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Applied and Environmental Microbiology, August 2007, p. 4785-4790, Vol. 73, No. 15
0099-2240/07/$08.00+0 doi:10.1128/AEM.00252-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

UMR181 Physiopathologie et Toxicologie Expérimentales, INRA, ENVT, Ecole Nationale Vétérinaire de Toulouse, 23 Chemin des Capelles, BP 87 614, 31076 Toulouse Cedex 3, France,1 UMR5100 Microbiologie et Génétique Moléculaires, CNRS, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France2
Received 31 January 2007/ Accepted 3 June 2007
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Antimicrobial resistance in food animals deserves special attention. One of the most heavily medicated sectors is pig farming, with worldwide antibiotic consumption in pigs accounting for 60% of the antibiotics used in animals (10). A relationship has been demonstrated between the high use of antimicrobials in pig herds and the increased occurrence of resistant bacterial strains in their digestive tracts (4, 13, 34, 37). When antibiotics are administered to pigs, both the level and time development of antibiotic exposure of the intestinal microflora are dependent on the mode of drug administration (38). This exposure is a key determinant of antibiotic resistance development in the gut flora, and the relation between antibiotic dosage regimen and resistance merits attention. The impact of different antibiotic dosage regimens on the emergence of resistance must be evaluated by appropriate quantitative indicators of the resistance level. Traditionally, this has involved phenotypic methods that measure bacterial antibiotic susceptibility (32). In addition, quantitative PCR has been recommended for resistance gene surveillance because (i) it is sensitive, (ii) unambiguous standard curves can be used to quantify the resistance genes from various matrices, and (iii) no bacterial cultivation is required (15, 20, 31, 39).
The aim of the present study was to both develop and validate a real-time PCR assay to quantify fecal blaTEM genes in swine stools and to explore the impact of three different ampicillin dosage regimens on fecal ampicillin resistance in swine by use of different indicators. Ampicillin resistance was evaluated by quantifying the blaTEM genes in feces by real-time PCR assay associated with two conventional phenotypic methods based on the determination of the MICs of Escherichia coli isolates and the percentage of resistant Enterobacteriaceae. The three dosage regimens tested were the intramuscular route, the oral route in fed swine, and the oral route in fasted swine.
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For phenotypic evaluation of ampicillin resistance, fecal samples were taken from each pig, by digital manipulation or immediately after spontaneous defecation, at days 0 (before ampicillin administration), 1, 4, and 7. The samples were immediately transferred to the laboratory, and the Enterobacteriaceae were counted. For the quantification of blaTEM genes in feces by real-time PCR, feces of each pig were collected two or three times before the treatment. The value given for day 0 is the mean of these samplings. Feces were then collected each day from day 1 to day 7. Samples were obtained as already described. Two hundred milligrams of feces from each sample was frozen in liquid nitrogen and stored at –80°C until assayed.
Phenotypic evaluation of ampicillin resistance.
Feces (5 g) from each pig were homogenized with 45 ml of peptone water, including 30% glycerol, with a BagMixer (Interscience, St. Nom, France). Tenfold serial dilutions of the filtrate were prepared, and 100-µl samples of the dilutions were spread on MacConkey plates (AEB 151602; AES, Ker Lann, France) containing 0 and 16 µg/ml of ampicillin. MacConkey agar is classically used for selective growth of Enterobacteriaceae (7, 8, 11, 30). Enterobacteriaceae growing in the presence of 16 µg/ml of ampicillin were classified as resistant. This concentration corresponds to the MIC breakpoint value (MIC of
32 µg/ml) proposed by the CLSI (23) and the French Society for Microbiology (http://www.sfm.asso.fr). The plates were incubated at 37°C for 24 h. Enterobacteriaceae counts from both plates were used to calculate the percentage of resistant Enterobacteriaceae at each sampling time.
