE E. faecium, multiple resistance was much more frequent among the human strains (90%) than among poultry (48.9%) and swine (26.5%) strains. These results show that in Italy VRE isolates from human clinical infections are usually more resistant than isolates from meat products and farm animals, and possess different antimicrobial resistance profiles.

Gene transfer of vancomycin and tetracycline resistances among Enterococcus faecalis during cheese and sausage fermentations

This study assessed the frequency of transfer of two mobile genetic elements coding for virulence determinants and antibiotic resistance factors, into food associated enterococci during fermentation processes. First, the transfer of the pheromone-inducible pCF10 plasmid, carrying tetracycline resistance and aggregation substance (AS) as virulence factor, between clinical and food strains of Enterococcus faecalis, was investigated in models of cheese and fermented sausage. The experiments demonstrated that even in the absence of selective tetracycline pressure, plasmid pCF10 was transferred from E. faecalis OG1rf cells to food strain E. faecalis BF3098c and that the plasmid subsequently persisted in these environments. Very high frequency of transfer was observed in sausage (10(-3)/recipient) if compared to cheese (10(-6)) and plate mating (10(-4)). Transconjugants were subsequently verified by PCR. The second transmissible element was the plasmid harbouring the vancomycin resistance (VanA phenotype) from E. faecalis A256. The transfer of this antibiotic resistance to a food strain of E. faecalis was studied in vitro and in food models. Although the transfer of vancomycin resistance was achieved in all the environments, the highest conjugation frequencies were observed during the ripening of fermented sausages, reaching 10(-3) transconjugants/recipient cell. PCR confirmed the transfer of the VanA genotype into a food associated Enterococcus strain. This study showed that even in the absence of selective pressure, mobile genetic elements carrying antibiotic resistance and virulence determinants can be transferred at high frequency to food associated enterococci during cheese and sausage fermentation.

Antimicrobial resistance in recent fecal enterococci from healthy volunteers and food handlers in Spain: genes and phenotypes

Susceptibility patterns to 15 different antibiotics and the presence of resistance genes were evaluated in recent fecal Enterococcus isolates recovered from 42 healthy volunteers (HV) and 43 food-handlers (FH). A total of 142 Enterococcus faecalis, 74 Enterococcus faecium, and 23 Enterococcus spp. with different antibiotic susceptibility patterns were studied. A higher percentage of resistance for moxifloxacin, erythromycin, glycopeptides and high-level resistance (HLR) to gentamicin were observed in the FH group. Ampicillin- or linezolid-resistant isolates were not recovered in any of the groups. The tet(M) gene was found in 96% and in 85% of tetracycline-resistant isolates from HV and FH, respectively. HLR-kanamycin was mediated by aph(3')-IIIa, or aac(6')-aph(2"), or both genes in all isolates from HV group and in 86% from FH group. The aac(6')-aph(2") gene was found in all HLR-gentamicin isolates. Ninety-one percent of HV and 71% of FH erythromycin-resistant isolates harbored the erm(B) gene (erythromycin MIC range of 8-128 microg/ml), whereas erm(A), erm(C), or mef(A) genes were not detected. Coexistence of erm(B), aph(3')-IIIa, and tet(M) genes was observed in 17% of the isolates of both groups. The HLR-gentamicin isolates presented unrelated PFGE patterns while 2 out of 3 vanA E. faecium isolates showed an indistinguishable SmaI-pulsed-field gel electrophoresis (PFGE) pattern. This study shows that despite 4 years of official banning of antibiotic growth promoters in animals, enterococci isolated from FH are more resistant than those from HV. This suggests the permanence of resistant clones or transferable resistance elements in farms and a possible exchange between food products and humans, or eventually the long-term permanence of certain clones in the FH intestinal tract.

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.

