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Cited by 50Salmonella and Campylobacter epidemiologyBacterial Infections and VaccinesAntibiotic Resistance in Bacteria

Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya

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Kariuki, Samuel, Dyson, Zoe A, Mbae, Cecilia, Ngetich, Ronald, Kavai, Susan M, Wairimu, Celestine, Anyona, Stephen, Gitau, Naomi +7 more·2021·eLife
DOI 10.7554/elife.67852PMC PMC8494480

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Abstract

Background: Understanding the dynamics of infection and carriage of typhoid in endemic settings is critical to finding solutions to prevention and control. Methods: In a 3-year case-control study, we investigated typhoid among children aged <16 years (4670 febrile cases and 8549 age matched controls) living in an informal settlement, Nairobi, Kenya. Results: 148 S . Typhi isolates from cases and 95 from controls (stool culture) were identified; a carriage frequency of 1 %. Whole-genome sequencing showed 97% of cases and 88% of controls were genotype 4.3.1 (Haplotype 58), with the majority of each (76% and 88%) being multidrug-resistant strains in three sublineages of the H58 genotype (East Africa 1 (EA1), EA2, and EA3), with sequences from cases and carriers intermingled. Conclusions: The high rate of multidrug-resistant H58 S . Typhi, and the close phylogenetic relationships between cases and controls, provides evidence for the role of carriers as a reservoir for the community spread of typhoid in this setting. Funding: National Institutes of Health (R01AI099525); Wellcome Trust (106158/Z/14/Z); European Commission (TyphiNET No 845681); National Institute for Health Research (NIHR); Bill and Melinda Gates Foundation (OPP1175797).

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  • Subclade 4.3.1 (previously haplotype 58) is the predominant multidrug-resistant genotype in sub-Saharan Africa, with a prevalence ranging from 60.4% to 97%.

    “Subclade 4.3.1 (previously haplotype 58) is the predominant MDR genotype in SSA, 75 with a prevalence ranging from 60.4% to 97%”

    From Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now? (2022) · cites this paper as [73]

    The Results identify H58 as genotype 4.3.1 and report that 97% of sampled Kenyan cases were H58; the Discussion describes MDR H58 as widespread across East Africa. The paper does not establish that it is the predominant MDR genotype throughout sub-Saharan Africa or report a prevalence range beginning at 60.4%. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 69

