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14. Antibiotic Resistance in the Environment: Expert Perspectives

Author

Manaia, Célia M., Graham, David, Topp, Edward, Martinez, José Luis, Collignon, Peter, Gaze, William H., Barceló, Damià, Series Editor, de Boer, Jacob, Editorial Board Member, Kostianoy, Andrey G., Series Editor, Garrigues, Philippe, Editorial Board Member, Hutzinger, Otto, Founding Editor, Gu, Ji-Dong, Editorial Board Member, Jones, Kevin C., Editorial Board Member, Knepper, Thomas P., Editorial Board Member, Negm, Abdelazim M., Editorial Board Member, Newton, Alice, Editorial Board Member, Nghiem, Duc Long, Editorial Board Member, Garcia-Segura, Sergi, Editorial Board Member, Manaia, Célia M., editor, Donner, Erica, editor, Vaz-Moreira, Ivone, editor, and Hong, Peiying, editor

Published
2020
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16. A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

Author

Marano, Roberto B.M., Fernandes, Telma, Manaia, Célia M., Nunes, Olga, Morrison, Donald, Berendonk, Thomas U., Kreuzinger, Norbert, Tenson, Tanel, Corno, Gianluca, Fatta-Kassinos, Despo, Merlin, Christophe, Topp, Edward, Jurkevitch, Edouard, Henn, Leonie, Scott, Andrew, Heß, Stefanie, Slipko, Katarzyna, Laht, Mailis, Kisand, Veljo, Di Cesare, Andrea, Karaolia, Popi, Michael, Stella G., Petre, Alice L., Rosal, Roberto, Pruden, Amy, Riquelme, Virginia, Agüera, Ana, Esteban, Belen, Luczkiewicz, Aneta, Kalinowska, Agnieszka, Leonard, Anne, Gaze, William H., Adegoke, Anthony A., Stenstrom, Thor A., Pollice, Alfieri, Salerno, Carlo, Schwermer, Carsten U., Krzeminski, Pawel, Guilloteau, Hélène, Donner, Erica, Drigo, Barbara, Libralato, Giovanni, Guida, Marco, Bürgmann, Helmut, Beck, Karin, Garelick, Hemda, Tacão, Marta, Henriques, Isabel, Martínez-Alcalá, Isabel, Guillén-Navarro, Jose M., Popowska, Magdalena, Piotrowska, Marta, Quintela-Baluja, Marcos, Bunce, Joshua T., Polo-López, Maria I., Nahim–Granados, Samira, Pons, Marie-Noëlle, Milakovic, Milena, Udikovic-Kolic, Nikolina, Ory, Jérôme, Ousmane, Traore, Caballero, Pilar, Oliver, Antoni, Rodriguez-Mozaz, Sara, Balcazar, Jose L., Jäger, Thomas, Schwartz, Thomas, Yang, Ying, Zou, Shichun, Lee, Yunho, Yoon, Younggun, Herzog, Bastian, Mayrhofer, Heidrun, Prakash, Om, Nimonkar, Yogesh, Heath, Ester, Baraniak, Anna, Abreu-Silva, Joana, Choudhury, Manika, Munoz, Leonardo P., Krizanovic, Stela, Brunetti, Gianluca, Maile-Moskowitz, Ayella, Brown, Connor, and Cytryn, Eddie

Published
2020
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23. 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., and Wernersson, Ann-Sofie

Published
2018
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30. The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.

Author

Manaia, Célia M., Aga, Diana S., Cytryn, Eddie, Gaze, William H., Graham, David W., Guo, Jianhua, Leonard, Anne F. C., Li, Liguan, Murray, Aimee K., Nunes, Olga C., Rodriguez‐Mozaz, Sara, Topp, Edward, and Zhang, Tong

Subjects
DRUG resistance in bacteria, HYGIENE products, HEALTH risk assessment, HORIZONTAL gene transfer, POLLUTANTS
Abstract

Antibiotic‐resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human‐impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self‐replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co‐occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man‐made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2024;43:637–652. © 2022 SETAC [ABSTRACT FROM AUTHOR]

Published
2024
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33. Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Author

Yin, Xiaole, Chen, Xi, Jiang, Xiao-Tao, Yang, Ying, Li, Bing, Shum, Marcus Ho-Hin, Lam, Tommy T Y, Leung, Gabriel M, Rose, Joan, Sanchez-Cid, Concepcion, Vogel, Timothy M, Walsh, Fiona, Berendonk, Thomas U, Midega, Janet, Uchea, Chibuzor, Frigon, Dominic, Wright, Gerard D, Bezuidenhout, Carlos, Picão, Renata C, Ahammad, Shaikh Z, Nielsen, Per Halkjær, Hugenholtz, Philip, Ashbolt, Nicholas J, Corno, Gianluca, Fatta-Kassinos, Despo, Bürgmann, Helmut, Schmitt, Heike, Cha, Chang-Jun, Pruden, Amy, Smalla, Kornelia, Cytryn, Eddie, Zhang, Yu, Yang, Min, Zhu, Yong-Guan, Dechesne, Arnaud, Smets, Barth F, Graham, David W, Gillings, Michael R, Gaze, William H, Manaia, Célia M, van Loosdrecht, Mark C M, Alvarez, Pedro J J, Blaser, Martin J, Tiedje, James M, Topp, Edward, and Zhang, Tong

Subjects
standardization, metagenomics, one-health, long-read sequencing, ARG copy per cell
Published
2023