For each sample, 20 colonies were randomly picked on the MacConkey plates without ampicillin and stored at –80°C until assayed. These colonies were considered to be E. coli on the basis of ß-glucuronidase production using TBX agar (tryptone bile X-glucuronide agar; AES Laboratoire, Bruz, France) (14). Only a few colonies were ß-glucuronidase negative. All ß-glucuronidase-negative isolates and a portion of ß-glucuronidase-positive isolates were tested by the API 20E Enterobacteriaceae identification system (bioMérieux, Marcy l'Etoile, France) to confirm their identification. For MIC determination, ampicillin susceptibility was tested by a microdilution broth dilution method according to the recommendations reported by the CLSI (22). The control strain was E. coli ATCC 25922.
Bacteria and growth conditions.
E. coli JS238(pOFX326), the plasmid of which carries a monocopy of the target gene blaTEM-1, was used to optimize real-time PCR, assess sensitivity, and generate quantification standards. The strain was cultured in Mueller-Hinton broth containing ampicillin at the concentration of 50 µg/ml at 37°C overnight.
DNA extraction.
pOFX326 was purified with the QIAprep Spin Miniprep kit (QIAGEN, Hilden, Germany). Quality was assessed by migration on gel electrophoresis in 1% agarose after digestion with HindIII, and concentration was assessed by spectrophotometry at 260 nm. The QIAamp DNA stool kit (QIAGEN, Hilden, Germany) was used to extract DNA from feces according to the manufacturer's recommendations. For each series of extractions, a positive control and a negative control were coextracted and subjected to real-time PCR.
Design of primers.
The PCR primers were designed with Primer 3 and Oligo Analyser. The specificity of the sequence was further checked against all the available GenBank DNA sequences. The forward and reverse primers chosen for blaTEM gene quantification were 5'-TTCCTGTTTTTGCTCACCCAG-3' and 5'-CTCAAGGATCTTACCGCTGTTG-3', respectively. These primers amplify a 112-bp segment of the blaTEM-1D gene (GenBank accession number AF 1888200) from nucleotide positions 270 to 382. A 100% homology was demonstrated with 130 blaTEM genes for which the nucleotide sequence was available, except for TEM-60.
Real-time PCR assay.
The PCR amplification was performed in a 25-µl reaction mixture with a SYBR green PCR core reagent kit (PerkinElmer Biosystems, Foster City, CA). The reaction mixture contained 5 µl of test DNA solution, 2.5 µl of 10x SYBR green PCR buffer, 1.6 µl of a deoxynucleoside triphosphate solution (2.5 mM each of dATP, dCTP, and dGTP and 5 mM of dUTP), 0.25 µl of each primer (20 µM), 4 µl of 25 mM MgCl2, 11.275 µl of ultrapure water (Qbiogene, Montréal, Canada), and 0.125 µl of AmpliTaq Gold DNA polymerase, LD (5 U/µl) (PerkinElmer Biosystems). Amplification was performed using a GeneAmp PCR system 5700 thermocycler (PerkinElmer Biosystems) with the following conditions: 95°C for 10 min followed by 45 cycles of 15 seconds at 95°C and 1 min at 60°C. A standard curve with three replicates of the control plasmid pOFX326 diluted in Tris-EDTA buffer was generated for each PCR assay. All sample PCRs were done in duplicate. The samples were checked for the absence of background levels of PCR-inhibiting compounds by spiking DNA extracted from the samples with target DNA and subjecting these spiked DNA samples to real-time PCR both undiluted and diluted (1:10).
The impact of DNA fecal environment on amplification sensitivity and performance was assessed by comparing standard curves obtained with the control plasmid diluted in Tris-EDTA or in swine fecal DNA. The accuracy and reproducibility of the entire assay (from DNA extraction to real-time PCR analysis) were measured by spiking 200 mg of feces with an overnight culture of E. coli JS238(pOFX326). Five aliquots per day were subjected to DNA extraction on three different days. The extraction recovery rate was calculated and checked to be the same for different concentrations of blaTEM genes in feces by spiking fecal samples with 10-fold serial dilutions of an overnight culture of E. coli JS238(pOFX326). These samples were subjected to DNA extraction and then to real-time PCR.
Statistical analysis.