  1. Accou-Demartin M Gaborieau V Song Y 2011 Salmonella enterica Serotype Typhi with nonclassical quinolone resistance phenotype Emerg Infect Dis 17 1091 1094 10.3201/eid/1706.101242 21749778 PMC3358197 · DOI
  2. Argimon S Abudahab K Goater RJE 2016 Microreact: visualizing and sharing data for genomic epidemiology and phylogeography Microbial Genomics 2 e000093 10.1099/mgen.0.000093 28348833 PMC5320705 · DOI · Paper page
  3. Argimón S Yeats CA Goater RJ Abudahab K Taylor B Underwood A Sánchez-Busó L Wong VK Dyson ZA Nair S Park SE Marks F Page AJ Keane JA Baker S Holt KE Dougan G Aanensen DM 2021 A global resource for genomic predictions of antimicrobial resistance and surveillance of salmonella typhi at pathogenwatch Nature Communications 12 2879 10.1038/s41467-021-23091-2 34001879 PMC8128892 · DOI
  4. Arnold C Edwards K Desai M Platt S Green J Setup CD 2018 Validation, and Quality Control of a Centralized Whole-Genome-Sequencing Laboratory: Lessons Learned Journal of Clinical Microbiology 56 00261-18 10.1128/JCM.00261-18 PMC6062811 29695528 · DOI
  5. Ashton PM Nair S Peters TM 2016 Identification of Salmonella for public health surveillance using whole genome sequencing PeerJ 4 e1752 10.7717/peerj.1752 27069781 PMC4824889 · DOI
  6. Baker S Holt KE Clements ACA 2011 Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission Open Biology 1 110008 10.1098/rsob.110008 22645647 PMC3352080 · DOI
  7. Britto CD Dyson ZA Duchene S 2018 Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy PLOS Neglected Tropical Diseases 12 e0006408 10.1371/journal.pntd.0006408 29684021 PMC5933809 · DOI
  8. Britto CD Dyson ZA Mathias S 2020 Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent The Journal of Antimicrobial Chemotherapy 75 337 341 10.1093/jac/dkz435 31665304 PMC7223262 · DOI
  9. Carattoli A Zankari E García-Fernández A 2014 In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing Antimicrobial Agents and Chemotherapy 58 3895 3903 10.1128/AAC.02412-14 24777092 PMC4068535 · DOI · Paper page
  10. Croucher NJ Page AJ Connor TR Delaney AJ Keane JA Bentley SD Parkhill J Harris SR 2015 Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins Nucleic Acids Research 43 e15 10.1093/nar/gku1196 25414349 PMC4330336 · DOI
  11. Crump JA Mintz ED 2010 Global trends in typhoid and paratyphoid Fever Clinical Infectious Diseases 50 241 246 10.1086/649541 20014951 PMC2798017 · DOI
  12. Dewan AM Corner R Hashizume M Ongee ET 2013 Typhoid Fever and its association with environmental factors in the Dhaka Metropolitan Area of Bangladesh: a spatial and time-series approach PLOS Neglected Tropical Diseases 7 e1998 10.1371/journal.pntd.0001998 23359825 PMC3554574 · DOI
  13. Dixon P 2003 VEGAN, a package of R functions for community ecology Journal of Vegetation Science 14 927 930 10.1111/j.1654-1103.2003.tb02228.x · DOI
  14. Duchene S Holt KE Weill FX 2016 Genome-scale rates of evolutionary change in bacteria Microbial Genomics 2 e000094 10.1099/mgen.0.000094 28348834 PMC5320706 · DOI
  15. Edwards DJ Duchêne S Pope B Holt KE 2020 SNPPAR: identifying convergent evolution and other homoplasies from microbial whole-genome alignments bioRxiv 10.1101/2020.07.08.194480 PMC8767352 34874243 · DOI
  16. Feasey NA Gaskell K Wong V Msefula C Selemani G Kumwenda S Allain TJ Mallewa J Kennedy N Bennett A Nyirongo JO Nyondo PA Zulu MD Parkhill J Dougan G Gordon MA Heyderman RS 2015 Rapid emergence of multidrug resistant, H58-lineage Salmonella typhi in Blantyre, Malawi PLOS Neglected Tropical Diseases 9 e0003748 10.1371/journal.pntd.0003748 25909750 PMC4409211 · DOI · Paper page
  17. Firth C Kitchen A Shapiro B Suchard MA Holmes EC Rambaut A 2010 Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses Molecular Biology and Evolution 27 2038 2051 10.1093/molbev/msq088 20363828 PMC3107591 · DOI
  18. Gauld JS Hu H Klein DJ Levine MM 2018 Typhoid fever in Santiago, Chile: Insights from a mathematical model utilizing venerable archived data from a successful disease control program PLOS Neglected Tropical Diseases 12 e0006759 10.1371/journal.pntd.0006759 30188904 PMC6143279 · DOI
  19. Gunn JS Marshall JM Baker S Dongol S Charles RC Ryan ET 2014 Salmonella chronic carriage: epidemiology, diagnosis, and gallbladder persistence Trends in Microbiology 22 648 655 10.1016/j.tim.2014.06.007 25065707 PMC4252485 · DOI
  20. Gupta SK Padmanabhan BR Diene SM 2014 ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes Antimicrobial Agents and Chemotherapy 58 212 220 10.1128/AAC.01310-13 24145532 PMC3910750 · DOI · Paper page
  21. Hawkey J Hamidian M Wick RR 2015 ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data BMC Genomics 16 667 10.1186/s12864-015-1860-2 26336060 PMC4558774 · DOI
  22. Hendriksen RS Leekitcharoenphon P Mikoleit M 2015 Genomic dissection of travel-associated extended-spectrum-beta-lactamase-producing Salmonella enterica serovar typhi isolates originating from the Philippines: a one-off occurrence or a threat to effective treatment of typhoid fever? Journal of Clinical Microbiology 53 677 680 10.1128/JCM.03104-14 25428145 PMC4298498 · DOI
