Abstract
The detection of multidrug-resistant bacteria is a growing problem; however, the role of domesticated animals in the propagation of antimicrobial resistance has barely been studied. The aim of this study was to identify extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains in domestic animal feces to assess their antimicrobial resistance profile and carry out molecular characterization of the β-lactamases. A total of 325 samples were collected from eight animal species. Of these, 34 bacterial isolates were identified as E. coli. The antibiotic resistance profile of the E. coli strains was as follows: 100% resistant to amoxicillin, aztreonam, and cephalosporins; 58.8% resistant to nalidixic acid, ciprofloxacin, and trimethoprim/sulfamethoxazole; 41.2% resistant to gentamicin and tobramycin; 11.8% resistant and 32.4% intermediate to cefoxitin; 97.1% sensible and 2.9% intermediate to amoxicillin/clavulanate; and 100% sensible to ertapenem, minocycline, imipenem, meropenem, amikacin, nitrofurantoin, fosfomycin, and colistin. All 34 E. coli strains met criteria for ESBL production. In total, 46 β-lactamase genes were detected: 43.5% blaTEM , 30.4% blaCTX-M (23.9% blaCTX-M-1 and 6.5% blaCTX-M-9 ), and 26.1% blaSHV (17.4% bla SHV-5 and 8.7% bla SHV-12). All the β-lactamases were found in dogs except for four bla SHV found in falcons. No plasmidic AmpC genes were found. The high prevalence of ESBL-producing E. coli strains in animals could become a zoonotic transmission vector.
Introduction
T
The role of domestic animals in the propagation of antimicrobial resistances is yet to be determined, possibly due to the fact that the administration of antibiotics in these animals is not as regulated as that of cattle (Guardabassi et al. 2004). This is a relevant fact, seeing as many of the antibiotics used in humans are also being used in animal therapy. Of all the antimicrobial agents used by veterinarians to treat bacterial infections, β-lactams are the most frequently prescribed due to their wide therapeutic range, their pharmacokinetics, and their broad spectrum of activity against pathogens (Prescott 2008). Furthermore, it is important to highlight that certain animals, such as dogs and cats, have frequent contact with humans and, therefore, may represent an important transmission vector of bacteria, their gut microbiota being a reservoir of β-lactam resistance genes (Hunter et al. 2010).
The main aim of this study was to detect and identify extended-spectrum beta-lactamase (ESBL) or plasmidic AmpC (pAmpC) β-lactamase-producing Escherichia coli in domesticated animal feces. Furthermore, the antimicrobial resistance profile of all isolated strains was assessed. Finally, the molecular characterization of these β-lactamases was carried out.
Materials and Methods
Sample collection
A total of 325 fecal samples were randomly collected from different species of healthy animals with frequent human contact: 140 dogs, 46 cats, 35 monkeys, 35 horses, 25 sheep, 20 goats, 12 falcons, and 12 pigeons. The samples were collected in different locations throughout Spain from February 2014 to February 2015, in veterinary diagnostics laboratories.
The Ethics and Animal Welfare Committee of the Universidad Cardenal Herrera-CEU approved this study. All animals were handled according to the principles of animal care published by Spanish Royal Decree 1201/2005 (BOE, 2005; BOE = Official Spanish State Gazette). The animal owners gave permission to take samples.
Bacterial identification
All samples were plated on selective and differential media (MacConkey and ChromID ESBL®) (Paterson and Bonomo 2005). After 24/48 h of incubation at 35–37°C, bacterial growth was determined along with colony colors.
Bacterial identification was verified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS; Burker Daltonics, Inc., Billerica, MA). Measurements were performed with Burker Microflex LT MALDI-TOF MS (Burker Daltonics, Inc.) using Flex Control software and a 60 Hz nitrogen laser (337 nm wavelength).
Antimicrobial resistance profile and phenotypic tests of E. coli strains
Susceptibility of the isolated strains identified as E. coli was assessed against amoxicillin (AMX), aztreonam (AZT), cephalothin (CEF), ceftazidime (CAZ), cefotaxime (CTX), cefoperazone (CFP), cefoxitin (FOX), cefuroxime (CXM), nalidixic acid (NAL), ciprofloxacin (CIP), cotrimoxazole (SXT), gentamicin (GEN), tobramycin (TOB), amikacin (AMK), amoxicillin/clavulanic acid (AMC), colistin (COL), erythromycin (ERY), fosfomycin (FOS), imipenem (IMI), meropenem (MER), minocycline (MIN), and nitrofurantoin (NFT) using a commercial broth microdilution method (Wider Panels, Soria-Melguizo, Spain). The criteria used for sensibility interpretation were those established by EUCAST (2013). Phenotypic tests using cefotaxime with/without clavulanate/cloxacillin disk-diffusion (Rosco Diagnostics, Denmark) and E-test (BioMérieux, France) were also performed.
