Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes

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• 作者：Akira Iwamoto (12)
  Toshihito Tanahashi (12) (13)
  Rina Okada (12)
  Yukio Yoshida (14)
  Kaoru Kikuchi (14)
  Yoshihide Keida (14)
  Yoshiki Murakami (15)
  Lin Yang (12)
  Koji Yamamoto (12)
  Shin Nishiumi (12)
  Masaru Yoshida (12)
  Takeshi Azuma (12)
  
  12. Department of Internal Medicine ; Division of Gastroenterology ; Kobe University Graduate School of Medicine ; 7-5-1 Kusunoki-cho ; Chuo-ku ; Kobe ; 650-0017 ; Japan
  13. Department of Medical Pharmaceutics ; Kobe Pharmaceutical University ; 4-19-1 Motoyama-kita ; Higashinada-ku ; Kobe ; 658-8558 ; Japan
  14. Division of Internal Medicine ; Okinawa Prefectural Chubu Hospital ; 281 Miyazato ; Uruma-city ; Okinawa ; 904-2293 ; Japan
  15. Department of Hepatology ; Osaka City University Graduate School of Medicine ; 1-4-3 Asahimachi ; Abeno-ku ; Osaka ; 545-8585 ; Japan
  
• 关键词：Whole ; genome sequencing ; Helicobacter pylori ; Clarithromycin ; Multidrug efflux ; TolC homolog
• 刊名：Gut Pathogens
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：6
• 期：1
• 全文大小：864 KB
• 参考文献：1. Gisbert, JP, Calvet, X (2011) Review article: the effectiveness of standard triple therapy for Helicobacter pylori has not changed over the last decade, but it is not good enough. Aliment Pharmacol Ther 34: pp. 1255-1268 CrossRef
  2. McColl, KE (2010) Clinical practice. Helicobacter pylori infection. N Engl J Med 362: pp. 1597-1604 CrossRef
  3. Malfertheiner, P, Megraud, F, O鈥橫orain, C, Bazzoli, F, El-Omar, E, Graham, D, Hunt, R, Rokkas, T, Vakil, N, Kuipers, EJ (2007) Current concepts in the management of Helicobacter pylori infection: the Maastricht III Consensus Report. Gut 56: pp. 772-781 CrossRef
  4. Gisbert, JP, Calvet, X, Gomollon, F, Mones, J (2005) [Eradication treatment of Helicobacter pylori. Recommendations of the II Spanish Consensus Conference]. Med Clin (Barc) 125: pp. 301-316 CrossRef
  5. Caselli, M, Zullo, A, Maconi, G, Parente, F, Alvisi, V, Casetti, T, Sorrentino, D, Gasbarrini, G (2007) 鈥淐ervia II Working Group Report 2006鈥? guidelines on diagnosis and treatment of Helicobacter pylori infection in Italy. Dig Liver Dis 39: pp. 782-789 CrossRef
  6. Chey, WD, Wong, BC (2007) American College of Gastroenterology guideline on the management of Helicobacter pylori infection. Am J Gastroenterol 102: pp. 1808-1825 CrossRef
  7. Jenks, PJ (2002) Causes of failure of eradication of Helicobacter pylori. BMJ 325: pp. 3-4 CrossRef
  8. Vakil, N, Megraud, F (2007) Eradication therapy for Helicobacter pylori. Gastroenterology 133: pp. 985-1001 CrossRef
  9. Graham, DY, Lu, H, Yamaoka, Y (2007) A report card to grade Helicobacter pylori therapy. Helicobacter 12: pp. 275-278 CrossRef
  10. Versalovic, J, Shortridge, D, Kibler, K, Griffy, MV, Beyer, J, Flamm, RK, Tanaka, SK, Graham, DY, Go, MF (1996) Mutations in 23S rRNA are associated with clarithromycin resistance in Helicobacter pylori. Antimicrob Agents Chemother 40: pp. 477-480
  11. Taylor, DE, Ge, Z, Purych, D, Lo, T, Hiratsuka, K (1997) Cloning and sequence analysis of two copies of a 23S rRNA gene from Helicobacter pylori and association of clarithromycin resistance with 23S rRNA mutations. Antimicrob Agents Chemother 41: pp. 2621-2628
  12. Rimbara, E, Noguchi, N, Kawai, T, Sasatsu, M (2008) Novel mutation in 23S rRNA that confers low-level resistance to clarithromycin in Helicobacter pylori. Antimicrob Agents Chemother 52: pp. 3465-3466 CrossRef
  13. Kim, JM, Kim, JS, Kim, N, Kim, YJ, Kim, IY, Chee, YJ, Lee, CH, Jung, HC (2008) Gene mutations of 23S rRNA associated with clarithromycin resistance in Helicobacter pylori strains isolated from Korean patients. J Microbiol Biotechnol 18: pp. 1584-1589
  14. Nash, KA, Brown-Elliott, BA, Wallace, RJ (2009) A novel gene, erm(41), confers inducible macrolide resistance to clinical isolates of Mycobacterium abscessus but is absent from Mycobacterium chelonae. Antimicrob Agents Chemother 53: pp. 1367-1376 CrossRef
  15. Roberts, M (2008) Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol Lett 282: pp. 147-159 CrossRef
  16. Hirata, K, Suzuki, H, Nishizawa, T, Tsugawa, H, Muraoka, H, Saito, Y, Matsuzaki, J, Hibi, T (2010) Contribution of efflux pumps to clarithromycin resistance in Helicobacter pylori. J Gastroenterol Hepatol 25: pp. S75-S79 CrossRef
  17. De Francesco, V, Margiotta, M, Zullo, A, Hassan, C, Valle, ND, Burattini, O, D鈥橝ngelo, R, Stoppino, G, Cea, U, Giorgio, F, Monno, R, Morini, S, Panella, C, Ierardi, E (2006) Claritromycin resistance and Helicobacter pylori genotypes in Italy. J Microbiol 44: pp. 660-664
  18. Tanuma, M, Rimbara, E, Noguchi, N, Boonyaritichaikij, S, Kuwabara, K, Fukunaga, Y, Sasatsu, M (2009) Analysis of clarithromycin resistance and CagA status in Helicobacter pylori by use of feces from children in Thailand. J Clin Microbiol 47: pp. 4144-4145 CrossRef
  19. MacLean, D, Jones, JD, Studholme, DJ (2009) Application of 鈥榥ext-generation鈥?sequencing technologies to microbial genetics. Nat Rev Microbiol 7: pp. 287-296
