Genotypic Characterization Of Antimicrobial Resistance Research Articles

Phenotypic and genotypic characterization of antimicrobial resistance of Campylobacterisolates from poultry meat in Turkey

Phenotypic and genotypic antimicrobial resistances of Campylobacter strains from chicken meat were investigated. A total of 19 isolates (Campylobacter jejuni=6 and Campylobacter coli=13) were identified by multiplex PCR. The C. jejuni and C. coli isolates were tested for resistance to ciprofloxacin, erythromycin, and tetracycline using the disc diffusion method. In addition, all the strains were analyzed for resistance gene tet-O and mutations in the gyrA and 23S rRNA genes by PCR. Overall, a high frequency of resistance was detected against tetracycline (14/19, 73.6%), followed by erythromycin (7/19, 36.8%), and ciprofloxacin (6/19, 31.5%). Two of C. coli isolates (15.3%) were multidrug resistant, whereas none of the C. jejuni isolates were resistant to three antibiotics at the same time. Ten of the 14 Campylobacter strains (71.4%) resistant to tetracycline carried tet-O gene. Mutations in the 23S rRNA and gyrA genes were identified in 57.1% (4/7), 66.6% (4/6) of the isolates resistant to erythromycin and ciprofloxacin, respectively.

Phenotypic and genotypic characterization of antimicrobial resistance in commonly isolated Salmonella serovars from chickens

Salmonellosis caused by Salmonella agents is the second most common zoonotic infection in humans. In recent years, Salmonella's increasing antimicrobial resistance (AMR) has been a concern. The major transmission route of Salmonella is consumption of contaminated poultry products. Therefore, monitoring of antimicrobial resistance in chicken-originated Salmonella is critically important. This study investigated AMR in four commonly isolated Salmonella serovars from chickens, namely Salmonella Enteritidis (S. Enteritidis), Salmonella Infantis (S. Infantis), Salmonella Kentucky (S. Kentucky), and Salmonella Typhimurium (S. Typhimurium). A total of 133 isolates were examined by phenotypic and genotypic AMR characterization. Resistance to 14 different antimicrobials and eight resistance genes were investigated in all isolates. The AMR test indicated that there was no resistant isolate to all antimicrobials while 14.3% were susceptible to all antimicrobials. The highest resistance was to sulfonamides (57.1%), nalidixic acid (48.1%), and tetracycline (39.1%). The highest susceptibilities were to cefotaxime (86.5%), cefoxitin (92.5%), ceftazidime (78.2%), and ceftriaxone (97%). S. Infantis and S. Kentucky isolates had higher resistance to all antimicrobials than S. Enteritidis and S. Typhimurium isolates. Significantly high multidrug-resistance (MDR) was detected in 50.4% of all isolates, although MDR prevalence varied widely between serovars: 78.7% of all S. Infantis isolates were MDR whereas only 18.8% of S. Enteritidis isolates were MDR. The most prevalent resistance genes were tetA (35.2%) and sul1 (31.6%), with 12.5% and 3.1% of S. Enteritidis isolates being positive for tetA and sul1, respectively, whereas 17.4% and 8.7% of S. Typhimurium isolates were positive. These rather low prevalence rates are probably due to effective monitoring of these serovars by control programs in Türkiye. The nondetection of mcr1 and mcr2 can be explained by the rare use of colistin in chicken flocks in Türkiye. The obtained findings emphasize the importance of AMR monitoring for Salmonella and the risks of chicken-originated isolates to humans.

P26 Phenotypic and genotypic characterization of antimicrobial resistance in Clostridioides difficile in North Wales

Background Clostridioides difficile poses a major infection control challenge and remains a huge burden to our healthcare system. The emergence of hypervirulent strains of C. difficile has highlighted the need for monitoring antimicrobial resistance (AMR) and continual epidemiological vigilance. Agar dilution is the current gold standard method for antimicrobial susceptibility testing of C. difficile and the method routinely utilized in the Public Health Wales (PHW) UK Anaerobe Reference Unit (UKARU) at the University Hospital of Wales, Cardiff. However, this method is laborious and time consuming. Meanwhile, the emergence of WGS introduces the possibility of acquiring rapid genotypic information in terms of AMR.MethodsIn this research project, isolates obtained from faecal samples submitted across the Betsi Cadwalader health board (BCUHB) that were either GDH or PCR positive were sequenced as part of the C. difficile Genomic Sequencing and Typing (DIGEST) pilot project performed at the PHW Pathogen Genomics Unit (PenGU) in Cardiff.ResultsResults highlights include the finding that 93% of the isolates analysed for the presence of AMR genes were found to have the cdeA gene associated with conferring resistance to fluoroquinolones such as ciprofloxacin. Other common genes observed included blaCDD-1 and blaCDD-2, associated with β-lactam resistance.ConclusionsWhile further work must be done to link genotypic characterization with phenotype, this study provides a valuable insight into AMR mechanisms in C. difficile and may in future become an important tool providing early indication of shift in C. difficile epidemiology or the emergence of a new hypervirulent and MDR strain.

