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 COVID-19 mathematical model of at-risk populations with non-pharmaceutical preventive measures

Asempapa, Reuben ; Oduro, Bismark ; Apenteng, Ofosuhene O. ; Magagula, Vusi M.
in: Infectious Disease Modelling, vol: 7, issue: 1, pages: 45-61

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1016/j.idm.2021.11.005

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 European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches

Félix, Benjamin ; Sevellec, Yann ; Palma, Federica ; Douarre, Pierre Emmanuel ; Felten, Arnaud ; Radomski, Nicolas ; Mallet, Ludovic ; Blanchard, Yannick ; Leroux, Aurélie ; Soumet, Christophe ; Bridier, Arnaud ; Piveteau, Pascal ; Ascensio, Eliette ; Hébraud, Michel ; Karpíšková, Renáta ; Gelbíčová, Tereza ; Torresi, Marina ; Pomilio, Francesco ; Cammà, Cesare ; Di Pasquale, Adriano ; Skjerdal, Taran ; Pietzka, Ariane ; Ruppitsch, Werner ; Canelhas, Monica Ricão ; Papić, Bojan ; Hurtado, Ana ; Wullings, Bart ; Bulawova, Hana ; Castro, Hanna ; Lindström, Miia ; Korkeala, Hannu ; Šteingolde, Žanete ; Kramarenko, Toomas ; Cabanova, Lenka ; Szymczak, Barbara ; Gareis, Manfred ; Oswaldi, Verena ; Marti, Elisabet ; Seyfarth, Anne-Mette ; Leblanc, Jean-Charles ; Guillier, Laurent ; Roussel, Sophie
in: Scientific Data, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1038/s41597-022-01278-6

Analysing the impact of migration on HIV/AIDS cases using epidemiological modelling to guide policy makers

Apenteng, Ofosuhene O. ; Osei, Prince P. ; Ismail, Noor Azina ; Chiabai, Aline
in: Infectious Disease Modelling, vol: 7, issue: 1, pages: 252-261

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1016/j.idm.2022.01.002

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2022 | DOI: https://doi.org/10.1016/j.mran.2022.100214

Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life Years for 29 Cancer Groups From 2010 to 2019

, ; Kocarnik, Jonathan M. ; Compton, Kelly ; Dean, Frances E ; Fu, Weijia ; Gaw, Brian L ; Harvey, James D ; Henrikson, Hannah Jacqueline ; Lu, Dan ; Pennini, Alyssa ; Xu, Rixing ; Ababneh, Emad ; Abbasi-Kangevari, Mohsen ; Abbastabar, Hedayat ; Abd-Elsalam, Sherief M ; Abdoli, Amir ; Abedi, Aidin ; Abidi, Hassan ; Abolhassani, Hassan ; Adedeji, Isaac Akinkunmi ; Adnani, Qorinah Estiningtyas Sakilah ; Advani, Shailesh M ; Afzal, Muhammad Sohail ; Aghaali, Mohammad ; Ahinkorah, Bright Opoku ; Ahmad, Sajjad ; Ahmad, Tauseef ; Ahmadi, Ali ; Ahmadi, Sepideh ; Ahmed Rashid, Tarik ; Ahmed Salih, Yusra ; Akalu, Gizachew Taddesse ; Aklilu, Addis ; Akram, Tayyaba ; Akunna, Chisom Joyqueenet ; Al Hamad, Hanadi ; Alahdab, Fares ; Al-Aly, Ziyad ; Ali, Saqib ; Alimohamadi, Yousef ; Alipour, Vahid ; Aljunid, Syed Mohamed ; Alkhayyat, Motasem ; Almasi-Hashiani, Amir ; Almasri, Nihad A ; Al-Maweri, Sadeq Ali Ali ; Arshad, Muhammad ; Ghith, Nermin
in: Jama Oncology, vol: 8, issue: 3, pages: 420-444

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1001/jamaoncol.2021.6987

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press | 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