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

Enterococci as a One Health indicator of antimicrobial resistance

The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.

Vancomycin Resistance in Enterococcus and Staphylococcus aureus

Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.

Barriers to genetic manipulation of Enterococci: Current Approaches and Future Directions

Enterococcus faecalis and Enterococcus faecium are Gram-positive commensal gut bacteria that can also cause fatal infections. To study clinically relevant multi-drug resistant E. faecalis and E. faecium strains, methods are needed to overcome physical (thick cell wall) and enzymatic barriers that limit the transfer of foreign DNA and thus prevent facile genetic manipulation. Enzymatic barriers to DNA uptake identified in E. faecalis and E. faecium include type I, II and IV restriction modification systems and CRISPR-Cas. This review examines E. faecalis and E. faecium DNA defence systems and the methods with potential to overcome these barriers. DNA defence system bypass will allow the application of innovative genetic techniques to expedite molecular-level understanding of these important, but somewhat neglected, pathogens.

Nigella sativaoil extract: A natural novel specific conjugal transfer inhibitor of vancomycin resistance from vanA/B Resistant Enterococcus faecium to Staphylococcus aureus

AIM

The emergence of vancomycin-resistant Staphylococcus aureus (VRSA) has been identified as one of the most challenging problems in healthcare settings worldwide. Specific conjugation inhibitors development are critical in the fight against the spread of emerging VRSA. The impact of Nigella sativa oil on VR genes conjugal transfer from Enterococcus faecium (VREtfm) to vancomycin sensitive S. aureus (VSSA) was investigated in this study.

METHODS AND RESULTS

Enterococci were isolated from retail broilers, fish, cows' milk, and human urine. VR Enterococcus faecalis and VREtfm VanA-phenotype' were prevalent in retail broiler samples. The VREtfm isolates were dominant, exhibiting high levels of resistance to gentamycin and ciprofloxacin antibiotics, as well as the existence of both vanA and vanB genes and virulence traits (ESP+, asa1+) as determined by PCR. VREtfm strains containing vanA/vanB genes and transconjugants containing 20Kb plasmids (transfer frequency around 10³ ) and carrying the Tn1546 transposon were identified. Tn1546 transposon transfer with its VR markers to VSSA was effectively inhibited in treated VREtfm donor strains with a sub-MIC of N. sativa oil.

THE SIGNIFICANCE AND IMPACT OF THE STUDY

This work offers new insights for overcoming VR conjugal transfer utilising natural N. sativa oil, as well as a suggestion for a novel specialized conjugation inhibitor that could effectively facilitate the difficulty of eliminating VR bacteria from healthcare settings.

Genomic, Antimicrobial Resistance, and Public Health Insights into Enterococcus spp. from Australian Chickens

Due to Australia's management of antimicrobial use in poultry, particularly the discontinued use of avoparcin for nearly 20 years, it is hypothesized that vancomycin-resistant enterococci associated with human disease are not derived from poultry isolates. This study evaluated antimicrobial resistance (AMR) of five enterococcal species isolated from Australian meat chickens, genomic features of Enterococcus faecium and Enterococcus faecalis, and the phylogenetic relationship of the poultry-derived E. faecium with isolates from human sepsis cases. All enterococcal isolates from chicken ceca were subjected to antimicrobial susceptibility testing. E. faecium and E. faecalis underwent whole-genome sequencing. E. faecium was compared at the core genome level to a collection of human isolates (n = 677) obtained from cases of sepsis over a 2-year period spanning 2015 to 2016. Overall, 205 enterococci were isolated consisting of five different species. E. faecium was the most frequently isolated species (37.6%), followed by E. durans (29.7%), E. faecalis (20%), E. hirae (12.2%), and E. gallinarum (0.5%). All isolates were susceptible to vancomycin and gentamicin, while one isolate was linezolid resistant (MIC 16 mg/liter). Core genome analysis of the E. faecium demonstrated two clades consisting predominantly of human or chicken isolates in each clade, with minimal overlap. Principal component analysis for total gene content revealed three clusters comprised of vanA-positive, vanB-positive, and both vanA- and vanB-negative E. faecium populations. The results of this study provide strong evidence that Australian chicken E. faecium isolates are unlikely to be precursor strains to the currently circulating vancomycin-resistant strains being isolated in Australian hospitals.

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.

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.

