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4. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?

Author

Bengtsson-Palme, Johan, Abramova, Anna, Berendonk, Thomas U., Coelho, Luis Pedro, Forslund, Sofia K., Gschwind, Rémi, Heikinheimo, Annamari, Jarquín-Díaz, Víctor Hugo, Khan, Ayaz Ali, Klümper, Uli, Löber, Ulrike, Nekoro, Marmar, Osińska, Adriana D., Ugarcina Perovic, Svetlana, Pitkänen, Tarja, Rødland, Ernst Kristian, Ruppé, Etienne, Wasteson, Yngvild, Wester, Astrid Louise, and Zahra, Rabaab

Published
2023
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7. Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Author

Brown, Peter, Tan, Aik-Choon, El-Esawi, Mohamed A, Liehr, Thomas, Blanck, Oliver, Gladue, Douglas P, Almeida, Gabriel MF, Cernava, Tomislav, Sorzano, Carlos O, Yeung, Andy WK, Engel, Michael S, Chandrasekaran, Arun Richard, Muth, Thilo, Staege, Martin S, Daulatabad, Swapna V, Widera, Darius, Zhang, Junpeng, Meule, Adrian, Honjo, Ken, Pourret, Olivier, Yin, Cong-Cong, Zhang, Zhongheng, Cascella, Marco, Flegel, Willy A, Goodyear, Carl S, van Raaij, Mark J, Bukowy-Bieryllo, Zuzanna, Campana, Luca G, Kurniawan, Nicholas A, Lalaouna, David, Hüttner, Felix J, Ammerman, Brooke A, Ehret, Felix, Cobine, Paul A, Tan, Ene-Choo, Han, Hyemin, Xia, Wenfeng, McCrum, Christopher, Dings, Ruud PM, Marinello, Francesco, Nilsson, Henrik, Nixon, Brett, Voskarides, Konstantinos, Yang, Long, Costa, Vincent D, Bengtsson-Palme, Johan, Bradshaw, William, Grimm, Dominik G, Kumar, Nitin, Martis, Elvis, Prieto, Daniel, Sabnis, Sandeep C, Amer, Said EDR, Liew, Alan WC, Perco, Paul, Rahimi, Farid, Riva, Giuseppe, Zhang, Chongxing, Devkota, Hari P, Ogami, Koichi, Basharat, Zarrin, Fierz, Walter, Siebers, Robert, Tan, Kok-Hian, Boehme, Karen A, Brenneisen, Peter, Brown, James AL, Dalrymple, Brian P, Harvey, David J, Ng, Grace, Werten, Sebastiaan, Bleackley, Mark, Dai, Zhanwu, Dhariwal, Raman, Gelfer, Yael, Hartmann, Marcus D, Miotla, Pawel, Tamaian, Radu, Govender, Pragashnie, Gurney-Champion, Oliver J, Kauppila, Joonas H, Zhang, Xiaolei, Echeverría, Natalia, Subhash, Santhilal, Sallmon, Hannes, Tofani, Marco, Bae, Taeok, Bosch, Oliver, Cuív, Páraic O, Danchin, Antoine, Diouf, Barthelemy, Eerola, Tuomas, Evangelou, Evangelos, Filipp, Fabian V, Klump, Hannes, Kurgan, Lukasz, Smith, Simon S, Terrier, Olivier, Tuttle, Neil, and Ascher, David B

Subjects
Cancer, Generic health relevance, RELISH Consortium, Data Format, Library and Information Studies
Abstract

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.

Published
2019

8. Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

Author

Nilsson, R Henrik, Taylor, Andy FS, Adams, Rachel I, Baschien, Christiane, Bengtsson-Palme, Johan, Cangren, Patrik, Coleine, Claudia, Daniel, Heide-Marie, Glassman, Sydney I, Hirooka, Yuuri, Irinyi, Laszlo, Iršėnaitė, Reda, Martin-Sanchez, Pedro M, Meyer, Wieland, Oh, Seung-Yoon, Sampaio, Jose Paulo, Seifert, Keith A, Sklenář, Frantisek, Stubbe, Dirk, Suh, Sung-Oui, Summerbell, Richard, Svantesson, Sten, Unterseher, Martin, Visagie, Cobus M, Weiss, Michael, Woudenberg, Joyce HC, Wurzbacher, Christian, Van den Wyngaert, Silke, Yilmaz, Neriman, Yurkov, Andrey, Kõljalg, Urmas, and Abarenkov, Kessy

Subjects
Microbiology, Biological Sciences, Indoor mycobiome, built environment, molecular identification, fungi, taxonomy, systematics, sequence annotation, metadata, open data, Ecology, Plant biology
Abstract

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.

