Item Type Date No Grouping

klebgenomics/KlebNNSsero. (2025) Holt, Kathryn E., Keegan, Shaun

Additional file 2 of A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs. (2025) Hetland, Marit A. K., Winkler, Mia A., Kaspersen, Håkon P., Håkonsholm, Fredrik, Bakksjø, Ragna-Johanne, Bernhoff, Eva, Delgado-Blas, Jose F., Brisse, Sylvain, Correia, Annapaula, Fostervold, Aasmund, Lam, Margaret M. C., Lunestad, Bjørn-Tore, Marathe, Nachiket P., Raffelsberger, Niclas, Samuelsen, Ørjan, Sunde, Marianne, Sundsfjord, Arnfinn, Urdahl, Anne Margrete, Wick, Ryan R., Löhr, Iren H., Holt, Kathryn E.

AmpliconTyper. (2025) Spadar, Anton, Mahindroo, Jaspreet, Troman, Catherine, Owusu, Michael, Adu-Sarkodie, Yaw, Abraham, Dilip, Blossom Benny, Govindan, Karthikeyan, Mohan, Venkata Raghava, Dyson, Zoe Anne, Grassly, Nicholas, Holt, Kathryn E.

typhoidgenomics/genotyphi. (2024) Holt, Kathryn E., Dyson, Zoe Anne, Hawkey, Jane, flashton2003

klebgenomics/Kleborate: v3.0.0. (2024) Ryan Wick, Holt, Kathryn E., marlam89, kelwyres, Maranga, Mary, Petit III, Robert A., da Silva, Anders Goncalves, Deveaud, Eric, Lampa, Samuel, Stanton, Tom

interpretAMR/AMRrules. (2024) Holt, Kathryn E., Hawkey, Jane

amrnet/amrnet: AMRnet-v1.0. (2024) Cerdeira, Louise, Sharma, Vandana, Maranga, Mary, Carey, Megan, Dyson, Zoe Anne, Holt, Kathryn E.

Supplemental Data for "A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex.". (2024) Cooper, Helena B., Vezina, Ben, Hawkey, Jane, Passet, Virginie, López-Fernández, Sebastián, Monk, Jonathan M., Brisse, Sylvain, Holt, Kathryn E., Wyres, Kelly L.

typhoidgenomics/TyphiNET. (2023) Cerdeira, Louise, Dyson, Zoe Anne, Holt, Kathryn E.

Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. (2023) Foster-Nyarko, Ebenezer, Holt, Kathryn E., Cottingham, Hugh, Wick, Ryan, Judd, Louise M., Lam, Margaret, Wyres, Kelly L., Stanton, Thomas, Tsang, Kara K., David, Sophia, Bridel, Sébastien, Palma, Federica, Aanensen, David M, Brisse, Sylvain

Global Typhoid Genomics Consortium 2022 - Genome Assemblies. (2023) Holt, Kathryn E.

Additional file 1 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. (2022) Hawkey, Jane, Wyres, Kelly L., Judd, Louise M., Harshegyi, Taylor, Blakeway, Luke, Wick, Ryan R., Jenney, Adam W. J., Holt, Kathryn E.

Additional file 3 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. (2022) Hawkey, Jane, Wyres, Kelly L., Judd, Louise M., Harshegyi, Taylor, Blakeway, Luke, Wick, Ryan R., Jenney, Adam W. J., Holt, Kathryn E.

Additional file 4 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. (2022) Hawkey, Jane, Wyres, Kelly L., Judd, Louise M., Harshegyi, Taylor, Blakeway, Luke, Wick, Ryan R., Jenney, Adam W. J., Holt, Kathryn E.

katholt/Kaptive. (2022) Wick, Ryan, kelwyres, Holt, Kathryn E.

katholt/RedDog. (2022) d-j-e, Holt, Kathryn E., Wyres, Kelly L

Accession numbers and data for S. Typhi sequences used in this study. (2022) Dyson, Zoe Anne, Malau, Elisheba, Horwood, Paul F, Ford, Rebecca, Siba, Valentine, Yoannes, Mition, Pomat, William, Passey, Megan, Judd, Louise M, Ingle, Danielle J, Williamson, Deborah A, Dougan, Gordon, Greenhill, Andrew R, Holt, Kathryn E

Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence. (2022) Dyson, Zoe Anne, Malau, Elisheba, Horwood, Paul F, Ford, Rebecca, Siba, Valentine, Yoannes, Mition, Pomat, William, Passey, Megan, Judd, Louise M, Ingle, Danielle J, Williamson, Deborah A, Dougan, Gordon, Greenhill, Andrew R, Holt, Kathryn E

Outgroups used for phylogenetic tree rooting. (2022) Dyson, Zoe Anne, Malau, Elisheba, Horwood, Paul F, Ford, Rebecca, Siba, Valentine, Yoannes, Mition, Pomat, William, Passey, Megan, Judd, Louise M, Ingle, Danielle J, Williamson, Deborah A, Dougan, Gordon, Greenhill, Andrew R, Holt, Kathryn E

Assembly and polishing details for the real-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Confusion matrices for the simulated-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Genome details for the simulated-read tests. (2022) Wick, Ryan R., Holt, Kathryn E.

