Data Collection

Holt, KE, Dyson, ZA, Hawkey, J and flashton2003 (2024). typhoidgenomics/genotyphi. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4707613

Ryan Wick, Holt, KE, marlam89, kelwyres, Maranga, M, Petit III, RA, da Silva, AG, Deveaud, E, Lampa, S and Stanton, T (2024). klebgenomics/Kleborate: v3.0.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.13683348

Holt, KE and Hawkey, J (2024). interpretAMR/AMRrules. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.12724318

Cerdeira, L, Sharma, V, Maranga, M, Carey, M, Dyson, ZA and Holt, KE (2024). amrnet/amrnet: AMRnet-v1.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10810218

Cooper, HB, Vezina, B, Hawkey, J, Passet, V, López-Fernández, S, Monk, JM, Brisse, S, Holt, KE and Wyres, KL (2024). Supplemental Data for "A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex.". [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.24871914.v1

Cerdeira, L, Dyson, ZA and Holt, KE (2023). typhoidgenomics/TyphiNET: New release. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.5338903

Foster-Nyarko, E, Holt, KE, Cottingham, H, Wick, R, Judd, LM, Lam, M, Wyres, KL, Stanton, T, Tsang, KK, David, S, Bridel, S, Palma, F, Aanensen, DM and Brisse, S (2023). Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.19745608.v2

Holt, KE (2023). Global Typhoid Genomics Consortium 2022 - Genome Assemblies. [Data Collection]. Monash University. https://doi.org/10.26180/21431883.v1

Hawkey, J, Wyres, KL, Judd, LM, Harshegyi, T, Blakeway, L, Wick, RR, Jenney, AWJ and Holt, KE (2022). Additional file 1 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20579653.v1

Hawkey, J, Wyres, KL, Judd, LM, Harshegyi, T, Blakeway, L, Wick, RR, Jenney, AWJ and Holt, KE (2022). Additional file 3 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20579659.v1

Hawkey, J, Wyres, KL, Judd, LM, Harshegyi, T, Blakeway, L, Wick, RR, Jenney, AWJ and Holt, KE (2022). Additional file 4 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20579662.v1

Wick, R, kelwyres and Holt, KE (2022). katholt/Kaptive. [Data Collection]. Github. https://github.com/katholt/Kaptive

d-j-e, Holt, KE and Wyres, KL (2022). katholt/RedDog. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6460229

Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Accession numbers and data for S. Typhi sequences used in this study. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s005

Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s006

Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Outgroups used for phylogenetic tree rooting. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s007

Wick, RR and Holt, KE (2022). Assembly and polishing details for the real-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s020

Wick, RR and Holt, KE (2022). Confusion matrices for the simulated-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s017

Wick, RR and Holt, KE (2022). Genome details for the simulated-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s015

Wick, RR and Holt, KE (2022). Predictors of assembly quality. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s018

Wick, RR and Holt, KE (2022). Raw results for the real-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s019

Wick, RR and Holt, KE (2022). Raw results for the simulated-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s016

Holt, KE, Gorrie, C and Wyres, K (2021). 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. [Data Collection]. Monash University. https://doi.org/10.26180/16811344

Wyres, KL, Hawkey, J, Mirčeta, M, Judd, LM, Wick, RR, Gorrie, CL, Pratt, NF, Garlick, JS, Watson, KM, Pilcher, DV, McGloughlin, SA, Abbott, IJ, Macesic, N, Spelman, DW, Jenney, AWJ and Holt, KE (2021). Additional file 2 of Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.14984870.v1

Inouye, M, Dashnow, H, Pope, B, Wick, R and Holt, KE (2021). katholt/srst2. [Data Collection]. Github. https://github.com/katholt/srst2

Holt, KE, Hawkey, J and Paranagama, K (2021). katholt/sonneityping: v20210201. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4609812

Holt, KE, Lam, M and Wick, R (2020). Kleborate v2.0.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4923014

Rahman, SIA, Dyson, ZA, Klemm, EJ, Khanam, F, Holt, KE, Chowdhury, EK, Dougan, G and Qadri, F (2020). Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0008036

Wyres, KL, Nguyen, TNT, Lam, MMC, Judd, LM, van Vinh Chau, N, Dance, DAB, Ip, M, Karkey, A, Ling, CL, Miliya, T, Newton, PN, Lan, NPH, Sengduangphachanh, A, Turner, P, Veeraraghavan, B, Vinh, PV, Vongsouvath, M, Thomson, NR, Baker, S and Holt, KE (2020). Data for, "Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.". [Data Collection]. Monash University. https://doi.org/10.26180/5c67982956721