Published
2018

14. List of Contributors

Author

Bengtsson-Palme, Johan, primary, Brocal, Francisco, additional, Brown, R. Stephen, additional, Courtier, Audrey, additional, De Battista, Margot, additional, González, Cristina, additional, Gotti, Alberto, additional, Götz, Konrad, additional, Hania, Patricia, additional, Hull, Matthew S., additional, Jaeger, Laura, additional, Janin, Myriam, additional, Karakitsios, Spyros P., additional, Liss, Steven N., additional, Majury, Anna, additional, McAllister, Tim A., additional, Michon, Julien, additional, Petrovic, Tamas, additional, Potkonjak, Aleksandar, additional, Rateau, Patrick, additional, Roig, Benoit, additional, Sanderson, Haley, additional, Sarigiannis, Denis A., additional, Savic, Sara, additional, A. Sebastián, Miguel, additional, Stein, Melina, additional, Strelau, Linda, additional, Sunderer, Georg, additional, Techer, Isabelle, additional, Thireau, Véronique, additional, Valette, Armance, additional, Vidaurre, Rodrigo, additional, Weiss, Karine, additional, Winker, Martina, additional, and Zekic-Stosic, Marina, additional

Published
2019
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15. Structure and function of the global topsoil microbiome

Author

Bahram, Mohammad, Hildebrand, Falk, Forslund, Sofia K., Anderson, Jennifer L., Soudzilovskaia, Nadejda A., Bodegom, Peter M., and Bengtsson-Palme, Johan

Subjects
Soil microbiology -- Identification and classification, Bacteria, pH, Bacterial genetics, Soil structure, Fungi, Precipitation (Meteorology), Soil acidity, Environmental associations, Microbial drug resistance, Soil carbon, Niches (Ecology), Oceans, Marine biology, Genes, Microorganisms, Soils, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities.sup.1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.Metagenomic, chemical and biomass analyses of topsoil samples from around the world reveal spatial and environmental trends in microbial community composition and genetic diversity., Author(s): Mohammad Bahram [sup.1] [sup.2] [sup.3] , Falk Hildebrand [sup.4] , Sofia K. Forslund [sup.4] [sup.16] [sup.17] , Jennifer L. Anderson [sup.2] , Nadejda A. Soudzilovskaia [sup.5] , Peter M. [...]

Published
2018
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16. Metaxa, Overview

Author

Bengtsson-Palme, Johan, Hartmann, Martin, Eriksson, K. Martin, Nilsson, R. Henrik, and Nelson, Karen E., editor

Published
2015
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18. Contributors

Author

Asha, Santhi, primary, Bacci, Giovanni, additional, Bargiela, Rafael, additional, Becerra, Manuel, additional, Bengtsson-Palme, Johan, additional, Beraud, Mélanie, additional, Boulund, Fredrik, additional, Chan, Chia Sing, additional, Chan, Kok-Gan, additional, Citlali, Fonseca-García, additional, Dave, Bharti P., additional, DeCastro, María-Eugenia, additional, Desgarennes, Damaris, additional, Dieleman, Levinus A., additional, Escuder-Rodríguez, Juan-José, additional, Ferrer, Manuel, additional, Flores-Núñez, Víctor M., additional, Foster, James A., additional, Goh, Kian Mau, additional, González-Siso, María-Isabel, additional, Gosai, Haren B., additional, Griffin, Timothy J., additional, Halgamuge, Saman K., additional, Jagtap, Pratik D., additional, Jayasundara, Duleepa, additional, Jonsson, Viktor, additional, Joshi, Chaitanya G., additional, Jovel, Juan, additional, Kadnikov, Vitaly V., additional, Kamalakkannan, Ranganathan, additional, Kao, Dina, additional, Kimura, Nobutada, additional, Kothari, Ramesh K., additional, Krishnaveni, Muthan, additional, Kristiansson, Erik, additional, Liew, Kok Jun, additional, Lim, Chia Chiu, additional, Ma, Zhanshan (Sam), additional, Mardanov, Andrey V., additional, Martínez-Martínez, Mónica, additional, Mary Josephine Punitha, Stanislaus, additional, Mason, Andrew L., additional, Matallana-Surget, Sabine, additional, Méndez-García, Celia, additional, Mootapally, Chandrashekar, additional, Nagarajan, Muniyandi, additional, Nathani, Neelam M., additional, Partida-Martínez, Laila P., additional, Pereira, Mariana Buongermino, additional, Prabhu, Vandana R., additional, Ramazzotti, Matteo, additional, Rank, Jalpa K., additional, Ravin, Nikolai V., additional, Rodríguez-Belmonte, Esther, additional, Salleh, Madihah Md, additional, Sani, Rajesh Kumar, additional, Sharmin Vini, Stephen, additional, Tang, Sen-Lin, additional, Wattiez, Ruddy, additional, Wei, Kwek Yan, additional, Wine, Eytan, additional, and Zhbannikov, Ilya Y., additional

Published
2018
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22. Contributors