  20. Didelot, X, Bowden, R, Wilson, DJ, Peto, TE, Crook, DW (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13: pp. 601-612 CrossRef
  21. Loman, NJ, Constantinidou, C, Chan, JZ, Halachev, M, Sergeant, M, Penn, CW, Robinson, ER, Pallen, MJ (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10: pp. 599-606 CrossRef
  22. Koser, CU, Ellington, MJ, Cartwright, EJ, Gillespie, SH, Brown, NM, Farrington, M, Holden, MT, Dougan, G, Bentley, SD, Parkhill, J, Peacock, SJ (2012) Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8: pp. e1002824 CrossRef
  23. van Amsterdam, K, Bart, A, van der Ende, A (2005) A Helicobacter pylori TolC efflux pump confers resistance to metronidazole. Antimicrob Agents Chemother 49: pp. 1477-1482 CrossRef
  24. Bentley, DR, Balasubramanian, S, Swerdlow, HP, Smith, GP, Milton, J, Brown, CG, Hall, KP, Evers, DJ, Barnes, CL, Bignell, HR, Boutell, JM, Bryant, J, Carter, RJ, Keira Cheetham, R, Cox, AJ, Ellis, DJ, Flatbush, MR, Gormley, NA, Humphray, SJ, Irving, LJ, Karbelashvili, MS, Kirk, SM, Li, H, Liu, X, Maisinger, KS, Murray, LJ, Obradovic, B, Ost, T, Parkinson, ML, Pratt, MR (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: pp. 53-59 CrossRef
  25. Clark, MJ, Chen, R, Lam, HY, Karczewski, KJ, Chen, R, Euskirchen, G, Butte, AJ, Snyder, M (2011) Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 29: pp. 908-914 CrossRef
  26. Howden, BP, McEvoy, CR, Allen, DL, Chua, K, Gao, W, Harrison, PF, Bell, J, Coombs, G, Bennett-Wood, V, Porter, JL, Robins-Browne, R, Davies, JK, Seemann, T, Stinear, TP (2011) Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR. PLoS Pathog 7: pp. e1002359 CrossRef
  27. Perkins, TT, Tay, CY, Thirriot, F, Marshall, B (2013) Choosing a benchtop sequencing machine to characterise Helicobacter pylori genomes. PLoS One 8: pp. e67539 CrossRef
  28. Quail, MA, Smith, M, Coupland, P, Otto, TD, Harris, SR, Connor, TR, Bertoni, A, Swerdlow, HP, Gu, Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13: pp. 341 CrossRef
  29. Emde, AK, Schulz, MH, Weese, D, Sun, R, Vingron, M, Kalscheuer, VM, Haas, SA, Reinert, K (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics 28: pp. 619-627 CrossRef
  30. Nishizawa, T, Suzuki, H, Umezawa, A, Muraoka, H, Iwasaki, E, Masaoka, T, Kobayashi, I, Hibi, T (2007) Rapid detection of point mutations conferring resistance to fluoroquinolone in gyrA of Helicobacter pylori by allele-specific PCR. J Clin Microbiol 45: pp. 303-305 CrossRef
  31. Nakamura, A, Furuta, T, Shirai, N, Sugimoto, M, Kajimura, M, Soya, Y, Hishida, A (2007) Determination of mutations of the 23S rRNA gene of Helicobacter pylori by allele specific primer-polymerase chain reaction method. J Gastroenterol Hepatol 22: pp. 1057-1063 CrossRef
  32. Furuta, T, Soya, Y, Sugimoto, M, Shirai, N, Nakamura, A, Kodaira, C, Nishino, M, Okuda, M, Okimoto, T, Murakami, K, Fujioka, T, Hishida, A (2007) Modified allele-specific primer-polymerase chain reaction method for analysis of susceptibility of Helicobacter pylori strains to clarithromycin. J Gastroenterol Hepatol 22: pp. 1810-1815 CrossRef
  33. McAdam, PR, Holmes, A, Templeton, KE, Fitzgerald, JR (2011) Adaptive evolution of Staphylococcus aureus during chronic endobronchial infection of a cystic fibrosis patient. PLoS One 6: pp. e24301 CrossRef
  34. Mutreja, A, Kim, DW, Thomson, NR, Connor, TR, Lee, JH, Kariuki, S, Croucher, NJ, Choi, SY, Harris, SR, Lebens, M, Niyogi, SK, Kim, EJ, Ramamurthy, T, Chun, J, Wood, JL, Clemens, JD, Czerkinsky, C, Nair, GB, Holmgren, J, Parkhill, J, Dougan, G (2011) Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477: pp. 462-465 CrossRef
  35. Okusu, H, Ma, D, Nikaido, H (1996) AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. J Bacteriol 178: pp. 306-308
  36. Murakami, S, Nakashima, R, Yamashita, E, Yamaguchi, A (2002) Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 419: pp. 587-593 CrossRef
  37. Nakashima, R, Sakurai, K, Yamasaki, S, Nishino, K, Yamaguchi, A (2011) Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket. Nature 480: pp. 565-569
  38. Johnson, JM, Church, GM (1999) Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps. J Mol Biol 287: pp. 695-715 CrossRef
  39. Bina, JE, Alm, RA, Uria-Nickelsen, M, Thomas, SR, Trust, TJ, Hancock, RE (2000) Helicobacter pylori uptake and efflux: basis for intrinsic susceptibility to antibiotics in vitro. Antimicrob Agents Chemother 44: pp. 248-254 CrossRef
  40. Alvarez-Ortega, C, Olivares, J, Martinez, JL (2013) RND multidrug efflux pumps: what are they good for?. Front Microbiol 4: pp. 7 CrossRef
  41. Tsugawa, H, Suzuki, H, Muraoka, H, Ikeda, F, Hirata, K, Matsuzaki, J, Saito, Y, Hibi, T (2011) Enhanced bacterial efflux system is the first step to the development of metronidazole resistance in Helicobacter pylori. Biochem Biophys Res Commun 404: pp. 656-660 CrossRef
  42. Binh, TT, Shiota, S, Suzuki, R, Matsuda, M, Trang, TT, Kwon, DH, Iwatani, S, Yamaoka, Y (2014) Discovery of novel mutations for clarithromycin resistance in Helicobacter pylori by using next-generation sequencing. J Antimicrob Chemother.
  Performance Standards for Antimicrobial Susceptibility Testing: Seventeenth Informational Supplement M100-S17. CLSI. Wayne, PA, USA
  