Molecular characterization of β-lactamases
Once the strains that were possibly producing ESBL and/or pAmpC were detected and identified, their characterization was carried out using multiplex PCR. To identify the β-lactamase genes detected in the multiplex PCR assays, DNA sequence analysis of the amplicons was performed (Dallene et al. 2010). First, bacterial DNA was extracted heating a colony suspended in 25 μL of distilled water (99°C for 10 min) to later centrifuge it, collecting the supernatant. That DNA was subdued to two multiplex PCRs. The first one (Dallene et al. 2010) was used to detect the following types of ESBL genes: bla TEM, bla SHV, bla OXA-1, and bla CTX-M. The process was carried out as follows: the extracted DNA (2 μL) was added to a reaction mixture containing PCR buffer 1 × (10 mM Tris-HCl, 50 mM KCl, and 1.5 mM MgCl2), dNTPs (200 μM), primers (variable concentration), and Taq polymerase (1 U). The total reaction volume was 50 μL. The amplification process consisted of an initial denaturalization at 94°C for 10 min; 30 cycles at 94°C for 40 s, 60°C for 40 s, and 72°C for 1 min; and a final extension at 75°C for 7 min.
To characterize the different types of pAmpC β-lactamases, a second multiplex PCR (Sundin 2009) was carried out for bla MOX, bla CIT, bla DHA, bla ACC, bla MIR-ACT, and bla FOX. For this PCR, mixers with a total volume of 50 μL containing DNA (2 μL), PCR buffer 1 × (20 mM Tris-HCl, 50 mM KCl, and 1.5 mM MgCl2), dNTPs (0.2 mM), primers (variable concentrations), and Taq polymerase (1.25 U) were prepared. In this case, the process of amplification consisted of an initial denaturalization at 94°C for 3 min, followed by 25 cycles of denaturalization at 94°C for 3 min, hybridization at 64°C for 30 s, and extension at 72°C for 1 min to finish with a final elongation at 72°C for 7 min.
All the PCRs were carried out in a 2720 Applied Biosystems thermocycler (Thermo Fisher Scientific, CA). Both positive (well-characterized β-lactamases-producing strains) and negative (distilled water) controls were included in all series. Finally, the amplicons were sequenced to confirm their identification.
Results
A total of 34 E. coli strains from healthy animals (25 dogs, 8 falcons, and 1 monkey) were isolated and studied. The antimicrobial resistance profile of these 34 isolated E. coli strains was as follows: 100% resistant to amoxicillin, aztreonam, cefalothin, ceftazidime, cefotaxime, cefoperazone, and cefuroxime; 58.8% resistant to nalidixic acid, ciprofloxacin, and trimethoprim/sulfamethoxazole; 41.2% resistant to gentamicin and tobramycin; 11.8% resistant and 32.4% intermediate to cefoxitin; 97.1% susceptible and 2.9% intermediate to amoxicillin/clavulanate; and 100% susceptible to erythromycin, minocycline, imipenem, meropenem, amikacin, nitrofurantoin, fosfomycin, and colistin. All 34 E. coli strains met criteria for ESBL production.
In regard to the molecular characterization of the β-lactamases produced by the 34 isolated E. coli strains, we were able to identify ESBL in 29 (85.3%) of them. Of these 29 strains with ESBL (Table 1), bla TEM-21 and bla CTX-M-1 were detected in six (17.6%) strains; bla TEM-52 and bla CTX-M-1 in five (14.7%) strains; bla SHV-5 in five (14.7%) strains; bla SHV-5 and bla TEM-21 in three (8.8%) strains; bla TEM-52 and bla CTX-M-9 in three (8.8%) strains; bla TEM-52 in three (8.8%) strains; and bla SHV-12 in four (11.7%). In total, 46 β-lactamase genes were detected in this study (Fig. 1), of which 43.5% were bla TEM (19.6% bla TEM-21 and 23.9% bla TEM-52), 30.4% bla CTX-M (23.9% bla CTX-M-1 and 6.5% bla CTX-M-9), and 26.1% were bla SHV (17.4% bla SHV-5 and 8.7% bla SHV-12). All β-lactamases were found in dogs except for four bla SHV-12 found in falcons. No pAmpC genes were found.

