Antibiotic residues and drug resistance in human intestinal flora

Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model

Studying potential dietary exposure to antimicrobial drug residues via meat and dairy products is essential to ensure human health and consumer safety. When studying how antimicrobial residues in food impact the development of antimicrobial drug resistance and disrupt normal bacteria community structure in the intestine, there are diverse methodological challenges to overcome. In this study, traditional cultures and molecular analysis techniques were used to determine the effects of tetracycline at chronic subinhibitory exposure levels on human intestinal microbiota using an in vitro continuous flow bioreactor. Six bioreactor culture vessels containing human fecal suspensions were maintained at 37 °C for 7 days. After a steady state was achieved, the suspensions were dosed with 0, 0.015, 0.15, 1.5, 15, or 150 µg/mL tetracycline, respectively. Exposure to 150 µg/mL tetracycline resulted in a decrease of total anaerobic bacteria from 1.9 × 10⁷ ± 0.3 × 10⁷ down to 2 × 10⁶ ± 0.8 × 10⁶ CFU/mL. Dose-dependent effects of tetracycline were noted for perturbations of tetB and tetD gene expression and changes in acetate and propionate concentrations. Although no-observed-adverse-effect concentrations differed, depending on the traditional cultures and the molecular analysis techniques used, this in vitro continuous flow bioreactor study contributes to the knowledge base regarding the impact of chronic exposure of tetracycline on human intestinal microbiota.

An in vitro study to assess the impact of tetracycline on the human intestinal microbiome

The human intestinal microbiome, a generally stable ecosystem, could be potentially altered by the ingestion of antimicrobial drug residues in foods derived from animals. Data and the scientific published literature on the effects of antimicrobial residues on the human intestinal microbiome are reviewed by national regulatory authorities as part of the human food safety evaluation of veterinary antimicrobial agents used in food-producing animals. In this study, we determined if tetracycline, at low residue concentrations, could impact the human intestinal microbiome structure and the resistance-gene profile, following acute and subchronic exposure. The effects of 0.15, 1.5, 15, and 150 μg/ml of tetracycline, after 24 h and 40 days of exposure, in 3% human fecal suspensions, collected from three individuals (A, B, and C) were investigated using in vitro batch cultures. Results were variable, with either no change or minor changes in total bacterial 16S rRNA gene copies after exposure of fecal samples to tetracycline, because of the inter-individual variation of human gastrointestinal tract microbiota. Bacterial community analysis using rRNA-based pyrosequencing revealed that Firmicutes and Bacteroidetes were the predominant phyla in the three fecal samples; the ratio of phylotypes varied among individuals. The evaluation of bacterial community changes at the genus level, from control to tetracycline-treated fecal samples, suggested that tetracycline under the conditions of this study could lead to slight differences in the composition of intestinal microbiota. The genus Bacteroides (of the Bacteroidetes) was consistently altered from 1.68 to 5.70% and 4.82-8.22% at tetracycline concentrations of 0.15 μg/ml or above at both time points for individual A, respectively, and increased 5.13-13.50% and 10.92-22.18% for individual B, respectively. Clostridium family XI increased 3.50-25.34% in the presence of tetracycline at 40 days for individual C. Principal Component Analysis (PCA) confirmed the pyrosequencing findings of inter-individual variability of the ratio of phylotypes and the effect of tetracycline. Among the 23 tetracycline resistance genes (TRGs) screened, four tet genes (tetO, Q, W, and X) were major TRGs in control and tetracycline-dosed fecal samples. A variable to slight increase of copy number of TRGs appeared to be related to tetracycline treatment, interindividual variability and duration of exposure. Despite, the inherent variability of the intestinal microbiota observed among or within individuals, this pilot study contributes to the knowledge base of the impact of low residue concentrations of tetracycline on the human intestinal microbiome on the potential for antimicrobial resistance.

An update discussion on the current assessment of the safety of veterinary antimicrobial drug residues in food with regard to their impact on the human intestinal microbiome