Predictors of assembly quality. (2022) Wick, Ryan R, Holt, Kathryn E

Raw results for the real-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Raw results for the simulated-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Genome assemblies and pan-genome data for 328 clinical isolates of Klebsiella pneumoniae species complex, representing one year of infections diagnosed in a hospital diagnostic lab. (2021) Holt, Kathryn E., Gorrie, Claire, Wyres, Kelly

Additional file 2 of Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. (2021) Wyres, Kelly L., Hawkey, Jane, Mirčeta, Mirianne, Judd, Louise M., Wick, Ryan R., Gorrie, Claire L., Pratt, Nigel F., Garlick, Jill S., Watson, Kerrie M., Pilcher, David V., McGloughlin, Steve A., Abbott, Iain J., Macesic, Nenad, Spelman, Denis W., Jenney, Adam W. J., Holt, Kathryn E.

katholt/srst2. (2021) Inouye, Michael, Dashnow, Harriet, Pope, Bernie, Wick, Ryan, Holt, Kathryn E.

katholt/sonneityping: v20210201. (2021) Holt, Kathryn E., Hawkey, Jane, Paranagama, Kalani

Kleborate v2.0.0. (2020) Holt, Kathryn E., Lam, Margaret, Wick, Ryan

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. (2020) Rahman, Sadia Isfat Ara, Dyson, Zoe A., Klemm, Elizabeth J., Khanam, Farhana, Holt, Kathryn E., Chowdhury, Emran Kabir, Dougan, Gordon, Qadri, Firdausi

Data for, "Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.". (2020) Wyres, Kelly L., Nguyen, To N. T., Lam, Margaret M. C., Judd, Louise M., van Vinh Chau, Nguyen, Dance, David A. B., Ip, Margaret, Karkey, Abhilasha, Ling, Clare L., Miliya, Thyl, Newton, Paul N., Lan, Nguyen Phu Huong, Sengduangphachanh, Amphone, Turner, Paul, Veeraraghavan, Balaji, Vinh, Phat Voong, Vongsouvath, Manivanh, Thomson, Nicholas R., Baker, Stephen, Holt, Kathryn E.

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. (2019) Ingle, Danielle J., Nair, Satheesh, Hartman, Hassan, Ashton, Philip M., Dyson, Zoe, Day, Martin, Freedman, Joanne, Chattaway, Marie A., Holt, Kathryn E., Dallman, Timothy J.

Additional file 2 of: Performance of neural network basecalling tools for Oxford Nanopore sequencing. (2019) Wick, Ryan R, Judd, Louise M, Holt, Kathryn E.

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. (2019) Wyres, Kelly L, Wick, Ryan R, Judd, Louise M, Froumine, Roni, Tokolyi, Alex, Gorrie, Claire L, Lam, Margaret MC, Duchêne, Sebastián, Jenney, Adam, Holt, Kathryn

hicap validation assembly set. (2019) Watts, Stephen, Holt, Kathryn E.

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. (2019) Boinett, Christine J., Cain, Amy K., Hawkey, Jane, Do Hoang, Nhu Tran, Khanh, Nhu Nguyen Thi, Thanh, Duy Pham, Dordel, Janina, Campbell, James I., Lan, Nguyen Phu Huong, Mayho, Matthew, Langridge, Gemma C., Hadfield, James, Chau, Nguyen Van Vinh, Thwaites, Guy E., Parkhill, Julian, Thomson, Nicholas R., Holt, Kathryn E., Baker, Stephen

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. (2018) M. C. Lam, Margaret, Wyres, Kelly L., Duchêne, Sebastian, Wick, Ryan R., Judd, Louise M., Gan, Yunn-Hwen, Hoh, Chu-Han, Archuleta, Sophia, Molton, James S., Kalimuddin, Shirin, Koh, Tse Hsien, Passet, Virginie, Brisse, Sylvain, Holt, Kathryn E.

Klebsiella ecology and genome plasticity compared to E. coli and Gram negative ESKAPE pathogens. (2018) Holt, Kathryn E., Wyres, Kelly

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. (2017) Perrin, Amandine, Larsonneur, Elise, Nicholson, Ainsley C., Edwards, David J., Gundlach, Kristin M., Whitney, Anne M., Gulvik, Christopher A., Bell, Melissa E., Rendueles, Olaya, Cury, Jean, Hugon, Perrine, Clermont, Dominique, Enouf, Vincent, Loparev, Vladimir, Juieng, Phalasy, Monson, Timothy, Warshauer, David, Elbadawi, Lina I., Walters, Maroya Spalding, Crist, Matthew B., Noble-Wang, Judith, Borlaug, Gwen, Rocha, Eduardo P. C., Criscuolo, Alexis, Touchon, Marie, Davis, Jeffrey P., Holt, Kathryn E., McQuiston, John R., Brisse, Sylvain

Bacteria genomic rates data: First release. (2016) Duchêne, Sebastian, Holt, Kathryn E., Weill, François-Xavier, Le Hello, Simon, Hawkey, Jane, Edwards, David J., Fourment, Mathieu, Holmes, Edward C.

Acinetobacter baumannii GC1 recombination analysis. (2016) Holt, Kathryn E.

The introduction and establishment of fluoroquinolone resistant Shigella sonnei into Bhutan. (2015) Chung The, Hao, Rabaa, Maia A., Pham Thanh, Duy, Ruekit, Sirigade, Wangchuk, Sonam, Dorji, Tshering, Pem Tshering, Kinzang, Nguyen Thi Nguyen, To, Voong Vinh, Phat, Ha Thanh, Tuyen, Nguyen Ngoc Minh, Chau, Turner, Paul, Sar, Poda, Thwaites, Guy, Holt, Kathryn E., Thomson, Nicholas R., Bodhidatta, Ladaporn, Mason, Carl Jeffries, Baker, Stephen