Exploring the differences of antibiotic resistance genes profiles between river surface water and sediments using metagenomic approach

To better understand the potential genic communication and dissemination of antibiotic resistance genes (ARGs) in different environmental matrices, the differences of ARG profiles between river surface water and sediments were explored. Metagenomic analysis was applied to investigate the comprehensive ARG profiles in water and sediment samples collected from the highly human-impacted catchment of the Beijiang River and its river source. A total of 135 ARG subtypes belonging to 18 ARG types were identified. Generally, ARGs in surface water were more diverse and abundant than those in sediments. ARG profiles in the surface water and sediment samples were distinct from each other, but some ARGs were shared by the surface water and sediments. Results revealed that multidrug and bacitracin resistance genes were the predominant ARGs types in both surface water (0.30, 0.17 copies/cell) and sediments (0.19, 0.15 copies/cell). 73 ARG subtypes were shared by the water and sediment samples and had taken over 90% of the total detected ARG abundance. Most of the shared ARGs are resistant to the clinically relevant antibiotics. Furthermore, significant correlations between the ARGs and 21 shared genera or mobile genetic elements (MGEs) (plasmids and integrons) were found in surface water and sediments, suggesting the important role of genera or MGEs in shaping ARGs profiles, propagation and distribution. These findings provide deeper insight into mitigating the propagation of ARGs and the associated risks to public health.

Tetracyclines, sulfonamides and quinolones and their corresponding resistance genes in the Three Gorges Reservoir, China

The Three Gorges Project significantly impacted water quality and ecological balance in this area. The special engineered aquatic environment could be an important reservoir for antibiotic resistance genes (ARGs). Fifteen ARGs corresponding to three groups of antibiotics (tetracyclines, sulfonamides and quinolones) were determined in surface water, soil and sediment in this study. Total concentrations of antibiotics ranged from 21.55 to 536.86ng/L, 3.69 to 438.76ng/g, 15.78 to 213.84ng/g in water, soil and sediment, respectively. Polymerase chain reaction (PCR) of ARGs revealed the presence of two sulfonamide resistance genes (sul1, sul2), five tetracycline resistance genes (tetA, tetB, tetM, tetQ, tetG) and class 1 integron gene (intI1) in all samples. And the relative abundance of sulfonamide resistance genes was generally higher than tetracycline resistance genes in three matrices. Significant correlations (p<0.05) were found between the concentrations of intI1 and ARGs (tetA, tetB, tetM, tetQ, tetG, sul1, sul2), indicating intI1 may facilitate the proliferation and propagation of these genes. Redundancy analysis (RDA) showed distribution of ARGs was related to the certain antibiotics residues, which may exert selective pressure on bacteria and thus enrich the abundance of ARGs. The results of this study could provide useful information for both better understanding and management of the contamination caused by ARGs and related antibiotics in engineered aquatic environments.

Mass spectrometry and multiplex antigen assays to assess microbial quality and toxin production of Staphylococcus aureus strains isolated from clinical and food samples

The aim of our study was to investigate the microbial quality of meat products and on some clinical samples in Abidjan focused on Staphylococcus genus and the toxin production profile of Staphylococcus aureus (S. aureus) isolated. Bacteria were collected from 240 samples of three meat products sold in Abidjan and 180 samples issued from clinical infections. The strains were identified by both microbiological and MALDI-TOF-MS methods. The susceptibility to antibiotics was determined by the disc diffusion method. The production of Panton-Valentine Leukocidin, LukE/D, and epidermolysins was screened using radial gel immunodiffusion. The production of staphylococcal enterotoxins and TSST-1 was screened by a Bio-Plex Assay. We observed that 96/240 of meat samples and 32/180 of clinical samples were contaminated by Staphylococcus. Eleven species were isolated from meats and 4 from clinical samples. Forty-two S. aureus strains were isolated from ours samples. Variability of resistance was observed for most of the tested antibiotics but none of the strains displays a resistance to imipenem and quinolones. We observed that 89% of clinical S. aureus were resistant to methicillin against 58% for those issued from meat products. All S. aureus isolates issued from meat products produce epidermolysins whereas none of the clinical strains produced these toxins. The enterotoxins were variably produced by both clinical and meat product samples.