The human gastrointestinal tract ecosystem consists of complex and diverse microbial communities that have now been collectively termed the intestinal microbiome. Recent scientific breakthroughs and research endeavours have increased our understanding of the important role the intestinal microbiome plays in human health and disease. The use of antimicrobial new animal drugs in food-producing animals may result in the presence of low levels of drug residues in edible foodstuffs. There is concern that antimicrobial new animal drugs in or on animal-derived food products at residue-level concentrations could disrupt the colonization barrier and/or modify the antimicrobial resistance profile of human intestinal bacteria. Therapeutic doses of antimicrobial drugs have been shown to promote shifts in the intestinal microbiome, and these disruptions promote the emergence of antimicrobial-resistant bacteria. To assess the effects of antimicrobial new animal drug residues in food on human intestinal bacteria, many national regulatory agencies and international committees follow a harmonized process, VICH GL36(R), which was issued by a trilateral organization of the European Union, the USA, and Japan called the International Cooperation on Harmonization of Technical Requirements for Veterinary Medicinal Products (VICH). The guidance describes a general approach currently used by national regulatory agencies and international committees to assess the effects of antimicrobial new animal drug residues in animal-derived food on human intestinal bacteria. The purpose of this review is to provide an overview of this current approach as part of the antimicrobial new animal drug approval process in participating countries, give insights on the microbiological endpoints used in this safety evaluation, and discuss the availability of new information. Copyright © 2016 John Wiley & Sons, Ltd.

Enhanced antibiotic multi-resistance in nasal and faecal bacteria after agricultural use of streptomycin

Streptomycin is used in arboriculture to control fire blight. Using sheep as a model, multidrug-resistant bacteria in mammals were found to be selected after the intentional release of streptomycin into the environment. Escherichia coli and Staphylococcus spp. were isolated from the faeces and nasal cavities, respectively, of sheep grazing on a field sprayed with streptomycin at concentrations used in orchards (test group) and on a field without streptomycin (control group). Before the application of streptomycin, the percentage of streptomycin-resistant E. coli isolates in faeces was 15.8% in the control group and 14.7% in the test group. After the application of streptomycin, the overall number of streptomycin-resistant E. coli isolates was significantly higher in the test group (39.9%) than in the control group (22.3%). Streptomycin-resistant Staphylococcus isolates were only detected after the application of streptomycin. Streptomycin resistance was frequently associated with resistance to sulfamethoxazole, ampicillin, tetracycline and chloramphenicol and less frequently to cefotaxime in E. coli, and to tetracycline, fusidic acid and tiamulin in Staphylococcus spp. This study shows that the application of low concentrations of streptomycin on grass, as occurs during the spraying of orchards, selects for multidrug-resistant nasal and enteric bacterial flora, including extended-spectrum beta-lactamase-producing E. coli.

Human flora-associated rodents--does the data support the assumptions?

There is little direct literature detailing exhaustive bacteriological studies comparing human donor faecal flora, human flora‐associated (HFA) mouse models and conventional rodent faecal flora. While there is a premise that the implanted donor faecal flora from humans is established in the rodent model the evidence is incomplete and indeed for groups such as Bifidobacterium spp. it is lacking. The reviewed bacteriology studies are generally lacking in detail with the exception of one study from which the data have mostly been overlooked when cited by other workers. While there are studies that suggest that the HFA rodent model is more relevant to man than studies with conventional rodents, the hypothesis remains to be proven. This review concludes that the established microbial flora in the HFA rodent model is different to that of donor human faecal flora, and this clearly raises the question as to whether this matters, after all a model is a model and as such models can be useful even should they fail to be a true representation of, in this case, the gastrointestinal tract. What matters is that there is a proper understanding of the limitations of the model as we attempt to unravel the significance of the components of the gastrointestinal flora in health and disease; examples of why such an analysis is important are provided with regard to obesity and nutritional studies. The data do unsurprisingly suggest that diet is an extremely influential variable when interpreting HFA and conventional rodent data. The microbiology data from direct bacteriology and indirect enzyme studies show that the established microbial flora in the HFA rodent model is different to that of donor human faecal flora. The significance of this conclusion remains to be established.

In vitroandin vivoevaluation of pectin beads for the colon delivery of β-lactamases

The aim of the present study was to provide a "proof of concept" of colon delivery of beta-lactamases by pectin beads aiming to degrade residual beta-lactam antibiotics, in order to prevent the emergence of resistant bacterial strains. Pectin beads were prepared according to ionotropic gelation method using CaCl2 as a gelling agent. Particles were then washed and soaked in polyethylenimine (PEI). Coating beads with PEI considerably improved their stability in simulated intestinal medium. In vitro studies showed that beta-lactamases were released from pectin beads in colonic medium due to the action of pectinolytic enzymes. When ampicillin was added to this medium, the release of beta-lactamases induced, as expected, the antibiotic inactivation. Finally, after oral administration of loaded-beads to CD1 mice, beta-lactamases were retrieved in high concentrations in faeces. Observation by SEM of beads extracted from mice intestinal tracts concluded the core degradation of beads without any modification of the PEI coating layer. This study demonstrates that a multiparticulate system with suitable characteristics for site-specific colonic delivery can be prepared. This system could be used to target beta-lactamases to the colon in order to hydrolyse antibiotic residues during treatment and prevent their impact on colonic microflora.