Author

Abdulla, Mohamed Hatha, Abramova, Anna, Akanmu, Akinlolu Olalekan, Ammini, Parvathi, Arockiaraj, Jesu, Arul Shiny, Mariadhason, Asha, Santhi, Ayangbenro, Ayansina Segun, Babalola, Olubukola Oluranti, Bacci, Giovanni, Bargiela, Rafael, Barik, Shubham, Becerra, Manuel, Bedse, Mandar, Bengtsson-Palme, Johan, Bhardwaj, Soumya, Bhavana, Karippadakam, Bombaywala, Sakina, Boulund, Fredrik, Casbarra, Lorenzo, Dafale, Nishant A., De, Rituparna, DeCastro, María-Eugenia, Deepthi, Mottakunja, Deo, Priya Nimish, Desgarennes, Damaris, Dhotre, Dhiraj Prakash, Escuder-Rodríguez, Juan-José, Fadiji, Ayomide Emmanuel, Ferrer, Manuel, Flores-Núñez, Víctor M., Fonseca-García, Citlali, González-Siso, María-Isabel, Gopinath, Devi, Grace, Tony, Guru, Ajay, Hassan, Saqib, Iyyadurai, Mariappan, Jairath, Gauri, Jonsson, Viktor, Jose, Mareena, Kadnikov, Vitaly V., Kamalakkannan, Ranganathan, Kannoth, Shalini, Karamveer, Karamveer, Karmarkar, Bhagyashree, Krishnaveni, Muthan, Kristiansson, Erik, Kumar, Anupam, Ma, Zhanshan (Sam), Mal, Gorakh, Malla, Muneer Ahmad, Mardanov, Andrey V., Martínez-Martínez, Mónica, Marunganathan, Vanitha, Meenatchi, Ramu, Méndez-García, Celia, Merlin Sobia, Poomani, Mohan, Suma, Nagarajan, Muniyandi, Nandi, Amartya, Nathan, Vinod Kumar, Partida-Martínez, Laila P., Pereira, Mariana Buongermino, Prabhu, Devachandana C., Prabhu, Vandana R., Prathiviraj, Ragothaman, Priya, P. Snega, Ramazzotti, Matteo, Rathika, Regurajan, Ravin, Nikolai V., Rialch, Ajayta, Rodríguez-Belmonte, Esther, Sadanandan, Shemmy, Sharma, Rinku, Singh, Birbal, Singh, Goldy, Singh, Kiran, Solanki, Jaykishan, Suravajhala, Prashanth, Suresh, Aparna, Tiwari, Arushi, Venkatesh, Subramanian, Vijayan, Jasna, and Yadav, Shweta

Published
2025
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25. The European technical report on aquatic effect-based monitoring tools under the water framework directive

Author

Wernersson, Ann-Sofie, Carere, Mario, Maggi, Chiara, Tusil, Petr, Soldan, Premysl, James, Alice, Sanchez, Wilfried, Dulio, Valeria, Broeg, Katja, Reifferscheid, Georg, Buchinger, Sebastian, Maas, Hannie, Van Der Grinten, Esther, O’Toole, Simon, Ausili, Antonella, Manfra, Loredana, Marziali, Laura, Polesello, Stefano, Lacchetti, Ines, Mancini, Laura, Lilja, Karl, Linderoth, Maria, Lundeberg, Tove, Fjällborg, Bengt, Porsbring, Tobias, Larsson, DG Joakim, Bengtsson-Palme, Johan, Förlin, Lars, Kienle, Cornelia, Kunz, Petra, Vermeirssen, Etienne, Werner, Inge, Robinson, Craig D, Lyons, Brett, Katsiadaki, Ioanna, Whalley, Caroline, den Haan, Klaas, Messiaen, Marlies, Clayton, Helen, Lettieri, Teresa, Carvalho, Raquel Negrão, Gawlik, Bernd Manfred, Hollert, Henner, Di Paolo, Carolina, Brack, Werner, Kammann, Ulrike, and Kase, Robert

Published
2015
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28. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 9: Polymyxins: colistin

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I., Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Indústries Alimentàries, Funcionalitat i Seguretat Alimentària, Koutsoumanis K., Allende A., Alvarez-Ordoñez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., and Peixe L.

Subjects
663/664, medicine.drug_class, Veterinary (miscellaneous), Polymyxin, Growth promotion, TP1-1185, Plant Science, Biology, Microbiology, Non target, Antibiotic resistance, growth promotion, medicine, TX341-641, antimicrobial resistance, colistin, yield increase, Animal health, Nutrition. Foods and food supply, business.industry, Chemical technology, sub-inhibitory concentration, sub‐inhibitory concentration, Contamination, Feed Antimicrobial Resistance Selection Concentration (FARSC), Antimicrobial, food-producing animal, Biotechnology, Colistin, Animal Science and Zoology, Parasitology, business, Food Science, medicine.drug
Abstract

The specific concentrations of colistin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of colistin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

Published
2021

29. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 13: Diaminopyrimidines: trimethoprim

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I., Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Indústries Alimentàries, Funcionalitat i Seguretat Alimentària, Koutsoumanis K., Allende A., Alvarez-Ordoñez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., and Peixe L.

