Publications from the Genomic Epidemiology Research Group

Absence of N-Acetylglucosamine Glycosylation on Listeria monocytogenes Wall Teichoic Acids Promotes Fatty Acid Tolerance by Repulsion From the Bacterial Surface

Thomasen, Rikke S. S. ; dos Santos, Patricia T. ; Lillebæk, Eva M. Sternkopf ; Skov, Marianne N. ; Kemp, Michael ; Kallipolitis, Birgitte H.
in: Frontiers in Microbiology, vol: 13

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.3389/fmicb.2022.897682

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome

Martiny, Hannah-Marie ; Munk, Patrick ; Brinch, Christian ; Aarestrup, Frank M. ; Petersen, Thomas N.
in: PLOS Biology, vol: 20, issue: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1371/journal.pbio.3001792

A European multicenter evaluation study to investigate the performance on commercially available selective agar plates for the detection of carbapenemase producing Enterobacteriaceae

, ; Dierikx, Cindy ; Börjesson, Stefan ; Perrin-Guyomard, Agnès ; Haenni, Marisa ; Norström, Madelaine ; Divon, Hege H. ; Ilag, Hanna Karin ; Granier, Sophie A. ; Hammerum, Annette ; Kjeldgaard, Jette Sejer ; Pauly, Natalie ; Randall, Luke ; Anjum, Muna F. ; Smialowska, Aleksandra ; Franco, Alessia ; Veldman, Kees ; Slettemeås, Jannice Schau
in: Journal of Microbiological Methods, vol: 193

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1016/j.mimet.2022.106418

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

Teseo, S. ; Otani, S. ; Brinch, C. ; Leroy, S. ; Ruiz, P. ; Desvaux, M. ; Forano, E. ; Aarestrup, F. M. ; Sapountzis, P.
in: Microbiome, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1186/s40168-022-01357-1

Assessing Campylobacter cross-contamination of Danish broiler flocks at slaughterhouses considering true flock prevalence estimates and ad-hoc sampling

Foddai, Alessandro ; Takeuchi-Storm, Nao ; Høg, Birgitte Borck ; Kjeldgaard, Jette Sejer ; Andersen, Jens Kirk ; Ellis-Iversen, Johanne
in: Microbial Risk Analysis, vol: 21

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1016/j.mran.2022.100214

Can Machine Learning Models Predict Asparaginase-associated Pancreatitis in Childhood Acute Lymphoblastic Leukemia

Nielsen, Rikke L. ; Wolthers, Benjamin O. ; Helenius, Marianne ; Albertsen, Birgitte K. ; Clemmensen, Line ; Nielsen, Kasper ; Kanerva, Jukka ; Niinimäki, Riitta ; Frandsen, Thomas L. ; Attarbaschi, Andishe ; Barzilai, Shlomit ; Colombini, Antonella ; Escherich, Gabriele ; Aytan-Aktug, Derya ; Liu, Hsi-Che ; Möricke, Anja ; Samarasinghe, Sujith ; van der Sluis, Inge M. ; Stanulla, Martin ; Tulstrup, Morten ; Yadav, Rachita ; Zapotocka, Ester ; Schmiegelow, Kjeld ; Gupta, Ramneek
in: Journal of Pediatric Hematology/Oncology, vol: 44, issue: 3, pages: e628-e636

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1097/MPH.0000000000002292

Clonal and plasmid-mediated flow of ESBL/AmpC genes in Escherichia coli in a commercial laying hen farm

Aldea, Irene ; Gibello, Alicia ; Hernández, Marta ; Leekitcharoenphon, Pimlapas ; Bortolaia, Valeria ; Moreno, Miguel A.
in: Veterinary Microbiology, vol: 270

