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. 2010 Apr 23;76(12):4118–4120. doi: 10.1128/AEM.02761-09

Genetic Detection of Extended-Spectrum β-Lactamase-Containing Escherichia coli Isolates from Birds of Prey from Serra da Estrela Natural Reserve in Portugal

Luís Pinto 1,2,3,4, Hajer Radhouani 1,2,3,4, Céline Coelho 1,2,3,4, Paulo Martins da Costa 5,6, Roméo Simões 5, Ricardo M L Brandão 7, Carmen Torres 8, Gilberto Igrejas 1,2, Patrícia Poeta 3,4,*
PMCID: PMC2893492  PMID: 20418435

Abstract

Extended-spectrum β-lactamase-containing Escherichia coli isolates were detected in 32 of 119 fecal samples (26.9%) from birds of prey at Serra da Estrela, and these isolates contained the following β-lactamases: CTX-M-1 (n = 13), CTX-M-1 plus TEM-1 (n = 14), CTX-M-1 plus TEM-20 (n = 1), SHV-5 (n = 1), SHV-5 plus TEM-1 (n = 2), and TEM-20 (n = 1).


The high and sometimes excessive use of antibiotics is directly related to the great spread and development of bacterial antibiotic resistance, a problem in public health nowadays. Thus, many studies have been done in order to understand the mechanisms of bacterial drug resistance, as many multidrug-resistant bacterial strains have been detected in domestic animals and humans (12). Recent studies from our research group have focused on wild animals, trying to understand how they acquire resistance to antibiotics without direct contact (11, 17, 20). One of the most clinically relevant antimicrobial resistance mechanisms is constituted by extended-spectrum β-lactamases (ESBLs) (3, 16) harbored by Enterobacteriaceae, such as Escherichia coli, commensals of the gastrointestinal tract of animals and humans, serving as a reservoir for resistances, namely, to β-lactam antibiotics (1, 15). Most ESBLs are derivatives of TEM or SHV enzymes, but a new family of plasmid-mediated ESBLs, CTX-M, has also been reported worldwide in E. coli and other Enterobacteriaceae. Different variants of the β-lactamase TEM, as in the case of TEM-1, are often reported in cases of plasmid-mediated β-lactamase resistance (2, 5, 8, 14, 21, 22). In this study, fecal samples from wild birds of prey at the Serra da Estrela Natural Reserve were analyzed in order to detect ESBL-containing E. coli isolates and characterize the type of ESBL-encoding genes and other associated resistance genes and the corresponding phylogenetic groups.

One hundred nineteen fecal samples from birds of prey were recovered from April to July 2008 and studied for the presence of ESBL-containing E. coli strains (Table 1). All the fecal samples were collected individually from each animal and obtained in collaboration with CERVAS (Center of Ecology, Collecting, Welcome and Handling of Wild Animals). This Center receives injured animals found in its natural environments, is located at the Serra da Estrela Natural Reserve, and belongs to the Portuguese Institute of the Nature Management. None of the animals had been previously fed by humans or had received antibiotics. Each bird that arrives at CERVAS is placed in an individual cage to be treated and released back into the environment. Sampling was performed by recovering the fecal material in the cloaca by using a sterile swab. They were immediately transferred to peptone water and manipulated during the first 24 h of arrival to the laboratory. Samples were seeded in Levine agar supplemented with cefotaxime (2 mg/liter), and colonies with typical E. coli morphology were selected, identified by classical biochemical methods and by the API 20E system (bioMérieux, La Balme Les Grottes, France), and further studied. Susceptibility to 16 antibiotics (ampicillin, amoxicillin plus clavulanic acid [AMC], cefoxitin, cefotaxime [CTX], ceftazidime [CAZ], aztreonam [ATM], imipenem, gentamicin, amikacin, tobramycin, streptomycin, nalidixic acid, ciprofloxacin, sulfamethoxazole-trimethoprim, tetracycline, and chloramphenicol) was tested by the disc diffusion method (7) for all recovered E. coli isolates. E. coli ATCC 25922 was used as a quality control strain. The double-disc diffusion test (CTX, CAZ, and ATM in the presence or absence of AMC) was performed to detect ESBL production (7).