Antimicrobial susceptibility of indicator bacteria isolated from chickens in Southeast Asian countries (Vietnam, Indonesia and Thailand)

To determine the prevalence of indicator bacteria resistant to antimicrobials among poultry in three Southeast Asian countries (Vietnam, Indonesia and Thailand), we examined the antimicrobial susceptibilities of commensal bacteria isolated from chickens. In total, 125, 117 and 180 isolates of Escherichia coli, Enterococcus faecalis and Enterococcus faecium, respectively, were used to test for antimicrobial susceptibility. Bacterial resistance to antimicrobial treatment was most frequently observed with oxytetracycline with a prevalence of 73.6% (E. coli), 69.2% (E. faecalis) and 92.2% (E. faecium). Resistance to fluoroquinolones, which are critically important medicines, was also frequently observed in E. coli (48.8%), E. faecalis (17.9%) and E. faecium (82.8%). The prevalence of indicator bacteria resistant to most of the antimicrobials tested in these countries was higher than those for developed countries. The factors underlying antimicrobial resistance may include inappropriate and/or excessive use of antimicrobials. These results highlight the need for monitoring the emergence and prevalence of antimicrobial resistance in developing countries.

Characterization of genes encoding for acquired bacitracin resistance in Clostridium perfringens

Phenotypic bacitracin resistance has been reported in Clostridium perfringens. However, the genes responsible for the resistance have not yet been characterized. Ninety-nine C. perfringens isolates recovered from broilers and turkeys were tested for phenotypic bacitracin resistance. Bacitracin MIC(90) (>256 µg/ml) was identical for both turkey and chicken isolates; whereas MIC(50) was higher in turkey isolates (6 µg/ml) than in chicken isolates (3 µg/ml). Twenty-four of the 99 isolates showed high-level bacitracin resistance (MIC breakpoint >256 µg/ml) and the genes encoding for this resistance were characterized in C. perfringens c1261_A strain using primer walking. Sequence analysis and percentages of amino acid identity revealed putative genes encoding for both an ABC transporter and an overproduced undecaprenol kinase in C. perfringens c1261_A strain. These two mechanisms were shown to be both encoded by the putative bcrABD operon under the control of a regulatory gene, bcrR. Efflux pump inhibitor thioridazine was shown to increase significantly the susceptibility of strain c1261_A to bacitracin. Upstream and downstream from the bcr cluster was an IS1216-like element, which may play a role in the dissemination of this resistance determinant. Pulsed-field gel electrophoresis with prior double digestion with I-CeuI/MluI enzymes followed by hybridization analyses revealed that the bacitracin resistance genes bcrABDR were located on the chromosome. Semi-quantitative RT-PCR demonstrated that this gene cluster is expressed under bacitracin stress. Microarray analysis revealed the presence of these genes in all bacitracin resistant strains. This study reports the discovery of genes encoding for a putative ABC transporter and an overproduced undecaprenol kinase associated with high-level bacitracin resistance in C. perfringens isolates from turkeys and broiler chickens.

Diversity of vanA-type vancomycin-resistant Enterococcus faecium isolated from broilers, poultry slaughterers and hospitalized humans in Greece

OBJECTIVES

This study investigated the prevalence of vancomycin-resistant enterococci (VRE) in the broiler production environment after the avoparcin ban and their epidemiological relationship with human clinical VRE from the same geographical regions in Greece.

METHODS

Caecal contents from broilers (n = 500) from eight livestock farms and faecal samples from poultry slaughterers (n = 50), all collected in two slaughterhouses during 2005-08, were analysed for species and vancomycin resistance gene identification using multiplex PCR. Sixty-three human clinical vancomycin-resistant Enterococcus faecium (VREF) isolates, obtained during 2006-09, were also examined. Discriminant analysis (DA) was used to establish the relationship of antimicrobial resistance profiles (ARPs) among broiler, poultry slaughterer and human clinical VREF. PFGE was conducted to study the genetic relatedness among VREF from the different sources.

RESULTS

A total of 120 VRE were recovered from 113 (22.6%) broiler samples. VREF carrying the vanA gene were predominant, being recovered from 72 (14.4%) samples from five (62.5%) broiler farms. Concerning poultry slaughterers, VREF were recovered from 10 (20%) samples. Susceptibility testing revealed that broiler VREF were consistently resistant to tetracycline, whereas 93.7% of clinical VREF were resistant to ampicillin. Furthermore, 92.1% of clinical VREF compared with 54.4% of broiler VREF were multiresistant (resistant to at least five antimicrobial classes). DA classified broiler and human clinical VREF into their corresponding source with high classification rates (100% and 85.7%, respectively), while the classification rate of poultry slaughterer VREF was relatively low (50%), with 40% of them classified closely to broiler VREF. PFGE patterns were clearly related to the source of the VREF, with broiler isolates being clustered distinctly from all human isolates.

