Seventeen multiple-antibiotic-resistant nonpathogenic Escherichia coli strains of human, animal, and food origins showed a wide variety of antibiotic resistance genes, many of them carried by class 1 and class 2 integrons. Amino acid changes in MarR and mutations in marO were identified for 15 and 14 E. coli strains, respectively.

DNA fingerprinting is a technique for comparing DNA patterns that has applications in a wide variety of contexts. Several commercial and freely-available tools can be used to analyze DNA fingerprint gel images; however, commercial tools are expensive and usually difficult to use; and, free tools support the basic functionality for DNA fingerprint analysis, but lack some instrumental features to obtain accurate results. In this paper, we present GelJ, a feather-weight, user-friendly, platform-independent, open-source and free tool for analyzing DNA fingerprint gel images. Some of the outstanding features of GelJ are mechanisms for accurate lane- and band-detection, several options for computing migration models, a number of band- and curve-based similarity methods, different techniques for generating dendrograms, comparison of banding patterns from different experiments, and database support. GelJ is an easy to use tool for analyzing DNA fingerprint gel images. It combines the best characteristics of both free and commercial tools: GelJ is light and simple to use (as free programs), but it also includes the necessary features to obtain precise results (as commercial programs). In addition, GelJ incorporates new functionality that is not supported by any other tool.

A multilocus sequence typing (MLST) scheme based on seven housekeeping genes was used to investigate the epidemiology and population structure of Enterococcus faecalis . MLST of 110 isolates from different sources and geographic locations revealed 55 different sequence types that grouped into four major clonal complexes (CC2, CC9, CC10, and CC21) by use of eBURST. Two of these clonal complexes, CC2 and CC9, are particularly fit in the hospital environment, as CC2 includes the previously described BVE clonal complex identified by an alternative MLST scheme and CC9 includes exclusively isolates from hospitalized patients. Identical alleles were found in genetically diverse isolates with no linkage disequilibrium, while the different MLST loci gave incongruent phylogenetic trees. This demonstrates that recombination is an important mechanism driving genetic variation in E. faecalis and suggests an epidemic population structure for E. faecalis . Our novel MLST scheme provides an excellent tool for investigating local and short-term epidemiology as well as global epidemiology, population structure, and genetic evolution of E. faecalis .

The blaESBL and blaAmpC genes in Enterobacteriaceae are spread by plasmid-mediated integrons, insertion sequences, and transposons, some of which are homologous in bacteria from food animals, foods, and humans. These genes have been frequently identified in Escherichia coli and Salmonella from food animals, the most common being blaCTX-M-1, blaCTX-M-14, and blaCMY-2. Identification of risk factors for their occurrence in food animals is complex. In addition to generic antimicrobial use, cephalosporin usage is an important risk factor for selection and spread of these genes. Extensive international trade of animals is a further risk factor. There are no data on the effectiveness of individual control options in reducing public health risks. A highly effective option would be to stop or restrict cephalosporin usage in food animals. Decreasing total antimicrobial use is also of high priority. Implementation of measures to limit strain dissemination (increasing farm biosecurity, controls in animal trade, and other general postharvest controls) are also important.

TEM-, SHV-, and OXA-type β-lactamases were studied by PCR with 124 ampicillin-resistant (AMP^r)Escherichia coliisolates recovered from foods of animal origin (n= 20) and feces of humans (n= 49) and healthy animals (n= 55). PCR showed that 103 isolates were positive for TEM and negative for SHV and OXA. ThreeE. coliisolates showed a positive reaction for OXA, and one showed a positive reaction for SHV. The remaining 17E. coliisolates were negative for the three enzymes by PCR. Fifty-seven of the 103bla_TEMamplicons were sequenced. Different molecular variants ofbla_TEM-1were found in 52 isolates:bla_TEM-1a(n= 9),bla_TEM-1b(n= 36),bla_TEM-1c(n= 6), andbla_TEM-1f(n= 1). Four inhibitor-resistant TEM (IRT) β-lactamase-encoding genes were also detected:bla_TEM-30c(IRT-2),bla_TEM-34b(IRT-6),bla_TEM-40b(IRT-11), andbla_TEM-51a(IRT-15). A newbla_TEMgene, namedbla_TEM-95b, which showed a mutation in amino acid 145 (P→A) was detected. It was found in a food isolate of chicken origin (AMP^r, amoxicillin-clavulanic acid susceptible). The promoter region in 24bla_TEMamplicons was analyzed, and the weakP3promoter was found in 23 of them (bla_TEM-1in 20 amplicons andbla_TEM-51a,bla_TEM-30c, andbla_TEM-95bin 1 amplicon each). The strongPa/Pbpromoter was found only in thebla_TEM-34bgene. No extended-spectrum β-lactamases were detected. Mutations at position −42 or −32 in theampCgene promoter were demonstrated in 4 of 10E. coliisolates for which the cefoxitin MIC was ≥16 μg/ml. Different variants ofbla_TEM-1and IRTbla_TEMgenes were found among the AMP^rE. coliisolates from foods and the feces of humans and healthy animals, and a new gene,bla_TEM-95b(P3), was detected.

Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover,Enterococcusis an important opportunistic pathogen, especially the speciesE. faecalisandE. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such asoptrAandcfr, is highlighted. The molecular epidemiology and the population structure ofE. faecalisandE. faeciumisolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.