Data Collection

Aiken, A and Rehman, AM (2023). MBIRA - Mortality from Bacterial Infections Resistant to Antibiotics study - underlying data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003168.

Asio, J, Watera, C, Namuwenge, N, Kirungi, W, Musinguzi, J, Mugagga, K, Busobozi, R, Tusiime, BJ, Lutalo, T, Mbidde, EK and Kaleebu, P (2020). Population-based monitoring of HIV drug resistance early warning indicators in Uganda: A nationally representative survey following revised WHO recommendations: S1 Data. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0230451.s001

Bronowski, C, Fookes, MC, Gilderthorp, R, Ashelford, KE, Harris, SR, Phiri, A, Hall, N, Gordon, MA, Wain, J, Hart, CA, Wigley, P, Thomson, NR and Winstanley, C (2013). Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0002557

Cameron, DW, Panesar, P, Jones, A, Aldous, A, Kranzer, K, Halpin, E, Fifer, H, Macrae, B, Curtis, C and Pollara, G (2016). Attitudes and Behaviours to Antimicrobial Prescribing following introduction of a Smartphone App. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0154202

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

Dorman, MJ, Kane, L, Domman, D, Turnbull, JD, Cormie, C, Fazal, M, Goulding, DA, Russell, JE, Alexander, S and Thomson, NR (2019). Additional materials from The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One. [Data Collection]. The Royal Society. https://doi.org/10.6084/m9.figshare.7951289.v1

Dyson, ZA and Holt, KE (2021). katholt/genotyphi: GenoTyphi. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4707613

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

Evangelopoulos, D, Prosser, GA, Rodgers, A, Dagg, BM, Khatri, B, Ho, MM, Gutierrez, MG and Cortes, T (2019). Comparative fitness analysis of D-cycloserine resistant mutants reveals both fitness-neutral and high-fitness cost genotypes. [Data Collection]. Nature Communications. https://doi.org/10.1038/s41467-019-12074-z

Guevara, PD, Maes, M, Thanh, DP, Duarte, C, Rodriguez, EC, Montaño, LA, Dan, THN, Nguyen, TNT, Carey, ME, Campos, J, Chinen, I, Perez, E and Baker, S (2021). Profile of the organisms selected for sequencing. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0009755.s001

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

Kim, C, Abbas, KM and vaccine-impact (2023). vaccine-impact/vaccine_amr. [Data Collection]. Github. https://github.com/vaccine-impact/vaccine_amr

Knight, G (2019). gwenknight/empiricprescribing. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3418998

Leclerc, QJ (2022). qleclerc/mrsa_phage_dynamics. [Data Collection]. Github. https://github.com/qleclerc/mrsa_phage_dynamics

Leclerc, QJ (2023). qleclerc/phage_antibiotic_dynamics. [Data Collection]. Github.

London School of Hygiene & Tropical Medicine (2019). Comparing antimicrobial resistance prediction pipelines from bacterial whole genome sequencing data: An inter-laboratory study. [Data Collection]. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/view/PRJEB34513

Lubell, Y, Mills, A, Whitty, CJ and Staedke, SG (2010). Model S1 - An Economic Evaluation of Home Management of Malaria in Uganda: An Interactive Markov Model. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0012439.s001

Ngufor, C, Critchley, J, Fagbohoun, J, N'guessan, R, Todjinou, D and Rowland, M (2016). Experimental hut data. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0162210.s001

Olaru, ID (2020). Evaluation of the InTray and Compact Dry culture systems for the diagnosis of urinary tract infections - ARGUS study dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001997.

Olaru, I (2021). ARGUS clinical and bacteriological outcomes dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002110.

Pickering, H, Hart, JD, Burr, S, Stabler, R, Maleta, K, Kalua, K, Bailey, RL and Holland, MJ (2022). Additional file 1 of Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.17982643.v1

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

Spadar, A (2022). AntonS-bio/entropy. [Data Collection]. GitHub. https://github.com/AntonS-bio/entropy

Thiha, N, Chinnakali, P, Harries, AD, Shwe, M, Balathandan, TP, Thein Than Tun, S, Das, M, Tin, HH, Yi, Y, Babin, FX, Lwin, TT and Clevenbergh, PA (2016). S1 Data for: "Is There a Need for Viral Load Testing to Assess Treatment Failure in HIV-Infected Patients Who Are about to Change to Tenofovir-Based First-Line Antiretroviral Therapy? Programmatic Findings from Myanmar". [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0160616.s001

Ugarte-Ruiz, M, Domínguez, L, Corcionivoschi, N, Wren, BW, Dorrell, N and Gundogdu, O (2018). Exploring the oxidative, antimicrobial and genomic properties of Campylobacter jejuni strains isolated from poultry. [Data Collection]. Research in Veterinary Science. https://doi.org/10.1016/j.rvsc.2018.06.016

van Kleef, E, Luangasanatip, N, Bonten, MJ and Cooper, BS (2017). R code: why sensitive bacteria are resistant to hospital infection control. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.1045530