CONCLUSIONS

A remarkable persistence of VREF was observed in the broiler production environment even >10 years after the avoparcin ban. Human and broiler VREF belonged to clearly unrelated populations, strongly indicating no clonal spread of VREF among the different sources, even between broilers and poultry slaughterers, despite them sharing common ARPs, as also supported by DA.

Effects of Sophy β-glucan on growth performance, carcass traits, meat composition, and immunological responses of Peking ducks

The response of Peking ducks to supplements of Sophy β-glucan was studied. A total of 160 healthy 1-d-old mixed-sex ducklings were randomly allocated to 3 groups: Sophy β-glucan (n = 80), bacitracin zinc (n = 40), and control (n = 40), which received the same antibiotics-deficient diet supplemented with 1% β-glucan, 5% bacitracin zinc, or nothing, respectively. During 2 mo of the study, growth performance, carcass composition, and meat quality of Peking ducks were evaluated. Additionally, a separate immunological study was conducted with a total of 105 healthy male Peking ducks in 7 groups (n = 15) and immunized with different doses of β-glucan (0, 0.5, 2.5, 12.5, and 62.5 μg/duck) and BSA (200 μg/duck). Blood was taken for detection of anti-BSA-IgG antibody and peripheral blood mononuclear cells proliferation assays. Groups subjected to different dietary treatments showed almost no differences in growth performance and slaughter traits except breast muscle percentage and intestinal length. These 2 indicators were significantly higher in the bacitracin zinc group than in the control and β-glucan groups (P < 0.05). Similarly, chemical compositions, fatty acids, and amino acids of breast muscle were not significantly influenced by the diet. Ducks immunized with Sophy β-glucan did not have enhanced level of anti-BSA-IgG antibodies but had significant peripheral blood mononuclear cells proliferation compared with unchallenged ducks (P < 0.01). With an increase in the glucan concentration, the proliferative responses approximately linearly increased. These findings indicate that 1% Sophy glucan did not improve duck growth performance, carcass composition, and meat quality significantly under the conditions of the present experiment and mainly had regulatory or enhancing properties on poultry nonspecific cellular immunity.

Genotypic-phenotypic discrepancies between antibiotic resistance characteristics of Escherichia coli isolates from calves in management settings with high and low antibiotic use

We hypothesized that bacterial populations growing in the absence of antibiotics will accumulate more resistance gene mutations than bacterial populations growing in the presence of antibiotics. If this is so, the prevalence of dysfunctional resistance genes (resistance pseudogenes) could provide a measure of the level of antibiotic exposure present in a given environment. As a proof-of-concept test, we assayed field strains of Escherichia coli for their resistance genotypes using a resistance gene microarray and further characterized isolates that had resistance phenotype-genotype discrepancies. We found a small but significant association between the prevalence of isolates with resistance pseudogenes and the lower antibiotic use environment of a beef cow-calf operation versus a higher antibiotic use dairy calf ranch (Fisher's exact test, P = 0.044). Other significant findings include a very strong association between the dairy calf ranch isolates and phenotypes unexplained by well-known resistance genes (Fisher's exact test, P < 0.0001). Two novel resistance genes were discovered in E. coli isolates from the dairy calf ranch, one associated with resistance to aminoglycosides and one associated with resistance to trimethoprim. In addition, isolates resistant to expanded-spectrum cephalosporins but negative for bla(CMY-2) had mutations in the promoter regions of the chromosomal E. coli ampC gene consistent with reported overexpression of native AmpC beta-lactamase. Similar mutations in hospital E. coli isolates have been reported worldwide. Prevalence or rates of E. coli ampC promoter mutations may be used as a marker for high expanded-spectrum cephalosporin use environments.