Relations between the occurrence of resistance to antimicrobial growth promoters among Enterococcus faecium isolated from broilers and broiler meat

From 1995 to 2001, Enterococcus faecium isolates were collected from broiler flocks at slaughter and broiler meat products at retail outlets and were tested for susceptibility to classes of antimicrobials used for growth promotion in broilers in Denmark, namely: evernimicin, glycopeptide, macrolide and streptogramin. By February 1998, all antimicrobial growth promoters (AGPs) were withdrawn from the Danish broiler production. The present study investigates, by logistic regression analyses, the (1) changes in the occurrence of AGP resistance among E. faecium from broilers and broiler meat from the fourth quarter of 1995 to the fourth quarter of 2001 and (2) relations between the occurrence of AGP resistance among E. faecium isolates from Danish broilers and AGP resistance among E. faecium isolates from the broiler meat of Danish and unknown origin collected in the same quarter within the year. In the present study, we showed that after the AGP withdrawal, a significant decline in resistance to avilamycin, erythromycin, vancomycin and virginiamycin was observed among E. faecium from broilers and broiler meat. In addition, a decline in the occurrence of AGP resistance among E. faecium from Danish broilers was associated with a decrease in the predicted probability of isolating an AGP-resistant E. faecium isolate from a randomly selected broiler meat product. In the analyses "relations between the occurrence of AGP resistance among E. faecium isolated from broilers and broiler meat collected in the same quarter" errors in the explanatory variable were expected. Therefore, a simulation study was performed to validate the results from logistic regression analyses. The results obtained by the two methods were similar.

Genetic linkage between erm(B) and vanA in Enterococcus hirae of poultry origin

Vancomycin-resistant enterococci (VRE) have frequently been isolated from Norwegian poultry production following the prohibition of the glycopeptide growth promoter avoparcin since 1995. In the present study, a close genetic linkage between the vanA and erm(B) determinants in an Enterococcus hirae isolate of poultry origin is demonstrated, a result that indicates a mechanism for co-selection and maintenance of vancomycin resistance in absence of selective pressure from avoparcin. A total of 36 vanA-positive enterococci of poultry origin, also phenotypically resistant to erythromycin and/or tetracycline, were analyzed by PCR for identification of erm and tet resistance determinants. An E. hirae isolate harbored erm(B) and tet(K), and in this isolate vanA and erm(B) were located on a BamHI fragment of an approximately 50-kb plasmid. Approximately 3 kb of this fragment was amplified by PCR with vanA and erm(B) primers. Sequence analysis of the region between erm(B) and vanZ of Tn1546 showed a truncated IS1216V inserted downstream of the erm(B) stop codon, aligned with a conserved copy of the 3'-inverted terminal repeat of Tn1546. Mating experiments with the E. hirae isolate as donor and E. faecalis JH2-2 as recipient did not result in any transconjugants, indicating that the vanA/erm(B)-carrying plasmid was nonconjugative under the given experimental conditions.

Persistence of vancomycin-resistant enterococci (VRE) in broiler houses after the avoparcin ban

The glycopeptide growth promoter avoparcin was banned from animal production in the EU in 1997 due to concern for the spread of vancomycin-resistant enterococci (VRE) from food animals to humans. In recent Norwegian and Danish studies, extensive occurrence of VRE on broiler farms and in broiler flocks after the avoparcin ban has been reported. The present study was undertaken to investigate the epidemiology of VRE on broiler farms in the absence of the selective pressure exerted by avoparcin. Environmental samples were obtained from five broiler houses after depopulation, cleaning, and disinfection of the houses between rotations, and two consecutive broiler flocks from each house were sampled by taking cloacal swabs from the broilers at the time of slaughter. A total of 69 vancomycin-resistant Enterococcus faecium isolates obtained from broiler flocks and broiler houses were subjected to molecular typing by pulsed-field gel electrophoresis (PFGE). Forty-one PFGE-profiles were observed. VRE with indistinguishable or highly similar PFGE profiles were isolated from consecutive broiler flocks and from environmental samples from the houses in which the flocks were reared, whereas VRE-isolates from different broiler houses and from flocks reared in different houses appeared to be genetically unrelated. These findings indicated that VRE was transmitted between consecutive broiler flocks by clones of resistant bacteria surviving in the broiler houses despite cleaning and disinfection between rotations. Thus, the extensive occurrence of VRE in broiler flocks after the avoparcin ban may be explained by persistence of VRE in the broiler house environment.

