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1. Author Correction: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance

Author

Becsei, Ágnes, Fuschi, Alessandro, Otani, Saria, Kant, Ravi, Weinstein, Ilja, Alba, Patricia, Stéger, József, Visontai, Dávid, Brinch, Christian, de Graaf, Miranda, Schapendonk, Claudia M. E., Battisti, Antonio, De Cesare, Alessandra, Oliveri, Chiara, Troja, Fulvia, Sironen, Tarja, Vapalahti, Olli, Pasquali, Frédérique, Bányai, Krisztián, Makó, Magdolna, Pollner, Péter, Merlotti, Alessandra, Koopmans, Marion, Csabai, Istvan, Remondini, Daniel, Aarestrup, Frank M., and Munk, Patrick

Published
2024
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2. Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance

Author

Becsei, Ágnes, Fuschi, Alessandro, Otani, Saria, Kant, Ravi, Weinstein, Ilja, Alba, Patricia, Stéger, József, Visontai, Dávid, Brinch, Christian, de Graaf, Miranda, Schapendonk, Claudia M. E., Battisti, Antonio, De Cesare, Alessandra, Oliveri, Chiara, Troja, Fulvia, Sironen, Tarja, Vapalahti, Olli, Pasquali, Frédérique, Bányai, Krisztián, Makó, Magdolna, Pollner, Péter, Merlotti, Alessandra, Koopmans, Marion, Csabai, Istvan, Remondini, Daniel, Aarestrup, Frank M., and Munk, Patrick

Published
2024
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4. Genomics Insights into Mycolicibacterium Hassiacum Causing Infection in a Cat with Pyogranulomatous Dermatitis and Panniculitis.

Author

Smedile, Daniele, Iurescia, Manuela, Carfora, Virginia, Cocumelli, Cristiano, Palmerini, Tiziana, Diaconu, Elena Lavinia, Congiu, Ilaria, Donati, Valentina, Stravino, Fiorentino, Sorbara, Luigi, Romano, Erica, Caprioli, Andrea, and Battisti, Antonio

Subjects
WHOLE genome sequencing, MYCOBACTERIA, ADIPOSE tissue diseases, MYCOBACTERIUM, MYCOBACTERIOSIS
Abstract

Mycolicibacterium hassiacum (homotypic synonym: Mycobacterium hassiacum) represents an ungrouped thermotolerant rapidly growing mycobacteria (RGM) species occasionally associated with infections and disease in humans. In this report, we describe a case of pyogranulomatous dermatitis and panniculitis due to M. hassiacum in an immunocompetent adult cat. To the best of our knowledge, this represents the first report of M. hassiacum infection in animals. We also report the results of the in-depth genome characterization of the isolate using a combined short- and long-read whole-genome sequencing (WGS) approach. We observed the lack of acquired-resistance genes and no evidence of mutations in housekeeping genes associated with resistance to rifampicin and isoniazid. We detected some virulence factors in our isolate, such as some associated with the interaction of mycobacteria with host cells, and the presence of multiple copies of heavy metal resistance genes (arsB, arsR, and arsL/cadL). In conclusion, M. hassiacum should be included among the RGM species associated with feline subcutaneous atypical mycobacteriosis (SAM). A reliable and fast RGM laboratory identification and characterization is important not only for an accurate etiological diagnosis but also for a correct approach to SAM treatment options. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Genomics insights into a Mycobacterium pinnipedii isolate causing tuberculosis in a captive South American sea lion (Otaria flavescens) from Italy

Author

Alba, Patricia, primary, Caprioli, Andrea, additional, Cocumelli, Cristiano, additional, Eleni, Claudia, additional, Diaconu, Elena Lavinia, additional, Donati, Valentina, additional, Ianzano, Angela, additional, Sorbara, Luigi, additional, Stravino, Fiorentino, additional, Cerini, Natalino, additional, Boniotti, Maria Beatrice, additional, Zanoni, Mariagrazia, additional, Franco, Alessia, additional, and Battisti, Antonio, additional

Published
2023
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6. Pathological and virological insights from an outbreak of European brown hare syndrome in the Italian hare (Lepus corsicanus)

Author

Domanico, Mariagiovanna, primary, Cavadini, Patrizia, additional, Nardini, Roberto, additional, Cecca, Daniele, additional, Mastrandrea, Giovanni, additional, Eleni, Claudia, additional, Galietta, Valentina, additional, Attili, Lorenzo, additional, Pizzarelli, Antonella, additional, Onorati, Roberta, additional, Amoruso, Cristina, additional, Stilli, Donatella, additional, Pacchiarotti, Giulia, additional, Merzoni, Francesca, additional, Caprioli, Andrea, additional, Ricci, Ida, additional, Battisti, Antonio, additional, Lavazza, Antonio, additional, and Scicluna, Maria Teresa, additional

Published
2023
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7. Brucella ceti Infection in Striped Dolphins from Italian Seas: Associated Lesions and Epidemiological Data

Author

Grattarola, Carla, primary, Petrella, Antonio, additional, Lucifora, Giuseppe, additional, Di Francesco, Gabriella, additional, Di Nocera, Fabio, additional, Pintore, Antonio, additional, Cocumelli, Cristiano, additional, Terracciano, Giuliana, additional, Battisti, Antonio, additional, Di Renzo, Ludovica, additional, Farina, Donatella, additional, Di Francesco, Cristina Esmeralda, additional, Crescio, Maria Ines, additional, Zoppi, Simona, additional, Dondo, Alessandro, additional, Iulini, Barbara, additional, Varello, Katia, additional, Mignone, Walter, additional, Goria, Maria, additional, Mattioda, Virginia, additional, Giorda, Federica, additional, Di Guardo, Giovanni, additional, Janowicz, Anna, additional, Tittarelli, Manuela, additional, De Massis, Fabrizio, additional, Casalone, Cristina, additional, and Garofolo, Giuliano, additional

Published
2023
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11. Evidence for Human Adaptation and Foodborne Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus

Author

Larsen, Jesper, Stegger, Marc, Andersen, Paal S., Petersen, Andreas, Larsen, Anders R., Westh, Henrik, Agersø, Yvonne, Fetsch, Alexandra, Kraushaar, Britta, Käsbohrer, Annemarie, Feßler, Andrea T., Schwarz, Stefan, Cuny, Christiane, Witte, Wolfgang, Butaye, Patrick, Denis, Olivier, Haenni, Marisa, Madec, Jean-Yves, Jouy, Eric, Laurent, Frederic, Battisti, Antonio, Franco, Alessia, Alba, Patricia, Mammina, Caterina, Pantosti, Annalisa, Monaco, Monica, Wagenaar, Jaap A., de Boer, Enne, van Duijkeren, Engeline, Heck, Max, Domínguez, Lucas, Torres, Carmen, Zarazaga, Myriam, Price, Lance B., and Skov, Robert L.