Multilocus sequence typing of Enterococcus faecalis isolates demonstrating different lesion types in broiler breeders

A total of 69 isolates of Enterococcus faecalis from broiler breeders demonstrating different lesion types and representing eight different flocks were characterized by multilocus sequence typing. Twenty isolates obtained from healthy birds representing two additional flocks were included for comparison. A total of 12 different sequence types (STs) was obtained. Correlation between ST and lesion type was not demonstrated. However, three STs (ST82, ST174, ST177) made up 81% of the isolates associated with lesions, indicating that these STs might be particularly associated with birds. In addition, ST174, the most frequently demonstrated ST, was only obtained from affected birds. Surprisingly, ST82, previously reported to be associated with amyloid arthropathy in layers worldwide, demonstrated a high degree of diversity as to lesion types, just as healthy carriers were demonstrated among broiler breeders. STs associated with healthy birds and lesions, respectively, did not demonstrate a phylogenetic relationship.

Trends in antibiotic resistance genes occurrence in the Haihe River, China

The occurrence of antibiotics and antibiotic resistance genes (ARGs) was quantified in water and sediment samples collected from a 72 km stretch of the Haihe River, China. Tetracycline resistance genes (tetW, tetQ, tetO, tetT, tetM, tetB, and tetS) were not detected by quantitative PCR in many samples. In contrast, sul1 and sul2 (coding for sulfonamide resistance) were present at relatively high concentrations in all (38) samples. The highest ARG concentrations detected were (7.8 ± 1.0) × 10(9) copies/g for sul1 and (1.7 ± 0.2) × 10(11) copies/g for sul2, in sediment samples collected during the summer. The corresponding total bacterial concentration (quantified with a universal 16S-rDNA probe) was (3.3 ± 0.4) × 10(12) cells/g. Sul1 and sul2 concentrations in sediments were 120-2000 times higher than that in water, indicating that sediments are an important ARG reservoir in the Haihe River. Statistical analysis indicated a positive correlation between the relative abundance of these ARGs (i.e., sul1/16S-rDNA and sul2/16S-rDNA) and the total concentration of sulfamethoxazole, sulfadiazine, plus sulfachlororyridazine, suggesting that sulfonamides exerted selective pressure for these ARGs. A class 1 integron was implicated in the propagation of sul1. Overall, the widespread distribution of sulfonamide ARGs underscores the need to better understand and mitigate their propagation in the environment and the associated risks to public health.

Isolation of VanA-type vancomycin-resistant Enterococcus strains from domestic poultry products with enrichment by incubation in buffered peptone water at 42 degrees C

Eight VanA-type enterococcal strains were isolated from 8 of 171 domestic poultry products by using enrichment by incubation in buffered peptone water at 35 degrees C and 42 degrees C. The pulsed-field gel electrophoresis patterns of all six VanA-type Enterococcus faecalis isolates were nearly indistinguishable, indicating the presence of a specific clone in Japan.

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.

Distribution of drug resistance among enterococci and Salmonella from poultry and cattle in Ethiopia

Enterococci and Salmonella were isolated from feces of chicken in intensive poultry farms and cattle which are maintained following traditional practices. Their resistance to different antibiotics was also determined. A total of 298 enterococcal isolates consisting of Enterococcus faecium (49.6%), Enterococcus durans (26.9%), Enterococcus hirea (11.9%), and Enterococcus faecalis (11.5%) were obtained. Among the enterococci, resistance to erythromycin (Ery), clindamicin (Cli), amoxicillin (Amo), ampicillin (Amp), and cephalothin (Cep) was high. Resistance to vancomycin (Van) was detected in all enterococcal species. Over 80% of the isolates showed multiple drug resistance. The most dominant patterns in poultry were Amo/Amp/Cep/Pen and Amo/Amp/Cep/Cli/Pen/Van. Among isolates from cattle, Amo/Amp/Cep/Cli/Ery/Pen/Van and Amo/Amp/Cli/Ery/Pen/Van constituted the most dominant multiple resistance patterns. A total of 51 Salmonella isolates were obtained from poultry (43/280) and cattle (8/450). About 70% of the isolates had varying resistance to the tested antibiotics. Multiple drug resistance was observed in over 30% of the Salmonella isolates. The most frequent resistance pattern was Amo/Amp/Cip/Gen/Str in cattle and Amo/Amp/Cep/Cip/Gen/Kan/Str in poultry. Enteroccoccal and Salmonella isolates showed multiple resistance to those antibiotics used in human and veterinary medicine. The high frequency of isolation of resistant enterococci is indicative of the wide dissemination of antibiotic resistant bacteria in the farm environment.