Phenotypic and Genotypic Characterization of Antimicrobial Resistance in <i>Escherichia Coli</i> Isolates from Chicken Meat

Phenotypic and Genotypic Characterization of Antimicrobial Resistance in <i>Escherichia Coli</i> Isolates from Chicken Meat

Phenotypic and genotypic characterization of antimicrobial resistance in clinical isolates of Vibrio cholerae over a decade (2002-2016)

PurposeEmergence and spread of resistance among Vibrio cholerae have become a global public health problem. In India, no consolidated data is available on antimicrobial susceptibility patterns and antibiotic resistance genes. MethodsA total of 110 representative isolates obtained over a period of 14 years were included. Antimicrobial susceptibility was tested by disc diffusion and micro broth dilution. Presence of 13 antimicrobial resistance genes was ascertained by using PCR. ResultsAntimicrobial resistance fluctuated for most of the antibiotics. Resistance to cotrimoxazole in our study was 92.72% and the SXT element was present in all isolates. Resistance to nalidixic acid, tetracycline, and cefotaxime was found to be 98.18%, 7.27%, and 10.9% respectively. Resistance to ampicillin saw a fluctuating trend with a recent fall. Resistance to ciprofloxacin and azithromycin was 12.72% and 29% by MIC. blaTEM was the most common ESBL gene (94.5%). Other were blaCMY (26.36%) and blaNDM (2.7%). We report blaCTX-M-15 and blaOXA-48 and ermB for the first time in the world. Newer antimicrobials like prulifloxacin and rifaximin were tested for the first time from India. ConclusionsOur study has shown very high levels of resistance to older antibiotics and the emergence of resistance to some of the newer classes of antibiotics. There is an urgent need for increased surveillance studies, rational use of the antimicrobials and preventive measures to control the disease.

Antimicrobial resistance genes and plasmids in Campylobacter jejuni from broiler production chain in Southern Brazil

Campylobacter jejuni is the main cause of foodborne gastroenteritis in humans throughout the world. Besides impairing the treatment of campylobacteriosis, the presence of resistant C. jejuni isolates in the food production chain raises a concern to human health. The aims of this study were to perform the phenotypic and genotypic characterization of antimicrobial resistance in C. jejuni isolates from broiler production chain in Southern Brazil, as well as to verify the presence of plasmids among the isolates. In this study, 82.2% of C. jejuni isolates presented resistance to at least one antimicrobial tested, and 46.4% were multidrug resistant. The cmeB and cmeG genes, which encode to multidrug efflux pumps, were reported in 91.3% of the resistant isolates. The tet(O) gene was found in 81.2% of the tetracycline-resistant isolates. All the isolates with phenotypic resistance to kanamycin were positive for the presence of the aphA-3 gene. Regarding the β-lactams, the blaoxa-61 gene was present in 66.7% of the ampicillin-resistant isolates. Thus, the high rates of antimicrobial resistance and the presence of plasmids harboring antimicrobial resistance genes found in C. jejuni isolates highlights the importance of a prudent and judicious use of antimicrobial agents in animal production in Brazil.

Genetic diversity, virulence and distribution of antimicrobial resistance among Listeria monocytogenes isolated from milk, beef, and bovine farm environment.