β-Lactamase genes characterized from the isolated Escherichia coli strains.
AMX, amoxicillin; AZT, aztreonam; CEF, cephalothin; CAZ, ceftazidime; CTX, cefotaxime; CFP, cefoperazone; FOX, cefoxitin; CXM, cefuroxime; NAL, nalidixic acid; CIP, ciprofloxacin; SXT, cotrimoxazole; GEN, gentamicin; TOB, tobramycin.
As for the antibiotic resistance profile in relation to the detected β-lactamases, Table 1 shows that most of the E. coli strains resistant to at least seven antibiotics were detected in dogs. The presence of the following combinations of β-lactamase genes: bla TEM-52/ bla CTX-M-9 (8.8%), bla TEM-21/bla CTX-M-1 (17.6%), and bla TEM-52/ bla CTX-M-1 (14.7%), has been detected in the E. coli strains that presented resistance to a higher number of antibiotics, 13 (AMX, AZT, CEF, CAZ, CTX, CFP, FOX, CXM, NAL, CIP, SXT, GEN, and TOB) and 12 (AMX, AZT, CEF, CAZ, CTX, CFP, CXM, NAL, CIP, SXT, GEN, and TOB) antibiotics, respectively, as it is specified in Table 1.
Table 2 compiles individual characteristics such as animal from which the sample was collected, antibiotic susceptibility minimum inhibitory concentrations, and ESBLs identified.
MIC (mg/L) values in bold character refer to resistance category.
Underlined MIC (mg/L) values refer to intermediate susceptibility category.
MIC, minimum inhibitory concentration; AMK, amikacin; AMC, amoxicillin/clavulanate; COL, colistin; ERT, erythromycin; FOS, fosfomycin; IMI, imipenem; MER, meropenem; MIN, minocycline; NFT, nitrofurantoin.
Discussion
To our knowledge, this is the first study reporting the presence of ESBL-producing E. coli in falcons. Similar studies focused on wild birds such as those of Alcalá et al. (2016) and Parker et al. (2016) reported prevalence rates of 14% and 2.7%, respectively. Coincidentally, both studies found E. coli strains containing bla SHV. Further studies should be carried out to determine the origin of these strains.
The study is focused on the molecular characterization of E. coli strains because ESBL production is the main mechanism of resistance to β-lactams in this species. This fact is corroborated by studies such as that of Mosquito et al. (2012), in which after analyzing 369 samples of E. coli from pediatric patients with diarrhea, it was observed that the production of bla TEM represented the main mechanism of resistance against β-lactams (31%).
When carrying out the antimicrobial resistance profile of all 34 strains of E. coli isolated in this study, it was observed that 100% were resistant to amoxicillin, aztreonam, cephalothin (first generation), cefuroxime (second generation), ceftazidime (third generation), cefotaxime (third generation), and cefepime (fourth generation), which indicates that all of them are resistant to monobactams and cephalosporins belonging to all generations. This is a disturbing fact, seeing as some of these compounds, such as ceftazidime, were considered strategic molecules within the therapeutic array in case of bacterial infections, used exclusively in the hospital setting. The existence of bacteria with animal origin resistant to these compounds strengthens the idea that veterinarians might be making an indiscriminate use of antibiotics, without taking into account the impact this could have on the public health.
In contrast, most ESBL-producing E. coli strains were susceptible to amoxicillin/clavulanate, which is consistent with the results obtained from a similar study by Rodrigues et al. (2002), in which of 104 strains of E. coli studied, only 1.9% were found to be resistant to amoxicillin/clavulanate. This fact is encouraging, seeing as this combination is one of the most widely used in clinical practice, in both veterinary and human medicine.
According to the National Committee for Clinical Laboratory Standards (2003) it is recommended to investigate systematically the production of ESBL in any isolate of Klebsiella or E. coli that presents resistance to aztreonam, ceftazidime, ceftriaxone, or cefotaxime. Three of these antibiotics, aztreonam, ceftazidime, and cefotaxime, were included in the resistance profile of the strains isolated in this study and, as it was mentioned earlier, all 34 strains of E. coli showed resistance, which is why we proceeded to the molecular characterization of ESBLs in all of them.