Classification and antimicrobial susceptibilities of enterococcus species isolated from apparently healthy food-producing animals in Japan

A total of 1024 enterococci were recovered from faeces of healthy animals from 178 cattle, 178 pig and 156 broiler farms. Enterococcus faecium was the predominant species recovered (35.8%), followed by E. faecalis (31.3%) and E. hirae (25.6%). Oxytetracycline resistance was most frequently found among E. faecalis (85.9%), E. faecium (58.8%) and E. hirae (48.1%). Resistance rates to almost all antimicrobials were higher in E. faecalis than E. faecium and E. hirae. Isolates from cattle were more susceptible to the antimicrobials studied than those from pigs and broilers. VanA- or VanB-type vancomycin-resistant enterococci have not been found since the ban of avoparcin use 5 years ago.

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.

Comparison of pulsed-field gel electrophoresis patterns of antimicrobial-resistant Escherichia coli and enterococci isolates from the feces of livestock and livestock farmers in Japan

Seven hundred thirty-nine animal strains and 662 livestock-farmer strains, consisting of Escherichia coli and enterococci, were examined for their pulsed-field gel electrophoresis (PFGE) and antimicrobial-resistance patterns. Two hundred fifty-eight and 203 PFGE patterns were found among 739 animal strains isolated from animals comprising broilers, pigs and cattle, and 662 human strains isolated from livestock farmers, respectively, from 27 farms in Japan. These results demonstrated that the PFGE patterns found among E. coli and enterococci strains from animals and livestock-farmers were heterogeneous and considerably diverse. The strains having both the identical PFGE pattern and the same drug-resistance pattern were defined as a single clone in this study. Seven types of E. coli and enterococci clones were shared among animals within the same farms and between the different farms housing the same animal species. The 25 strains (3.4%) of 739 E. coli and enterococci animal strains belonged to these seven types of clones. Only three types of E. coli clones were shared among animals between the different farms housing different animal species, but no identical E. faecalis or E. faecium clones were found between different animal species farms. The 15 strains (2.0%) of 739 E. coli and enterococci animal strains belonged to these three types of clones. Additionally, the 11 strains (1.5%) of 739 E. coli and enterococci strains isolated from animals were identical clones to strains isolated from livestock farmers of the same farm. These results suggest that the transmission of animal clones to livestock farmers or vice versa is less common.

Emergence of CC17 Enterococcus faecium: from commensal to hospital-adapted pathogen

For many years, Enterococcus faecium was considered to be a commensal of the digestive tract, which only sporadically caused opportunistic infections in severely ill patients. Over the last two decades, vancomycin-resistant E. faecium (VREF) has emerged worldwide as an important cause of nosocomial infections, especially in immunocompromised patients. The global Vancomycin-resistant enterococci (VRE) epidemic was preceded by the emergence of ampicillin-resistant E. faecium (AREfm) in the United States in the early 1980s, followed by the rapid emergence of VRE in the 1990s. A similar increase of VRE may occur in countries with still low levels of VRE in hospitals (such as The Netherlands), but increasing incidence of AREfm infections. Molecular epidemiological studies of both human- and animal-derived E. faecium isolates using multilocus sequence typing revealed the existence of host-specific genogroups, including a specific genetic lineage designated CC17, associated with hospital-related isolates. These strains were characterized by ampicillin and quinolone resistance. In addition, the majority of these CC17 isolates contain over hundred hospital-clade-specific genes, including mobile elements, phage genes and plasmid sequences, hypothetical and membrane proteins and antibiotic and regulatory genes and a putative pathogenicity island including the esp gene.

Enterococci and streptococci

Besides Staphylococcus aureus, other Gram-positive bacteria have become multidrug-resistant and cause therapeutic problems, particularly amongst hospitalised patients. The acquisition of vancomycin resistance by strains of Enterococcus faecium and Enterococcus faecalis is of particular concern and has resulted in treatment failures. Some of the infections caused by these bacteria do respond to treatment with new antibiotics that have been released in the last few years, however more options are required as not all enterococci are inherently susceptible and resistance is beginning to emerge amongst those that were susceptible. Resistance to commonly used antibiotics is also emerging in Streptococcus spp., particularly to the tetracyclines and macrolides. In both genera, multiresistant strains spread between patients and between hospitals. In the laboratory, these bacteria show considerable susceptibility to tigecycline, with little propensity to develop resistance, indicating that tigecycline could assume an important role in controlling infections caused by these Gram-positive bacteria.