Listeria monocytogenes is an opportunistic intracellular foodborne pathogen and is ubiquitous in nature. The occurrence of L. monocytogenes in animal production units coupled with their presence in milk, faeces, feed, water, sewage, and soil is a contributory factor for foodborne listeriosis in humans and animals. The study was aimed to characterize genotype and serogroup of L. monocytogenes recovered from different types of samples and also to study antimicrobial patterns by phenotypic and genotypic methods. Multiplex polymerase chain reaction (PCR) was used for the confirmation of L. monocytogenes, the identification of its serogroup and lineage, and the detection of virulence markers. Enterobacterial repetitive intergenic consensus (ERIC), and randomly amplified polymorphic DNA (RAPD)-PCR were used to characterize those isolates, and antimicrobial patterns were studied phenotypically by Kirby-Bauer method and genotypically by PCR. Out of the screened 474 samples (274 milk and 50 each of soil, feed, sewage, and beef), ten L. monocytogenes isolates (milk=8, soil=1, and beef=1) were confirmed by PCR targeting the hlyA gene and found to belong to the 1/2a, 3a serogroup and fall under type II lineage. Virulence potential assessment revealed that all the ten isolates harbored the iap gene while the presence of plcA and plcB genes were noticed in seven and eight isolates respectively. Six isolates from milk were found to group in the same cluster by ERIC and RAPD fingerprinting, suggesting both methods to be efficient molecular typing tools for L. monocytogenes. Genotypic characterization of antimicrobial resistance (AMR) genes revealed that seven isolates were positive for tetM, five for mefA, four for msrA, and one for lnuA genes while none of the isolates showed tetK, ermA, ermB, and lnuB genes. The presence of L. monocytogenes in bovine farm environments coupled with virulence markers, and multidrug resistance from the study area suggest a possible transmission from the environment to humans and animals which needs to be monitored regularly to ensure food safety and the well-being of animals and humans.

Phenotypic and Genotypic Characterization of Antimicrobial Resistance in Salmonella Strains Isolated from Chicken Carcasses and Parts Collected at Different Stages during Processing

Chicken carcass and parts rinsate samples and fecal samples were collected at different stages in a commercial poultry processing facility. Microbiological analysis was conducted to determine the levels of multiple indicator microorganisms and prevalence of Salmonella. Antibiotic susceptibility testing was conducted on Salmonella isolates to determine antimicrobial resistance profiles. Whole genome sequencing was performed for tracing isolates in the processing chain, serotyping, and determining genetic features associated with virulence and antimicrobial resistance in the bacterial genome. The overall contamination rate was 55% for Salmonella. Prevalence increased by 80% in chicken parts compared with the previous processing site (postchill carcasses), suggesting possible cross-contamination during the cutting and deboning processes. The levels of indicator organisms were reduced significantly from the prescalding to the parts processing sites, by 3.22 log CFU/mL for aerobic plate count, 3.92 log CFU/mL for E. coli, 3.70 log CFU/mL for coliforms, and 3.40 log CFU/mL for Enterobacteriaceae. The most frequent resistance in Salmonella was associated with tetracycline (49 of 50, 98%) and streptomycin (43 of 50, 86%). Some Salmonella isolates featured resistance to the cephems class of antibiotics (up to 15%). Whole genome sequencing analysis of Salmonella isolates identified nine different clonal populations distributed throughout the samples taken at different stages; serotype Kentucky was the most commonly isolated. This study provides insights into microbial profiling and antibiotic-resistant strains of chicken rinsate samples during poultry processing.

Epidemiology and antibiotic resistance trends in clinical isolates of Pseudomonas aeruginosa from Rio de janeiro - Brazil: Importance of mutational mechanisms over the years (1995–2015)

Pseudomonas aeruginosa is a major health concern globally and treating infections caused by MDR-isolates unarguably a humongous challenge that remains an unmet need in modern medicine. To determine patterns and mechanisms of antimicrobial resistance and its spread over the years in Rio de Janeiro, Brazil, 88 P. aeruginosa isolates were selected from 1995 to 2015. Phenotypic and genotypic characterization of antimicrobial resistance was evaluated and isolates were submitted to clonality by PFGE and MLST. PFGE analysis showed a great variability of clonal groups mainly over the past 10 years of this study. STs predominant in the early years (ST804, ST1860, ST487 and ST1602) associated to multidrug resistance (MDR) phenotype were replaced by ST277, ST244, ST1945, ST1791 with extensive drug resistance (XDR) in last years, with significant increase in resistance to carbapenems, fluoroquinolones and aminoglycosides. Colistin resistance was detected in 3.5%. The main mechanisms of antimicrobial resistance were mutational mechanisms (mutations in oprD, mexT and gyrA genes). We found the ESBL genes blaTEM (n = 2), blaSHV (n = 3) and blaCTX (n = 1).The carbapenemases genes was present in ST277 (blaSPM, n = 3), ST1560 (blaKPC, n = 3) and ST1944 (blaKPC, n = 2). The 16S RNA methylase gene (rmtD) was found in five isolates belonged to ST277. In conclusion, molecular epidemiological investigation reveals an increase of antimicrobial resistance in P. aeruginosa over 21 years in Rio de Janeiro with higher population structure and occurrence of high risk clone in the last years. The mutational mechanisms of resistance were present in all XDR isolates.