  23. Holt KE Parkhill J Mazzoni CJ 2008 High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi Nature Genetics 40 987 993 10.1038/ng.195 18660809 PMC2652037 · DOI
  24. Holt KE Thomson NR Wain J 2009 Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi BMC Genomics 10 36 10.1186/1471-2164-10-36 19159446 PMC2658671 · DOI
  25. Holt KE Phan MD Baker S Duy PT Nga TVT Nair S Turner AK Walsh C Fanning S Farrell-Ward S Dutta S Kariuki S Weill F-X Parkhill J Dougan G Wain J 2011 Emergence of a globally dominant inchi1 plasmid type associated with multiple drug resistant typhoid PLOS Neglected Tropical Diseases 5 e1245 10.1371/journal.pntd.0001245 21811646 PMC3139670 · DOI
  26. Ingle DJ Nair S Hartman H 2019 Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers PLOS Neglected Tropical Diseases 13 e0007620 10.1371/journal.pntd.0007620 31513580 PMC6741848 · DOI
  27. Inouye M Dashnow H Raven LA 2014 SRST2: Rapid genomic surveillance for public health and hospital microbiology labs Genome Medicine 6 90 10.1186/s13073-014-0090-6 25422674 PMC4237778 · DOI
  28. Jaillard M Lima L Tournoud M 2018 A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events PLOS Genetics 14 e1007758 10.1371/journal.pgen.1007758 30419019 PMC6258240 · DOI
  29. Jolley KA Maiden MCJ 2010 BIGSdb: Scalable analysis of bacterial genome variation at the population level BMC Bioinformatics 11 595 10.1186/1471-2105-11-595 21143983 PMC3004885 · DOI
  30. Kanungo S Dutta S Sur D 2008 Epidemiology of typhoid and paratyphoid fever in India Journal of Infection in Developing Countries 2 454 460 10.3855/jidc.161 19745523 · DOI
  31. Kariuki S Revathi G Kiiru J 2010 Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia Journal of Clinical Microbiology 48 2171 2176 10.1128/JCM.01983-09 20392916 PMC2884483 · DOI · Paper page
  32. Kariuki S Gordon MA Feasey N Parry CM 2015 Antimicrobial resistance and management of invasive Salmonella disease Vaccine 33 C21 C29 10.1016/j.vaccine.2015.03.102 25912288 PMC4469558 · DOI
  33. Kariuki S Mbae C Onsare R 2019 Multidrug-resistant Nontyphoidal Salmonella Hotspots as Targets for Vaccine Use in Management of Infections in Endemic Settings Clinical Infectious Diseases 68 S10 S15 10.1093/cid/ciy898 30767004 PMC6376148 · DOI · Paper page
  34. Kariuki S Mbae C Van Puyvelde S 2020 High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya PLOS Neglected Tropical Diseases 14 e0008440 10.1371/journal.pntd.0008440 32745137 PMC7425985 · DOI
  35. Klemm EJ Shakoor S Page AJ Qamar FN Judge K Saeed DK Wong VK Dallman TJ Nair S Baker S Shaheen G Qureshi S Yousafzai MT Saleem MK Hasan Z Dougan G Hasan R 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 e00105-18 10.1128/mBio.00105-18 29463654 PMC5821095 · DOI
  36. Köser CU Ellington MJ Cartwright EJP 2012 Routine use of microbial whole genome sequencing in diagnostic and public health microbiology PLOS Pathogens 8 e1002824 10.1371/journal.ppat.1002824 22876174 PMC3410874 · DOI
  37. Kyobutungi C Ziraba AK Ezeh A Yé Y 2008 The burden of disease profile of residents of Nairobi’s slums: results from a demographic surveillance system Population Health Metrics 6 1 10.1186/1478-7954-6-1 18331630 PMC2292687 · DOI
  38. Langmead B Salzberg SL 2012 Fast gapped-read alignment with Bowtie 2 Nat Meth 9 357 359 10.1038/nmeth.1923 PMC3322381 22388286 · DOI · Paper page
  39. Levine MM Black RE Lanata C 1982 Precise estimation of the numbers of chronic carriers of Salmonella typhi in Santiago, Chile, an endemic area The Journal of Infectious Diseases 146 724 726 10.1093/infdis/146.6.724 7142746 · DOI
  40. Li H Handsaker B Wysoker A 2009 The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2078 2079 10.1093/bioinformatics/btp352 19505943 PMC2723002 · DOI · Paper page
  41. Lutterloh E Likaka A Sejvar J 2012 Multidrug-resistant typhoid fever with neurologic findings on the Malawi-Mozambique border Clinical Infectious Diseases 54 1100 1106 10.1093/cid/cis012 22357702 · DOI
  42. Marchello CS Hong CY Crump JA 2019 Global Typhoid Fever Incidence: A Systematic Review and Meta-analysis Clinical Infectious Diseases 68 S105 S116 10.1093/cid/ciy1094 30845336 PMC6405273 · DOI
  43. Marchello CS Birkhold M Crump JA 2020 Complications and mortality of typhoid fever: A global systematic review and meta-analysis The Journal of Infection 81 902 910 10.1016/j.jinf.2020.10.030 33144193 PMC7754788 · DOI
  44. Marks F von K Aaby P 2017 Incidence of invasive salmonella disease in sub-Saharan Africa: a multicentre population-based surveillance study The Lancet Global Health 5 310 323 10.1016/S2214-109X(17)30022-0 28193398 PMC5316558 · DOI
  45. Mbae C Mwangi M Gitau N 2020 Factors associated with occurrence of salmonellosis among children living in Mukuru slum, an urban informal settlement in Kenya BMC Infectious Diseases 20 422 10.1186/s12879-020-05134-z 32552753 PMC7302364 · DOI