Statistical analysis was performed using Systat 10 (Systat Software Inc., Richmond, CA). Changes in the level of ampicillin resistance were analyzed using a generalized linear mixed-effects model with the following equation:
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ijk an error term. Y, the measure of resistance, was monitored in various ways. For the phenotypic evaluation of resistance, Y was the log-transformed percentage of the resistant Enterobacteriaceae population or the log-transformed percentage of E. coli isolates with MICs of >16 µg/ml. For the genotypic evaluation, Y was the log-transformed quantity of blaTEM genes. Multiple comparisons were performed using the Tukey test. The selected level of significance was a P value of <0.05. |
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FIG. 1. Standard curves calculated with the control plasmid diluted in Tris-EDTA buffer ( ) or in DNA extracted from swine feces ( ). Amplification was repeated four times for each dilution.
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FIG. 2. (a) Percentages of ampicillin-resistant Enterobacteriaceae for each mode of ampicillin administration. These percentages were calculated from the total counts of Enterobacteriaceae in the absence or presence of ampicillin (16 µg/ml). (b) Percentages of ampicillin-resistant E. coli isolates (i.e., with MICs above 16 µg/ml) for each mode of ampicillin administration. Ampicillin susceptibility was tested at each sampling point on 20 isolates from each pig. Treated pigs received ampicillin at 20 mg/kg from day 0 to day 6 by the intramuscular route ( ) (n = 4), by the oral route in fasted pigs ( ) (n = 4), or by the oral route in fed pigs ( ) (n = 4). Six pigs were used as a control (). Values are the means of the results, and error bars represent the standard deviations.
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Genotypic evaluation of ampicillin resistance.
Ampicillin resistance in feces was measured by blaTEM gene quantification using a validated PCR assay. blaTEM gene copy numbers per gram of wet feces were measured on each day of treatment for each pig (Fig. 3). The baseline values for all pigs were below 107 copies/g of feces. blaTEM quantities increased after ampicillin administration. The between-day fluctuations for a given animal were large. The blaTEM quantities for the oral routes fluctuated between 107 and 109 copies/g of feces, but only between 105 and 108 copies/g of feces for the intramuscular route. Two fed pigs treated by oral route excreted the highest blaTEM quantities, with values above 109 copies/g of feces. The blaTEM quantities for the control group were lower than those of the three ampicillin-treated groups and fluctuated between 104 and 106 copies/g of feces.
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FIG. 3. Copy numbers of blaTEM genes per gram of feces detected by real-time PCR for each pig. Ampicillin was administered at 20 mg/kg from day 0 to day 6. Modes of administration were the oral route in fed pigs (n = 4) (a), the oral route in fasted pigs (n = 4) (b), and the intramuscular route (n = 4) (c); six pigs were used as a control (d).
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FIG. 4. Copy numbers of blaTEM genes per gram of feces for each mode of ampicillin administration. Treated pigs received ampicillin at 20 mg/kg from day 0 to day 6 by the intramuscular route ( ) (n = 4), by the oral route in fasted pigs ( ) (n = 4), or by the oral route in fed pigs ( ) (n = 4). Six pigs were used as a control (). Values are the means of the results, and error bars represent the standard deviations.
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FIG. 5. Relationship between the log of the blaTEM copy number/gram of feces and the log of counts of ampicillin-resistant Enterobacteriaceae/gram of feces.
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Antibiotic impact on the gut microflora is generally measured by phenotypic evaluation of antibiotic resistance on a limited bacterial population by using isolates of indicator bacteria or families of bacteria. E. coli and Enterobacteriaceae are good candidates for studies of the antibiotic resistance level of the fecal flora and are commonly used for this purpose in pigs (32). These bacteria are easily culturable, and their isolation is facilitated by specific culture media. In the present experiment, results obtained with the two phenotypic indicators of ampicillin resistance implied that all treatments had similar negative impacts on the gut microflora, with the emergence of a high level of resistance with all three dosage regimens. These results are consistent with those of previous studies demonstrating that ampicillin treatment could have a marked effect on the level of resistance in the intestinal microbiota of several species (9, 21, 33). Nevertheless, the phenotypic indicators commonly used to assess antibiotic resistance exhibit methodological features that impact both their metrological performances and their relevance. First, the selected indicator bacteria must be cultured, and the reliability of results has been questioned due to considerable variation originating from the culture medium, bacterial inoculum, antibiotic preparation, and incubation conditions (26). Second, the isolates might not be representative of the whole population of bacteria (6). These limits impair the sensitivity and precision of phenotypic indicators for the assessment of resistance levels and have prompted investigators to develop molecular techniques as alternatives—in particular, quantitative PCR (15, 20, 31, 39).
