@misc{BuchananLewisParisetal., author = {Buchanan, Erin M. and Lewis, Savannah C. and Paris, Bastien and Forscher, Patrick S. and Pavlacic, Jeffrey M. and Beshears, Julie E. and Drexler, Shira Meir and Gourdon-Kanhukamwe, Am{\´e}lie and Mallik, Peter R and Silan, Miguel Alejandro A. and Miller, Jeremy K. and IJzerman, Hans and Moshontz, Hannah and Beaudry, Jennifer L. and Suchow, Jordan W. and Chartier, Christopher R. and Coles, Nicholas A. and Sharifian, MohammadHasan and Todsen, Anna Louise and Levitan, Carmel A. and Azevedo, Fl{\´a}vio and Legate, Nicole and Heller, Blake and Rothman, Alexander J. and Dorison, Charles A. and Gill, Brian P. and Wang, Ke and Rees, Vaughan W. and Gibbs, Nancy and Goldenberg, Amit and Thi Nguyen, Thuy-vy and Gross, James J. and Kaminski, Gwena{\^e}l and von Bastian, Claudia C. and Paruzel-Czachura, Mariola and Mosannenzadeh, Farnaz and Azouaghe, Soufian and Bran, Alexandre and Ruiz-Fernandez, Susana and Santos, Anabela Caetano and Reggev, Niv and Zickfeld, Janis H. and Akkas, Handan and Pantazi, Myrto and Ropovik, Ivan and Korbmacher, Max and Arriaga, Patr{\´i}cia and Gjoneska, Biljana and Warmelink, Lara and Alves, Sara G. and de Holanda Coelho, Gabriel Lins and Stieger, Stefan and Schei, Vidar and Hanel, Paul H. P. and Szaszi, Barnabas and Fedotov, Maksim and Antfolk, Jan and Marcu, Gabriela-Mariana and Schr{\"o}tter, Jana and Kunst, Jonas R. and Geiger, Sandra J. and Adetula, Adeyemi and Kocalar, Halil Emre and Kielińska, Julita and Kačm{\´a}r, Pavol and Bokkour, Ahmed and Galindo-Caballero, Oscar J. and Djamai, Ikhlas and P{\"o}ntinen, Sara Johanna and AGESIN, Bamikole Emmanuel and Jerns{\"a}ther, Teodor and Urooj, Anum and Rachev, Nikolay R. and Koptjevskaja-Tamm, Maria and Kurfal{\i}, Murathan and Pit, Ilse L. and Li, Ranran and {\c{C}}oksan, Sami and Dubrov, Dmitrii and Paltrow, Tamar Elise and Ban{\´i}k, Gabriel and Korobova, Tatiana and Studzinska, Anna and Jiang, Xiaoming and Aruta, John Jamir Benzon R. and Vintr, J{\´a}chym and Chiu, Faith and Kaliska, Lada and Berkessel, Jana B. and T{\"u}mer, Murat and Morales-Izquierdo, Sara and Chuan-Peng, Hu and Vezirian, Kevin and Rosa, Anna Dalla and Bialobrzeska, Olga and Vasilev, Martin R. and Beitner, Julia and K{\´a}cha, Ondřej and Žuro, Barbara and Westerlund, Minja and Nedelcheva-Datsova, Mina and Findor, Andrej and Krupić, Dajana and Kowal, Marta and Askelund, Adrian Dahl and Pourafshari, Razieh and Đorđević, Jasna Milošević and Schmidt, Nadya-Daniela and Baklanova, Ekaterina and Szala, Anna and Zakharov, Ilya and Vranka, Marek A. and Ihaya, Keiko and Grano, Caterina and Cellini, Nicola and Białek, Michał and Anton-Boicuk, Lisa and Dalgar, Ilker and Ad{\i}g{\"u}zel, Arca and Verharen, Jeroen P. H. and Maturan, Princess Lovella G. and Kassianos, Angelos P. and Oliveira, Raquel and Čadek, Martin and Adoric, Vera Cubela and {\"O}zdoğru, Asil Ali and Sverdrup, Therese E. and Aczel, Balazs and Zambrano, Danilo and Ahmed, Afroja and Tamnes, Christian K. and Yamada, Yuki and Volz, Leonhard and Sunami, Naoyuki and Suter, Lilian and Vieira, Luc and Groyecka-Bernard, Agata and Kamburidis, Julia Arhondis and Reips, Ulf-Dietrich and Harutyunyan, Mikayel and Adetula, Gabriel