Ingle, DJ, Nair, S, Hartman, H, Ashton, PM, Dyson, ZA, Day, M, Freedman, J, Chattaway, MA, Holt, KE and Dallman, TJ (2019). Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. [Data Collection]. PLoS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0007620

Wick, RR, Judd, LM and Holt, KE (2019). Additional file 2 of: Performance of neural network basecalling tools for Oxford Nanopore sequencing. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.8319506.v1

Hawkey, J, Le Hello, S, Doublet, B, Granier, SA, Hendriksen, RS, Fricke, WF, Ceyssens, P, Gomart, C, Billman-Jacobe, H, Holt, KE and Weill, F (2019). Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. [Data Collection]. Microbial Genomics. https://doi.org/10.1099/mgen.0.000269

Wyres, KL, Wick, RR, Judd, LM, Froumine, R, Tokolyi, A, Gorrie, CL, Lam, MM, Duchêne, S, Jenney, A and Holt, K (2019). Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. [Data Collection]. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1008114

Watts, S and Holt, KE (2019). hicap validation assembly set. [Data Collection]. Monash University. https://doi.org/10.26180/5c352c5110712

Lam, MMC, Wyres, KL, Wick, RR, Judd, LM, Fostervold, A, Holt, KE and Löhr, IH (2019). Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15. [Data Collection]. Journal of Antimicrobial Chemotherapy. https://doi.org/10.1093/jac/dkz028

Boinett, CJ, Cain, AK, Hawkey, J, Do Hoang, NT, Khanh, NNT, Thanh, DP, Dordel, J, Campbell, JI, Lan, NPH, Mayho, M, Langridge, GC, Hadfield, J, Chau, NVV, Thwaites, GE, Parkhill, J, Thomson, NR, Holt, KE and Baker, S (2019). Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. [Data Collection]. Microbial genomics. https://doi.org/10.1099/mgen.0.000246

M. C. Lam, M, Wyres, KL, Duchêne, S, Wick, RR, Judd, LM, Gan, Y, Hoh, C, Archuleta, S, Molton, JS, Kalimuddin, S, Koh, TH, Passet, V, Brisse, S and Holt, KE (2018). Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. [Data Collection]. Nature Communications. https://doi.org/10.1038/s41467-018-05114-7

Holt, KE and Wyres, K (2018). Klebsiella ecology and genome plasticity compared to E. coli and Gram negative ESKAPE pathogens. [Data Collection]. University of Melbourne, Australia. https://doi.org/10.4225/49/5ac3670f83717

Perrin, A, Larsonneur, E, Nicholson, AC, Edwards, DJ, Gundlach, KM, Whitney, AM, Gulvik, CA, Bell, ME, Rendueles, O, Cury, J, Hugon, P, Clermont, D, Enouf, V, Loparev, V, Juieng, P, Monson, T, Warshauer, D, Elbadawi, LI, Walters, MS, Crist, MB, Noble-Wang, J, Borlaug, G, Rocha, EPC, Criscuolo, A, Touchon, M, Davis, JP, Holt, KE, McQuiston, JR and Brisse, S (2017). Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. [Data Collection]. Nature Communications. https://doi.org/10.1038/ncomms15483

Duchêne, S, Holt, KE, Weill, F, Le Hello, S, Hawkey, J, Edwards, DJ, Fourment, M and Holmes, EC (2016). Bacteria genomic rates data: First release. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.45951

Holt, KE (2016). Acinetobacter baumannii GC1 recombination analysis. [Data Collection]. University of Melbourne. https://doi.org/10.4225/49/5690B341A0FDB

Chung The, H, Rabaa, MA, Pham Thanh, D, Ruekit, S, Wangchuk, S, Dorji, T, Pem Tshering, K, Nguyen Thi Nguyen, T, Voong Vinh, P, Ha Thanh, T, Nguyen Ngoc Minh, C, Turner, P, Sar, P, Thwaites, G, Holt, KE, Thomson, NR, Bodhidatta, L, Mason, CJ and Baker, S (2015). The introduction and establishment of fluoroquinolone resistant Shigella sonnei into Bhutan. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1610693.v1