Antibiotic resistance genes as emerging contaminants: studies in northern Colorado

This study explores antibiotic resistance genes (ARGs) as emerging environmental contaminants. The purpose of this study was to investigate the occurrence of ARGs in various environmental compartments in northern Colorado, including Cache La Poudre (Poudre) River sediments, irrigation ditches, dairy lagoons, and the effluents of wastewater recycling and drinking water treatment plants. Additionally, ARG concentrations in the Poudre River sediments were analyzed at three time points at five sites with varying levels of urban/agricultural impact and compared with two previously published time points. It was expected that ARG concentrations would be significantly higher in environments directly impacted by urban/agricultural activity than in pristine and lesser-impacted environments. Polymerase chain reaction (PCR) detection assays were applied to detect the presence/absence of several tetracycline and sulfonamide ARGs. Quantitative real-time PCR was used to further quantify two tetracycline ARGs (tet(W) and tet(O)) and two sulfonamide ARGs (sul(I) and sul(II)). The following trend was observed with respect to ARG concentrations (normalized to eubacterial 16S rRNA genes): dairy lagoon water > irrigation ditch water > urban/agriculturally impacted river sediments (p < 0.0001), except for sul(II), which was absent in ditch water. It was noted that tet(W) and tet(O) were also present in treated drinking water and recycled wastewater, suggesting that these are potential pathways for the spread of ARGs to and from humans. On the basis of this study, there is a need for environmental scientists and engineers to help address the issue of the spread of ARGs in the environment.

Vancomycin-resistant enterococci from animal sources in Korea

Enterococci for which the minimum inhibitory concentration (MIC) of vancomycin was >/=8 mg/l were isolated from meat, feces, and raw milk samples collected in Korea from March to November 2003. Among the 243 vancomycin-resistant enterococci (VRE) that were identified the vanA vancomycin resistance gene was carried by 51 Enterococcus faecium and one Enterococcus sp., vanC1 was carried by 151 Enterococcus gallinarum, vanC2 was carried by 39 Enterococcus casseliflavus, and one Enterococcus sp. carried no van genes. Of the isolated enterococci carrying vanA, 4% were found to be highly resistant to gentamicin and 11% were resistant to ampicillin. Further genotyping of the E. faecium isolates carrying vanA using pulsed-field gel electrophoresis (PFGE) revealed extensive heterogeneity. The vancomycin resistance transferability test revealed that only two of the 52 enterococci carrying the vanA gene were able to transfer vancomycin resistance to other enterococci. The VRE were recovered from various animal sources with a particularly high prevalence of E. faecium carrying the vanA gene being found in poultry meat.

Isolation of antibiotic-resistant bacteria from the air plume downwind of a swine confined or concentrated animal feeding operation

OBJECTIVE

In this study we evaluated the levels of antibiotic- and multidrug-resistant bacteria in bioaerosols upwind, within, and downwind at locations 25 m, 50 m, 100 m, and 150 m from a swine confined animal feeding operation.

DESIGN

We used Andersen two-stage samplers to collect bacterial samples, the replicate plate method to isolate organisms, and the Kirby-Bauer disk diffusion method to determine antibiotic resistance.

RESULTS

The percentage of organisms resistant to at least two antibiotic classes and all four classes evaluated were, respectively, 2.1 and 3.0 times higher inside (n = 69) than upwind (n = 59) of the facility. Staphylococcus aureus was the most prevalent organism recovered. Concentrations of antibiotic-resistant S. aureus decreased with increasing distance from the facility. Using Fisher's exact methods, the change in distribution of antibiotic resistance profiles for each antibiotic was statistically significant (oxytetracycline, p = 0.010; tetracycline, p = 0.014; ampicillin, p = 0.007; erythromycin, p = 0.035); however, this relationship was not seen with lincomycin and penicillin (p > 0.05) . In addition, the levels of antibiotic-resistant S.aureus 25 m downwind were significantly greater than the levels from samples taken upwind from the facility for the same four antibiotics (p < 0.05) . The percentage of resistant group A streptococci and fecal coliform increased within the facility compared with upwind values for all antibiotics evaluated,except for lincomycin. The percentage of resistant total coliform organisms increased within the facility compared with upwind values for oxytetracycline and tetracycline.