Impact of residual and therapeutic doses of ciprofloxacin in the human-flora-associated mice model

A study was conducted to evaluate the effects of therapeutic and residual doses of ciprofloxacin on the human intestinal flora implanted into germ-free mice. Ciprofloxacin was administered daily via drinking water at concentrations to provide doses of 0, 0.125, 1.25, and 12.5mg/kg b.w. Changes in the intestinal flora composition, alteration in bacterial enzyme activities, fecal short chain fatty acid concentration and bacterial cellular fatty acid profiles, overgrowth of resistant bacteria, and disruption of the colonization barrier were the endpoints evaluated in the feces of human-flora-associated (HFA) mice. Ciprofloxacin at all tested doses decreased significantly the aerobic populations and particularly the population of Enterobacteriaceae. Selection of resistant Bacteroides fragilis group was noticed in HFA mice receiving 12.5mg/kg b.w. In mice challenged with a Salmonella strain, exogenous Salmonella persisted in the feces of all treated mice indicating that the flora responsible for the colonization barrier effect was disturbed by the antibiotic treatment. None of the studied metabolic parameters of the flora were affected by ciprofloxacin at any dose level. Under the experimental conditions of the study, the no-observed-effect level of ciprofloxacin was found to be less than 0.125 mg/kg b.w.

Influence of tetracycline exposure on tetracycline resistance and the carriage of tetracycline resistance genes within commensal Escherichia coli populations

AIMS

To assess the influence of incremental tetracycline exposure on the genetic basis of tetracycline resistance within faecal Escherichia coli.

METHODS AND RESULTS

Through the adoption of a novel combination of multiple breakpoint selection, phenotypic characterization and the application of a polymerase chain reaction based gene identification system it proved possible to monitor the influence of antibiotic exposure on resistance gene possession. Using tetracycline as a case study a clear hierarchy was revealed between tet genes, strongly influenced by host antimicrobial exposure history.

CONCLUSIONS

The antimicrobial exposure regime under which an animal is produced affects both the identity and magnitude of resistance gene possession of a selected bacterial population within its enteric microflora. Among the ramifications associated with such resistance gene selection is the degree of resistance conferred and the carriage of linked resistance determinants. This selection is applied by exposure to antibiotic concentrations well below recognized minimum inhibitory tetracycline concentration breakpoints widely adopted to characterize bacterial 'susceptibility'.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study confirms the ability of minimal antibiotic exposure to select for the continued persistence of resistance genes within the enteric microflora. It is clearly demonstrated that different antimicrobial regimes select for different resistance genes, the implications of which are discussed.

Risk assessment in regulatory policy making for human and veterinary public health

Risk assessment is the method of systematically identifying and assessing factors that influence the probability and consequences of a negative event occurring. One responsibility of veterinary medicine is to protect animal and human health. Food animal production uses antibiotics to enhance production. Regulators evaluate new production technology to ensure animal safety and safe, edible products and to make public policy decisions by assessing risks/benefits. The U.S. Food and Drug Administration, Center for Veterinary Medicine's (CVM's) first risk assessment addressed the potential human health impact of campylobacter effects associated with the use of fluoroquinolines in food-producing animals. CVM used the Monte Carlo method to estimate risk byprobability distributions that reflect the uncertainty and variability in the data used for the assessment. Enterococci faecium is a species more likely to be resistant to antibiotics of last resort. Effective control of multidrug-resistant enterococci will requirea better understanding of the transfer of E. faeciumfrom animals to humans and the interaction between E. faecium, the hospital environment, and humans; prudent antibiotic use; better contact isolation in hospitals; and better surveillance. CVM will model these factors in a second, more complex risk assessment designed to examine the indirect transfer of resistance from animals to humans. Use of risk assessments allows researchers, the industry, regulatory authorities, and educators to make better policy decisions regarding antimicrobial use in food animals and humans and the development of resistance. Today the question of whether the use of antimicrobials for growth enhancement infood animals should or should not be terminated for the benefit of human health remains unresolved.