  46. Mogasale V Maskery B Ochiai RL 2014 Burden of typhoid fever in low-income and middle-income countries: a systematic, literature-based update with risk-factor adjustment The Lancet Global Health 2 e570 e580 10.1016/S2214-109X(14)70301-8 25304633 · DOI
  47. Mutai WC Muigai AWT Waiyaki P Kariuki S 2018 Multi-drug resistant Salmonella enterica serovar typhi isolates with reduced susceptibility to ciprofloxacin in Kenya BMC Microbiology 18 187 10.1186/s12866-018-1332-3 30428828 PMC6236932 · DOI
  48. Mutisya E Yarime M 2011 Understanding the grassroots dynamics of slums in Nairobi: The dilemma of Kibera informal settlements International Transaction Journal of Engineering, Management, and Applied Sciences and Technologies 2011 1 18
  49. Neil KP Sodha SV Lukwago L 2012 A large outbreak of typhoid fever associated with a high rate of intestinal perforation in Kasese District, Uganda, 2008-2009 Clinical Infectious Diseases 54 1091 1099 10.1093/cid/cis025 22357703 · DOI
  50. Olack B Burke H Cosmas L 2011 Nutritional status of under-five children living in an informal urban settlement in Nairobi, Kenya Journal of Health, Population, and Nutrition 29 357 363 10.3329/jhpn.v29i4.8451 21957674 PMC3190366 · DOI
  51. Paradis E Claude J Strimmer K 2004 APE: Analyses of Phylogenetics and Evolution in R language Bioinformatics 20 289 290 10.1093/bioinformatics/btg412 14734327 · DOI
  52. Park SE Pham DT Boinett C 2018 The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa Nature Communications 9 5094 10.1038/s41467-018-07370-z 30504848 PMC6269545 · DOI · Paper page
  53. Parkhill J Dougan G James KD 2001 Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 Nature 413 848 852 10.1038/35101607 11677608 · DOI
  54. Parry CM Hien TT Dougan G White NJ Farrar JJ 2002 Typhoid fever The New England Journal of Medicine 347 1770 1782 10.1056/NEJMra020201 12456854 · DOI · Paper page
  55. Pham Thanh D Karkey A Dongol S 2016 A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure eLife 5 e14003 10.7554/eLife.14003 26974227 PMC4805543 · DOI
  56. Phan MD Kidgell C Nair S 2009 Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever Antimicrobial Agents and Chemotherapy 53 716 727 10.1128/AAC.00645-08 19015365 PMC2630618 · DOI
  57. Pitzer VE Feasey NA Msefula C 2015 Mathematical modeling to assess the drivers of the recent emergence of Typhoid fever in blantyre, malawi Clinical Infectious Diseases 61 251 258 10.1093/cid/civ710 26449939 PMC4596932 · DOI
  58. Rahman SIA Dyson ZA Klemm EJ 2020 Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016 PLOS Neglected Tropical Diseases 14 e0008036 10.1371/journal.pntd.0008036 32106221 PMC7064254 · DOI
  59. Rambaut A Lam TT Max Carvalho L Pybus OG 2016 Exploring the temporal structure of heterochronous sequences using TEMPEST (formerly Path-o-gen) Virus Evolution 2 vew007 10.1093/ve/vew007 27774300 PMC4989882 · DOI
  60. Saad NJ Bowles CC Grenfell BT 2017 The impact of migration and antimicrobial resistance on the transmission dynamics of typhoid fever in Kathmandu, Nepal: A mathematical modelling study PLOS Neglected Tropical Diseases e0005547 10.1371/journal.pntd.0005547 28475605 PMC5435358 · DOI
  61. Stamatakis A 2014 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Bioinformatics 30 1312 1313 10.1093/bioinformatics/btu033 24451623 PMC3998144 · DOI · Paper page
  62. Suchard MA Lemey P Baele G Ayres DL Drummond AJ Rambaut A 2018 Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Virus Evolution 4 vey016 10.1093/ve/vey016 29942656 PMC6007674 · DOI
  63. Thanh Duy P Thieu NTV Nguyen Thi Nguyen T Ngoc Dan Thanh H Dongol S Karkey A Carey M Basnyat B Dougan G Rabaa MA Baker S 2020 Gallbladder carriage generates genetic variation and genome degradation in salmonella typhi PLOS Pathogens 16 e1008998 10.1371/journal.ppat.1008998 33085725 PMC7605710 · DOI
  64. Thindwa D Chipeta MG Henrion MYR Gordon MA 2019 Distinct climate influences on the risk of typhoid compared to invasive non-typhoid Salmonella disease in Blantyre Malawi. Sci Rep 9 20310 20311 10.1038/s41598-019-56688-1 31889080 PMC6937328 · DOI
  65. Tinline RR Gregory D 1988 The Universal Transverse Mercator Code: A location code for disease reporting The Canadian Veterinary Journal = La Revue Veterinaire Canadienne 29 825 829 17423142 PMC1680870
  66. Wick RR Schultz MB Zobel J Holt KE 2015 Bandage: interactive visualization of de novo genome assemblies Bioinformatics 31 3350 3352 10.1093/bioinformatics/btv383 26099265 PMC4595904 · DOI
  67. Wick RR Judd LM Gorrie CL Holt KE 2017 Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads PLOS Computational Biology 13 e1005595 10.1371/journal.pcbi.1005595 28594827 PMC5481147 · DOI
  68. Wong VK Baker S Pickard DJ 2015 Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events Nature Genetics 47 632 639 10.1038/ng.3281 25961941 PMC4921243 · DOI
  69. Wong VK Baker S Connor TR 2016 An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid Nature Communications 7 12827 10.1038/ncomms12827 27703135 PMC5059462 · DOI