Vancomycin resistance is maintained in enterococci in the viable but nonculturable state and after division is resumed

Stressed vancomycin-resistant enterococci (VRE) can activate a survival strategy known as the viable but nonculturable (VBNC) state and are able to maintain vancomycin resistance. During restoration of division they continue to express the vancomycin resistance trait. We suggest that VBNC enterococci may constitute further reservoirs of VRE and therefore represent an additional risk for human health.

Vancomycin-resistant enterococci in shellfish, unchlorinated waters, and chicken

Vancomycin-resistant enterococci (VRE) have been a cause of increasing concern chiefly regarding the infection of hospital patients. There is suspicion, but limited evidence, that food and environmental spread may be important. Biomonitoring by examination of bivalve shellfish was used to assess the occurrence of VRE entering the environment. Using pre-enrichment and Lewisham and Slanetz and Bartley agars, 2/125 (1.6%) of shellfish were found to contain enterococci resistant to high levels of vancomycin. Lewisham agar allows relatively rapid identification of VRE. In a second phase of the work using pre-enrichment and Slanetz and Bartley agar, 4/151 (2.7%) shellfish and 5/27 (18.5%) raw chickens contained VRE. Using filtration and pre-enrichment, no VRE were found in 54 unchlorinated water samples. The study shows that environmental prevalence of VRE is low, and that raw chickens are frequently contaminated.

Antibiotic resistance in food-related bacteria--a result of interfering with the global web of bacterial genetics

A series of antibiotic resistance genes have been sequenced and found to be identical or nearly identical in various ecological environments. Similarly, genetic vectors responsible for assembly and mobility of antibiotic resistance genes, such as transposons, integrons and R plasmids of similar or identical type are also widespread in various niches of the environment. Many zoonotic bacteria carry antibiotic resistance genes directly from different food-producing environments to the human being. These circumstances may have a major impact on the degree for success in treating infectious diseases in man. Several recent examples demonstrate that use of antibiotics in all parts of the food production chain contributes to the increasing level of antibiotic resistance among the food-borne pathogenic bacteria. Modern industrialized food production adds extra emphasis on lowering the use of antibiotics in all parts of agriculture, husbandry and fish farming because these food products are distributed to very large numbers of humans compared to more traditional smaller scale niche production.

Enterococci from foods

Enterococci have recently emerged as nosocomial pathogens. Their ubiquitous nature determines their frequent finding in foods as contaminants. In addition, the notable resistance of enterococci to adverse environmental conditions explains their ability to colonise different ecological niches and their spreading within the food chain through contaminated animals and foods. Enterococci can also contaminate finished products, such as fermented foods and, for this reason, their presence in many foods (such as cheeses and fermented sausages) can only be limited but not completely eliminated using traditional processing technologies. Enterococci are low grade pathogens but their intrinsic resistance to many antibiotics and their acquisition of resistance to the few antibiotics available for treatment in clinical therapy, such as the glycopeptides, have led to difficulties and a search for new drugs and therapeutic options. Enterococci can cause food intoxication through production of biogenic amines and can be a reservoir for worrisome opportunistic infections and for virulence traits. Clearly, there is no consensus on the acceptance of their presence in foodstuffs and their role as primary pathogens is still a question mark. In this review, the following topics will be covered: (i) emergence of the enterococci as human pathogens due to the presence of virulence factors such as the production of adhesins and aggregation substances, or the production of biogenic amines in fermented foods; (ii) their presence in foods; (iii) their involvement in food-borne illnesses; (iv) the presence, selection and spreading of antibiotic-resistant enterococci as opportunistic pathogens in foods, with particular emphasis on vancomycin-resistant enterococci.

Vancomycin-resistant Enterococcus faecium (VREF) from Norwegian poultry cluster with VREF from poultry from the United Kingdom and The Netherlands in an amplified fragment length polymorphism genogroup

The genetic relationship between 197 vancomycin-resistant Enterococcus faecium (VREF) isolates and 21 vancomycin-susceptible E. faecium isolates from Norwegian poultry was analyzed by amplified fragment length polymorphism (AFLP). The isolates were compared to 255 VREF isolates from various sources and countries. The Norwegian isolates constituted a relatively homogeneous population of E. faecium and clustered in a previously defined poultry AFLP genogroup.