Subjects
Complete data, 663/664, Veterinary (miscellaneous), Growth promotion, TP1-1185, Plant Science, Biology, Microbiology, Trimethoprim, Non target, Antibiotic resistance, growth promotion, medicine, TX341-641, antimicrobial resistance, yield increase, Animal health, Nutrition. Foods and food supply, business.industry, Chemical technology, sub-inhibitory concentration, food-producing animals, Biol5012, food‐producing animals, sub‐inhibitory concentration, Contamination, Feed Antimicrobial Resistance Selection Concentration (FARSC), Antimicrobial, food-producing animal, Biotechnology, Scientific Opinion, Animal Science and Zoology, Parasitology, business, Food Science, medicine.drug
Abstract

The specific concentrations of trimethoprim in non-target feed for food-producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for trimethoprim was estimated. Uncertainties and data gaps associated to the levels reported were addressed. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for trimethoprim. info:eu-repo/semantics/publishedVersion

Published
2021
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30. Maximum levels of cross‐contamination for 24 antimicrobial active substances in non‐target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and doxycycline

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Indústries Alimentàries, Funcionalitat i Seguretat Alimentària, Koutsoumanis K., Allende A., Alvarez-Ordonez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., and Peixe L.

Subjects
Chlortetracycline, 663/664, Tetracycline, Veterinary (miscellaneous), Growth promotion, TP1-1185, Plant Science, Oxytetracycline, Biology, Microbiology, Antibiotic resistance, growth promotion, medicine, TX341-641, antimicrobial resistance, Food science, chlortetracycline, tetracycline, Doxycycline, doxycycline, Nutrition. Foods and food supply, Chemical technology, food-producing animals, Contamination, Antimicrobial, food-producing animal, Animal Science and Zoology, Parasitology, oxytetracycline, Food Science, medicine.drug
Abstract

The specific concentrations of tetracycline, chlortetracycline, oxytetracycline and doxycycline in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for these four tetracyclines was estimated. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tetracycline, chlortetracycline, oxytetracycline, whilst for doxycycline no suitable data for the assessment were available. Uncertainties and data gaps associated with the levels reported were addressed. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

Published
2021
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31. Maximum levels of cross‐contamination for 24 antimicrobial active substances in non‐target feed. Part 10: Quinolones: flumequine and oxolinic acid

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Koutsoumanis K., Allende A., Alvarez-Ordoñez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., Peixe L., Indústries Alimentàries, and Funcionalitat i Seguretat Alimentària

Subjects
663/664, Veterinary (miscellaneous), Growth promotion, flumequine, TP1-1185, Plant Science, Microbiology, Non target, Antibiotic resistance, growth promotion, oxolinic acid, Oxolinic acid, medicine, TX341-641, Food science, antimicrobial resistance, Food8822, yield increase, Animal health, Nutrition. Foods and food supply, Chemical technology, sub-inhibitory concentration, food-producing animals, food‐producing animals, Contamination, sub‐inhibitory concentration, Antimicrobial, food-producing animal, Scientific Opinion, Flumequine, Environmental science, Animal Science and Zoology, Parasitology, Food Science, medicine.drug
Abstract

The specific concentrations of flumequine and oxolinic acid in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

Published
2021
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32. Maximum levels of cross‐contamination for 24 antimicrobial active substances in non‐target feed. Part 4: β‐Lactams: amoxicillin and penicillin V

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Indústries Alimentàries, Funcionalitat i Seguretat Alimentària, Koutso111umanis K., Allende A., Alvarez-Ordonez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., and Peixe L.

Subjects
663/664, Veterinary (miscellaneous), Growth promotion, TP1-1185, Plant Science, Biology, Microbiology, Antibiotic resistance, Non target, growth promotion, β lactams, medicine, TX341-641, antimicrobial resistance, Food science, yield increase, amoxicillin, Nutrition. Foods and food supply, sub-inhibitory concentration, Chemical technology, food-producing animals, Biol5012, food‐producing animals, sub‐inhibitory concentration, Contamination, Amoxicillin, penicillin V, Antimicrobial, food-producing animal, Penicillin, Scientific Opinion, Animal Science and Zoology, Parasitology, Food Science, medicine.drug
Abstract

The specific concentrations of amoxicillin and penicillin V in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for amoxicillin, whilst for penicillin V no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials. info:eu-repo/semantics/publishedVersion

Published
2021
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33. Maximum levels of cross‐contamination for 24 antimicrobial active substances in non‐target feed. Part 6: Macrolides: tilmicosin, tylosin and tylvalosin

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Koutsoumanis K., Allende A., Alvarez-Ordoñez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., Peixe L., Indústries Alimentàries, and Funcionalitat i Seguretat Alimentària

