Comprehensive diagnosis of bacterial infection associated with acute cholecystitis using metagenomic approach

Frontiers in Microbiology

Volumn 8, Issue APR, 2017, Pages

  Kujiraoka, Manabu ^a,b   Kuroda, Makoto ^b   Asai, Koji ^a   Sekizuka, Tsuyoshi ^b   Kato, Kengo ^b   Watanabe, Manabu ^a   Matsukiyo, Hiroshi ^a   Saito, Tomoaki ^a   Ishii, Tomotaka ^a   Katada, Natsuya ^a   Saida, Yoshihisa ^a   Kusachi, Shinya ^a  

^a TOHO UNIVERSITY OHASHI MEDICAL CENTER   (Japan)

^b NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

Author keywords

Acute cholecystitis; Bacteriological analysis; Gut microbiota; Metagenome analysis; Next generation sequencing

Indexed keywords

BETA LACTAMASE CTX M; CEFOPERAZONE PLUS SULBACTAM; CEFTRIAXONE; DNA;

ACUTE CHOLECYSTITIS; ADULT; AGED; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL INFECTION; BILE; BIOINFORMATICS; CHOLECYSTECTOMY; CHOLESTASIS; CLINICAL ARTICLE; DISEASE ASSOCIATION; ESCHERICHIA COLI INFECTION; FECES ANALYSIS; FEMALE; GENOME ANALYSIS; HUMAN; INFECTION; KLEBSIELLA PNEUMONIAE INFECTION; MALE; METAGENOME; METAGENOMICS; MIDDLE AGED; POLYMERASE CHAIN REACTION; SALIVA ANALYSIS; STREPTOCOCCUS INFECTION; VERY ELDERLY;

EID: 85018326977     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2017.00685     Document Type: Article

References (38)

