Item Type Date Title No Grouping

Dataset

typhoidgenomics/TyphoidGenomicsConsortiumMykrobe. (2025) Ingle, Danielle J.; Holt, Kathryn E.; Dyson, Zoe Anne

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

Additional file 3 of The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health. (2025) Dyson, Zoe A.; Cerdeira, Louise; Sharma, Vandana; Carey, Megan E.; Holt, Kathryn E.

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.

klebgenomics/Kaptive. (2025) Wick, Ryan R.; Stanton, Thomas; Wyres, Kelly L; Holt, Kathryn E.

Genomic and functional analysis of rmp locus variants in Klebsiella pneumoniae. (2025) Lam, Margaret M. C.; Salisbury, Stephen M.; Treat, Logan P.; Wick, Ryan R.; Judd, Louise M.; Wyres, Kelly L; Brisse, Sylvain; Walker, Kimberly A; Miller, Virginia L; 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.

Polypolish: Short-read polishing of long-read bacterial genome assemblies. (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