TABLE 1.

Animal species in which ESBL-positive E. coli isolates were recovered

Animal species No. of tested animals No. of animals with ESBL-positive E. coli isolates
Common buzzard (Buteo buteo) 23 11
Common barn owl (Tyto alba) 8 4
Eurasian tawny owl (Strix aluco) 10 2
Booted eagle (Hieraaetus pennatus) 11 5
Montagu's harrier (Circus pygargus) 5 2
Black kite (Milvus migrans) 16 2
Eurasian black vulture (Aegypius monachus) 2 1
Bonelli's eagle (Hieraaetus fasciatus) 2 1
Eurasian eagle owl (Bubo bubo) 8 2
Common raven (Corvus corax) 3 2
Other speciesa 31 0
a

Northern goshawk (Accipiter gentilis; n = 5); European scops owl (Otus scops; n = 5); Eurasian sparrowhawk (Accipiter nisus; n = 4); common crane (Grus grus; n = 2); honey buzzard (Pernis apivorus; n = 2); carrion crow (Corvus corone; n = 2); yellow-legged gull (Larus cachinnans; n = 2); little owl (Athene noctua; n = 2); Eurasian marsh harrier (Circus aeruginosus; n = 1); Egyptian vulture (Neophron percnopterus; n = 1); common kestrel (Falco tinnunculus; n = 1); azure-winged magpie (Cyanopica cyanus; n = 1); European magpie (Pica pica; n = 1); common swift (Apus apus; n = 1); and red kite (Milvus milvus; n = 1).

The presence of genes encoding TEM, SHV, OXA, CTX-M, and CMY type β-lactamases was studied by specific PCRs (17). All obtained amplicons were sequenced on both strands, and sequences were compared with those included in the GenBank database and at the Lahey Clinic website (http://www.lahey.org/Studies/) to identify the β-lactamase genes.

Non-β-lactamase genes [tetA/tetB, aadA, aac(3)-II/aac(3)-IV, aac(6′), cmlA, and sul1/sul2/sul3, associated with tetracycline, streptomycin, gentamicin, amikacin, chloramphenicol, and trimethoprim-sulfamethoxazole resistance, respectively] were also studied by PCR (17). The presence of the genes intI1 and intI2, encoding class 1 and 2 integrases, respectively, was studied by PCR. Positive and negative controls from the bacterial collection of the University of Trás-os-Montes and Alto Douro were used in all assays. The ESBL-positive isolates were classified into one of the four main phylogenetic groups, A, B1, B2, and D, by PCR as described previously based on the presence or absence of the chuA, yjaA, or tspE4.C2 gene (6).