Subjects
663/664, Veterinary (miscellaneous), Growth promotion, TP1-1185, Plant Science, Tylosin, Biology, tilmicosin, Microbiology, chemistry.chemical_compound, Antibiotic resistance, Non target, growth promotion, TX341-641, antimicrobial resistance, Food science, Tilmicosin, yield increase, tylosin, Nutrition. Foods and food supply, Chemical technology, food-producing animals, tylvalosin, Contamination, Antimicrobial, food-producing animal, chemistry, Animal Science and Zoology, Parasitology, Tylvalosin, Food Science
Abstract

The specific concentrations of tilmicosin, tylosin and tylvalosin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tilmicosin and tylosin, whilst for tylvalosin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these three antimicrobials. info:eu-repo/semantics/publishedVersion

Published
2021
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34. Maximum levels of cross‐contamination for 24 antimicrobial active substances in non‐target feed. Part 11: Sulfonamides

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I., Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Koutsoumanis K., Allende A., Alvarez-Ordoñez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., Peixe L., Indústries Alimentàries, and Funcionalitat i Seguretat Alimentària

Subjects
Sulfamerazine, 663/664, Veterinary (miscellaneous), Growth promotion, TP1-1185, Plant Science, Sulfonamide, Microbiology, Antibiotic resistance, Non target, growth promotion, medicine, TX341-641, antimicrobial resistance, Food science, yield increase, Sulfonamides, Animal health, Nutrition. Foods and food supply, Chemical technology, sub-inhibitory concentration, food‐producing animals, food-producing animals, sub‐inhibitory concentration, Contamination, Antimicrobial, food-producing animal, Sulfathiazole, Environmental science, Animal Science and Zoology, Parasitology, Food Science, medicine.drug
Abstract

The specific concentrations of sulfonamides in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were identified for three sulfonamides: sulfamethazine, sulfathiazole and sulfamerazine. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

Published
2021
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35. Improving ITS sequence data for identification of plant pathogenic fungi

Author

Nilsson, R. Henrik, Hyde, Kevin D., Pawłowska, Julia, Ryberg, Martin, Tedersoo, Leho, Aas, Anders Bjørnsgard, Alias, Siti A., Alves, Artur, Anderson, Cajsa Lisa, Antonelli, Alexandre, Arnold, A. Elizabeth, Bahnmann, Barbara, Bahram, Mohammad, Bengtsson-Palme, Johan, Berlin, Anna, Branco, Sara, Chomnunti, Putarak, Dissanayake, Asha, Drenkhan, Rein, Friberg, Hanna, Frøslev, Tobias Guldberg, Halwachs, Bettina, Hartmann, Martin, Henricot, Beatrice, Jayawardena, Ruvishika, Jumpponen, Ari, Kauserud, Håvard, Koskela, Sonja, Kulik, Tomasz, Liimatainen, Kare, Lindahl, Björn D., Lindner, Daniel, Liu, Jian-Kui, Maharachchikumbura, Sajeewa, Manamgoda, Dimuthu, Martinsson, Svante, Neves, Maria Alice, Niskanen, Tuula, Nylinder, Stephan, Pereira, Olinto Liparini, Pinho, Danilo Batista, Porter, Teresita M., Queloz, Valentin, Riit, Taavi, Sánchez-García, Marisol, de Sousa, Filipe, Stefańczyk, Emil, Tadych, Mariusz, Takamatsu, Susumu, Tian, Qing, Udayanga, Dhanushka, Unterseher, Martin, Wang, Zheng, Wikee, Saowanee, Yan, Jiye, Larsson, Ellen, Larsson, Karl-Henrik, Kõljalg, Urmas, and Abarenkov, Kessy

Published
2014
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37. Metaxa, Overview

Author

Bengtsson-Palme, Johan, primary, Hartmann, Martin, additional, Eriksson, K. Martin, additional, and Nilsson, R Henrik, additional

Published
2014
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38. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides: lincomycin

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Indústries Alimentàries, Funcionalitat i Seguretat Alimentària, Koutsoumanis K., Allende A., Alvarez-Ordonez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., and Peixe L.