Agboola and Allred, Tara Bulut and Barzykowski, Krystian and Antazo, Benedict G and Zsido, Andras N. and Šakan, Dušana Dušan and Cyrus-Lai, Wilson and Ahlgren, Lina Pernilla and Hruška, Matej and Vega, Diego and Manunta, Efisio and Mokady, Aviv and Capizzi, Mariagrazia and Martončik, Marcel and Say, Nicolas and Filip, Katarzyna and Vilar, Roosevelt and Staniaszek, Karolina and Vdovic, Milica and Adamkovic, Matus and Johannes, Niklas and Hajdu, Nandor and Cohen, Noga and Overkott, Clara and Krupić, Dino and Hubena, Barbora and Nilsonne, Gustav and Mioni, Giovanna and Solorzano, Claudio Singh and Ishii, Tatsunori and Chen, Zhang and Kushnir, Elizaveta and Karaarslan, Cemre and Ribeiro, Rafael R. and Khaoudi, Ahmed and Kossowska, Małgorzata and Bavolar, Jozef and Hoyer, Karlijn and Roczniewska, Marta and Karababa, Alper and Becker, Maja and Monteiro, Renan P. and Kunisato, Yoshihiko and Metin-Orta, Irem and Adamus, Sylwia and Kozma, Luca and Czarnek, Gabriela and Domurat, Artur and Štrukelj, Eva and Alvarez, Daniela Serrato and Parzuchowski, Michal and Massoni, S{\´e}bastien and Czamanski-Cohen, Johanna and Pronizius, Ekaterina and Muchembled, Fany and van Schie, Kevin and Sa{\c{c}}akl{\i}, Asl{\i} and Hristova, Evgeniya and Kuzminska, Anna O. and Charyate, Abdelilah and Bijlstra, Gijsbert and Afhami, Reza and Majeed, Nadyanna M. and Musser, Erica D. and Sirota, Miroslav and Ross, Robert M. and Yeung, Siu Kit and Papadatou-Pastou, Marietta and Foroni, Francesco and Almeida, In{\^e}s A. T. and Grigoryev, Dmitry and Lewis, David M. G. and Holford, Dawn L. and Janssen, Steve M. J. and Tatachari, Srinivasan and Batres, Carlota and Olofsson, Jonas K. and Daches, Shimrit and Belaus, Anabel and Pfuhl, Gerit and Corral-Frias, Nadia Sarai and Sousa, Daniela and R{\"o}er, Jan Philipp and Isager, Peder Mortvedt and Godbersen, Hendrik and Walczak, Radoslaw B. and Van Doren, Natalia and Ren, Dongning and Gill, Tripat and Voracek, Martin and DeBruine, Lisa M. and Anne, Michele and Očovaj, Sanja Batić and Thomas, Andrew G. and Arvanitis, Alexios and Ostermann, Thomas and Wolfe, Kelly and Arinze, Nwadiogo Chisom and Bundt, Carsten and Lamm, Claus and Calin-Jageman, Robert J and Davis, William E. and Karekla, Maria and Zorjan, Saša and Jaremka, Lisa M. and Uttley, Jim and Hricova, Monika and Koehn, Monica A and Kiselnikova, Natalia and Bai, Hui and Krafnick, Anthony J. and Balci, Busra Bahar and Ballantyne, Tonia and Lins, Samuel and Vally, Zahir and Esteban-Serna, Celia and Schmidt, Kathleen and Macapagal, Paulo Manuel L. and Szwed, Paulina and Zdybek, Przemysław Marcin and Moreau, David and Collins, W. Matthew and Joy-Gaba, Jennifer A. and Vilares, Iris and Tran, Ulrich S. and Boudesseul, Jordane and Albayrak-Aydemir, Nihan and Dixson, Barnaby James Wyld and Perillo, Jennifer T and Ferreira, Ana and Westgate, Erin C. and Aberson, Christopher L. and Arinze, Azuka Ikechukwu and Jaeger, Bastian and Butt, Muhammad Mussaffa and Silva, Jaime R. and Storage, Daniel Shafik and Janak, Allison P and Jim{\´e}nez-Leal, William and Soto, Jose A. and Sorokowska, Agnieszka and McCarthy, Randy and Tullett, Alexa M and Frias-Armenta, Martha and Ribeiro, Matheus Fernando Felix