Evaluation of residual and therapeutic doses of tetracycline in the human-flora-associated (HFA) mice model

In order to evaluate an in vivo model system for assessing the effect of therapeutic and residue levels of tetracycline on human intestinal microflora, tetracycline was administered via drinking water (1, 10, and 100 mg/liter) to human-flora-associated (HFA) male and female mice. The effects of the antibiotic on fecal aerobic and anaerobic populations, selection of bacteria resistant to tetracycline, metabolic parameters of the microflora, and maintenance of the intestinal barrier against exogenous Salmonella (resistance to colonization) were recorded. In both sexes of mice, tetracycline exposure at 10 and 100 mg/liter induced the selection of several resistant bacterial species (Gram-positive anaerobes, Bacteroides fragilis, enterobacteria, and enterococci). This effect was also observed at the lowest dose (1 mg/liter) in female mice and indicates the potential sensitivity of this endpoint for evaluating the microbiological risk of tetracycline residues. The resistance to colonization was impaired at 100 mg/liter, a concentration corresponding to about half of the therapeutic doses in humans and animals. Metabolic parameters of the microflora were not affected by tetracycline at all levels. In this study, the no-observed-effect level (NOEL) of tetracycline on intestinal flora in this study was less than 1 mg of tetracycline per liter of drinking water. This concentration in the mouse corresponds to 0.125 mg of tetracycline per kilogram of body weight per day. Within the constraints of the experimental design employed here, the HFA mice model proved to be acceptable for studying dose-related effects of tetracycline on human intestinal microflora.

[Consequences of antibiotic therapy to the intestinal ecosystem]

Ecological impact of antibiotherapy results from the interaction between microorganisms in the ecosystems and antibiotics at which they are exposed. The amount of antibiotics use in the world is continuously increasing. The fraction devoted to human care is only about half the total amount. There are multiple other fields of usage, in agriculture, breeding and veterinary medicine. Bacterial ecosystems exposed at antibiotherapy in man are mainly the skin and the gastrointestinal and respiratory tracts. The gastrointestinal system is quantitatively predominant and the consequences of the bacterial imbalance induced by antibiotics are potentially severe. It is the reason why it is the most extensively studied, in the literature and in the present review. The origin of resistant bacteria will be briefly discussed.

Evaluation of veterinary drug residues in food for their potential to affect human intestinal microflora

The use of veterinary drugs in food-producing animals may result in trace quantities of the drugs or their metabolites being present as residues in food. The effects of veterinary drugs intended for use in food-producing animals on intestinal microflora are evaluated in drug registration since these residues may pose a risk due to their antibiotic activity. This article reviews the different in vivo and in vitro experimental test systems and approaches used by animal health industries, contract laboratories, and regulatory authorities to assess the safety of veterinary drug residues in foods for human consumption. Furthermore, we propose a systematic approach to assess the effects and safety of veterinary drug residues on the human intestinal microflora.

Screening for antimicrobial resistance in fecal samples by the replica plating method

Replica plating can be used for the detection of antibiotic resistance in normal flora. We have evaluated this application of the replica plating method by comparing it with a five-colony method. The replica plating method uses a single plate for each antibiotic, with a concentration just above that for borderline resistance. By the five-colony method, five colonies per sample were picked, chosen to represent all different colony morphologies present, and MICs were determined by a standard agar dilution method. The gram-negative, aerobic floras of 131 fecal samples were screened for resistance to ampicillin, cefuroxime, nalidixic acid, trimethoprim, sulfamethoxazole, and tetracycline by both methods. The rate of resistance detection by the two methods did not differ statistically for any of the antibiotics tested. The breakpoint concentrations used for the replica plates in the study gave results similar to those produced by the agar dilution method and the breakpoint values of the National Committee for Clinical Laboratory Standards and can thus be recommended. As the only currently used resistance detection method, replica plating facilitates an exact determination of the percentage of resistant colonies/total number of colonies (between 1 and 100%) in a sample. This revealed an uneven distribution, with only 23% of the samples having resistance frequencies in the range of 10 to 85%; usually, the resistant flora either was a small minority or was very dominant in samples with resistance. This phenomenon was present for all of the antibiotics.

Effects of sarafloxacin hydrochloride on human enteric bacteria under simulated human gut conditions

The effects of sarafloxacin, a newly developed veterinary fluoroquinolone antimicrobial, on 15 strains of aerobic and anaerobic bacteria of human origin were assessed under simulated human gut conditions. An in vitro gut simulation model was designed to mimic the situation of sarafloxacin (free and bound to meat) passing through the human gastrointestinal tract. The survival of bacteria in the simulation model and any subsequent change in the sensitivity of isolates to sarafloxacin were measured. The inhibitory level of sarafloxacin for the tested bacteria was strain dependent. It appeared that in broth culture Escherichia coli isolates were sensitive to sarafloxacin concentrations 5-fold lower than the concentrations present in the simulated gut model, suggesting that sarafloxacin may be partially unavailable due to absorption to organic matter in the model. There was no significant observed change in the sarafloxacin sensitivity of the bacterial strains exposed to the compound in the model.

