The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study
Tài liệu tham khảo
Dougan, 2014, Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever, Annu Rev Microbiol, 68, 317, 10.1146/annurev-micro-091313-103739
Antillón, 2017, The burden of typhoid fever in low- and middle-income countries: a meta-regression approach, PLoS Negl Trop Dis, 11, 10.1371/journal.pntd.0005376
Stanaway, 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
Mogasale, 2014, Burden of typhoid fever in low-income and middle-income countries: a systematic, literature-based update with risk-factor adjustment, Lancet Glob Health, 2, e570, 10.1016/S2214-109X(14)70301-8
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
Dyson, 2019, Antibiotic resistance and typhoid, Clin Infect Dis, 68, S165, 10.1093/cid/ciy1111
Andrews, 2018, Extensively drug-resistant typhoid - are conjugate vaccines arriving just in time?, N Engl J Med, 379, 1493, 10.1056/NEJMp1803926
Hooda, 2019, Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance, PLoS Negl Trop Dis, 13, 10.1371/journal.pntd.0007868
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, e00105, 10.1128/mBio.00105-18
Sajib, 2021, Tracking the emergence of azithromycin resistance in multiple genotypes of typhoidal salmonella, MBio, 12, 1, 10.1128/mBio.03481-20
2019, Typhoid vaccines: WHO position paper, March 2018 – Recommendations, Vaccine, 37, 214, 10.1016/j.vaccine.2018.04.022
Carey, 2020, Clin Infect Dis, 71, S102, 10.1093/cid/ciaa367
Andrews, 2018, High rates of enteric fever diagnosis and lower burden of culture-confirmed disease in peri-urban and rural Nepal, J Infect Dis, 218, S214, 10.1093/infdis/jix221
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
Rahman, 2020, Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016, PLoS Negl Trop Dis, 14, 10.1371/journal.pntd.0008036
Ingle, 2019, Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers, PLoS Negl Trop Dis, 13, 10.1371/journal.pntd.0007620
Tanmoy, 2018, Salmonella enterica serovar typhi in Bangladesh: exploration of genomic diversity and antimicrobial resistance, MBio, 9, e02112, 10.1128/mBio.02112-18
Britto, 2020, Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent, J Antimicrob Chemother, 75, 337
Pragasam, 2020, Phylogenetic analysis indicates a longer term presence of the globally distributed H58 haplotype of Salmonella Typhi in southern India, Clin Infect Dis, 71, 1856, 10.1093/cid/ciz1112
Pham Thanh, 2016, A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure, eLife, 5, 10.7554/eLife.14003
Britto, 2018, Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: antimicrobial resistance and implications for vaccine policy, PLoS Negl Trop Dis, 12, 10.1371/journal.pntd.0006408
Dyson, 2017, Whole genome sequence analysis of Salmonella Typhi isolated in Thailand before and after the Introduction of a National Immunization Program, PLoS Negl Trop Dis, 11, 10.1371/journal.pntd.0005274
Wong, 2016, An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid, Nat Commun, 7, 10.1038/ncomms12827
Park, 2018, The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa, Nat Commun, 9, 10.1038/s41467-018-07370-z
Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033
Rambaut, 2016, Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen), Virus Evol, 2, 10.1093/ve/vew007
Didelot, 2018, Bayesian inference of ancestral dates on bacterial phylogenetic trees, Nucleic Acids Res, 46, e134, 10.1093/nar/gky783
Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol Biol, 7, 214, 10.1186/1471-2148-7-214
Volz, 2017, Scalable relaxed clock phylogenetic dating, Virus Evol, 3, 10.1093/ve/vex025
Tanabe, 2010, Plasmodium falciparum accompanied the human expansion out of Africa, Curr Biol, 20, 1283, 10.1016/j.cub.2010.05.053
Wirth, 2015, Massive lineage replacements and cryptic outbreaks of Salmonella Typhi in eastern and southern Africa, Nat Genet, 47, 565, 10.1038/ng.3318
Carter, 2020, Introducing Typhoid conjugate vaccine in south Asia: lessons from the Surveillance for Enteric Fever in Asia Project, Clin Infect Dis, 71, S191, 10.1093/cid/ciaa1296
Balaji, 2018, Longitudinal Typhoid fever trends in India from 2000 to 2015, Am J Trop Med Hyg, 99, 34, 10.4269/ajtmh.18-0139
Qamar, 2020, Antimicrobial resistance in Typhoidal Salmonella: Surveillance for Enteric Fever in Asia Project, 2016-2019, Clin Infect Dis, 71, S276, 10.1093/cid/ciaa1323
Holt, 2012, Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe, Nat Genet, 44, 1056, 10.1038/ng.2369
Wong, 2016, Molecular surveillance identifies multiple transmissions of Typhoid in west Africa, PLoS Negl Trop Dis, 10
2021, Extensively drug-resistant Salmonella Typhi infections among U.S. residents without international travel, HAN Arch, CDCHAN-00439, 0
Octavia, 2021, Azithromycin-resistant Salmonella enterica serovar Typhi AcrB-R717Q/L, Singapore, Emerg Infect Dis J, 27, 624, 10.3201/eid2702.203874
Carey, 2021, Spontaneous emergence of azithromycin resistance in independent lineages of Salmonella Typhi in northern India, Clin Infect Dis, 72, e120, 10.1093/cid/ciaa1773