CONCLUSIONS

Bacterial concentrations with multiple antibiotic resistances or multidrug resistance were recovered inside and outside to (at least) 150 m downwind of this facility at higher percentages than upwind. Bacterial concentrations with multiple antibiotic resistances were found within and downwind of the facility even after subtherapeutic antibiotics were discontinued. This could pose a potential human health effect for those who work within or live in close proximity to these facilities.

Absence of VanA- and VanB-containing enterococci in poultry raised on nonintensive production farms in Brazil

We examined cloacal samples from poultry raised on nonintensive production farms in Brazil for the presence of vancomycin-resistant enterococci. No VanA- or VanB-containing enterococci were identified in a total of 200 cloacal swabs. The most prevalent species were Enterococcus gallinarum (vanC1; 13.0%) and E. casseliflavus (vanC2/3; 5.5%).

Prevalence, persistence, and molecular characterization of glycopeptide-resistant enterococci in Norwegian poultry and poultry farmers 3 to 8 years after the ban on avoparcin

Environmental reservoirs of glycopeptide-resistant enterococci (GRE) in Norway have been linked to former growth promoting use of the glycopeptide avoparcin in poultry production. We have examined the prevalence of fecal GRE in poultry and poultry farmers 3 to 8 years after the Norwegian avoparcin ban in 1995 and performed molecular analyses of the GRE population. Fecal samples from poultry farmers and their flocks on 29 previously avoparcin-exposed farms were collected on five occasions during the study period (1998 to 2003). All flocks (100%) were GRE positive in 1998. Throughout the study period, 78.5% of the poultry samples were GRE positive. Glycopeptide-resistant Enterococcus faecium (GREF) was isolated from 27.6% of the farmer samples in 1998 and from 27.8% of the samples collected between 1998 and 2003. The prevalence of fecal GRE in poultry declined significantly during the study period, but prevalence in samples from the farmers did not decline. PCR analysis revealed a specific Tn1546-plasmid junction fragment in 93.9% of E. faecium isolates. A putative postsegregation killing (PSK) system linked to Tn1546 was detected in 97.1% of the isolates examined. Multilocus sequence typing of glycopeptide-susceptible (n = 10) and -resistant (n = 10) E. faecium isolates from humans (n = 10) and poultry (n = 10) on two farms displayed 17 different sequence types. The study confirms the continuing persistence of a widespread common plasmid-mediated vanA-pRE25-PSK element within a heterogeneous GRE population on Norwegian poultry farms 8 years after the avoparcin ban. Moreover, it suggests an important role of PSK systems in the maintenance of antimicrobial resistance determinants in reservoirs without apparent antimicrobial selection.

Antibiotics and gastrointestinal colonization by vancomycin-resistant enterococci

Although several classes of antimicrobial agents have been associated with colonization or infection with glycopeptide-resistant enterococci (GRE) in individual clinical studies, the agents most commonly implicated are extended-spectrum cephalosporins and compounds with potent activity against anaerobic bacteria, including ticarcillin-clavulanic acid. In some clinical studies, formulary alterations designed to minimize the use of extended-spectrum cephalosporins or ticarcillin-clavulanic acid have resulted in significant decreases in colonization and infection by GRE. Experimental data using a mouse model of GRE gastrointestinal colonization indicate that persistence of high-level GRE colonization of the mouse gastrointestinal tract is promoted by exposure to agents with potent activity against anaerobic bacteria, suggesting that reduction of competing flora is the major factor leading to persistence of high-level colonization. One study performed in humans is consistent with this model and suggests that high levels of colonization may promote spread of resistant organisms in the nosocomial setting. Establishing colonization with GRE in uncolonized mice correlates with exposure to agents that are (a) secreted into the bile in significant concentrations and (b) have negligible activity against the colonizing enterococcal strain. Differences between piperacillin-tazobactam and ceftriaxone in the establishment model can be attributed directly to differences in their anti-enterococcal activity. Modification of antimicrobial prescribing practices may play an important role in facilitating successful infection control efforts to limit GRE in the nosocomial setting.

High prevalence of VanA-type vancomycin-resistant Enterococci in Austrian poultry

Fecal samples from humans and food-producing animals were analyzed for the presence of vancomycin-resistant enterococci (VRE). The VRE carriage rate in humans was 6%, and there was a predominance of VanC-type resistance. Enterococcus faecium with vanA-mediated resistance was frequent in broiler chickens (42%) but rare in cattle and pig samples.

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.