Shedding of antibiotic-resistant members of the family Enterobacteriaceae in healthy residents of France and Jordan

We compared the frequency of shedding of members of the family Enterobacteriaceae resistant to ampicillin, tetracycline, chloramphenicol, kanamycin, gentamicin and ceftazidime in 83 French residents of the Paris urban area and in 101 subjects in Jordan, 64 of whom resided in the urban area of Irbid, 15 in rural areas, and 22 of whom had a nomadic lifestyle. There was no significant difference between these populations regarding (i) the percentages of subjects with strains resistant to any of the antimicrobial agents tested and (ii) the proportions of total counts of organisms of the Enterobacteriaceae resistant to these agents. The simultaneous shedding of strains resistant to ampicillin, chloramphenicol, tetracycline and kanamycin was significantly associated with (i) exposure to antibiotic treatment during the six months preceding the study and (ii) the presence of many children at home.

Establishment of a microbiologically acceptable daily intake of antimicrobial drug residues

A model is presented to calculate the microbiologically acceptable daily intake (ADIm) of antibiotic residues in food products. The ADIm calculation is based on MIC values for indicator bacteria Escherichia coli, Bacteroides fragilis, Bifidobacterium spp. and Eubacterium spp., established under gut-like conditions in an in vitro simulation model. The maximum residue level (MRL) for residues in food products can be derived from the ADIm. Four phases can be distinguished in this gastro-intestinal simulation model, namely: 1. In vitro determination of the MIC for each bacterial strain by a standard method. 2. Incorporation of the drug into food (meat, milk) followed by testing of the stability of the antibiotic under gut-like conditions. 3. Adjustment of the 'gastric' fluid to the duodenal situation, inoculation with the test bacteria and anaerobic incubation at 37 degrees C for at least 18 h. 4. MIC reading confirmed by counting bacteria growing on specific solidified media. In this study the method for calculation of ADIm and MRL is given for flumequine as model drug. On the basis of MIC50 values for E. coli strains, a MRL for flumequine of 1.0 microgram/g meat or 0.25 microgram/ml milk was calculated. It is suggested that, depending on the antibacterial spectrum of the antibiotic involved, the ADIm can be determined with selected indicator bacteria, incubated under simulated gastrointestinal conditions.

An evaluation of methods to assess the effect of antimicrobial residues on the human gut flora

1. Barrier effect. Relevant models should include an anaerobic dominant flora that antagonizes minor bacterial populations such as drug resistant E. coli. 2. Anaerobes vs. aerobes. Aerobe counts are more precise and much less time consuming than anaerobe counts. Minor populations of drug resistant aerobes are sensitive markers of the ecosystem balance, and are directly relevant to the potential risk of antimicrobial residues. 3. MIC vs. plate counts. The determination of minimum inhibitory concentrations (MIC) of selected clones in time consuming, does not detect subdominant resistance (less than 1%), and the MIC shift is difficult to test statistically. In contrast, direct counts of bacteria on drug supplemented media allows a rapid measure of minor resistant populations. 4.

STATISTICS

Most published designs do not include adequate statistical evaluation. This is critical for trials made in conventional humans and animals, where data are highly variable. 5. Human trials: The lowest concentration of antibiotic tested in human volunteers (2 mg oxytetracycline/d for 7d in 6 subjects) significantly increased the proportion of resistant fecal enterobacteria (P = 0.05). However, the huge day-to-day and interindividual variations of human floras make this evidence rather weak. 6. Gnotobiotic mice inoculated with human flora are living isolated models in which the effect of any antimicrobial on the human gut flora can be tested. This in vivo model does include the barrier effect of dominant anaerobes. Interindividual and day-to-day variations of bacterial populations are lower in those mice than in humans. 7. Most resistant enterobacteria in the human gut of untreated people come from bacterial contamination of raw foods. The relative contribution of residues in selecting antibiotic resistance seems to be low when compared to bacterial contamination.

Minimum antibiotic levels for selecting a resistance plasmid in a gnotobiotic animal model

The minimum antibiotic concentrations for selecting an R plasmid in vivo were determined in germfree mice colonized by two isogenic strains of Escherichia coli, one of which carried an R plasmid. Seventy groups of three gnotobiotic mice were given low doses of ampicillin, colistin, flumequin, gentamicin, tetracycline, or streptomycin via drinking water for 2 weeks. The equilibrium between susceptible and resistant populations of bacteria was monitored daily in feces and compared with that of control mice given pure water. This model yielded reproducible data, and dose and response were strongly correlated. The minimum selecting doses ranged from 0.9 to 12.8 micrograms/ml of water, depending on the antibiotic and the R plasmid. The use of mathematical models and complementary in vitro experiments accounted for the effect of the low antibiotic levels.