Published
2016
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14. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Author

Munk, Patrick, Brinch, Christian, Møller, Frederik Duus, Petersen, Thomas N., Hendriksen, Rene S., Seyfarth, Anne Mette, Kjeldgaard, Jette S., Svendsen, Christina Aaby, van Bunnik, Bram, Berglund, Fanny, Bego, Artan, Power, Pablo, Rees, Catherine, Lambrinidis, Dionisia, Neilson, Elizabeth Heather Jakobsen, Gibb, Karen, Coventry, Kris, Collignon, Peter, Cassar, Susan, Allerberger, Franz, Begum, Anowara, Hossain, Zenat Zebin, Worrell, Carlon, Vandenberg, Olivier, Pieters, Ilse, Victorien, Dougnon Tamègnon, Gutierrez, Angela Daniela Salazar, Soria, Freddy, Grujić, Vesna Rudić, Mazalica, Nataša, Rahube, Teddie O., Tagliati, Carlos Alberto, Rodrigues, Dalia, Oliveira, Guilherme, de Souza, Larissa Camila Ribeiro, Ivanov, Ivan, Juste, Bonkoungou Isidore, Oumar, Traoré, Sopheak, Thet, Vuthy, Yith, Ngandijo, Antoinette, Nzouankeu, Ariane, Olivier, Ziem A. Abah Jacques, Yost, Christopher K., Kumar, Pratik, Brar, Satinder Kaur, Tabo, Djim-Adjim, Adell, Aiko D., Paredes-Osses, Esteban, Martinez, Maria Cristina, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Lau, Lok Ting, Chung, Teresa, Jiao, Xiaoyang, Yu, Yongjie, JiaYong, Zhao, Morales, Johan F. Bernal, Valencia, Maria Fernanda, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Deogratias, Zozo Nyarukweba, Elsborg, Bodil, Hansen, Lisbeth Truelstrup, Jensen, Pernille Erland, Abouelnaga, Mohamed, Salem, Mohamed Fathy, Koolmeister, Marliin, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Le Guyader, Soizick, Schaeffer, Julien, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Schubert, Sara, Hesse, Sina, Berendonk, Thomas U., Saba, Courage Kosi Setsoafia, Mohammed, Jibril, Feglo, Patrick Kwame, Banu, Regina Ama, Kotzamanidis, Charalampos, Lytras, Efthymios, Lickes, Sergio A., Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Ballal, Mamatha, Bangera, Sohan Rodney, Fani, Fereshteh, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Diaconu, Elena Lavinia, Corno, Gianluca, Di Cesare, Andrea, Alba, Patricia, Hisatsune, Junzo, Yu, Liansheng, Kuroda, Makoto, Sugai, Motoyuki, Kayama, Shizuo, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Jamil, Kazi, Fakhraldeen, Saja Adel, Alaati, Tareq, Bērziņš, Aivars, Avsejenko, Jeļena, Kokina, Kristina, Streikisa, Madara, Bartkevics, Vadims, Matar, Ghassan M., Daoud, Ziad, Pereckienė, Asta, Butrimaite-Ambrozeviciene, Ceslova, Penny, Christian, Bastaraud, Alexandra, Rasolofoarison, Tiavina, Collard, Jean-Marc, Samison, Luc Hervé, Andrianarivelo, Mala Rakoto, Banda, Daniel Lawadi, Amin, Arshana, Rajandas, Heraa, Parimannan, Sivachandran, Spiteri, David, Haber, Malcolm Vella, Santchurn, Sunita J., Vujacic, Aleksandar, Djurovic, Dijana, Bouchrif, Brahim, Karraouan, Bouchra, Vubil, Delfino Carlos, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, Jeunen, Gert-Jan, Gemmell, Neil, Chambers, Stephen T., Mendoza, Fania Perez, Huete-Pιrez, Jorge, Vilchez, Samuel, Ahmed, Akeem Olayiwola, Adisa, Ibrahim Raufu, Odetokun, Ismail Ayoade, Fashae, Kayode, Sørgaard, Anne-Marie, Wester, Astrid Louise, Ryrfors, Pia, Holmstad, Rune, Mohsin, Mashkoor, Hasan, Rumina, Shakoor, Sadia, Gustafson, Natalie Weiler, Schill, Claudia Huber, Rojas, Maria Luz Zamudio, Velasquez, Jorge Echevarria, Magtibay, Bonifacio B., Catangcatang, Kris, Sibulo, Ruby, Yauce, Felipe Campos, Wasyl, Dariusz, Manaia, Celia, Rocha, Jaqueline, Martins, Jose, Álvaro, Pedro, Di Yoong Wen, Doris, Shin, Hanseob, Hur, Hor-Gil, Yoon, Sukhwan, Bosevska, Golubinka, Kochubovski, Mihail, Cojocaru, Radu, Burduniuc, Olga, Hong, Pei-Ying, Perry, Meghan Rose, Gassama, Amy, Radosavljevic, Vladimir, Tay, Moon Y. F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Pastuchová, Katarína, Truska, Peter, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Song, Min Joon, Quintela-Baluja, Marcos, Lopez, Mariano Gomez, Cerdà-Cuéllar, Marta, Perera, R.R.D.P., Bandara, N.K.B.K.R.G.W., Premasiri, H.I., Pathirage, Sujatha, Charlemagne, Kareem, Rutgersson, Carolin, Norrgren, Leif, Örn, Stefan, Boss, Renate, Van der Heijden, Tanja, Hong, Yu-Ping, Kumburu, Happiness Houka, Mdegela, Robinson Hammerthon, Hounmanou, Yaovi Mahuton Gildas, Chonsin, Kaknokrat, Suthienkul, Orasa, Thamlikitkul, Visanu, de Roda Husman, Ana Maria, Bidjada, Bawimodom, Njanpop-Lafourcade, Berthe-Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Kurekci, Cemil, Ejobi, Francis, Kalule, John Bosco, Thomsen, Jens, Obaidi, Ouidiane, Jassim, Laila Mohamed, Moore, Andrew, Leonard, Anne, Graham, David W., Bunce, Joshua T., Zhang, Lihong, Gaze, William H., Lefor, Brett, Capone, Drew, Sozzi, Emanuele, Brown, Joe, Meschke, John Scott, Sobsey, Mark D., Davis, Michael, Beck, Nicola Koren, Sukapanpatharam, Pardi, Truong, Phuong, Lilienthal, Ronald, Kang, Sanghoon, Wittum, Thomas E., Rigamonti, Natalia, Baklayan, Patricia, Van, Chinh Dang, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Larsson, D. G. Joakim, Koopmans, Marion, Woolhouse, Mark, Aarestrup, Frank M., Virology, Producció Animal, and Sanitat Animal

Subjects
genomic analysis, sewage, antimicrobial resistance, Multidisciplinary, Sewage, Drug Resistance, Bacterial, Metagenome, General Physics and Astronomy, Drug Resistance, Bacterial/genetics, Genomics, General Chemistry, General Biochemistry, Genetics and Molecular Biology, Anti-Bacterial Agents/pharmacology, Anti-Bacterial Agents
Abstract

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention. Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Published
2022

15. The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals

Author

Carfora, Virginia, primary, Diaconu, Elena Lavinia, additional, Ianzano, Angela, additional, Di Matteo, Paola, additional, Amoruso, Roberta, additional, Dell'Aira, Elena, additional, Sorbara, Luigi, additional, Bottoni, Francesco, additional, Guarneri, Flavia, additional, Campana, Laura, additional, Franco, Alessia, additional, Alba, Patricia, additional, and Battisti, Antonio, additional

Published
2022
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16. The New SPARC_LAB RF Photo-Injector

Author

Alesini, David, Anania, Maria Pia, Battisti, Antonio, Bellaveglia, Marco, Biagioni, Angelo, Cardelli, Fabio, Carillo, Martina, Chiadroni, Enrica, Cianchi, Alessandro, Costa, Gemma, Del Franco, Mario, Di Pirro, Giampiero, Di Raddo, Gianluca, Faillace, Luigi, Ferrario, Massimo, Franzini, Giovanni, Galletti, Mario, Gallo, Alessandro, Giribono, Anna, Liedl, Andrea, Lollo, Valerio, Pellegrino, Luigi, Piersanti, Luca, Pompili, Riccardo, Romeo, Stefano, Sabbatini, Lucia, Shpakov, Vladimir, Stella, Angelo, Vaccarezza, Cristina, Vannozzi, Alessandro, and Villa, Fabio

Subjects
MC3: Novel Particle Sources and Acceleration Techniques, Physics::Accelerator Physics, Accelerator Physics
Abstract

