Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China

Gut Pathogens

Volumn 6, Issue 1, 2014, Pages

  You, Yuanhai ^a   Liu, Lin ^b   Zhang, Maojun ^a   Zhu, Yuanfang ^b   He, Lihua ^a   Li, Dongfang ^b   Zhang, Jianzhong ^a  

^a CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^b BGI SHENZHEN   (China)

Author keywords

Gastric cancer; Genomic features; Helicobacter pylori; Next generation sequencing

Indexed keywords

EID: 84897599705     PISSN: None     EISSN: 17574749     Source Type: Journal    
DOI: 10.1186/1757-4749-6-5     Document Type: Article

References (25)

1. Helicobacter pylori infection and the development of gastric cancer. Uemura N, Okamoto S, Yamamoto S, Matsumura N, Yamaguchi S, Yamakido M, Taniyama K, Sasaki N, Schlemper RJ, N Engl J Med 2001 345 784 789 10.1056/NEJMoa001999 11556297
2. Helicobacter pylori. Marshall B, Am J Gastroenterol 1994 89 116 S128 8048402
3. Pathogenesis of Helicobacter pylori infection. Gerhard M, Rad R, Prinz C, Naumann M, Helicobacter 2002 7 Suppl 1 17 23 12197905
4. Replicative genomics can help Helicobacter fraternity usher in good times. Ahmed N, Gut Pathog 2010 2 25 10.1186/1757-4749-2-25 21182772
5. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Falush D, Kraft C, Taylor NS, Correa P, Fox JG, Achtman M, Suerbaum S, Proc Natl Acad Sci USA 2001 98 15056 15061 10.1073/pnas.251396098 11742075
6. Gain and loss of multiple genes during the evolution of Helicobacter pylori. Gressmann H, Linz B, Ghai R, Pleissner KP, Schlapbach R, Yamaoka Y, Kraft C, Suerbaum S, Meyer TF, Achtman M, PLoS Genet 2005 1 43 10.1371/journal.pgen.0010043 16217547
7. Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Ahmed N, Dobrindt U, Hacker J, Hasnain SE, Nat Rev Microbiol 2008 6 387 394 10.1038/nrmicro1889 18392032
8. A flood of microbial genomes-do we need more? Ahmed N, PLoS One 2009 4 5831 10.1371/journal.pone.0005831 19513110
9. Helicobacter pylori-a seasoned pathogen by any other name. Ahmed N, Tenguria S, Nandanwar N, Gut Pathog 2009 1 24 10.1186/1757-4749-1-24 20030808
10. Helicobacter pylori in 2013: multiplying genomes, emerging insights. Ahmed N, Loke MF, Kumar N, Vadivelu J, Helicobacter 2013 18 Suppl 1 1 4
11. Comparative analysis of the full genome of Helicobacter pylori isolate Sahul64 identifies genes of high divergence. Lu W, Wise MJ, Tay CY, Windsor HM, Marshall BJ, Peacock C, Perkins T, J Bacteriol 2014 196 5 1073 1083 10.1128/JB.01021-13 24375107
12. Next-generation sequencing and de novo assembly, genome organization, and comparative genomic analyses of the genomes of two Helicobacter pylori isolates from duodenal ulcer patients in India. Kumar N, Mukhopadhyay AK, Patra R, De R, Baddam R, Shaik S, Alam J, Tiruvayipati S, Ahmed N, J Bacteriol 2012 194 21 5963 5964 10.1128/JB.01371-12 23045484
13. Genome sequences of three Helicobacter pylori strains isolated from atrophic gastritis and gastric ulcer patients in China. Yuanhai Y, Lin L, Maojun Z, Xifang H, Lihua H, Yuanfang Z, Peixiang N, Jianzhong Z, J Bacteriol 2012 194 22 6314 6315 10.1128/JB.01399-12 23105058
14. Genomic diversity in Helicobacter and related organisms. Linz B, Schuster SC, Res Microbiol 2007 158 737 744 10.1016/j.resmic.2007.09.006 18023330
15. Genomes of Two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient. Avasthi TS, Devi SH, Taylor TD, Kumar N, Baddam R, Kondo S, Suzuki Y, Lamouliatte H, Mégraud F, Ahmed N, J Bacteriol 2011 193 13 3385 3386 10.1128/JB.05006-11 21515762
16. Genotypic and phenotypic stability of Helicobacter pylori markers in a nine-year follow-up study of patients with noneradicated infection. Gustavsson A, Unemo M, Blomberg B, Danielsson D, Dig Dis Sci 2005 50 375 380 10.1007/s10620-005-1613-1 15745103
17. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Israel DA, Salama N, Krishna U, Rieger UM, Atherton JC, Falkow S, Peek RM Jr, Proc Natl Acad Sci USA 2001 98 14625 14630 10.1073/pnas.251551698 11724955
18. Stewart BW, Kleihues P, World Cancer Report Lyon: IARC Press 2003
19. Epidemiology of gastric cancer. Crew KD, Neugut AI, World J Gastroenterol 2006 12 3 354 362 16489633
20. Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome. Yuanhai Y, Lihua H, Maojun Z, Jianying F, Yixin G, Binghua Z, Xiaoxia T, Jianzhong Z, PLoS ONE 2012 7 6 38528 10.1371/journal.pone.0038528 22701658
21. The RAST Server: rapid annotations using subsystems technology. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O, BMC Genomics 2008 9 75 10.1186/1471-2164-9-75 18261238
22. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Darling AC, Mau B, Blattner FR, Perna NT, Genome Res 2004 14 7 1394 1403 10.1101/gr.2289704 15231754
23. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP, BMC Bioinforma 2010 11 461 10.1186/1471-2105-11-461
24. Traces of human migrations in Helicobacter pylori populations. Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Mégraud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S, Science 2003 299 1582 1585 10.1126/science.1080857 12624269
25. Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. Suzuki R, Shiota S, Yamaoka Y, Infect Genet Evol 2012 12 2 203 213 10.1016/j.meegid.2011.12.002 22197766