Subjects
663/664, medicine.drug_class, Veterinary (miscellaneous), Growth promotion, Plant Science, TP1-1185, Biology, Microbiology, Antibiotic resistance, Non target, growth promotion, medicine, TX341-641, Food science, antimicrobial resistance, yield increase, Lincosamides, Animal health, Nutrition. Foods and food supply, sub-inhibitory concentration, Chemical technology, Biol5012, food‐producing animals, food-producing animals, Contamination, sub‐inhibitory concentration, Antimicrobial, Feed Antimicrobial Resistance Selection Concentration (FARSC), food-producing animal, Lincomycin, Scientific Opinion, Animal Science and Zoology, Parasitology, lincomycin, Food Science, medicine.drug
Abstract

The specific concentrations of lincomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of lincomycin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for lincomycin. info:eu-repo/semantics/publishedVersion

Published
2021
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39. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 2: Aminoglycosides/aminocyclitols: apramycin, paromomycin, neomycin and spectinomycin

Author

EFSA Panel on Biological Hazards (BIOHAZ), Allende, Ana, Koutsoumanis, Konstantinos, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Allende A., Koutsoumanis K., Alvarez-Ordoñez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., Peixe L., Indústries Alimentàries, and Funcionalitat i Seguretat Alimentària

Subjects
Spectinomycin, 663/664, spectinomycin, Veterinary (miscellaneous), Growth promotion, Paromomycin, TP1-1185, Plant Science, Biology, Apramycin, Microbiology, Antibiotic resistance, growth promotion, medicine, TX341-641, Food science, antimicrobial resistance, Nutrition. Foods and food supply, Chemical technology, neomycin, food-producing animals, Neomycin, Contamination, Antimicrobial, food-producing animal, Animal Science and Zoology, Parasitology, paromomycin, Food Science, medicine.drug, apramycin
Abstract

The specific concentrations of apramycin, paromomycin, neomycin and spectinomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC for these antimicrobials, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for apramycin and neomycin, whilst for paromomycin and spectinomycin, no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these four antimicrobials. info:eu-repo/semantics/publishedVersion

Published
2021
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40. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 3: Amprolium

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, Koutsoumanis K., Allende A., Alvarez-Ordoñez A., Bolton D., Bover-Cid S., Chemaly M., Davies R., De Cesare A., Herman L., Hilbert F., Lindqvist R., Nauta M., Ru G., Simmons M., Skandamis P., Suffredini E., Andersson D.I., Bampidis V., Bengtsson-Palme J., Bouchard D., Ferran A., Kouba M., Lopez Puente S., Lopez-Alonso M., Nielsen S.S., Pechova A., Petkova M., Girault S., Broglia A., Guerra B., Innocenti M.L., Liebana E., Lopez-Galvez G., Manini P., Stella P., Peixe L., Indústries Alimentàries, and Funcionalitat i Seguretat Alimentària

Subjects
663/664, Veterinary (miscellaneous), Growth promotion, TP1-1185, Plant Science, Biology, Microbiology, chemistry.chemical_compound, Antibiotic resistance, Non target, Amprolium, growth promotion, TX341-641, Food science, antimicrobial resistance, yield increase, Animal health, Nutrition. Foods and food supply, Chemical technology, Biol5012, food‐producing animals, food-producing animals, Feed Antimicrobial Resistance Selection Concentration (FARSC), growth promotion, Contamination, Antimicrobial, Feed Antimicrobial Resistance Selection Concentration (FARSC), food-producing animal, Scientific Opinion, subinhibitory concentration, chemistry, Animal Science and Zoology, Parasitology, Food Science, amprolium
Abstract

The specific concentrations of amprolium in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC for amprolium, it was not possible to conclude the assessment. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of amprolium in feed that showed to have an effect on growth promotion/increased yield were reported. The lack of antibacterial activity at clinically relevant concentrations for amprolium suggests that further studies relating to bacterial resistance are not a priority. info:eu-repo/semantics/publishedVersion

Published
2021
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41. CAFE : a software suite for analysis of paired-sample transposon insertion sequencing data

Author

Abramova, Anna, Osińska, Adriana, Kunche, Haveela, Burman, Emil, Bengtsson-Palme, Johan, Abramova, Anna, Osińska, Adriana, Kunche, Haveela, Burman, Emil, and Bengtsson-Palme, Johan

Abstract

SUMMARY: Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE-Coefficient-based Analysis of Fitness by read Enrichment-a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition, and perform appropriate statistical testing on these fitness coefficients. AVAILABILITY AND IMPLEMENTATION: CAFE is implemented in Perl and R. The source code is freely available for download under the MIT License from https://github.com/bengtssonpalme/cafe and http://microbiology.se/software/cafe/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. The evaluation data can be obtained from https://microbiology.se/sw/cafe/example_data.tgz., CC BY 4.0

Published
2021
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42. What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach

Author

Bengtsson-Palme, Johan, Jonsson, Viktor, Heß, Stefanie, Bengtsson-Palme, Johan, Jonsson, Viktor, and Heß, Stefanie

Abstract

It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in transmission of resistant bacteria, its role in the emergence of novel antibiotic resistance genes (ARGs) is less clear. It has been suggested that the environment constitutes an enormous recruitment ground for ARGs to pathogens, but its extent is practically unknown. We have constructed a model framework for resistance emergence and used available quantitative data on relevant processes to identify limiting steps in the appearance of ARGs in human pathogens. We found that in a majority of possible scenarios, the environment would only play a minor role in the emergence of novel ARGs. However, the uncertainty is enormous, highlighting an urgent need for more quantitative data. Specifically, more data is most needed on the fitness costs of ARG carriage, the degree of dispersal of resistant bacteria from the environment to humans, and the rates of mobilization and horizontal transfer of ARGs. This type of data is instrumental to determine which processes should be targeted for interventions to curb development and transmission of ARGs in the environment.