E. coli isolates were detected in Levine-CTX plates for 32 of the 119 samples (26.9%) from wild birds of prey at the Serra da Estrela Natural Reserve (Table 1). All 32 isolates recovered in this survey resulted in a positive ESBL screening test, which also indicated a resistant phenotype to CTX and/or CAZ. The β-lactamase genes detected in these isolates were as follows: blaCTX-M-1 (n = 13), blaCTX-M-1 plus blaTEM-1b (n = 8), blaCTX-M-1 plus blaTEM-1d (n = 6), blaCTX-M-1 plus blaTEM-20 (n = 1), blaSHV-5 plus blaTEM-1b (n = 2), blaSHV-5 (n = 1), and blaTEM-20 (n = 1) (Table 2). The blaCTX-M-1 gene was found in most of our ESBL-positive E. coli isolates (n = 28); this ESBL was also reported in studies of healthy poultry (13) and by our research group in healthy pets (9) and wild animals (10, 17). It is interesting to underline that approximately half of the blaCTX-M-1-containing E. coli isolates also harbored a variant of a blaTEM gene, concretely blaTEM-1b, blaTEM-1d, or blaTEM-20. The blaTEM-1b gene is the most frequent variant found in β-lactam-resistant E. coli isolates of food, humans, and healthy animals or in wild boars in other studies (4, 18). The blaTEM-1d genetic variant is relatively infrequent, although it has been detected in some other studies (19). Two ESBL-containing E. coli isolates were positive for the presence of blaTEM-20, and another three isolates carried the blaSHV-5 gene. Most ESBL-positive E. coli isolates of this study were classified into the A or B1 phylogenetic group (72%), although nine isolates which harbored blaCTX-M-1 with or without blaTEM-1b were included in the B2 phylogenetic group. The predominance of CTX-M-1-producing isolates belonging to phylogenetic group B2 is of great concern, as, in fact, this phylogenetic group often carries virulence determinants that are less frequently present in other phylogenetic groups. Similar results were found in wild boars by our research group (18).

TABLE 2.

Characteristics of the ESBL-positive fecal E. coli isolates recovered from birds of prey

Isolate no. Animal species Resistance pattern to β-lactam antibioticsa β-Lactamase-encoding genes detected Resistance pattern to non-β-lactam antibioticsb Resistance genes for non-β-lactam antibiotics Integron-related genes Phylogenetic group
B1 Buteo buteo AMP-CTX blaCTX-M-1 plus blaTEM-20 CIP-NAL-TET-STR-SXT tetA, sul2 intI1 B1
B2 Buteo buteo AMP-CTX-ATM blaCTX-M-1 plus blaTEM-1D CIP-NAL-TET-SXT tetA, sul2 intI1 B1
B3 Buteo buteo AMP-CTX blaCTX-M-1 NAL-SXT sul2, sul3 intI1 B1
B9 Buteo buteo AMP-CTX-ATM blaCTX-M-1 plus blaTEM-1b CIP-NAL-TET-SXT tetA, sul2 intI1 B1
B10 Buteo buteo AMP-CTX blaCTX-M-1 plus blaTEM-1b CIP-NAL-TET-STR-SXT tetA, sul2 intI1 B1
B14 Buteo buteo AMP-CTX-ATM blaCTX-M-1 plus blaTEM-1D NAL-TET-STR-CHL-SXT tetA, sul2 intI1 A
B15 Buteo buteo AMP-CTX blaCTX-M-1 plus blaTEM-1D NAL-TET-STR-SXT aadA, tetA, sul2 intI1, intI2 A
B17 Buteo buteo AMP-CTX blaCTX-M-1 CIP-NAL-STR-SXT sul2, sul3 intI1 B2
B18 Buteo buteo AMP-CTX-CAZ blaTEM-20 NAL-TET-STR-SXT-KAN tetA, sul2 intI1 B1
B19 Buteo buteo AMP-CTX blaCTX-M-1 CIP-NAL-STR-SXT sul2, sul3 intI1 B2
B24 Buteo buteo AMP-CTX blaCTX-M-1 CIP-NAL-TET-SXT tetA, sul3 B2
H6 Hieraaetus pennatus AMP-CTX blaCTX-M-1 NAL-TET-SXT sul2, sul3 intI1 B1
H7 Hieraaetus pennatus AMP-CTX blaCTXM-1 TET-SXT sul2 intI1 A
H8 Hieraaetus pennatus AMP-CTX blaCTX-M-1 plus blaTEM-1b CIP-NAL-TET-SXT tetA, sul2 intI1 B1
H11 Hieraaetus pennatus AMP-CTX blaCTX-M-1 plus blaTEM-1d CIP- NAL-TET-SXT tetA, sul2 A
H12 Hieraaetus pennatus AMP-CTX blaCTX-M-1 plus blaTEM-1d CIP- NAL-TET-SXT tetA, sul2 A
T4 Tyto alba AMP-CTX-ATM blaCTX-M-1 plus blaTEM-1d NAL-TET-STR-SXT aadA, tetA, sul2 intI1, intI2 A
T28 Tyto alba AMP-CTX-AMC blaCTX-M-1 plus blaTEM-1b NAL-TET-STR-SXT aadA, tetA, sul1 intI1 B2
T29 Tyto alba AMP-CTX-ATM-CAZ-AMC blaSHV-5 CIP-NAL-TET-STR-CHL- SXT-KAN-TOB-GEN aadA, sul1 intI1 A
T30 Tyto alba AMP-CTX-ATM blaCTX-M-1 plus blaTEM-1b TET-STR-CHL-SXT-KAN aadA, sul1 intI1, intI2 B1
S5 Strix aluco AMP-CTX blaCTX-M-1 NAL-TET-SXT sul2, sul3 intI1 B1
S20 Strix aluco AMP-CTX blaCTX-M-1 CIP-NAL-STR-SXT sul2, sul3 B2
M13 Milvus migrans AMP-CTX blaCTX-M-1 plus blaTEM-1b CIP- NAL-TET-STR-SXT sul1, sul2 B1
M21 Milvus migrans AMP-CTX-ATM blaCTX-M-1 NAL-SXT sul3 intI1 B1
C22 Circus pygargus AMP-CTX blaCTX-M-1 plus blaTEM-1b NAL-TET-STR-SXT tetA B2
C23 Circus pygargus AMP-CTX blaCTX-M-1 NAL-TET-SXT sul3 intI1 A
BU26 Bubo bubo AMP-CTX blaCTX-M-1 CIP- NAL-SXT sul3 intI1 B2
BU27 Bubo bubo AMP-CTX blaCTX-M-1 CIP-NAL-SXT sul3 intI1 B2
CO31 Corvus corax AMP-CTX-ATM blaSHV-5 plus blaTEM-1b TET-STR-CHL-SXT cmlA, tetA, sul3 intI1 B1
CO32 Corvus corax AMP-CTX-ATM-CAZ blaSHV-5 plus blaTEM-1b TET- STR-CHL-SXT cmlA, aadA, tetA, sul3 intI1 B1
A16 Aegypius monachus AMP-CTX blaCTX-M-1 plus blaTEM-1b CIP-NAL-STR-CHL-SXT sul1, sul2 intI1 B1
HI25 Hieraaetus fasciatus AMP-CTX blaCTX-M-1 CIP-NAL-SXT sul3 intI1 B2
a