A new RF photo-injector has been designed, realized and successfully installed at the SPARC_LAB facility (INFN-LNF, Frascati, Rome). It is based on a 1.6 cell RF gun fabricated with the new brazing free technology recently developed at the National Laboratories of Frascati. The electromagnetic design has been optimized to have a full compensation of the dipole and quadrupole field components introduced by the coupling hole with an improvement of the effective pumping speed with two added pumping ports. The gun is overcoupled (\beta=2) to reduce the filling time and to allow the operation with short RF pulses. The overall injector integrates a new solenoid with a remote control of the transverse position and a variable skew quadrupole for the compensation of residual quadrupole field components. It also allows an on axis laser injection system with the last mirror in air, and the possibility of a future integration of an X/C band cavity linearizer. In the paper we report the main characteristics of the electromagnetic and mechanical design and the low and high power test results that shows the extremely good perfomances of the new device., Proceedings of the 13th International Particle Accelerator Conference, IPAC2022, Bangkok, Thailand

Published
2022
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17. Genomic evolution of antimicrobial resistance in Escherichia coli

Author

Leekitcharoenphon, Pimlapas, Johansson, Markus Hans Kristofer, Munk, Patrick, Malorny, Burkhard, Skarzynska, Magdalena, Wadepohl, Katharina, Moyano, Gabriel, Hesp, Ayla, Veldman, Kees T., Bossers, Alex, Graveland, Haitske, van Essen, Alieda, Battisti, Antonio, Caprioli, Andrea, Blaha, Thomas, Hald, Tine, Daskalov, Hristo, Saatkamp, Helmut W., Staerk, Katharina D. C., Luiken, Roosmarijn E. C., Van Gompel, Liese, Hansen, Rasmus Borup, Dewulf, Jeroen, Duarte, Ana Sofia Ribeiro, Zajac, Magdalena, Wasyl, Dariusz, Sanders, Pascal, Gonzalez-Zorn, Bruno, Brouwer, Michael S. M., Wagenaar, Jaap A., Heederik, Dick J. J., Mevius, Dik, Aarestrup, Frank M., EFFORT Consortium, for the, Technical University of Denmark [Lyngby] (DTU), Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), European Project: 613754,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,EFFORT(2013), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I RA, and Faculteit Diergeneeskunde

Subjects
0301 basic medicine, Genomic alteration, antibiotic resistance, Swine, Epidemiology, résistance aux antibiotiques, veterinary drug, medicine.disease_cause, Genome, Poultry, Feces, animal, évolution, bacteria, Escherichia coli Infections, Phylogeny, médicament humainélevage, 2. Zero hunger, Genetics, human drug, bactérie, Multidisciplinary, Virulence, Bacteriologie, transmission, Genomics, Bacteriology, Host Pathogen Interaction & Diagnostics, Text, Anti-Bacterial Agents, Europe, Medicine, médicament, médicament vétérinaire, Bioinformatica & Diermodellen, Science, 030106 microbiology, Microbial Sensitivity Tests, GENETIC-STRUCTURE, Biology, Article, Evolution, Molecular, 03 medical and health sciences, Antibiotic resistance, résistance aux antimicrobiens, Drug Resistance, Bacterial, Bio-informatics & Animal models, medicine, Escherichia coli, Animals, Life Science, Epidemiology, Bio-informatics & Animal models, ddc:610, Veterinary Sciences, antimicrobial resistance, microbiologie, General, genome, Host Pathogen Interaction & Diagnostics, Epidemiologie, Whole genome sequencing, génome, microbiology, Bacteriology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Host Pathogen Interactie & Diagnostiek, livestock, Red Meat, 030104 developmental biology, Metagenomics, Genetic marker, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Molecular evolution, Cattle, POULTRY, Mobile genetic elements, humain, Genome, Bacterial
Abstract

The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

Published
2021

18. Zinc resistance of Staphylococcus aureus of animal origin is strongly associated with methicillin resistance

Author

Cavaco, Lina M., Hasman, Henrik, Aarestrup, Frank M., Members of MRSA-CG, Wagenaar, Jaap A., Graveland, Haitske, Veldman, Kees, Mevius, Dik, Fetsch, Alexandra, Tenhagen, Bernd-Alois, Concepcion Porrero, M., Dominguez, Lucas, Granier, Sophie A., Jouy, Eric, Butaye, Patrick, Kaszanyitzky, Eva, Dán, Adam, Zmudzki, Jacek, Battisti, Antonio, Franco, Alessia, Schwarz, Stefan, Gutierrez, Montserrat, Weese, J. Scott, Cui, Shengui, and Pomba, Constança

Published
2011
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19. Evidence of structural rearrangements and variability in pESI(like) megaplasmids of S.Infantis by resolving the pESI-like-blaCTX-M-1 positive variant.

Author

Alba, Patricia, primary, Carfora, Virginia, additional, Feltrin, Fabiola, additional, Iurescia, Manuela, additional, Diaconu, Elena Lavinia, additional, Cordaro, Gessica, additional, Dell'Aira, Elena, additional, Marani, Ilaria, additional, Giacomi, Angelo, additional, Franco, Alessia, additional, and Battisti, Antonio, additional

Published
2021
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20. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Author

Hendriksen, Rene S., Munk, Patrick, Njage, Patrick, van Bunnik, Bram, McNally, Luke, Lukjancenko, Oksana, Röder, Timo, Nieuwenhuijse, David, Pedersen, Susanne Karlsmose, Kjeldgaard, Jette, Kaas, Rolf S., Clausen, Philip Thomas Lanken Conradsen, Vogt, Josef Korbinian, Leekitcharoenphon, Pimlapas, van de Schans, Milou G.M., Zuidema, Tina, de Roda Husman, Ana Maria, Rasmussen, Simon, Petersen, Bent, Bego, Artan, Rees, Catherine, Cassar, Susan, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Vuthy, Yith, Sopheak, Thet, Yost, Christopher K., Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Jergović, Matijana, Hrenovic, Jasna, Karpíšková, Renáta, Villacis, Jose Eduardo, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, Cormican, Martin, O’Connor, Louise, Moran-Gilad, Jacob, Alba, Patricia, Battisti, Antonio, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Avsejenko, Jeļena, Bērziņš, Aivars, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljevic, Vladimir, Wuertz, Stefan, Zuniga-Montanez, Rogelio, Tay, Moon Y.F., Gavačová, Dagmar, Pastuchova, Katarina, Truska, Peter, Trkov, Marija, Esterhuyse, Kerneels, Keddy, Karen, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Norrgren, Leif, Örn, Stefan, Larsson, D. G.Joakim, Heijden, Tanja Van der, Kumburu, Happiness Houka, Sanneh, Bakary, Bidjada, Pawou, Njanpop-Lafourcade, Berthe Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van, Chinh Dang, Tran, Doan Minh Nguyen, Kwenda, Geoffrey, Tabo, Djim adjim, Wester, Astrid Louise, Cuadros-Orellana, Sara, Amid, Clara, Cochrane, Guy, Sicheritz-Ponten, Thomas, Schmitt, Heike, Alvarez, Jorge Raul Matheu, Aidara-Kane, Awa, Pamp, Sünje J., Lund, Ole, Hald, Tine, Woolhouse, Mark, Koopmans, Marion P., Vigre, Håkan, Petersen, Thomas Nordahl, Aarestrup, Frank M., Sub RIVM, dIRAS RA-I&I RA, One Health Microbieel, dIRAS RA-I&I I&I, University of Helsinki, Food Hygiene and Environmental Health, Producció Animal, Sanitat Animal, Tilraunastöð í meinafræði að Keldum (HÍ), Institute for Experimental Pathology, Keldur (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, University of Iceland, Food Hygiene and Environmental Health, Helsinki One Health (HOH), Zoonotic Antimicrobial Resistance, and Virology