Determination of antimicrobial resistance in Salmonella spp.

Infections with Salmonella are an important public health problem worldwide. Salmonella are one of the most common causes of food-borne illness in humans. There are many types of Salmonella but they can be divided into two broad categories: those that cause typhoid and those that do not. The typhoidal Salmonella (TS), such as S. enterica subsp. enterica serovars Typhi and S. Paratyphi only colonize humans and are usually acquired by the consumption of food or water contaminated with human fecal material. The much broader group of non-typhoidal Salmonella (NTS) usually results from improperly handled food that has been contaminated by animal or human fecal material. Antimicrobials are critical to the successful outcome of invasive Salmonella infections and enteric fever. Due to resistance to the older antimicrobials, ciprofloxacin [fluoroquinolone (FQ)] has become the first-line drug for treatment. Nevertheless, switch to FQ has led to a subsequent increase in the occurrence of salmonellae resistant to this antimicrobial agent. The exact mechanism of this FQ resistance is not fully understood. FQ resistance has driven the use of third-generation cephalosporins and azithromycin. However, there are sporadic worldwide reports of high level resistance to expanded-spectrum cephalosporins (such as ceftriaxone) in TS and in NTS it has been recognized since 1988 and are increasing in prevalence worldwide. Already there are rare reports of azithromycin resistance leading to treatment failure. Spread of such resistance would further greatly limit the available therapeutic options, and leave us with only the reserve antimicrobials such as carbapenem and tigecycline as possible treatment options. Here, we describe the methods involved in the genotypic characterization of antimicrobial resistance in clinical isolates of salmonellae.

Phenotypic and genotypic characterization of antimicrobial resistance in Escherichia coli isolates

Background:Themajor influenceson the increase and spreadof antimicrobial resistant bacteria are the use of antimicrobial agents in human medicine and their use in livestock for therapy and growth promotion. To generate baseline data to use in future risk assessment of antimicrobial resistance, a number of surveillance program on the local, continental and global scale have been initiated. The prevalence of resistance in commensal E. coli is a good indicator for the selective pressure by antibiotics use and resistance problems to be expected in pathogenic bacteria. The aim of this studywas to determine and compare the occurrence of antimicrobial resistance phenotypes and genotypes among E. coli strains recovered from animal sources. Methods & Materials: Fifty-eight (58) E. coli strains were isolated from animal sources (Cattle, pig and chicken). MIC was determined according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Strains were screened and mapped by PCR methods for antimicrobial resistant genes, integrons and gene cassettes. Results: The resistance profile of E. coli for ampicillin (100%), cefotaxime (100%), ceftazidime (83%), ciprofloxacin (43%) (C), tetracycline (100%) (T), gentamicin (90%) (G), kanamycin (77%) (K), streptomycin (100%) (S), chloramphenicol (97%) (Ch) sulphamethoxazole (100%) (Su) and trimethoprime (97%) (T). Eight-Five per cent (85%) of E. coli harbored class 1 integron and variable gene cassettes were revealed. A prevalence of gene cassettes that present resistance to streptomycin and trimethoprime was observed. The resistance genes determinant present in gentamicin resistance were aac(3’)-IIc, aac(6’)-Ib and ant(2”)-1a. The occurrence of aph(3)-Ia in kanamycin resistant strainswas 68%. The prevalence of sul1 (80%) and sul2 (100%) was observed. The prevalence of tet(A) is higher than tet(B) in tetracycline-resistant strains. The gene determinants for chloramphenicol resistance (cat1 and catB) were detected. Differences in the rates and profile of resistance were observed, possibly reflecting differences in antibiotic use regimens among these strains. Conclusion: This study shows that multi-drug resistant E. coli isolates are prevalent in animal sources and a considerable proportion of E. coli strains are resistant to a variety of antimicrobial agents.Genotypic characterization revealedhighnumberofdiverse resistance determinants.