AMP, ampicillin; AMC, amoxicillin-clavulanic acid; ATM, aztreonam.

b

GEN, gentamicin; TOB, tobramycin; STR, streptomycin; TET, tetracycline; SXT, sulfamethoxazole-trimethoprim; NAL, nalidixic acid; CIP, ciprofloxacin; CHL, chloramphenicol; KAN, kanamycin.

The common phenotype of resistance to multiple antibiotics among our ESBL-producing isolates is probably due to the coexistence of blaCTX-M-1 with other antibiotic resistance genes in the same plasmid, contributing to maintain ESBL-producing populations under different antibiotic selective pressures. With this study, it was possible to detect and characterize ESBL-producing E. coli isolates from birds of prey at the Serra da Estrela Natural Reserve in Portugal, with two types of ESBLs detected as CTX-M-1 and SHV-5. However, we cannot exclude the possibility that these wild animals had been exposed to fecal material of farm animals or even that of humans. These facts might be involved in the acquisition and dissemination of antibiotic-resistant bacteria even in the absence of direct antibiotic pressure and might explain the presence of ESBL-positive E. coli isolates. However, more studies should be performed to better understand the role of these animals in the spread of this type of resistance.

Acknowledgments

We thank CERVAS, Portugal, for its contribution to the collection of samples.

Footnotes

Published ahead of print on 23 April 2010.

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