Subjects
0301 basic medicine, Water microbiology, global surveillance, Sanitation, Kwantitatieve Veterinaire Epidemiologie, Drug Resistance, General Physics and Astronomy, Sewage, 02 engineering and technology, Drug resistance, Antimicrobial resistance, 413 Veterinary science, BU Veterinary Drugs, Abundance (ecology), Drug Resistance, Multiple, Bacterial, Genamengi, AMR, lcsh:Science, resistome, Ónæmisfræði, Multidisciplinary, Population Health, 021001 nanoscience & nanotechnology, 3. Good health, Europe, machine learning, Geography, Epidemiological Monitoring, 0210 nano-technology, Asia, Science, Microbial Consortia, Oceania, Article, General Biochemistry, Genetics and Molecular Biology, BU Dierbehandelingsmiddelen, 03 medical and health sciences, Antibiotic resistance, SDG 3 - Good Health and Well-being, Environmental health, Erfðafræði, Life Science, Humans, ddc:610, wastewater, Ecological epidemiology, Bacteria, business.industry, Quantitative Veterinary Epidemiology, prediction, General Chemistry, South America, Resistome, 030104 developmental biology, Genes, Socioeconomic Factors, 416 Food Science, Genes, Bacterial, Metagenomics, ENVIRONMENTAL SURVEILLANCE, Africa, North America, Metagenome, UPDATE, lcsh:Q, business, 610 Medizin und Gesundheit
Abstract

Publisher's version (útgefin grein), Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR., We are grateful to Hanne Nørgaard Nielsen, Christina Aaby Svendsen, Jacob Dyring Jensen, Birthe S. Rosenqvist Lund, Kate Vina Vibefeldt, Inge Marianne Hansen, Gunhild Larsen, Hanne Mordhorst, and Carsten Bidstrup for technical assistance. We also thank Jeffrey Edward Skiby for internal review. This study has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 643476 (COMPARE), the World Health Organization, The Villum Foundation (VKR023052), and The Novo Nordisk Foundation (NNF16OC0021856: Global Surveillance of Antimicrobial Resistance).

Published
2019

21. Antimicrobial resistance genes aph(3')-III, erm(B), sul2 and tet(W) abundance in animal faeces, meat, production environments and human faeces in Europe

Author

Yang, Dongsheng, Heederik, Dick J.J., Scherpenisse, Peter, Van Gompel, Liese, Luiken, Roosmarijn E.C., Wadepohl, Katharina, Skarżyńska, Magdalena, Van Heijnsbergen, Eri, Wouters, Inge M., Greve, Gerdit D., Jongerius-Gortemaker, Betty G.M., Tersteeg-Zijderveld, Monique, Portengen, Lützen, Juraschek, Katharina, Fischer, Jennie, Zajac, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A., Mevius, Dik J., Smit, Lidwien A.M., Schmitt, Heike, Graveland, Haitske, Joosten, Philip, Sarrazin, Steven, Dewulf, Jeroen, Van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, David, Julie, Soumet, Christophe, Battisti, Antonio, Caprioli, Andrea, Blaha, Thomas, Brandt, Maximiliane, Aarestrup, Frank, Hald, Tine, Duarte, Ana Sofia Ribeiro, Hoszowski, Andrzej, Pekala-Safinnska, Agnieszka, Pazdzior, Ewa, Daskalov, Hristo, Saatkamp, Helmut W., Stark, Katharina D.C., IRAS OH Epidemiology Microbial Agents, Faculteit Diergeneeskunde, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, Klinische infectiologie en microb. lab., LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, and dI&I I&I-4

Subjects
Microbiology (medical), Livestock, Meat, Drivers, Swine, Epidemiology, Bioinformatica & Diermodellen, GTB Gewasgez. Bodem en Water, Bedrijfseconomie, WASS, Escherichia-coli, Feces, Crop health, Anti-Infective Agents, Business Economics, RNA, Ribosomal, 16S, Drug Resistance, Bacterial, Bio-informatics & Animal models, Mechanisms, Animals, Humans, Life Science, Epidemiology, Bio-informatics & Animal models, Pharmacology (medical), Host Pathogen Interaction & Diagnostics, Epidemiologie, Pharmacology, Carriage, Ecology, Bacteriologie, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, Chicken, Host Pathogen Interactie & Diagnostiek, Anti-Bacterial Agents, Risk-factors, Cross-Sectional Studies, Infectious Diseases, Genes, Bacterial, Epidemiologie, Bioinformatica & Diermodellen, Gewasgezondheid, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Cattle, Pigs, Chickens
Abstract

Background Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains. Objectives We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed. Methods A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3′)-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman’s rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data. Results ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains (‘farm to fork’) was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman’s ρ > 0.7) between qPCR data and metagenomic data of pooled samples. Conclusions qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.

Published
2022

22. Technical specifications for a baseline survey on the prevalence of methicillin‐resistant Staphylococcus aureus (MRSA) in pigs.

Author

Aerts, Marc, Battisti, Antonio, Hendriksen, Rene, Larsen, Jesper, Nilsson, Oskar, Abrahantes, José Cortiñas, Guerra, Beatriz, Papanikolaou, Alexandra, and Beloeil, Pierre‐Alexandre

Subjects
*SWINE breeding, *METHICILLIN-resistant staphylococcus aureus, *SWINE farms, *TECHNICAL specifications, *SWINE, *REQUIREMENTS engineering
Abstract

The European Commission requested scientific and technical assistance in the preparation of a EU‐wide baseline survey protocol for a European Union (EU) coordinated monitoring programme on the prevalence of methicillin‐resistant Staphylococcus Aureus (MRSA) in pigs. The objective of the survey is to estimate the MRSA prevalence in batches of fattening pigs at slaughter at both European and national levels, with a 95% level of confidence and a level of precision of 10% considering an expected prevalence of 50%. The survey protocol defines the target population, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic testing of MRSA isolates), the data reporting requirements and the plan of analysis. The samples are to be analysed according to the laboratory protocols available on the European Union Reference Laboratory (EURL‐AR) website. Generalised linear models will be used to estimate proportion (with 95% confidence intervals) of batches of slaughter pigs tested positive to MRSA. The necessary data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA data collection framework. [ABSTRACT FROM AUTHOR]

Published
2022
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23. Livestock-Associated Methicillin-Resistant Staphylococcus aureus and Related Risk Factors in Holdings of Veal Calves in Northwest Italy

Author

Zoppi, Simona, primary, Dondo, Alessandro, additional, Di Blasio, Alessia, additional, Vitale, Nicoletta, additional, Carfora, Virginia, additional, Goria, Maria, additional, Chiavacci, Laura, additional, Giorgi, Ilaria, additional, D'Errico, Valeria, additional, Irico, Lara, additional, Franco, Alessia, additional, and Battisti, Antonio, additional

Published
2021
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24. Plasmodium matutinum Causing Avian Malaria in Lovebirds (Agapornis roseicollis) Hosted in an Italian Zoo

Author

Cocumelli, Cristiano, primary, Iurescia, Manuela, additional, Diaconu, Elena Lavinia, additional, Galietta, Valentina, additional, Raso, Caterina, additional, Buccella, Carmela, additional, Stravino, Fiorentino, additional, Grande, Francesco, additional, Fiorucci, Letizia, additional, De Liberato, Claudio, additional, Caprioli, Andrea, additional, and Battisti, Antonio, additional

Published
2021
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25. Plasmodium matutinum Transmitted by Culex pipiens as a Cause of Avian Malaria in Captive African Penguins (Spheniscus demersus) in Italy

Author

Iurescia, Manuela, primary, Romiti, Federico, additional, Cocumelli, Cristiano, additional, Diaconu, Elena Lavinia, additional, Stravino, Fiorentino, additional, Onorati, Roberta, additional, Alba, Patricia, additional, Friedrich, Klaus Gunther, additional, Maggi, Flavio, additional, Magliano, Adele, additional, Ermenegildi, Arianna, additional, Carfora, Virginia, additional, Caprioli, Andrea, additional, De Liberato, Claudio, additional, and Battisti, Antonio, additional

Published
2021
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27. Setting a baseline for global urban virome surveillance in sewage