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1016/j.vetmic.2022.109453

Critical Assessment of Metagenome Interpretation

Meyer, Fernando ; Fritz, Adrian ; Deng, Zhi-Luo ; Koslicki, David ; Lesker, Till Robin ; Gurevich, Alexey ; Robertson, Gary ; Alser, Mohammed ; Antipov, Dmitry ; Beghini, Francesco ; Bertrand, Denis ; Brito, Jaqueline J. ; Brown, C. Titus ; Buchmann, Jan ; Buluç, Aydin ; Chen, Bo ; Chikhi, Rayan ; Clausen, Philip T.L.C. ; Cristian, Alexandru ; Dabrowski, Piotr Wojciech ; Darling, Aaron E. ; Egan, Rob ; Eskin, Eleazar ; Georganas, Evangelos ; Goltsman, Eugene ; Gray, Melissa A. ; Hansen, Lars Hestbjerg ; Hofmeyr, Steven ; Huang, Pingqin ; Irber, Luiz ; Jia, Huijue ; Jørgensen, Tue Sparholt ; Kieser, Silas D. ; Klemetsen, Terje ; Kola, Axel ; Kolmogorov, Mikhail ; Korobeynikov, Anton ; Kwan, Jason ; LaPierre, Nathan ; Lemaitre, Claire ; Li, Chenhao ; Limasset, Antoine ; Malcher-Miranda, Fabio ; Mangul, Serghei ; Marcelino, Vanessa R. ; Marchet, Camille ; Marijon, Pierre ; Meleshko, Dmitry ; Mende, Daniel R. ; Milanese, Alessio ; Nagarajan, Niranjan ; Nissen, Jakob ; Nurk, Sergey ; Oliker, Leonid ; Paoli, Lucas ; Peterlongo, Pierre ; Piro, Vitor C. ; Porter, Jacob S. ; Rasmussen, Simon ; Rees, Evan R. ; Reinert, Knut ; Renard, Bernhard ; Robertsen, Espen Mikal ; Rosen, Gail L. ; Ruscheweyh, Hans-Joachim ; Sarwal, Varuni ; Segata, Nicola ; Seiler, Enrico ; Shi, Lizhen ; Sun, Fengzhu ; Sunagawa, Shinichi ; Sørensen, Søren Johannes ; Thomas, Ashleigh ; Tong, Chengxuan ; Trajkovski, Mirko ; Tremblay, Julien ; Uritskiy, Gherman ; Vicedomini, Riccardo ; Wang, Zhengyang ; Wang, Ziye ; Wang, Zhong ; Warren, Andrew ; Willassen, Nils Peder ; Yelick, Katherine ; You, Ronghui ; Zeller, Georg ; Zhao, Zhengqiao ; Zhu, Shanfeng ; Zhu, Jie ; Garrido-Oter, Ruben ; Gastmeier, Petra ; Hacquard, Stephane ; Häußler, Susanne ; Khaledi, Ariane ; Maechler, Friederike ; Mesny, Fantin ; Radutoiu, Simona ; Schulze-Lefert, Paul ; Smit, Nathiana ; Strowig, Till ; Bremges, Andreas ; Sczyrba, Alexander ; McHardy, Alice Carolyn
in: Nature Methods, vol: 19, issue: 4, pages: 429-440

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1038/s41592-022-01431-4

Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient

Wei, Shaodong ; Jespersen, Marie Louise ; Baunwall, Simon Mark Dahl ; Myers, Pernille Neve ; Smith, Emilie Milton ; Dahlerup, Jens Frederik ; Rasmussen, Simon ; Nielsen, Henrik Bjørn ; Licht, Tine Rask ; Bahl, Martin Iain ; Hvas, Christian Lodberg
in: Microbiome, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1186/s40168-022-01394-w

Draft Genome Sequences of Six Isolates of the Bacillus cereus Group Isolated from Pet Reptiles

Skóra, Milena ; Zając, Magdalena ; Kwit, Renata ; Skarżyńska, Magdalena ; Pasim, Paulina ; Mikos-Wojewoda, Emilia ; Bomba, Arkadiusz ; Giza, Aleksandra ; Chesneau, Olivier ; Hendriksen, Rene S. ; Wasyl, Dariusz
in: Microbiology Resource Announcements, vol: 11, issue: 9

Type: Letter (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1128/mra.00385-22