and Hartanto, Andree and Forbes, Paul A. G. and Willis, Megan L. and del Carmen Tejada R, Mar{\´i}a and Torres, Adriana Julieth Olaya and Stephen, Ian D and Vaidis, David C. and de la Rosa-G{\´o}mez, Anabel and Yu, Karen and Sutherland, Clare A. M. and Manavalan, Mathi and Behzadnia, Behzad and Urban, Jan and Baskin, Ernest and McFall, Joseph P. and Ogbonnaya, Chisom Esther and Fu, Cynthia H. Y. and Rahal, Rima-Maria and Ndukaihe, Izuchukwu L. G. and Hostler, Thomas J. and Kappes, Heather Barry and Sorokowski, Piotr and Khosla, Meetu and Lazarevic, Ljiljana B. and Eudave, Luis and Vilsmeier, Johannes K. and Luis, Elkin O. and Muda, Rafał and Agadullina, Elena and C{\´a}rcamo, Rodrigo A. and Reeck, Crystal and Anjum, Gulnaz and Venegas, M{\´o}nica Camila Toro and Misiak, Michal and Ryan, Richard M. and Nock, Nora L. and Travaglino, Giovanni A. and Mensink, Michael C. and Feldman, Gilad and Wichman, Aaron L. and Chou, Weilun and Ziano, Ignazio and Seehuus, Martin and Chopik, William J. and Kung, Franki Y. H. and Carpentier, Joelle and Vaughn, Leigh Ann and Du, Hongfei and Xiao, Qinyu and Lima, Tiago J. S. and Noone, Chris and Onie, Sandersan and Verbruggen, Frederick and Radtke, Theda and Primbs, Maximilian A.}, title = {The psychological science accelerator's COVID-19 rapid-response dataset}, series = {Scientific Data}, volume = {10}, journal = {Scientific Data}, number = {1}, publisher = {Springer Science and Business Media LLC}, issn = {2052-4463}, doi = {10.1038/s41597-022-01811-7}, pages = {1 -- 15}, language = {en} } @misc{FroemmelLehmannRoedigeretal., author = {Fr{\"o}mmel, Ulrike and Lehmann, Werner and R{\"o}diger, Stefan and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Weinreich, J{\"o}rg and Groß, Julia and Roggenbuck, Dirk and Zinke, Olaf and Ansorge, Hermann and Vogel, Steffen and Klemm, Per and Wex, Thomas and Schr{\"o}der, Christian and Wieler, Lothar H. and Schierack, Peter}, title = {Adhesion of human and animal Escherichia coli strains in association with their virulence-associated genes and phylogenetic origins}, series = {Applied and environmental microbiology}, volume = {79}, journal = {Applied and environmental microbiology}, number = {19}, issn = {1098-5336}, doi = {10.1128/AEM.01384-13}, pages = {5814 -- 5829}, abstract = {Intestinal colonization is influenced by the ability of the bacterium to inhabit a niche, which is based on the expression of colonization factors. Escherichia coli carries a broad range of virulence-associated genes (VAGs) which contribute to intestinal (inVAGs) and extraintestinal (exVAGs) infection. Moreover, initial evidence indicates that inVAGs and exVAGs support intestinal colonization. We developed new screening tools to genotypically and phenotypically characterize E. coli isolates originating in humans, domestic pigs, and 17 wild mammal and avian species. We analyzed 317 isolates for the occurrence of 44 VAGs using a novel multiplex PCR microbead assay (MPMA) and for adhesion to four epithelial cell lines using a new adhesion assay. We correlated data for the definition of new adhesion genes. inVAGs were identified only sporadically, particularly in roe deer (Capreolus capreolus) and the