Author

Nieuwenhuijse, David F., Oude Munnink, Bas B., Phan, My V.T., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Bērziņš, Aivars, Avsejenko, Jeļena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G.M., Zuidema, Tina, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama†, Amy, Radosavljevic, Vladimir, Tay, Moon Y.F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Larsson, D. G.Joakim, Norrgren, Leif, Örn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van Dang, Chinh, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P.G., IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Singapore Centre for Environmental Life Sciences and Engineering, Nanyang Technological University Food Technology Centre (NAFTEC), Producció Animal, Sanitat Animal, Virology, University of Helsinki, Food Hygiene and Environmental Health, Helsinki One Health (HOH), Zoonotic Antimicrobial Resistance, IRAS OH Epidemiology Microbial Agents, and dIRAS RA-I&I I&I

Subjects
0301 basic medicine, lcsh:Medicine, Sewage, Pilot Projects, POLIOVIRUS, Disease, CORONAVIRUS, Disease Outbreaks, BU Veterinary Drugs, 0302 clinical medicine, Vegetables, lcsh:Science, metagenomic sequencing, sewage, viral pathogens, virome, virus, 11832 Microbiology and virology, Public health, Multidisciplinary, Virome, ENTEROVIRUSES, 3142 Public health care science, environmental and occupational health, Environmental engineering [Engineering], Geography, Public Health, Environmental Monitoring, VIRUSES, High density, Early detection, Food Contamination, CLASSIFICATION, BU Dierbehandelingsmiddelen, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Environmental health, Humans, Life Science, Human virome, Author Correction, business.industry, lcsh:R, Outbreak, SEASONALITY, Cross-Sectional Studies, 030104 developmental biology, Megacity, Metagenomics, PATTERNS, Metagenome, lcsh:Q, business, 030217 neurology & neurosurgery
Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Published
2020

28. Antimicrobial usage and resistance in companion animals: A cross-sectional study in three european countries

Author

Joosten, Philip, Ceccarelli, Daniela, Odent, Evelien, Sarrazin, Steven, Graveland, Haitske, Van Gompel, Liese, Battisti, Antonio, Caprioli, Andrea, Franco, Alessia, Wagenaar, Jaap A, Mevius, Dik, Dewulf, Jeroen, dI&I I&I-4, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, One Health Microbieel, Klinische infectiologie en microb. lab., dI&I I&I-4, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, One Health Microbieel, and Klinische infectiologie en microb. lab.

Subjects
0301 basic medicine, Veterinary medicine, Cross-sectional study, critically important antimicrobials, Epidemiology, Colistin resistance, medicine.disease_cause, Antimicrobial resistance, Toxicology and Pharmaceutics, Biochemistry, 0403 veterinary science, Ampicillin, companion animals, Pharmacology (medical), General Pharmacology, Toxicology and Pharmaceutics, Critically important antimicrobials, One health, Incidence (epidemiology), 04 agricultural and veterinary sciences, Companion animals, Antimicrobial, Antimicrobial use, Infectious Diseases, DOGS, colistin resistance, Staphylococcus aureus, ESCHERICHIA-COLI, PIG PRODUCTION, medicine.drug, Microbiology (medical), 040301 veterinary sciences, Bioinformatica & Diermodellen, 030106 microbiology, PET ANIMALS, Biology, MULTIDRUG-RESISTANT, Microbiology, Article, 03 medical and health sciences, one health, Antibiotic resistance, General Pharmacology, Bio-informatics & Animal models, medicine, Epidemiology, Bio-informatics & Animal models, Veterinary Sciences, antimicrobial resistance, Feces, STAPHYLOCOCCUS-AUREUS, Epidemiologie, lcsh:RM1-950, VETERINARY PRACTICES, ANTIBIOTIC-RESISTANCE, antimicrobial use, HOUSEHOLD TRANSMISSION, Multiple drug resistance, lcsh:Therapeutics. Pharmacology, Epidemiologie, Bioinformatica & Diermodellen, PATTERNS
Abstract

Companion animals have been described as potential reservoirs of antimicrobial resistance (AMR), however data remain scarce. Therefore, the objectives were to describe antimicrobial usage (AMU) in dogs and cats in three European countries (Belgium, Italy, and The Netherlands) and to investigate phenotypic AMR. A questionnaire and one fecal sample per animal (n = 303) were collected over one year and AMU was quantified using treatment incidence (TI). Phenotypic resistance profiles of 282 Escherichia coli isolates were determined. Nineteen percent of the animals received at least one antimicrobial treatment six months preceding sampling. On average, cats and dogs were treated with a standard daily dose of antimicrobials for 1.8 and 3.3 days over one year, respectively. The most frequently used antimicrobial was amoxicillin-clavulanate (27%). Broad-spectrum antimicrobials and critically important antimicrobials for human medicine represented 83% and 71% of the total number of treatments, respectively. Resistance of E. coli to at least one antimicrobial agent was found in 27% of the isolates. The most common resistance was to ampicillin (18%). Thirteen percent was identified as multidrug resistant isolates. No association between AMU and AMR was found in the investigated samples. The issue to address, regarding AMU in companion animal, lies within the quality of use, not the quantity. Especially from a One-Health perspective, companion animals might be a source of transmission of resistance genes and/or resistant bacteria to humans.

Published
2020

29. Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid

Author

Alba, Patricia, Leekitcharoenphon, Pimlapas, Carfora, Virginia, Amoruso, Roberta, Cordaro, Gessica, Di Matteo, Paola, Ianzano, Angela, Iurescia, Manuela, Diaconu, Elena L, Study Group, Engage-Eurl-Ar Network, Karlsmose Pedersen, Susanne, Guerra, Beatriz, Hendriksen, Rene S., Franco, Alessia, Battisti, Antonio, Alba, Patricia, Leekitcharoenphon, Pimlapas, Carfora, Virginia, Amoruso, Roberta, Cordaro, Gessica, Di Matteo, Paola, Ianzano, Angela, Iurescia, Manuela, Diaconu, Elena L, Study Group, Engage-Eurl-Ar Network, Karlsmose Pedersen, Susanne, Guerra, Beatriz, Hendriksen, Rene S., Franco, Alessia, and Battisti, Antonio

Abstract

Salmonella Infantis is one of the five serovars most frequently causing human salmonellosis in Europe, mainly associated with poultry. A clone harbouring a conjugative plasmid of emerging S. Infantis (pESI)-like megaplasmid, carrying multidrug resistant (MDR) and extended-spectrum beta-lactamases (ESBL) genes, has spread in the Italian broiler chicken industry also causing human illness. This work is aimed at elucidating the molecular epidemiology of S. Infantis and pESI-like in Europe using whole-genome sequencing and bioinformatics analysis, and to investigate the genetic relatedness of S. Infantis clones and pESI-like from animals, meat, feed and humans provided by institutions of nine European countries. Two genotyping approaches were used: chromosome or plasmid SNP-based analysis and the minimum spanning tree (MST) algorithm based on core-genome multilocus sequence typing (cgMLST). The European S. Infantis population appeared heterogeneous, with different genetic clusters defined at core-genome level. However, pESI-like variants present in 64.1 % of the isolates were more genetically homogeneous and capable of infecting different clonal lineages in most of the countries. Two different pESI-like with ESBL genes (n=82) were observed: bla CTX-M-1-positive in European isolates and bla CTX-M-65-positive in American isolates (study outgroup). Both variants had toxin-antitoxin systems, resistance genes towards tetracyclines, trimethoprim, sulphonamides and aminoglycosides, heavy metals (merA) and disinfectants (qacEΔ). Worryingly, 66 % of the total isolates studied presented different gyrA chromosomal point mutations associated with (fluoro)quinolone resistance (MIC range 0.125-0.5 mg/L), while 18 % displayed transferable macrolide resistance mediated by mph, mef and erm(B) genes. Proper intervention strategies are needed to prevent further dissemination/transmission of MDR S. Infantis and pESI-like along the food chain in Europe.

