FBOS. Population and housing census 2017. Suva, Fiji Islands 2018.
Kumar, 2012, The incidence of typhoid fever in Fiji from 1995-2009, Fiji J Public Health, 1, 31
Dunn, 2005, Laboratory-based Salmonella surveillance in Fiji, 2004-2005, Pac Health Dialog, 12, 53
Thompson, 2014, Typhoid fever in Fiji: a reversible plague?, Trop Med Int Health, 19, 1284, 10.1111/tmi.12367
Getahun Strobel, 2019, A retrospective study of patients with blood culture-confirmed typhoid fever in Fiji during 2014-2015: epidemiology, clinical features, treatment and outcome, Trans R Soc Trop Med Hyg, 113, 764, 10.1093/trstmh/trz075
Watson, 2017, A cross-sectional seroepidemiological survey of typhoid fever in Fiji, PLoS Negl Trop Dis, 11, 10.1371/journal.pntd.0005786
Walsh, 2019, Tropical cyclones and climate change, Trop Cycl Res Rev, 8, 240, 10.1016/j.tcrr.2020.01.004
Kidgell, 2002, Salmonella Typhi, the causative agent of typhoid fever, is approximately 50,000 years old, Infect Genet Evol, 2, 39, 10.1016/S1567-1348(02)00089-8
Roumagnac, 2006, Evolutionary history of Salmonella Typhi, Science, 314, 1301, 10.1126/science.1134933
Wong, 2016, An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid, Nat Commun, 7, 12827, 10.1038/ncomms12827
Wong, 2015, Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events, Nat Genet, 47, 632, 10.1038/ng.3281
Parry, 2002, Typhoid fever, N Engl J Med, 347, 1770, 10.1056/NEJMra020201
Saha, 2019, Evaluating PCR-based detection of Salmonella Typhi and Paratyphi A in the environment as an enteric fever surveillance tool, Am J Trop Med Hyg, 100, 43, 10.4269/ajtmh.18-0428
Klemm, 2018, Emergence of an extensively drug-resistant Salmonella enterica serovar Typhi clone harboring a promiscuous plasmid encoding resistance to fluoroquinolones and third-generation cephalosporins, mBio, 9, 10.1128/mBio.00105-18
2019, Typhoid vaccines: WHO position paper, March 2018 - Recommendations, Vaccine, 37, 214, 10.1016/j.vaccine.2018.04.022
Prasad, 2018, Epidemiology and risk factors for typhoid fever in Central Division, Fiji, 2014-2017: a case-control study, PLoS Negl Trop Dis, 12, 10.1371/journal.pntd.0006571
Wick, 2017, Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads, PLoS Comput Biol, 13, 10.1371/journal.pcbi.1005595
Hunt, 2015, Circlator: automated circularization of genome assemblies using long sequencing reads, Genome Biol, 16, 294, 10.1186/s13059-015-0849-0
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv:12073907 [q-bioGN]2012.
Cingolani, 2012, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly, 6, 80, 10.4161/fly.19695
Croucher, 2015, Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Res, 43, e15, 10.1093/nar/gku1196
International Typhoid Consortium, 2016, Molecular surveillance identifies multiple transmissions of typhoid in West Africa, PLoS Negl Trop Dis, 10
Park, 2018, The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa, Nat Commun, 9, 5094, 10.1038/s41467-018-07370-z
Pragasam, 2020, Phylogenetic analysis indicates a longer term presence of the globally distributed H58 haplotype of Salmonella Typhi in Southern India, Clin Infect Dis, 10.1093/cid/ciz1112
Argimon, 2021, A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch, Nat Commun, 12, 2879, 10.1038/s41467-021-23091-2
Song, 2013, Structure and function of the Salmonella Typhi chimaeric A(2)B(5) typhoid toxin, Nature, 499, 350, 10.1038/nature12377
Davies, 2019, Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics, Nat Genet, 51, 1035, 10.1038/s41588-019-0417-8
Nguyen, 2015, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, 32, 268, 10.1093/molbev/msu300
Suchard, 2018, Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10, Virus Evol, 4, vey016, 10.1093/ve/vey016
Ho, 2015, Simulating and detecting autocorrelation of molecular evolutionary rates among lineages, Mol Ecol Resour, 15, 688, 10.1111/1755-0998.12320
Ho, 2011, Skyline-plot methods for estimating demographic history from nucleotide sequences, Mol Ecol Resour, 11, 423, 10.1111/j.1755-0998.2011.02988.x
Dearlove, 2013, Coalescent inference for infectious disease: meta-analysis of hepatitis C, Philos Trans R Soc Lond B, 368, 10.1098/rstb.2012.0314
Paradis, 2019, ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R, Bioinformatics, 35, 526, 10.1093/bioinformatics/bty633
Yu, 2018, Two methods for mapping and visualizing associated data on phylogeny using ggtree, Mol Biol Evol, 35, 3041, 10.1093/molbev/msy194
Parkhill, 2001, Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18, Nature, 413, 848, 10.1038/35101607
Eaves, 2004, Prevalence of mutations within the quinolone resistance-determining region of gyrA, gyrB, parC, and parE and association with antibiotic resistance in quinolone-resistant Salmonella enterica, Antimicrob Agents Chemother, 48, 4012, 10.1128/AAC.48.10.4012-4015.2004
Duchene, 2016, Genome-scale rates of evolutionary change in bacteria, Microb Genom, 2
de Alwis, 2018, Role of environmental factors in shaping spatial distribution of Salmonella enterica serovar Typhi, Fiji, Emerg Infect Dis, 24, 284, 10.3201/eid2402.170704
Scobie, 2014, Impact of a targeted typhoid vaccination campaign following cyclone Tomas, Republic of Fiji, 2010, Am J Trop Med Hyg, 90, 1031, 10.4269/ajtmh.13-0728
Knutson, 2010, Tropical cyclones and climate change, Nature Geoscience, 3, 157, 10.1038/ngeo779
Pablo, 2015, Investigation on the typhoid outbreak in Wailoku, Tamavua, Suva, Fiji J Public Health, 4, 27
Clegg, 1995, The role of the laboratory in the diagnosis and management of typhoid fever, PNG Med J, 38, 315
Sikorski, 2020, Tenacious endemic typhoid fever in Samoa, Clin Infect Dis, 71, S120, 10.1093/cid/ciaa314
2019, The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017, Lancet Infect Dis, 19, 369, 10.1016/S1473-3099(18)30685-6