Phenotypic and Genotypic Characterization of Antimicrobial Resistance in Enterohemorrhagic Escherichia Coli and Atypical Enteropathogenic E. Coli Strains from Ruminants

Two hundred and twenty-six attaching and effacing Escherichia coli (AEEC) strains (20 enterohemorrhagic E. coli and 206 atypical enteropathogenic E. coli) isolated from calves, lambs, and goat kids with diarrhea and from healthy cattle, sheep, and goats were tested for their resistance to 10 antimicrobial agents by the disc diffusion method. Resistant and intermediate strains were analyzed by polymerase chain reaction for the presence of the major resistance genes. The overall percentage of resistant strains to tetracycline, streptomycin, erythromycin, and sulfamethoxazole was very high (>65%). Moreover, a high level of resistance (approximately 30%) to ampicillin, chloramphenicol, trimethoprim, and trimethoprim-sulfamethoxazole was also detected. The AEEC strains were very susceptible (>90%) to gentamicin and colistin. Because AEEC from ruminants can cause diseases in human beings, the high frequency of antimicrobial resistance detected in the current study is a source of concern. For each antimicrobial agent, the predominant resistance genes in the resistant strains were ampicillin, bla(TEM) (97.1%); tetracycline, tetA (76.7%); gentamicin, aac(3)II (80%); streptomycin, strA/strB (76.7%) and aadA (71.7%); chloramphenicol, catI (85.1%); trimethoprim, dhfrI (76.3%); and sulfamethoxazole, sul1 (60%) and sul2 (63.3%). In the majority of cases, resistance to a given antimicrobial, except for streptomycin, was caused by a single gene. A negative association between tetA and tetB, between aac(3)II and aac(3)IV, and between dhfrI and dhfrV was observed. The present study gives baseline data on frequency and molecular basis of antimicrobial resistance in AEEC strains from ruminants.

Detection of multiple-antimicrobial resistance and characterization of the implicated genes in Escherichia coli isolates from foods of animal origin in Tunis.

Phenotypic and genotypic characterization of antimicrobial resistance was conducted for 98 Escherichia coli isolates recovered from 40 food samples of animal origin (poultry, sheep, beef, fish, and others) obtained in supermarkets and local butcheries in Tunis during 2004 and 2005. Susceptibility to 15 antimicrobial agents was tested by disk diffusion and agar dilution methods, the mechanisms of resistance were evaluated using PCR and sequencing methods, and the clonal relationship among isolates was evaluated using pulsed-field gel electrophoresis. High resistance was detected to tetracycline, sulphonamides, nalidixic acid, ampicillin, streptomycin, and trimethoprim-sulfamethoxazole (29 to 43% of isolates), but all isolates were susceptible to cefotaxime, ceftazidime, cefoxitin, azthreonam, and amikacin. One-third of the isolates had multiresistant phenotypes (resistance to at least five different families of antimicrobial agents). Different variants of blaTEM, tet, sul, dfrA, aadA, and aac(3) genes were detected in most of the strains resistant to ampicillin, tetracycline, sulphonamide, trimethoprim, streptomycin, and gentamicin, respectively. The presence of class 1 and class 2 integrons was studied in 15 sulphonamide-resistant unrelated E. coli strains, and 14 of these strains harbored class 1 integrons with five different arrangements of gene cassettes, and a class 2 integron with the dfrA 1 + sat + aadA 1 arrangement was found in one strain. This study revealed the high diversity of antimicrobial resistance genes, some of them included in integrons, in E. coli isolates of food origin.

Phenotypic and genotypic characterization of antimicrobial resistance in faecal enterococci from wild boars ( Sus scrofa)

The objective was to study the prevalence of antimicrobial resistance and the mechanisms implicated in faecal enterococci of wild boars in Portugal. One hundred and thirty-four enterococci (67 E. faecium, 54 E. hirae, 2 E. faecalis, 2 E. durans and 9 Enterococcus spp.) were recovered from 67 wild boars (two isolates/sample), and were further analysed. High percentages of resistance were detected for erythromycin, tetracycline, and ciprofloxacin (48.5%, 44.8%, and 17.9%, respectively), and lower values were observed for high-level-kanamycin, -streptomycin, chloramphenicol, and ampicillin resistance (9%, 6.7%, 4.5%, and 3.7%, respectively). No isolates showed vancomycin or high-level-gentamicin resistance. The erm(B), tet(M), aph(3′)-IIIa, and ant( 6)-I genes were demonstrated in all erythromycin-, tetracycline-, kanamycin-, and streptomycin-resistant isolates, respectively. Specific genes of Tn 916/Tn 1545 and Tn5397 transposons were detected in 78% and 47% of our tet(M)-positive enterococci, respectively. The tet(S) and tet(K) genes were detected in one isolate of E. faecium and E. hirae, respectively. Three E. faecium isolates showed quinupristin–dalfopristin resistance and the vat(E) gene was found in all of them showing the erm(B)– vat(E) linkage. Four E. faecium isolates showed ampicillin-resistance and all of them presented seven amino acid substitutions in PBP5 protein (461Q → K, 470H → Q, 485M → A, 496N → K, 499A → T, 525E → D, and 629E → V), in relation with the reference one; a serine insertion at 466′ position was found in three of the isolates. Faecal enterococci from wild boars harbour a variety of antimicrobial resistance mechanisms and could be a reservoir of antimicrobial resistance genes and resistant bacteria that could eventually be transmitted to other animals or even to humans.