Published
2020

30. Setting a baseline for global urban virome surveillance in sewage

Author

IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Nieuwenhuijse, David F., Oude Munnink, Bas B., Phan, My V.T., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Bērziņš, Aivars, Avsejenko, Jeļena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G.M., Zuidema, Tina, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama†, Amy, Radosavljevic, Vladimir, Tay, Moon Y.F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Larsson, D. G.Joakim, Norrgren, Leif, Örn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van Dang, Chinh, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P.G., IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Nieuwenhuijse, David F., Oude Munnink, Bas B., Phan, My V.T., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Bērziņš, Aivars, Avsejenko, Jeļena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G.M., Zuidema, Tina, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama†, Amy, Radosavljevic, Vladimir, Tay, Moon Y.F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Larsson, D. G.Joakim, Norrgren, Leif, Örn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van Dang, Chinh, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, and Koopmans, Marion P.G.

Published
2020

31. Antimicrobial Usage and Resistance in Companion Animals: A Cross-Sectional Study in Three European Countries

Author

dI&I I&I-4, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, One Health Microbieel, Klinische infectiologie en microb. lab., Joosten, Philip, Ceccarelli, Daniela, Odent, Evelien, Sarrazin, Steven, Graveland, Haitske, Van Gompel, Liese, Battisti, Antonio, Caprioli, Andrea, Franco, Alessia, Wagenaar, Jaap A, Mevius, Dik, Dewulf, Jeroen, dI&I I&I-4, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, One Health Microbieel, Klinische infectiologie en microb. lab., Joosten, Philip, Ceccarelli, Daniela, Odent, Evelien, Sarrazin, Steven, Graveland, Haitske, Van Gompel, Liese, Battisti, Antonio, Caprioli, Andrea, Franco, Alessia, Wagenaar, Jaap A, Mevius, Dik, and Dewulf, Jeroen

Published
2020

32. Setting a baseline for global urban virome surveillance in sewage

Author

Nieuwenhuijse, David, Munnink, Bas B. Oude, Phan, My V. T., Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim-adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Li, Baisheng, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenović, Jasna, Jergović, Matijana, Karpiskova, Renata, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Eduardo Villacis, Jose, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafa, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O'Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng'eno, Eric, Raka, Lul, Berzins, Aivars, Avsejenko, Jelena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G. M., Zuidema, Tina, Jeunen, Gert-Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Zamudio Rojas, Maria Luz, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljević, Vladimir, Tay, Moon Y. F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavacova, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerda-Cuellar, Marta, Pathirage, Sujatha, Larsson, D. G. Joakim, Norrgren, Leif, Orn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe-Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Chinh, Van Dang, Doan Minh Nguyen, Tran, Nguyen, Do Phuc, Kwenda, Geofrey, Nieuwenhuijse, David, Munnink, Bas B. Oude, Phan, My V. T., Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim-adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Li, Baisheng, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenović, Jasna, Jergović, Matijana, Karpiskova, Renata, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Eduardo Villacis, Jose, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafa, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O'Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng'eno, Eric, Raka, Lul, Berzins, Aivars, Avsejenko, Jelena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G. M., Zuidema, Tina, Jeunen, Gert-Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Zamudio Rojas, Maria Luz, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljević, Vladimir, Tay, Moon Y. F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavacova, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerda-Cuellar, Marta, Pathirage, Sujatha, Larsson, D. G. Joakim, Norrgren, Leif, Orn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe-Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Chinh, Van Dang, Doan Minh Nguyen, Tran, Nguyen, Do Phuc, and Kwenda, Geofrey

Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Published
2020

33. West Nile virus epidemic in horses, Tuscany region, Italy. (Research)

Author

Autorino, Gian Luca, Battisti, Antonio, Deubel, Vincent, Ferrari, Giancarlo, Forletta, Riccardo, Giovannini, Armando, Lelli, Rossella, Murri, Severine, and Scicluna, Maria Teresa

Subjects
Horses -- Health aspects, West Nile fever -- Development and progression, Communicable diseases -- Research
Abstract

During the late summer of 1998, veterinary authorities in Tuscany, Italy, received reports of cases of neurologic disease among homes residing in a large wetland area located in the provinces [...]

Published
2002

34. International collaborative study on the occurrence of plasmid-mediated quinolone resistance in Salmonella enterica and Escherichia coli isolated from animals, humans, food and the environment in 13 European countries

Author

Veldman, Kees, Cavaco, Lina M., Mevius, Dik, Battisti, Antonio, Franco, Alessia, Botteldoorn, Nadine, Bruneau, Mireille, Perrin-Guyomard, Agnès, Cerny, Tomas, De Frutos Escobar, Cristina, Guerra, Beatriz, Schroeter, Andreas, Gutierrez, Montserrat, Hopkins, Katie, Myllyniemi, Anna-Liisa, Sunde, Marianne, Wasyl, Dariusz, and Aarestrup, Frank M.

Published
2011
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36. Molecular epidemiology of methicillin-resistant Staphylococcus aureus from dairy farms in North-eastern Italy

Author

Tomao, Paola, primary, Pirolo, Mattia, additional, Agnoletti, Fabrizio, additional, Pantosti, Annalisa, additional, Battisti, Antonio, additional, Di Martino, Guido, additional, Visaggio, Daniela, additional, Monaco, Monica, additional, Franco, Alessia, additional, Pimentel de Araujo, Fernanda, additional, Palei, Manlio, additional, Benini, Nicola, additional, Motta, Cesare, additional, Bovo, Chiara, additional, Di Renzi, Simona, additional, Vonesch, Nicoletta, additional, and Visca, Paolo, additional

Published
2020
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38. Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid

Author

Alba, Patricia, primary, Leekitcharoenphon, Pimlapas, additional, Carfora, Virginia, additional, Amoruso, Roberta, additional, Cordaro, Gessica, additional, Di Matteo, Paola, additional, Ianzano, Angela, additional, Iurescia, Manuela, additional, Diaconu, Elena L., additional, Study Group, ENGAGE-EURL-AR Network, additional, Pedersen, Susanne K., additional, Guerra, Beatriz, additional, Hendriksen, Rene S., additional, Franco, Alessia, additional, and Battisti, Antonio, additional

Published
2020
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39. Molecular analysis of methicillin-resistant Staphylococcus pseudintermedius of feline origin from different European countries and North America

Author

Kadlec, Kristina, Schwarz, Stefan, Perreten, Vincent, Grönlund Andersson, Ulrika, Finn, Maria, Greko, Christina, Moodley, Arshnee, Kania, Stephen A., Frank, Linda A., Bemis, David A., Franco, Alessia, Iurescia, Manuela, Battisti, Antonio, Duim, Birgitta, Wagenaar, Jaap A., van Duijkeren, Engeline, Weese, J. Scott, Fitzgerald, J. Ross, Rossano, Alexandra, and Guardabassi, Luca

Published
2010
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40. Clonal spread of methicillin-resistant Staphylococcus pseudintermedius in Europe and North America: an international multicentre study

Author

Perreten, Vincent, Kadlec, Kristina, Schwarz, Stefan, Grönlund Andersson, Ulrika, Finn, Maria, Greko, Christina, Moodley, Arshnee, Kania, Stephen A., Frank, Linda A., Bemis, David A., Franco, Alessia, Iurescia, Manuela, Battisti, Antonio, Duim, Birgitta, Wagenaar, Jaap A., van Duijkeren, Engeline, Weese, J. Scott, Fitzgerald, J. Ross, Rossano, Alexandra, and Guardabassi, Luca

Published
2010
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42. Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries

Author

Luiken, Roosmarijn, van Gompel, Liese, Munk, Patrick, Sarrazin, Steven, Joosten, Philip, Dorado-García, Alejandro, Borup Hansen, Rasmus, Knudsen, Berith, Bossers, Alex, Wagenaar, Jaap, Aarestrup, Frank, Dewulf, Jeroen, Mevius, Dik, Heederik, Dick, Smit, Lidwien, Schmitt, Heike, Graveland, Haitske, Vanessen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Hald, Tine, Ribeiro Duarte, Ana Sofia, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut, Stärk, Katharina, One Health Microbieel, dI&I I&I-4, Dep IRAS, dIRAS RA-I&I RA, Part of Wageningen UR, Central Veterinary Institute, Obstetrics, Reproduction and Herd Health, Universiteit Gent = Ghent University (UGENT), Environmental and Occupational Health Group, Wageningen University and Research [Wageningen] (WUR), Division of Environmental Epidemiology [Utrecht, The Netherlands], Utrecht University [Utrecht]- Institute of Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Institute for Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Utrecht University [Utrecht], Facultad de Veterinaria, Dpto. de Sanidad Animal - VISAVET, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Pharmacoepidemiologie et évaluation de l'impact des produits de santé sur les populations, Université Bordeaux Segalen - Bordeaux 2-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT), Department of Microbiology, National Veterinary Research Institute [Pulawy, Pologne] (NVRI), European Project: 613754,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,EFFORT(2013), Universiteit Gent = Ghent University [Belgium] (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bordeaux Segalen - Bordeaux 2-Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Normandie Université (NU)

Subjects
Veterinary medicine, antibiotic resistance, Epidemiology, animal diseases, Biosecurity, Drug resistance, veterinary drug, antibiotique, Anti-Infective Agents, Risk Factors, Pharmacology (medical), Veterinary drug, bacteria, Original Research, agriculture, 2. Zero hunger, bactérie, 0303 health sciences, Lincosamides, Microbiota, poultry, Bacteriologie, Bacteriology, Host Pathogen Interaction & Diagnostics, Antimicrobial, usage, médicamentvétérinaire, Europe, Infectious Diseases, farm, Microbiology (medical), Farms, medicine.drug_class, Bioinformatica & Diermodellen, Biology, 03 medical and health sciences, Antibiotic resistance, Drug Resistance, Bacterial, Bio-informatics & Animal models, medicine, Animals, Life Science, Epidemiology, Bio-informatics & Animal models, antimicrobial resistance, microbiologie, 030304 developmental biology, Pharmacology, Host Pathogen Interaction & Diagnostics, Epidemiologie, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, 030306 microbiology, microbiology, Computational Biology, Bacteriology, antimicrobial use, Host Pathogen Interactie & Diagnostiek, Resistome, volaille, Cross-Sectional Studies, feces, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Flock, Metagenomics, antimicrobien, Chickens
Abstract

Objectives To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms. Methods In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored. Results Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity. Conclusions The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes.

Published
2019

43. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Author

Sub RIVM, dIRAS RA-I&I RA, One Health Microbieel, dIRAS RA-I&I I&I, Hendriksen, Rene S., Munk, Patrick, Njage, Patrick, van Bunnik, Bram, McNally, Luke, Lukjancenko, Oksana, Röder, Timo, Nieuwenhuijse, David, Pedersen, Susanne Karlsmose, Kjeldgaard, Jette, Kaas, Rolf S., Clausen, Philip Thomas Lanken Conradsen, Vogt, Josef Korbinian, Leekitcharoenphon, Pimlapas, van de Schans, Milou G.M., Zuidema, Tina, de Roda Husman, Ana Maria, Rasmussen, Simon, Petersen, Bent, Bego, Artan, Rees, Catherine, Cassar, Susan, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Vuthy, Yith, Sopheak, Thet, Yost, Christopher K., Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Jergović, Matijana, Hrenovic, Jasna, Karpíšková, Renáta, Villacis, Jose Eduardo, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, Cormican, Martin, O’Connor, Louise, Moran-Gilad, Jacob, Alba, Patricia, Battisti, Antonio, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Avsejenko, Jeļena, Bērziņš, Aivars, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljevic, Vladimir, Wuertz, Stefan, Zuniga-Montanez, Rogelio, Tay, Moon Y.F., Gavačová, Dagmar, Pastuchova, Katarina, Truska, Peter, Trkov, Marija, Esterhuyse, Kerneels, Keddy, Karen, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Norrgren, Leif, Örn, Stefan, Larsson, D. G.Joakim, Heijden, Tanja Van der, Kumburu, Happiness Houka, Sanneh, Bakary, Bidjada, Pawou, Njanpop-Lafourcade, Berthe Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van, Chinh Dang, Tran, Doan Minh Nguyen, Kwenda, Geoffrey, Tabo, Djim adjim, Wester, Astrid Louise, Cuadros-Orellana, Sara, Amid, Clara, Cochrane, Guy, Sicheritz-Ponten, Thomas, Schmitt, Heike, Alvarez, Jorge Raul Matheu, Aidara-Kane, Awa, Pamp, Sünje J., Lund, Ole, Hald, Tine, Woolhouse, Mark, Koopmans, Marion P., Vigre, Håkan, Petersen, Thomas Nordahl, Aarestrup, Frank M., Sub RIVM, dIRAS RA-I&I RA, One Health Microbieel, dIRAS RA-I&I I&I, Hendriksen, Rene S., Munk, Patrick, Njage, Patrick, van Bunnik, Bram, McNally, Luke, Lukjancenko, Oksana, Röder, Timo, Nieuwenhuijse, David, Pedersen, Susanne Karlsmose, Kjeldgaard, Jette, Kaas, Rolf S., Clausen, Philip Thomas Lanken Conradsen, Vogt, Josef Korbinian, Leekitcharoenphon, Pimlapas, van de Schans, Milou G.M., Zuidema, Tina, de Roda Husman, Ana Maria, Rasmussen, Simon, Petersen, Bent, Bego, Artan, Rees, Catherine, Cassar, Susan, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Vuthy, Yith, Sopheak, Thet, Yost, Christopher K., Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Jergović, Matijana, Hrenovic, Jasna, Karpíšková, Renáta, Villacis, Jose Eduardo, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, Cormican, Martin, O’Connor, Louise, Moran-Gilad, Jacob, Alba, Patricia, Battisti, Antonio, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Avsejenko, Jeļena, Bērziņš, Aivars, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljevic, Vladimir, Wuertz, Stefan, Zuniga-Montanez, Rogelio, Tay, Moon Y.F., Gavačová, Dagmar, Pastuchova, Katarina, Truska, Peter, Trkov, Marija, Esterhuyse, Kerneels, Keddy, Karen, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Norrgren, Leif, Örn, Stefan, Larsson, D. G.Joakim, Heijden, Tanja Van der, Kumburu, Happiness Houka, Sanneh, Bakary, Bidjada, Pawou, Njanpop-Lafourcade, Berthe Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van, Chinh Dang, Tran, Doan Minh Nguyen, Kwenda, Geoffrey, Tabo, Djim adjim, Wester, Astrid Louise, Cuadros-Orellana, Sara, Amid, Clara, Cochrane, Guy, Sicheritz-Ponten, Thomas, Schmitt, Heike, Alvarez, Jorge Raul Matheu, Aidara-Kane, Awa, Pamp, Sünje J., Lund, Ole, Hald, Tine, Woolhouse, Mark, Koopmans, Marion P., Vigre, Håkan, Petersen, Thomas Nordahl, and Aarestrup, Frank M.

Published
2019

44. Cross-Border Transmission of Salmonella Choleraesuis var. Kunzendorf in European Pigs and Wild Boar: Infection, Genetics, and Evolution

Author

Leekitcharoenphon, Pimlapas, Sørensen, Gitte, Lofstrom, Charlotta, Battisti, Antonio, Szabo, Istvan, Wasyl, Dariusz, Slowey, Rosemarie, Zhao, Shaohua, Brisabois, Anne, Kornschober, Christian, Karssin, Age, Szilard, Janosi, Cerny, Tomas, Svendsen, Christina Aaby, Pedersen, Karl, Aarestrup, Frank Møller, Hendriksen, Rene S., Leekitcharoenphon, Pimlapas, Sørensen, Gitte, Lofstrom, Charlotta, Battisti, Antonio, Szabo, Istvan, Wasyl, Dariusz, Slowey, Rosemarie, Zhao, Shaohua, Brisabois, Anne, Kornschober, Christian, Karssin, Age, Szilard, Janosi, Cerny, Tomas, Svendsen, Christina Aaby, Pedersen, Karl, Aarestrup, Frank Møller, and Hendriksen, Rene S.