1. Asai, K., Watanabe, M., Kusachi, S., Tanaka, H., Matsukiyo, H., Osawa, A., et al. (2012). Bacteriological analysis of bile in acute cholecystitis according to the Tokyo guidelines. J. Hepatobiliary Pancreat. Sci. 19, 476-486. doi: 10.1007/s00534-011-0463-9
2. Banerjee, R., and Johnson, J. R. (2014). A new clone sweeps clean: the enigmatic emergence of Escherichia coli sequence type 131. Antimicrob. Agents Chemother. 58, 4997-5004. doi: 10.1128/AAC.02824-14
3. Barzon, L., Lavezzo, E., Militello, V., Toppo, S., and Palu, G. (2011). Applications of next-generation sequencing technologies to diagnostic virology. Int. J. Mol. Sci. 12, 7861-7884. doi: 10.3390/ijms12117861
4. Becker, C., Neurath, M. F., and Wirtz, S. (2015). The intestinal microbiota in inflammatory bowel disease. ILAR J. 56, 192-204. doi: 10.1093/ilar/ilv030
5. Bonnet, R. (2004). Growing group of extended-spectrum β-lactamases: the CTX-M enzymes. Antimicrob. Agents Chemother. 48, 1-14. doi: 10.1128/AAC.48.1.1-14.2004
6. Chan, J. Z., Pallen, M. J., Oppenheim, B., and Constantinidou, C. (2012). Genome sequencing in clinical microbiology. Nat. Biotechnol. 30, 1068-1071. doi: 10.1038/nbt.2410
7. Clemente, J. C., Ursell, L. K., Parfrey, L. W., and Knight, R. (2012). The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258-1270. doi: 10.1016/j.cell.2012.01.035
8. Clinical and Laboratory Standards Institute (2012). Performance Standards for Antimicrobial Susceptibility Testing; Twenty-second Informational Supplement. Wayne, PA: Clinical and Laboratory Standards Institute.
9. Csendes, A., Burdiles, P., Maluenda, F., Diaz, J. C., Csendes, P., and Mitru, N. (1996). Simultaneous bacteriologic assessment of bile from gallbladder and common bile duct in control subjects and patients with gallstones and common duct stones. Arch Surg. 131, 389-394. doi: 10.1001/archsurg.1996.01430160047008
10. Dalal, S. R., and Chang, E. B. (2014). The microbial basis of inflammatory bowel diseases. J. Clin. Invest. 124, 4190-4196. doi: 10.1172/JCI72330
11. Faria, N. R., Azevedo Rdo, S., Kraemer, M. U., Souza, R., Cunha, M. S., Hill, S. C., et al. (2016). Zika virus in the Americas: early epidemiological and genetic findings. Science 352, 345-349. doi: 10.1126/science.aaf5036
12. Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., and Pace, N. R. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U.S.A. 104, 13780-13785. doi: 10.1073/pnas.0706625104
13. Hawkey, P. M., and Jones, A. M. (2009). The changing epidemiology of resistance. J. Antimicrob. Chemother. 64(Suppl. 1), i3-10. doi: 10.1093/jac/dkp256
14. Huson, D. H., Auch, A. F., Qi, J., and Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Res. 17, 377-386. doi: 10.1101/gr.5969107
15. Huson, D. H., Beier, S., Flade, I., Gorska, A., El-Hadidi, M., Mitra, S., et al. (2016). MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12:e1004957. doi: 10.1371/journal.pcbi.1004957
16. Larsen, M. V., Cosentino, S., Rasmussen, S., Friis, C., Hasman, H., Marvig, R. L., et al. (2012). Multilocus sequence typing of total-genome-sequenced bacteria. J. Clin. Microbiol. 50, 1355-1361. doi: 10.1128/JCM.06094-11
17. Lavezzo, E., Toppo, S., Franchin, E., Di Camillo, B., Finotello, F., Falda, M., et al. (2013). Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak. BMC Infect. Dis. 13:554. doi: 10.1186/1471-2334-13-554
18. Liu, J., Yan, Q., Luo, F., Shang, D., Wu, D., Zhang, H., et al. (2015). Acute cholecystitis associated with infection of Enterobacteriaceae from gut microbiota. Clin. Microbiol. Infect. 21, 851.e1-e9. doi: 10.1016/j.cmi.2015.05.017
19. Lloyd-Price, J., Abu-Ali, G., and Huttenhower, C. (2016). The healthy human microbiome. Genome Med. 8:51. doi: 10.1186/s13073-016-0307-y
20. Matsumura, Y., Johnson, J. R., Yamamoto, M., Nagao, M., Tanaka, M., Takakura, S., et al. (2015). CTX-M-27-and CTX-M-14-producing, ciprofloxacin-resistant Escherichia coli of the H30 subclonal group within ST131 drive a Japanese regional ESBL epidemic. J. Antimicrob. Chemother. 70, 1639-1649. doi: 10.1093/jac/dkv017
21. Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., et al. (2012). Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13:R79. doi: 10.1186/gb-2012-13-9-r79
22. Nicolas-Chanoine, M. H., Bertrand, X., and Madec, J. Y. (2014). Escherichia coli ST131, an intriguing clonal group. Clin. Microbiol. Rev. 27, 543-574. doi: 10.1128/CMR.00125-13
23. Nicolas-Chanoine, M. H., Blanco, J., Leflon-Guibout, V., Demarty, R., Alonso, M. P., Canica, M. M., et al. (2008). Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15. J. Antimicrob. Chemother. 61, 273-281. doi: 10.1093/jac/dkm464
24. Odamaki, T., Kato, K., Sugahara, H., Hashikura, N., Takahashi, S., Xiao, J. Z., et al. (2016). Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiol. 16:90. doi: 10.1186/s12866-016-0708-5
25. Ondov, B. D., Bergman, N. H., and Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12:385. doi: 10.1186/1471-2105-12-385
26. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65. doi: 10.1038/nature08821
27. Rogers, B. A., Sidjabat, H. E., and Paterson, D. L. (2011). Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. J. Antimicrob. Chemother. 66, 1-14. doi: 10.1093/jac/dkq415
28. Shibasaki, M., Komatsu, M., Sueyoshi, N., Maeda, M., Uchida, T., Yonezawa, H., et al. (2016). Community spread of extended-spectrum beta-lactamase-producing bacteria detected in social insurance hospitals throughout Japan. J. Infect. Chemother. 22, 395-399. doi: 10.1016/j.jiac.2016.03.001
29. Takada, T., Kawarada, Y., Nimura, Y., Yoshida, M., Mayumi, T., Sekimoto, M., et al. (2007). Background: Tokyo Guidelines for the management of acute cholangitis and cholecystitis. J. Hepatobiliary. Pancreat. Surg. 14, 1-10. doi: 10.1007/s00534-006-1150-0
30. Takada, T., Strasberg, S. M., Solomkin, J. S., Pitt, H. A., Gomi, H., Yoshida, M., et al. (2013). TG13: updated Tokyo guidelines for the management of acute cholangitis and cholecystitis. J. Hepatobiliary Pancreat. Sci. 20, 1-7. doi: 10.1007/s00534-012-0566-y
31. Takeuchi, F., Sekizuka, T., Yamashita, A., Ogasawara, Y., Mizuta, K., and Kuroda, M. (2014). MePIC, metagenomic pathogen identification for clinical specimens. Jpn. J. Infect. Dis. 67, 62-65. doi: 10.7883/yoken.67.62
32. Tang, P., and Chiu, C. (2010). Metagenomics for the discovery of novel human viruses. Future Microbiol. 5, 177-189. doi: 10.2217/fmb.09.120
33. Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J. P., et al. (2009). Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11, 2574-2584. doi: 10.1111/j.1462-2920.2009.01982.x
34. van der Linden, W., and Sunzel, H. (1970). Early versus delayed operation for acute cholecystitis. A controlled clinical trial. Am. J. Surg. 120, 7-13. doi: 10.1016/S0002-9610(70)80133-7
35. Wang, C. H., Wu, C. Y., Yang, J. C., Lien, W. C., Wang, H. P., Liu, K. L., et al. (2016). Long-term outcomes of patients with acute cholecystitis after successful percutaneous cholecystostomy treatment and the risk factors for recurrence: a decade experience at a single center. PLoS ONE 11:e0148017. doi: 10.1371/journal.pone.0148017
36. Wells, J. E., Berr, F., Thomas, L. A., Dowling, R. H., and Hylemon, P. B. (2000). Isolation and characterization of cholic acid 7a-dehydroxylating fecal bacteria from cholesterol gallstone patients. J. Hepatol. 32, 4-10. doi: 10.1016/S0168-8278(00)80183-X
37. Wu, T., Zhang, Z., Liu, B., Hou, D., Liang, Y., Zhang, J., et al. (2013). Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study. BMC Genomics 14:669. doi: 10.1186/1471-2164-14-669
38. Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., et al. (2012). Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640-2644. doi: 10.1093/jac/dks261