European hedgehog ( Erinaceus europaeus). The prevalence of exVAGs depended on isolation from a specific host. Human uropathogenic E. coli isolates carried exVAGs with the highest prevalence, followed by badger (Meles meles) and roe deer isolates. Adhesion was found to be very diverse. Adhesion was specific to cells, host, and tissue, though it was also unspecific. Occurrence of the following VAGs was associated with a higher rate of adhesion to one or more cell lines: afa-dra, daaD, tsh, vat, ibeA, fyuA, mat, sfa-foc, malX, pic, irp2, and papC. In summary, we established new screening methods which enabled us to characterize large numbers of E. coli isolates. We defined reservoirs for potential pathogenic E. coli. We also identified a very broad range of colonization strategies and defined potential new adhesion genes.}, language = {en} } @misc{FroemmelBoehmNitschkeetal., author = {Fr{\"o}mmel, Ulrike and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Weinreich, J{\"o}rg and Groß, Julia and R{\"o}diger, Stefan and Wex, Thomas and Ansorge, Hermann and Zinke, Olaf and Schr{\"o}der, Christian and Roggenbuck, Dirk and Schierack, Peter}, title = {Adhesion patterns of commensal and pathogenic Escherichia coli from humans and wild animals on human and porcine epithelial cell lines}, series = {Gut Pathogens}, volume = {5}, journal = {Gut Pathogens}, number = {31}, issn = {1757-4749}, doi = {10.1186/1757-4749-5-31}, pages = {8}, abstract = {Abstract BACKGROUND: Different strategies of colonization or infection by E. coli result in formation of certain adhesion patterns which help also in classifying intestinal E. coli into pathotypes. Little is known about adhesion patterns and host- and tissue adaption of commensal E. coli and about E. coli originating in clinically healthy hosts carrying pathotype-specific virulence-associated genes. FINDINGS: Adhesion pattern of E. coli (n = 282) from humans and from 18 animal species were verified on intestinal human Caco-2 and porcine IPEC-J2 cells and, furthermore, for comparison on human urinary bladder 5637, porcine kidney PK-15 epithelial and HEp-2 cells. The analysis was carried out on 150,000 images of adhesion assays.Adhesion patterns were very diverse; 88 isolates were completely non-adherent, whereas 194 adhered to at least one cell line with the dominant adhesion patterns "diffusely distributed" and "microcolony formation". Adhesion patterns "chains" and "clumps" were also visible. Chain formation was mediated by the presence of epithelial cells. Clump formation was very specific on only the 5637 cell line. All enteropathogenic (eae+) E. coli (EPEC; n = 14) were able to form microcolonies which was cell line specific for each isolate. Most EPEC formed microcolonies on intestinal IPEC-J2 and Caco-2 but several also on urinary tract cells. Shigatoxin-producing (stx+) E. coli (n = 10) showed no specific adhesion patterns. CONCLUSIONS: E. coli isolates were highly diverse. Commensal and pathogenic isolates can adhere in various forms, including diffuse distribution, microcolonies, chains and clumps. Microcolony formation seems to be a global adhesion strategy also for commensal E. coli.}, language = {en} }