Phenotypic and genotypic characterization of antimicrobial resistance in Escherichia coli O111 isolates

The aim of this study was to generate baseline data on the prevalence and molecular basis of antimicrobial resistance in Escherichia coli O111 isolates. A total of 105 epidemiologically unrelated E. coli O111 isolates from humans and cattle (isolated between 1983 and 2003) were tested for susceptibility to 17 antimicrobial agents by broth microdilution. Resistant isolates were screened by molecular methods for resistance genes, class 1 and 2 integrons and mutations in the quinolone-resistance determining regions. Resistance was found in 76% of the isolates, with a prevalence of 72% for multiresistance. The most prevalent resistances were to streptomycin, sulfamethoxazole and tetracycline (72-68%), followed by spectinomycin, ampicillin and kanamycin/neomycin (39-25%). For each antimicrobial agent, the predominant resistance genes were ampicillin, bla(TEM) (94%); chloramphenicol, catA1 (100%); gentamicin, aac(3)-IV and aac(3)-II (50% each); kanamycin, aphA1 (100%); streptomycin, aadA1- like (66%); sulfamethoxazole, sul1 (59%); tetracycline, tet(A) (86%); and trimethoprim, dfrA1-like (83%). Class 1 integrons were found in 41% of the isolates. They carried aadA1, dfrA1-aadA1 and dfrA15-aadA1. A class 2 integron (dfrA1-sat1-aadA1) was found in one isolate. Only three isolates (3%) were resistant to nalidixic acid (reduced susceptibility to ciprofloxacin), with a single mutation in the gyrA gene. E. coli O111 strains exhibit a wide repertoire of genetic elements to sustain antimicrobial pressure. Two specific antimicrobial resistance pheno/genotypes, [STR-SPT]-SUL-TET/aadA1-sul1-tet(A) and STR-SUL-TET-AMP-[KAN-NEO]/strA/B-sul2-tet(A)-bla(TEM)-aphA1, are predominant.

Phenotypic and genotypic characterization of antimicrobial resistance in German Escherichia coli isolates from cattle, swine and poultry.

Phenotypic and genotypic characterization of the antimicrobial resistance of German Escherichia coli strains isolated during 1999-2001 from cattle, swine and poultry. Three hundred and seventeen isolates were tested for their resistance to 17 antimicrobial agents by broth microdilution. Resistant strains were screened by molecular methods for resistance genes, integrons and mutations in quinolone-resistance determining regions. Resistance was found in 40% and multiresistance in 32% of the strains. The resistance was significantly higher in isolates from poultry (61%) and swine (60%) than from cattle (25%) (P < 0.01). The most prevalent resistances were to sulfamethoxazole, tetracycline, streptomycin, ampicillin and spectinomycin (30-15%). For each antibiotic, the predominant resistance genes were: ampicillin, blaTEM1-like (92%); chloramphenicol, catA (68%) and cmlA1-like (36%); gentamicin, aac(3)-IV (60%); kanamycin, aphA1 (100%); streptomycin, aadA1-like (61%) and strA/B (59%); sulfamethoxazole, sul2 (66%), sul1 (42%) and sul3 (14%); tetracycline, tet(A) (66%) and tet(B) (42%); and trimethoprim, dfrA1-like (77%), dfrA17 (13%) and dfrA12 (7%). Class 1 integrons were found in 30% of the strains. They carried dfrA1-aadA1a (40%), aadA1a (29%), sat1-aadA1a (16%), dfrA17-aadA5 (11%), oxa1-aadA1a (5%) and dfrA12-aadA2 (3%). Eleven percent of the strains were resistant to nalidixic acid. Of these, 61% presented a reduced susceptibility to ciprofloxacin (MIC = 0.12-2 mg/L) and single mutations in gyrA or gyrA and parC genes, and 39%, full resistance to ciprofloxacin (MIC > or = 4 mg/L) and double and single mutations in gyrA and parC, respectively. The study gives baseline information on the magnitude of the resistance problem and its genetic background in contemporary German E. coli from food-producing animals.