Abstract

Salmonella enterica subspecies enterica serotype Choleraesuis is a swine adapted serovar. S. Choleraesuis variant Kunzendorf is responsible for the majority of outbreaks among pigs. S. Choleraesuis is rare in Europe, although there have been serious outbreaks in pigs including two outbreaks in Denmark in 1999-2000 and 2012-2013. Here, we elucidate the epidemiology, possible transmission routes and sources, and clonality of European S. Choleraesuis isolates including the Danish outbreak isolates. A total of 102 S. Choleraesuis isolates from different European countries and the United States, covering available isolates from the last two decades were selected for whole genome sequencing. We applied a temporally structured sequence analysis within a Bayesian framework to reconstruct a temporal and spatial phylogenetic tree. MLST type, resistance genes, plasmid replicons, and accessory genes were identified using bioinformatics tools. Fifty-eight isolates including 11 out of 12 strains from wild boars were pan-susceptible. The remaining isolates carried multiple resistance genes. Eleven different plasmid replicons in eight plasmids were determined among the isolates. Accessory genes were associated to the identified resistance genes and plasmids. The European S. Choleraesuis was estimated to have emerged in ∼ 1837 (95% credible interval, 1733-1983) with the mutation rate of 1.02 SNPs/genome/year. The isolates were clustered according to countries and neighbor countries. There were transmission events between strains from the United States and European countries. Wild boar and pig isolates were genetically linked suggesting cross-border transmission and transmission due to a wildlife reservoir. The phylogenetic tree shows that multiple introductions were responsible for the outbreak of 2012-2013 in Denmark, and suggests that poorly disinfected vehicles crossing the border into Denmark were potentially the source of the outbreak. Low levels of single nucleotide polymorphi

Published
2019

45. Community-acquired methicillin-resistant Staphylococcus aureus ST398 infection, Italy

Author

Pan, Angelo, Battisti, Antonio, Zoncada, Alessia, Bernieri, Francesco, Boldini, Massimo, Franco, Alessia, Giorgi, Maurilio, Iurescia, Manuela, Lorenzotti, Silvia, Martinotti, Mario, Monaco, Monica, and Pantosti, Annalisa

Subjects
Staphylococcus aureus -- Health aspects, Pork industry -- Health aspects
Abstract

To the Editor: Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has been identified in livestock animals (particularly pigs), veterinarians, and animal farm workers (1,2). CA-MRSA strains from pigs have been classified most [...]

Published
2009

46. Erratum to: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries (Nature Microbiology, (2018), 3, 8, (898-908), 10.1038/s41564-018-0192-9)

Author

Munk, Patrick, Knudsen, Berith Elkær, Lukjancenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., dIRAS RA-I&I I&I, One Health Microbieel, dIRAS RA-I&I RA, Dep IRAS, dI&I I&I-4, and LS Klinisch Onderzoek Wagenaar

Subjects
Coronacrisis-Taverne
Abstract

In the version of this Article originally published, the surname of author Oksana Lukjancenko was spelt incorrectly as ‘Lukjacenko’. This has now been corrected.

Published
2018

47. Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes

Author

Rebelo, Ana Rita, Bortolaia, Valeria, Kjeldgaard, Jette S., Karlsmose Pedersen, Susanne, Leekitcharoenphon, Pimlapas, Hansen, Inge M., Guerra, Beatriz, Malorny, Burkhard, Borowiak, Maria, Hammerl, Jens Andre, Battisti, Antonio, Franco, Alessia, Alba, Patricia, Perrin-Guyomard, Agnes, Granier, Sophie A., de Frutos, Cristina, Escobar, Malhotra-Kumar, Surbhi, Villa, Laura, Carattoli, Alessandra, Hendriksen, Rene S., Technical University of Denmark [Lyngby] (DTU), European Food Safety Authority = Autorité européenne de sécurité des aliments, Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT), Laboratoire de Fougères, Bâtiment Bioagropolis, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Laboratorio Central de Veterinaria (LCV Algete), University of Antwerp (UA), Istituto Superiore di Sanità [Rome, Italy], European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR), WHO Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR), and WHO Global Antimicrobial Resistance Surveillance System (GLASS)

Subjects
0301 basic medicine, antibiotic resistance, Epidemiology, polymerase chain reaction, [SDV]Life Sciences [q-bio], Colistin resistance, Transferases (Other Substituted Phosphate Groups), résistance aux antibiotiques, law.invention, Plasmid, law, Salmonella, mcr, Multiplex, colistin, Colistine, Polymerase chain reaction, Surveillance, Colistin, antiinfective agent, Escherichia coli protein, MCR-1 protein, E coli, mcr-2 protein, E coli, MCR-3 protein, E coli, MCR-4 protein, E coli, MCR-5 protein, E coli, membrane protein, phosphotransferase, amplicon, Article, bacterial gene, bacterium isolate, calf (bovine), controlled study, Escherichia coli, France, gene amplification, gene identification, genetic variability, Germany, Italy, mcr 1 gene, mcr 2 gene, mcr 3 gene, mcr 4 gene, mcr 5 gene, minimum inhibitory concentration, multiplex polymerase chain reaction, nonhuman, pig, plasmid, process development, Salmonella enterica serovar Paratyphi B, Spain, whole genome sequencing, drug effect, Enterobacteriaceae, Enterobacteriaceae infection, genetics, human, isolation and purification, metabolism, microbial sensitivity test, microbiology, plasmid, Anti-Bacterial Agents, Enterobacteriaceae Infections, Escherichia coli Proteins, Humans, Membrane Proteins, Microbial Sensitivity Tests, Multiplex Polymerase Chain Reaction, Plasmids, transferable resistance, Amplicon, Surveillance systems, 3. Good health, Anti-Bacterial Agents, PCR, sécurité alimentaire, Erratum, hormones, hormone substitutes, and hormone antagonists, medicine.drug, Research Article, 030106 microbiology, Computational biology, Biology, 03 medical and health sciences, Virology, Multiplex polymerase chain reaction, polymyxin E, medicine, Polymerase Chain Reaction PCR, antimicrobial resistance, Whole genome sequencing, Public Health, Environmental and Occupational Health, multiplex, MCR-1, Human medicine, mcr-4.3
Abstract

Background and aim Plasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.6**, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing.

Published
2018

48. DS1_JVDI_10.1177_1040638718764786 – Supplemental material for Non-toxigenic Corynebacterium ulcerans sequence types 325 and 339 isolated from two dogs with ulcerative lesions in Italy

Author

Carfora, Virginia, Scarampella, Fabia, Iurescia, Manuela, Donati, Valentina, Stravino, Fiorentino, Lorenzetti, Serena, Menichini, Erika, Franco, Alessia, Caprioli, Andrea, and Battisti, Antonio

Subjects
70706 Veterinary Medicine, FOS: Clinical medicine, FOS: Veterinary sciences, 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
Abstract

Supplemental material, DS1_JVDI_10.1177_1040638718764786 for Non-toxigenic Corynebacterium ulcerans sequence types 325 and 339 isolated from two dogs with ulcerative lesions in Italy by Virginia Carfora, Fabia Scarampella, Manuela Iurescia, Valentina Donati, Fiorentino Stravino, Serena Lorenzetti, Erika Menichini, Alessia Franco, Andrea Caprioli, Antonio Battisti in Journal of Veterinary Diagnostic Investigation

Published
2018
Full Text
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50. Death of captive-bred vultures caused by flunixin poisoning in Italy

Author

Eleni, Claudia, primary, Neri, Bruno, additional, Giannetti, Luigi, additional, Grifoni, Goffredo, additional, Meoli, Roberta, additional, Stravino, Fiorentino, additional, Friedrich, Klaus Gunther, additional, Scholl, Francesco, additional, Di Cerbo, Pilar, additional, and Battisti, Antonio, additional

Published
2019
Full Text
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