Variation at HLA-DRB1 is associated with resistance to enteric fever

Nature Genetics

Volumn 46, Issue 12, 2014, Pages 1333-1336

  Dunstan, Sarah J ^a,b,c   Hue, Nguyen Thi ^a,d   Han, Buhm ^e,f,g   Li, Zheng ⁱ   Tram, Trinh Thi Bich ^a   Sim, Kar Seng ⁱ   Parry, Christopher M ^a,j   Chinh, Nguyen Tran ^k   Vinh, Ha ^k   Lan, Nguyen Phu Huong ^k   Thieu, Nga Tran Vu ^a   Vinh, Phat Voong ^a   Koirala, Samir ^a   Dongol, Sabina ^a   Arjyal, Amit ^a   Karkey, Abhilasha ^a   Shilpakar, Olita ^a   Dolecek, Christiane ^a,b   Foo, Jia Nee ⁱ   Phuong, Le Thi ^l   Lanh, Mai Ngoc ^l   Do, Tan ^m   Aung, Tin ⁿ   Hon, Do Nu ^m   Teo, Yik Ying ^o   Hibberd, Martin L ^i,p   Anders, Katherine L ^a,b   Okada, Yukinori ^q,r   Raychaudhuri, Soumya ^f,g,h,s   Simmons, Cameron P ^a,b,t   Baker, Stephen ^a,b,p   De Bakker, Paul I W ^u   Basnyat, Buddha ^a   Hien, Tran Tinh ^a   Farrar, Jeremy J ^a,b   Khor, Chiea Chuen ^i,n,o,v   more..

^a OXFORD UNIVERSITY CLINICAL RESEARCH UNIT   (Viet Nam)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d UNIVERSITY OF NATURAL SCIENCES   (Viet Nam)

^e University of Ulsan College of Medicine   (South Korea)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

^g BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^h LABORATORY FOR MOLECULAR MEDICINE   (United States)

ⁱ GENOME INSTITUTE OF SINGAPORE   (Singapore)

^j LIVERPOOL SCHOOL OF TROPICAL MEDICINE   (United Kingdom)

^k UNIVERSITY COLLEGE LONDON HOSPITALS   (United Kingdom)

^l Dong Thap Provincial Hospital   (Viet Nam)

^m Vietnam National Institute of Ophthalmology   (Viet Nam)

ⁿ SINGAPORE EYE RESEARCH INSTITUTE   (Singapore)

^o NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^p LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^q TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^r Institute of Physical and Chemical Research   (Japan)

^s UNIVERSITY OF MANCHESTER   (United Kingdom)

^t UNIVERSITY OF MELBOURNE   (Australia)

^u UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^v NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

more..

Author keywords

[No Author keywords available]

Indexed keywords

HLA DPB1 ANTIGEN; HLA DQA1 ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN; BIOLOGICAL MARKER; GENETIC MARKER; HLA-DRB1*04 ANTIGEN;

ALLELE; ARTICLE; BACTERIAL SURVIVAL; BACTERIAL VIRULENCE; CD4+ T LYMPHOCYTE; CONTROLLED STUDY; DENDRITIC CELL; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HEREDITY; HETEROZYGOTE; HUMAN; IMMUNE RESPONSE; INFECTION RESISTANCE; MAJOR CLINICAL STUDY; MAJOR HISTOCOMPATIBILITY COMPLEX; PRIORITY JOURNAL; TYPHOID FEVER; VIET NAM; ANTIGEN PRESENTATION; CHROMOSOME MAP; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; NEPAL; ODDS RATIO; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI;

ALLELES; ANTIGEN PRESENTATION; BIOMARKERS; CHROMOSOME MAPPING; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HLA-DRB1 CHAINS; HUMANS; MODELS, STATISTICAL; NEPAL; ODDS RATIO; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; TYPHOID FEVER; VIETNAM;

EID: 84927578188     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3143     Document Type: Article

References (56)