Published
2021
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43. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7:Amphenicols: florfenicol and thiamphenicol

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, and Peixe, Luisa

Abstract

The specific concentrations of florfenicol and thiamphenicol in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for florfenicol was estimated. However, due to the lack of data, the calculation of the FARSC for thiamphenicol was not possible until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for florfenicol, whilst for thiamphenicol no suitable data for the assessment were available. Uncertainties and data gaps associated to the levels reported were addressed. For florfenicol, it was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC, whereas for thiamphenicol, the recommendation was to generate the data required to fill the gaps which prevented the FARSC calculation.

Published
2021

44. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 1: Methodology, general data gaps and uncertainties

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, and Peixe, Luisa

Abstract

The European Commission requested EFSA to assess, in collaboration with EMA, the specific concentrations of antimicrobials resulting from cross-contamination in non-target feed for food-producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in microbial agents relevant for human and animal health, as well as the levels of the antimicrobials which could have a growth promotion/increase yield effect. The assessment was performed for 24 antimicrobial active substances, as specified in the mandate. This scientific opinion describes the methodology used, and the main associated data gaps and uncertainties. To estimate the antimicrobial levels in the non-target feed that would not result in emergence of, and/or selection for, resistance, a model was developed. This ‘Feed Antimicrobial Resistance Selection Concentration’ (FARSC) model is based on the minimal selective concentration (MSC), or the predicted MSC (PMSC) if MSC for the most susceptible bacterial species is unavailable, the fraction of antimicrobial dose available for exposure to microorganisms in the large intestine or rumen (considering pharmacokinetic parameters), the daily faecal output or rumen volume and the daily feed intake. Currently, lack of data prevents the establishment of PMSC and/or FARSC for several antimicrobials and animal species. To address growth promotion, data from an extensive literature search were used. Specific assessments of the different substances grouped by antimicrobial classes are addressed in separate scientific opinions. General conclusions and recommendations were made.

Published
2021

45. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8::Pleuromutilins: tiamulin and valnemulin

Author

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, Peixe, Luisa, EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis, Konstantinos, Allende, Ana, Alvarez-Ordóñez, Avelino, Bolton, Declan, Bover-Cid, Sara, Chemaly, Marianne, Davies, Robert, De Cesare, Alessandra, Herman, Lieve, Hilbert, Friederike, Lindqvist, Roland, Nauta, Maarten, Ru, Giuseppe, Simmons, Marion, Skandamis, Panagiotis, Suffredini, Elisabetta, Andersson, Dan I, Bampidis, Vasileios, Bengtsson-Palme, Johan, Bouchard, Damien, Ferran, Aude, Kouba, Maryline, López Puente, Secundino, López-Alonso, Marta, Nielsen, Søren Saxmose, Pechová, Alena, Petkova, Mariana, Girault, Sebastien, Broglia, Alessandro, Guerra, Beatriz, Innocenti, Matteo Lorenzo, Liébana, Ernesto, López-Gálvez, Gloria, Manini, Paola, Stella, Pietro, and Peixe, Luisa

Abstract

The specific concentrations of tiamulin and valnemulin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tiamulin, while for valnemulin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials.

Published
2021

48. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Author

Nilsson, Rolf Henrik, Larsson, Karl-Henrik, Taylor, Andy F S, Bengtsson-Palme, Johan, Jeppesen, Thomas S, Schigel, Dmitry, Kennedy, Peter, Picard, Kathryn, Glöckner, Frank Oliver, Tedersoo, Leho, Saar, Irja, Kõljalg, Urmas, and Abarenkov, Kessy

Subjects
Fungi, Database Issue, Computational Biology, DNA Barcoding, Taxonomic, Genomics, Genome, Fungal, Web Browser, Databases, Nucleic Acid, Software
Abstract

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcodethe nuclear ribosomal internal transcribed spacer(ITS) regionand offers all approximate to 1 000000 public fungal ITS sequences for reference. These are clustered into approximate to 459000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.