• 刊物主题：Gastroenterology; Medical Microbiology; Parasitology;
• 出版者：BioMed Central
• ISSN：1757-4749

文摘

Background Clarithromycin (CLR) is the key drug in eradication therapy of Helicobacter pylori (H. pylori) infection, and widespread use of CLR has led to an increase in primary CLR-resistant H. pylori. The known mechanism of CLR resistance has been established in A2146G and A2147G mutations in the 23S rRNA gene, but evidence of the involvement of other genetic mechanisms is lacking. Using the MiSeq platform, whole-genome sequencing of the 19 clinical strains and the reference strain ATCC26695 was performed to identify single nucleotide variants (SNVs) of multi-drug resistant efflux pump genes in the CLR-resistant phenotype. Results Based on sequencing data of ATCC26695, over one million sequencing reads with over 50-fold coverage were sufficient to detect SNVs, but not indels in the bacterial genome. Sequencing reads of the clinical isolates ranged from 1.82 to 10.8 million, and average coverage ranged from 90.9- to 686.3-fold, which were acceptable criteria for detecting SNVs. Utilizing the conventional approach of allele-specific PCR, point mutations in the 23S rRNA gene were detected in 12 clinical resistant isolates, but not in 7 clinical susceptible isolates. All sequencing reads of CLR-resistant strains had a G mutation in an identical position of the 23S rRNA gene. In addition, genetic variants of four gene clusters (hp0605-hp0607, hp0971-hp0969, hp1327-hp1329, and hp1489-hp1487) of TolC homologues, which have been implicated in multi-drug resistance, were examined. Specific SNVs were dominantly found in resistant strains. Conclusions Gene clusters of TolC homologues are involved in CLR susceptibility profiles in individual H. pylori strains. Whole-genome sequencing has yielded novel understanding of genotype-phenotype relationships.