1. Buckle, G.C., Walker, C.L. & Black, R.E. Typhoid fever and paratyphoid fever: systematic review to estimate global morbidity and mortality for 2010. J. Glob. Health 2, 010401 (2012)
2. Crump, J.A., Luby, S.P. & Mintz, E.D. The global burden of typhoid fever. Bull. World Health Organ. 82, 346-353 (2004)
3. Cvjetanović, B., Grab, B. & Uemura, K. Epidemiological model of typhoid fever and its use in the planning and evaluation of antityphoid immunization and sanitation programmes. Bull. World Health Organ. 45, 53-75 (1971)
4. Crump, J.A. & Mintz, E.D. Global trends in typhoid and paratyphoid fever. Clin. Infect. Dis. 50, 241-246 (2010)
5. McGregor, A.C., Waddington, C.S. & Pollard, A.J. Prospects for prevention of Salmonella infection in children through vaccination. Curr. Opin. Infect. Dis. 26, 254-262 (2013)
6. Karki, S., Shakya, P., Cheng, A.C., Dumre, S.P. & Leder, K. Trends of etiology and drug resistance in enteric fever in the last two decades in Nepal: a systematic review and meta-analysis. Clin. Infect. Dis. 57, e167-e176 (2013)
7. Kingsley, R.A. et al. Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. MBio 4, e00565-13 (2013)
8. Wong, V.K. et al. Characterization of the yehUT two-component regulatory system of Salmonella enterica serovar Typhi and Typhimurium. PLoS ONE 8, e84567 (2013)
9. de Jong, R. et al. Severe mycobacterial and Salmonella infections in interleukin-12 receptor-deficient patients. Science 280, 1435-1438 (1998)
10. Dunstan, S.J. et al. Typhoid fever and genetic polymorphisms at the natural resistance-associated macrophage protein 1. J. Infect. Dis. 183, 1156-1160 (2001)
11. Dunstan, S.J. et al. Genes of the class II and class III major histocompatibility complex are associated with typhoid fever in Vietnam. J. Infect. Dis. 183, 261-268 (2001)
12. Dunstan, S.J. et al. A TNF region haplotype offers protection from typhoid fever in Vietnamese patients. Hum. Genet. 122, 51-61 (2007)
13. Dharmana, E. et al. HLA-DRB1∗12 is associated with protection against complicated typhoid fever, independent of tumour necrosis factor?. Eur. J. Immunogenet. 29, 297-300 (2002)
14. Fakiola, M. et al. Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis. Nat. Genet. 45, 208-213 (2013)
15. Huyghe, J.R. et al. Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion. Nat. Genet. 45, 197-201 (2013)
16. Helgason, A. et al. Refining the impact of TCF7L2 gene variants on type 2 diabetes and adaptive evolution. Nat. Genet. 39, 218-225 (2007)
17. Pereyra, F. et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330, 1551-1557 (2010)
18. Jia, X. et al. Imputing amino acid polymorphisms in human leukocyte antigens. PLoS ONE 8, e64683 (2013)
19. Pillai, N.E. et al. Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations. Hum. Mol. Genet. 23, 4443-4451 (2014)
20. Raychaudhuri, S. et al. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat. Genet. 44, 291-296 (2012)
21. Gockel, I. et al. Common variants in the HLA-DQ region confer susceptibility to idiopathic achalasia. Nat. Genet. 46, 901-904 (2014)
22. Okada, Y. et al. Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations. Hum. Mol. Genet. doi:10.1093/hmg/ddu387 (28 July 2014)
23. Huang, L., Wang, C. & Rosenberg, N.A. The relationship between imputation error and statistical power in genetic association studies in diverse populations. Am. J. Hum. Genet. 85, 692-698 (2009)
24. Jantsch, J., Chikkaballi, D. & Hensel, M. Cellular aspects of immunity to intracellular Salmonella enterica. Immunol. Rev. 240, 185-195 (2011)
25. Malik-Kale, P. et al. Salmonella-at home in the host cell. Front. Microbiol. 2, 125 (2011)
26. Haraga, A., Ohlson, M.B. & Miller, S.I. Salmonellae interplay with host cells. Nat. Rev. Microbiol. 6, 53-66 (2008)
27. Cheminay, C., Mohlenbrink, A. & Hensel, M. Intracellular Salmonella inhibit antigen presentation by dendritic cells. J. Immunol. 174, 2892-2899 (2005)