Published
2018

49. Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance

Author

Larsson, D.G. Joakim, Andremont, Antoine, Bengtsson-Palme, Johan, Brandt, Kristian Koefoed, de Roda Husman, Ana Maria, Fagerstedt, Patriq, Fick, Jerker, Flach, Carl-Fredrik, Gaze, William H., Kuroda, Makoto, Kvint, Kristian, Laxminarayan, Ramanan, Manaia, Celia M., Nielsen, Kaare Magne, Plant, Laura, Ploy, Marie-Cécile, Segovia, Carlos, Simonet, Pascal, Smalla, Kornelia, Snape, Jason, Topp, Edward, van Hengel, Arjon J., Verner-Jeffreys, David W., Virta, Marko P.J., Wellington, Elizabeth M., Wernersson, Ann-Sofie, Sub RIVM, dIRAS RA-I&I RA, Horizon 2020, Sub RIVM, dIRAS RA-I&I RA, Department of Microbiology, Helsinki Institute of Sustainability Science (HELSUS), Antibiotic resistance in human impacted environments, Doctoral Programme in Microbiology and Biotechnology, University of Gothenburg (GU), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Copenhagen = Københavns Universitet (KU), Department of Chemistry, Umeå University, University of Exeter, Center for Disease Dynamics, Economics & Policy (CDDEP), Anti-infectieux : supports moléculaires des résistances et innovations thérapeutiques (RESINFIT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-CHU Limoges, Instituto de Salud Carlos III [Madrid] (ISC), Ampère, Département Bioingénierie (BioIng), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Plant Virology, Microbiology and Biosafety, Federal Biological Research Centre for Agriculture and Forestry, Berlin and Braunschweig (BBA), Agriculture and Agri-Food [Ottawa] (AAFC), JRC Institute for Reference Materials and Measurements [Geel] (IRMM), European Commission - Joint Research Centre [Geel] (JRC), Unión Europea. Comisión Europea. H2020, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), and Veritati - Repositório Institucional da Universidade Católica Portuguesa

Subjects
0301 basic medicine, Value (ethics), Antimicrobial resistance markers, Psychological intervention, Infektionsmedicin, POLICY INTERVENTIONS, Environmental pollution, 010501 environmental sciences, Antimicrobial resistance, 01 natural sciences, HORIZONTAL GENE-TRANSFER, Environmental Microbiology, lcsh:Environmental sciences, Risk management, Risk assessment, General Environmental Science, lcsh:GE1-350, 2. Zero hunger, PROTECTION GOALS, Bacterial Infections, Anti-Bacterial Agents, 3. Good health, Risk assessments, ESCHERICHIA-COLI, BACTERIA, Infectious diseases, RISK-ASSESSMENT, Infectious Medicine, 030106 microbiology, Resistance (psychoanalysis), 03 medical and health sciences, Antibiotic resistance, WASTE-WATER, Drug Resistance, Bacterial, Animals, Humans, Environmental planning, 1172 Environmental sciences, 0105 earth and related environmental sciences, PATHOGENS, Bacteria, business.industry, [SPI.NRJ]Engineering Sciences [physics]/Electric power, Research needs, EVOLUTION, 13. Climate action, business
Abstract

There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1. The workshop was organized and supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), the Swedish Research Council (SRC) and the Centre for Antibiotic Resistance Research at University of Gothenburg, Sweden (CARe). This project received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement JPI-EC-AMR No 681055. Individual member states of the JPIAMR also covered travel costs for participants. Sí

Published
2018
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50. Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site

Author

Wahlgren, Weixiao Y., Dunevall, Elin, North, Rachel A., Paz, Aviv, Scalise, Mariafrancesca, Bisignano, Paola, Bengtsson-Palme, Johan, Goyal, Parveen, Claesson, Elin, Caing-Carlsson, Rhawnie, Andersson, Rebecka, Beis, Konstantinos, Nilsson, Ulf J., Farewell, Anne, Pochini, Lorena, Indiveri, Cesare, Grabe, Michael, Dobson, Renwick C. J., Abramson, Jeff, Ramaswamy, S., Friemann, Rosmarie, Biotechnology and Biological Sciences Research Council (BBSRC), and Medical Research Council (MRC)

Subjects
Protein Folding, Science, Organic Anion Transporters, DOPAMINE TRANSPORTER, VIRULENCE FACTOR, HAEMOPHILUS-INFLUENZAE, Article, Substrate Specificity, MD Multidisciplinary, CRYSTAL-STRUCTURE, Amino Acid Sequence, lcsh:Science, Science & Technology, Sequence Homology, Amino Acid, Symporters, Sodium, BETAINE TRANSPORTER BETP, MACROMOLECULAR CRYSTALLOGRAPHY, N-Acetylneuraminic Acid, Multidisciplinary Sciences, carbohydrates (lipids), X-RAY STRUCTURES, ESCHERICHIA-COLI, MOLECULAR-DYNAMICS, SEROTONIN TRANSPORTER, Science & Technology - Other Topics, lcsh:Q
Abstract

Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 Å resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na+ gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na+ ions. One Na+ binds to the conserved Na2 site, while the second Na+ binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na+ sites regulate N-acetylneuraminic acid transport., Sialic acid transporters (SiaT) are required for sialic acid uptake in a number of human pathogens and are of interest as targets for antimicrobial drug development. Here the authors present the substrate bound SiaT structure from the uropathogen Proteus mirabilis and provide insights into the mechanism of sialic acid transport.

Published
2018
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