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      Agriculture and food animals as a source of antimicrobial-resistant bacteria

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          Abstract

          One of the major breakthroughs in the history of medicine is undoubtedly the discovery of antibiotics. Their use in animal husbandry and veterinary medicine has resulted in healthier and more productive farm animals, ensuring the welfare and health of both animals and humans. Unfortunately, from the first use of penicillin, the resistance countdown started to tick. Nowadays, the infections caused by antibiotic-resistant bacteria are increasing, and resistance to antibiotics is probably the major public health problem. Antibiotic use in farm animals has been criticized for contributing to the emergence of resistance. The use and misuse of antibiotics in farm animal settings as growth promoters or as nonspecific means of infection prevention and treatment has boosted antibiotic consumption and resistance among bacteria in the animal habitat. This reservoir of resistance can be transmitted directly or indirectly to humans through food consumption and direct or indirect contact. Resistant bacteria can cause serious health effects directly or via the transmission of the antibiotic resistance traits to pathogens, causing illnesses that are difficult to treat and that therefore have higher morbidity and mortality rates. In addition, the selection and proliferation of antibiotic-resistant strains can be disseminated to the environment via animal waste, enhancing the resistance reservoir that exists in the environmental microbiome. In this review, an effort is made to highlight the various factors that contribute to the emergence of antibiotic resistance in farm animals and to provide some insights into possible solutions to this major health issue.

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          Sampling the antibiotic resistome.

          Microbial resistance to antibiotics currently spans all known classes of natural and synthetic compounds. It has not only hindered our treatment of infections but also dramatically reshaped drug discovery, yet its origins have not been systematically studied. Soil-dwelling bacteria produce and encounter a myriad of antibiotics, evolving corresponding sensing and evading strategies. They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms.
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            Metagenomics: genomic analysis of microbial communities.

            Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.
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              Update on acquired tetracycline resistance genes.

              This mini-review summarizes the changes in the field of bacterial acquired tetracycline resistance (tet) and oxytetracycline (otr) genes identified since the last major review in 2001. Thirty-eight acquired tetracycline resistant (Tc(r)) genes are known of which nine are new and include five genes coding for energy-dependent efflux proteins, two genes coding for ribosomal protection proteins, and two genes coding for tetracycline inactivating enzymes. The number of inactivating enzymes has increased from one to three, suggesting that work needs to be done to determine the role these enzymes play in bacterial resistance to tetracycline. In the same time period, 66 new genera have been identified which carry one or more of the previously described 29 Tc(r) genes. Included in the new genera is, for the first time, an obligate intracellular pathogen suggesting that this sheltered group of bacteria is capable of DNA exchange with non-obligate intracellular bacteria. The number of genera carrying ribosomal protection genes increased dramatically with the tet(M) gene now identified in 42 genera as compared with 24 and the tet(W) gene found in 17 new genera as compared to two genera in the last major review. New conjugative transposons, carrying different ribosomal protection tet genes, have been identified and an increase in the number of antibiotic resistance genes linked to tet genes has been found. Whether these new elements may help to spread the tet genes they carry to a wider bacterial host range is discussed.
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                Author and article information

                Journal
                Infect Drug Resist
                Infect Drug Resist
                Infection and Drug Resistance
                Infection and Drug Resistance
                Dove Medical Press
                1178-6973
                2015
                01 April 2015
                : 8
                : 49-61
                Affiliations
                [1 ]Department of Hygiene and Technology of Food of Animal Origin, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
                [2 ]Food-Water Microbiology Unit, Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
                Author notes
                Correspondence: Vangelis Economou, Laboratory of Hygiene of Food of Animal Origin, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece, Tel +30 2310 999875, Fax +30 2310 999833, Email boikonom@ 123456vet.auth.gr
                Article
                idr-8-049
                10.2147/IDR.S55778
                4388096
                25878509
                a641f529-487e-4996-9a52-2ba0bed2042e
                © 2015 Economou and Gousia. This work is published by Dove Medical Press Limited, and licensed under Creative Commons Attribution – Non Commercial (unported, v3.0) License

                The full terms of the License are available at http://creativecommons.org/licenses/by-nc/3.0/. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed.

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                Categories
                Review

                Infectious disease & Microbiology
                antimicrobial resistance,farm animals,food safety,foodborne pathogens,alternatives to antibiotics

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