28. van den Bergh, E.T., Gasem, M.H., Keuter, M. & Dolmans, M.V. Outcome in three groups of patients with typhoid fever in Indonesia between 1948 and 1990. Trop. Med. Int. Health 4, 211-215 (1999)
29. Khor, C.C. & Hibberd, M.L. Host-pathogen interactions revealed by human genome-wide surveys. Trends Genet. 28, 233-243 (2012)
30. Freudenberg, J. et al. Genome-wide association study of rheumatoid arthritis in Koreans: population-specific loci as well as overlap with European susceptibility loci. Arthritis Rheum. 63, 884-893 (2011)
31. Yamazaki, K. et al. A genome-wide association study identifies 2 susceptibility loci for Crohn's disease in a Japanese population. Gastroenterology 144, 781-788 (2013)
32. Sfriso, P. et al. Infections and autoimmunity: the multifaceted relationship. J. Leukoc. Biol. 87, 385-395 (2010)
33. Karlsson, E.K., Kwiatkowski, D.P. & Sabeti, P.C. Natural selection and infectious disease in human populations. Nat. Rev. Genet. 15, 379-393 (2014)
34. de Bakker, P.I. et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat. Genet. 38, 1166-1172 (2006)
35. de Bakker, P.I. & Telenti, A. Infectious diseases not immune to genome-wide association. Nat. Genet. 42, 731-732 (2010)
36. Davila, S. et al. Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease. Nat. Genet. 42, 772-776 (2010)
37. Thye, T. et al. Common variants at 11p13 are associated with susceptibility to tuberculosis. Nat. Genet. 44, 257-259 (2012)
38. Thye, T. et al. Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2. Nat. Genet. 42, 739-741 (2010)
39. Fellay, J. et al. A whole-genome association study of major determinants for host control of HIV-1. Science 317, 944-947 (2007)
40. Khor, C.C. et al. Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1. Nat. Genet. 43, 1139-1141 (2011)
41. Dean, M. et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 273, 1856-1862 (1996)
42. Huang, Y. et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat. Med. 2, 1240-1243 (1996)
43. Modiano, D. et al. Haemoglobin C protects against clinical Plasmodium falciparum malaria. Nature 414, 305-308 (2001)
44. Cao, X.T. et al. A comparative study of ofloxacin and cefixime for treatment of typhoid fever in children. The Dong Nai Pediatric Center Typhoid Study Group. Pediatr. Infect. Dis. J. 18, 245-248 (1999)
45. Chinh, N.T. et al. A randomized controlled comparison of azithromycin and ofloxacin for treatment of multidrug-resistant or nalidixic acid-resistant enteric fever. Antimicrob. Agents Chemother. 44, 1855-1859 (2000)
46. Luxemburger, C. et al. Risk factors for typhoid fever in the Mekong delta, southern Viet Nam: a case-control study. Trans. R. Soc. Trop. Med. Hyg. 95, 19-23 (2001)
47. Vinh, H. et al. Double blind comparison of ibuprofen and paracetamol for adjunctive treatment of uncomplicated typhoid fever. Pediatr. Infect. Dis. J. 23, 226-230 (2004)
48. House, D. et al. Cytokine release by lipopolysaccharide-stimulated whole blood from patients with typhoid fever. J. Infect. Dis. 186, 240-245 (2002)
49. Arjyal, A. et al. Gatifloxacin versus chloramphenicol for uncomplicated enteric fever: an open-label, randomised, controlled trial. Lancet Infect. Dis. 11, 445-454 (2011)
50. Pandit, A. et al. An open randomized comparison of gatifloxacin versus cefixime for the treatment of uncomplicated enteric fever. PLoS ONE 2, e542 (2007)
51. Koirala, S. et al. Gatifloxacin versus ofloxacin for the treatment of uncomplicated enteric fever in Nepal: an open-label, randomized, controlled trial. PLoS Negl. Trop. Dis. 7, e2523 (2013)
52. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007)
53. Tall, A.R. CETP inhibitors to increase HDL cholesterol levels. N. Engl. J. Med. 356, 1364-1366 (2007)
54. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010)
55. Purcell, S., Cherny, S.S. & Sham, P.C. Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 19, 149-150 (2003)
56. Purdue, M.P. et al. Genome-wide association study of renal cell carcinoma identifies two susceptibility loci on 2p21 and 11q13.3. Nat. Genet. 43, 60-65 (2011)