The first case of an ESBL-producing E. coli strain from animal origin was detected in Spain in the year 2000 when analyzing a sample of a dog with recurring chronic cystitis, having found bla SHV-12 (Teshager et al. 2000). It was only a few years later when Carattoli et al. (2005) detected the first cases of bla CTX-M producing bacteria, exactly bla CTX-M-1, in dogs and cats with and without pathology. As it was previously mentioned, the only genes detected were bla TEM, bla SHV, and bla CTX-M, which is not surprising seeing as other studies (Costa et al. 2008, Moreno et al. 2008, Harada et al. 2011) performed on animals with no pathology showed similar results. A study (Harada et al. 2011) performed in Japan isolated bla SHV-12 producing E. coli strains in healthy puppies in two different breeding grounds. Likewise, two other studies performed in Portugal (Costa et al. 2008) and Chile (Moreno et al. 2008) identified E. coli strains producing bla CTX-M-1 and bla CTX-M-9 in fecal samples of healthy dogs that had previously received antibiotic treatment.
The β-lactamase gene most frequently identified in this study has been bla TEM, representing a 43.5% of the total. As it was mentioned by Philippon et al. (1989) type bla TEM β-lactamases are responsible for most of the resistances to β-lactam antibiotics in Enterobacteria.
bla CTX-M was the second most frequently detected β-lactamase, being present in 30.4% of the ESBL-producing E. coli strains. This was expected seeing as, since the year 2000, the presence of this ESBL has increased exponentially, with cases of E. coli strains producing bla CTX-M being detected in Europe, Asia, Africa, and America, reaching a point at which the scientific community is considering it “the bla CTX-M pandemic” (Cantón and Coque 2006). Even though this ESBL is predominantly found in E. coli, bla CTX-M has also been detected in other Enterobacteria, having become the most extended and detected type of ESBL worldwide (Pitout and Laupland 2008). Moreover, the relevance of the presence of this β-lactamase is corroborated by similar studies, such as those of Schmiedel et al. (2014) and Schink et al. (2013). Both studies, carried out in Germany, analyzed fecal samples from dogs, cats, and horses, and concluded that bla CTX-M-1 was a predominant subtype in animals with prevalence rates of 25.8% and 81.48%, respectively.
Interestingly, of the eight animal species studied, ESBLs were only detected in dogs and falcons, whereas none were found in animals such as horses, sheep, monkeys, or goats which, while domesticated, have less contact with their owners. Along these lines, it is surprising that no ESBL-producing bacteria were found in cats, seeing as similar studies on domestic animals did report these strains in cat pets (Bogaerts et al. 2015).
The increasing number of studies on the prevalence of ESBL-producing bacteria in domestic animals is contributing to a rise in the awareness of the scientific community in relation to what could become a serious public health issue. The potential zoonotic transmission of ESBL-producing bacteria is corroborated by studies such as that conducted by Rocha-García et al. (2015), in which feces of healthy domestic dogs were analyzed, having found ESBL-producing E. coli strains in 6% of the samples. Furthermore, a study (Meyer et al. 2012) carried out on 231 volunteers in 2011 analyzing possible risk factors for colonization with ESBL-producing E. coli concluded that contact with pets increases by almost sevenfold the chance of being colonized.
Conclusions
The results obtained from this study show that the animal feces analyzed presented a high prevalence of ESBL-producing E. coli. This fact could become a serious threat to the public health, seeing as the presence of these microorganisms in pets should be considered a possible zoonotic transmission vector. Moreover, all the E. coli strains studied were resistant to, at least, seven of the antibiotics studied, which reinforces the idea that there is a real need to implement control methods over veterinary antibiotic prescriptions in domestic animals. Finally, it is important to emphasize that this is the first report of ESBL-producing E. coli strains in falcons, suggesting that more studies should be carried out to determine their prevalence and the transmission route by which these falcons could have acquired drug-resistant bacteria.
Footnotes
Acknowledgment
This work was funded in part by grants from the Universidad Cardenal Herrera-CEU (INDI16/27, INDI 15/21, INDI14/20).
Author Disclosure Statement
No conflicting financial interests exist.