Molecular techniques can be used to reveal the presence of genetic determinants without bacterial cultivation and irrespective of the bacterial species carrying these genetic determinants (5, 35). However, a requisite to this approach is the knowledge of the underlying resistance mechanisms, and when few genes are involved in resistance, they may provide candidates for resistance markers (3). blaTEM genes code for the most commonly encountered ß-lactamases in gram-negative bacteria (24). We therefore developed and validated a real-time PCR assay to quantify blaTEM genes in swine feces. This PCR assay was suitable for the quantification of blaTEM genes from 104 to 109 copies/g of feces.
Examination of the agreement between resistant Enterobacteriaceae counts and blaTEM concentrations revealed a significant correlation between the quantities of blaTEM genes and the counts of ampicillin-resistant Enterobacteriaceae. The observed scatter is probably due in part to the inaccuracy of both techniques and to the fact that amplified blaTEM genes may be harbored by bacteria other than Enterobacteriaceae (16).
During our experiment to monitor blaTEM gene excretion, we found that treated pigs excreted more blaTEM genes than control pigs. Moreover, as in the phenotypic evaluations, the fecal excretion of blaTEM genes showed large, individual, day-to-day fluctuations. As indicated above, these fluctuations were correlated with counts of ampicillin-resistant Enterobacteriaceae. Similarly, Belloc et al. (2) studied the effect of quinolone treatment on the selection and persistence of quinolone-resistant E. coli in swine fecal flora and observed great variability in both the percentages of resistant strains and the patterns of emergence of resistance. In the present study, despite the great variability and the small number of pigs per mode of treatment, at least two of the three modes of drug administration (i.e., the intramuscular route and the oral route in fed pigs) could be differentiated by quantifying the blaTEM genes excreted in feces, but not by phenotypic evaluation. These results imply that a genotypic indicator can be used advantageously as a complement to phenotypic approaches to quantitatively evaluate the intestinal reservoir of resistance genes. For example, blaTEM gene quantification has already been used to evaluate ampicillin-induced selective pressure on the gut microbiota in dogs (15).
Our results, showing that oral administration of ampicillin in fed pigs was associated with the highest excretion level of fecal blaTEM genes, are consistent with both our pharmacokinetic measurements (not shown) and published data. The latter indicate that ß-lactam absorption following oral administration is largely incomplete in pigs (1, 17) and that feeding decreases ß-lactam absorption in pigs, as it does in dogs (18) and humans (36). As a consequence, these expected high concentrations of unabsorbed ampicillin in the intestine are likely to exert great pressure on the gut microflora, and this all the more if ampicillin is administered to fed pigs. Following intramuscular administration, ampicillin can gain access to the gastrointestinal lumen by biliary excretion (12), which explains why the intramuscular route was also associated with an increase in fecal blaTEM gene excretion. Thus, the pharmacokinetic profiles of the three modes of ampicillin administration tested in the present study were apparently different and resulted in different intestinal exposures.
In conclusion, our study indicates that fecal blaTEM gene quantification might be a useful tool to evaluate and discriminate the impact of different modes of ampicillin administration on the gut microflora. In the future, this quantitative tool might help to quantify the flux of resistance genes in epidemiological investigations.
We thank Nathalie Arpaillange and Nadine Gauthier for their technical support and Jean-Pierre Gau, Patrice Rouby, Joseph Maligoy, and Jean Denjean for taking care of the animals.
Published ahead of print on 8 June 2007. ![]()
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