35. Assessing the Impact of Recreational Water Use on Carriage of Antimicrobial Resistant Organisms

Author

Farrell, Maeve Louise, primary, Chueiri, Alexandra, additional, O' Connor, Louise, additional, Duane, Sinead, additional, Maguire, Mark, additional, Miliotis, Georgios, additional, Cormican, Martin, additional, Hooban, Brigid, additional, Leonard, Anne, additional, Gaze, William H., additional, Devane, Genevieve, additional, Tuohy, Alma, additional, Burke, Liam P., additional, and Morris, Dearbháile, additional

Published
2023
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36. 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
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37. The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment

Author

Manaia, Célia M., primary, Aga, Diana S., additional, Cytryn, Eddie, additional, Gaze, William H, additional, Graham, David W., additional, Guo, Jianhua, additional, Leonard, Anne F. C., additional, Liguan, Li, additional, Murray, Aimee K, additional, Nunes, Olga C., additional, Rodriguez‐Mozaz, Sara, additional, Topp, Edward, additional, and Zhang, Tong, additional

Published
2022
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46. Additional file 1 of Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level

Author

Wang, Yue, Yu, Zhigang, Ding, Pengbo, Lu, Ji, Klümper, Uli, Murray, Aimee K., Gaze, William H., and Guo, Jianhua

Abstract

Additional file 1: Text S1. Stability of RP4 plasmid. Text S2. Effect of antibiotic chloramphenicol (Chl) on conjugative transfer. Text S3. ROS production in the mixed culture. Figure S1. Plasmid stability in bacterial cells. a, Set-up of plasmid stability assays over 5 days. In each cycle, 1% of cultures were grown in fresh LB medium. b, Dynamic analysis of plasmid stability in LB media. Figure S2. FACS sorting of transconjugant cells from a mixture initiated with activated sludge and P. putida KT2440 carrying gfp-RP4 plasmid. Gate I sorts for bacterial size based on forward-H and side scatter-H; Gate II sorts for singlet based on forward-H and forward-W; and Gate III selects only those green cells (left corner) [1]. Panel (a) shows the results from the donor, panel (b) shows the results from positive control (green transconjugants), while panel (c) shows the results from activated sludge. Figure S3. Fold change in conjugative transfer of plasmid-borne antibiotic resistance in activated sludge bacteria under exposure to antibiotic Chl (N = 6). Significant differences between carbamazepine-treated groups and the control groups were analyzed by Independent-sample t test and the Bonferroni correction, * P < 0.05 and ** P < 0.01. Figure S4. Fold changes in ROS production in the mixed culture (the donor and activated sludge) under exposure to carbamazepine. Significant differences between the control and the treated groups were tested with Independent-sample t test and the Bonferroni correction, * P < 0.05 and ** P < 0.01.

Published
2022
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47. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

Author

Sheridan, Paul O., Raguideau, Sebastien, Quince, Christopher, Holden, Jennifer, Zhang, Lihong, Gaze, William H., Mead, Andrew, Singer, Andrew C., Wellington, Elizabeth M.H., Williams, Tom A., Gubry-Rangin, Cécile, Thames Consortium, Gaze, William H., Holden, Jennifer, Mead, Andrew, Raguideau, Sébastien, Quince, Christopher, Singer, Andrew C., Wellington, Elizabeth M. H., and Zhang, Lihong

Subjects
0301 basic medicine, Genome evolution, Thaumarchaeota, Carbohydrate transport, Gene Transfer, Horizontal, Proteome, Science, Lineage (evolution), 030106 microbiology, General Physics and Astronomy, Genome, General Biochemistry, Genetics and Molecular Biology, Article, Evolution, Molecular, 03 medical and health sciences, Genome, Archaeal, Gene Duplication, Gene duplication, Gene family, lcsh:Science, Gene, Ecosystem, Phylogeny, Multidisciplinary, biology, Archaeal genomics, QH, General Chemistry, biology.organism_classification, Archaea, QR, Phylogenetics, 030104 developmental biology, Biology and Microbiology, Evolutionary biology, lcsh:Q, Metagenomics
Abstract

Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea., Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle. Using 12 new genomes, this study finds evidence that Nitrososphaerales evolution was marked by lateral gene transfer followed by gene duplication.

Published
2020
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50. Human Health and Ocean Pollution

Author

Landrigan, Philip J., primary, Stegeman, John J., additional, Fleming, Lora E., additional, Allemand, Denis, additional, Anderson, Donald M., additional, Backer, Lorraine C., additional, Brucker-Davis, Françoise, additional, Chevalier, Nicolas, additional, Corra, Lilian, additional, Czerucka, Dorota, additional, Bottein, Marie-Yasmine Dechraoui, additional, Demeneix, Barbara, additional, Depledge, Michael, additional, Deheyn, Dimitri D., additional, Dorman, Charles J., additional, Fénichel, Patrick, additional, Fisher, Samantha, additional, Gaill, Françoise, additional, Galgani, François, additional, Gaze, William H., additional, Giuliano, Laura, additional, Grandjean, Philippe, additional, Hahn, Mark E., additional, Hamdoun, Amro, additional, Hess, Philipp, additional, Judson, Bret, additional, Laborde, Amalia, additional, McGlade, Jacqueline, additional, Mu, Jenna, additional, Mustapha, Adetoun, additional, Neira, Maria, additional, Noble, Rachel T., additional, Pedrotti, Maria Luiza, additional, Reddy, Christopher, additional, Rocklöv, Joacim, additional, Scharler, Ursula M., additional, Shanmugam, Hariharan, additional, Taghian, Gabriella, additional, Van de Water, Jeroen A. J. M., additional, Vezzulli, Luigi, additional, Weihe, Pál, additional, Zeka, Ariana, additional, Raps, Hervé, additional, and Rampal, Patrick, additional

Published
2020
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