Cited by

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Authors
Kariuki, S., Dyson, Z. A., Mbae, C., Ngetich, R., Kavai, S. M., Wairimu, C., Anyona, S., Gitau, N., Onsare, R. S., Ongandi, B., Duchene, S., Ali, M., Clemens, J. D., Holt, K. E., & Dougan, G.
Affiliations
  • Wellcome Sanger Institute (GB)
  • University of Cambridge (GB)
  • Kenya Medical Research Institute (KE)
  • Centre for Microbiology Research, Kenya Medical Research Institute
  • Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
  • Johns Hopkins University (US)
  • International Centre for Diarrhoeal Disease Research (BD)
  • London School of Hygiene & Tropical Medicine (GB)
  • Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge
Corresponding author
Kariuki, Samuel
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2021-09-13
Volume
10
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.67852
PMC
PMC8494480
OpenAlex
W3198916444
Cited by
50
References
4
Citations by year
2026: 2 · 2025: 5 · 2024: 18 · 2023: 11 · 2022: 11 · 2021: 3
FWCI
6.42
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • Apollo
  • Apollo (cc-by)
Funders
  • National Institutes of Health (R01AI099525)
  • Wellcome Trust (106158/Z/14/Z)
  • European Commission (TyphiNET No 845681)
  • National Institute for Health Research (AMR Theme)
  • Bill and Melinda Gates Foundation (OPP1175797)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Salmonella and Campylobacter epidemiology
  • Life Sciences › Immunology and Microbiology › Microbiology › Bacterial Infections and Vaccines
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
Keywords
typhoid fever, asymptomatic carriage, informal settlements, Nairobi, children, community transmission, reservoirs, whole genome sequencing, phylogenetic analysis
MeSH terms
Adolescent, Anti-Bacterial Agents, Carrier State, Child, Child, Preschool, Female, Humans, Infant, Kenya, Male, Phylogeny, Salmonella typhi, Typhoid Fever, Case-Control Studies, Drug Resistance, Multiple, Bacterial

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