Abstract
Pyogenic liver abscess (PLA) is a severe disease with considerable mortality and is often polymicrobial. Understanding the pathogens that cause PLA is the basis for PLA treatment. Here, we profiled the bacterial composition in PLA fluid by pyrosequencing the 16S ribosomal RNA (rRNA) gene based on next-generation sequencing (NGS) technology to identify etiological agents of PLA and to provide information of their 16S rRNA sequences for application to DNA-based techniques in the hospital. Twenty patients with PLA who underwent percutaneous catheter drainage, abscess culture, and blood culture for isolates were included. Genomic DNAs from abscess fluids were subjected to polymerase chain reaction and pyrosequencing of the 16S rRNA gene with a 454 GS Junior System. The abscess and blood cultures were positive in nine (45%) and four (20%) patients, respectively. Pyrosequencing of 16S rRNA gene showed that 90% of the PLA fluid samples contained single or multiple genera of known bacteria such as Klebsiella, Fusobacterium, Streptococcus, Bacteroides, Prevotella, Peptostreptococcus, unassigned Enterobacteriaceae, and Dialister. Klebsiella was predominantly found in the PLA fluid samples. All samples that carried unassigned bacteria had 26.8% reads on average. We demonstrated that the occurrence of PLA was associated with eight known bacterial genera as well as unassigned bacteria and that 16S rRNA gene sequencing was more useful than conventional culture methods for accurate identification of bacterial pathogens from PLA.
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Ali A.H., Smalligan R.D., Ahmed M., and Khasawneh F.A. 2013. Pyogenic liver abscess and the emergence of Klebsiella as an etiology: a retrospective study. Int. J. Gen. Med. 7, 37–42.
Bourbeau P.P., Heiter B.J., and Figdore M. 1997. Use of Gen-Probe AccuProbe Group B streptococcus test to detect group B streptococci in broth cultures of vaginal-anorectal specimens from pregnant women: comparison with traditional culture method. J. Clin. Microbiol. 35, 144–147.
Cerwenka H. 2010. Pyogenic liver abscess: differences in etiology and treatment in Southeast Asia and Central Europe. World J. Gastroenterol. 16, 2458–2462.
Chung D.R., Lee H., Park M.H., Jung S.I., Chang H.H., Kim Y.S., Son J.S., Moon C., Kwon K.T., Ryu S.Y., and et al. 2012. Fecal carriage of serotype K1 Klebsiella pneumoniae ST23 strains closely related to liver abscess isolates in Koreans living in Korea. Eur. J. Clin. Microbiol. Infect. Dis. 31, 481–486.
Clarridge J.E., 3rd. 2004. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 17, 840–862.
Corbella X., Vadillo M., Torras J., Pujol M., Rafecas A., and Gudiol F. 1995. Presentation, diagnosis and treatment of pyogenic liver abscess: analysis of a series of 63 cases. Enferm. Infect. Microbiol. Clin. 13, 80–84.
Costa M.C., Arroyo L.G., Allen-Vercoe E., Stämpfli H.R., Kim P.T., Sturgeon A., and Weese J.S. 2012. Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene. PLoS ONE 7, e41484.
Denys G.A. and Carey R.B. 1992. Identification of Streptococcus pneumoniae with a DNA probe. J. Clin. Microbiol. 30, 2725–2727.
Fredericks D.N. and Relman D.A. 1996. Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clin. Microbiol. Rev. 9, 18–33.
Hiyari S. and Bennett K.M. 2011. Dental diagnostics: molecular analysis of oral biofilms. J. Dent. Hyg. 85, 256–263.
Holder R.C., Kirse D.J., Evans A.K., Peters T.R., Poehling K.A., Swords W.E., and Reid S.D. 2012. One third of middle ear effusions from children undergoing tympanostomy tube placement had multiple bacterial pathogens. BMC Pediatr. 12, 87.
Hooda S., Minamoto Y., Suchodolski J.S., and Swanson K.S. 2012. Current state of knowledge: the canine gastrointestinal microbiome. Anim. Health. Res. Rev. 13, 78–88.
Huse S.M., Ye Y., Zhou Y., and Fodor A.A. 2012. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7, e34242.
Kiratisin P., Li L., Murray P.R., and Fischer S.H. 2003. Identification of bacteria recovered from clinical specimens by 16S rRNA gene sequencing. Eur. J. Clin. Microbiol. Infect. Dis. 22, 628–631.
Kolbert C.P. and Persing D.H. 1999. Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr. Opin. Microbiol. 2, 299–305.
Lebrun L., Espinasse F., Poveda J.D., and Vincent-Levy-Frebault V. 1992. Evaluation of nonradioactive DNA probes for identification of mycobacteria. J. Clin. Microbiol. 30, 2476–2478.
Lee K.T., Wong S.R., and Sheen P.C. 2001. Pyogenic liver abscess: an audit of 10 years’ experience and analysis of risk factors. Dig. Surg. 18, 459–465.
Li J., Fu Y., Wang J.Y., Tu C.T., Shen X.Z., Li L., and Jiang W. 2010. Early diagnosis and therapeutic choice of Klebsiella pneumoniae liver abscess. Front. Med. China 4, 308–316.
Li W. and Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659.
Liu Y., Wang J.Y., and Jiang W. 2013. An increasing prominent disease of liver abscess: etiology, diagnosis, and treatment. Gastroenterol. Res. Pract. 2013, 2585–4.
Lopez-Cano Gomez M., Laguna Del Estal P., Garcia Montero P., Gil Navarro M., and Castaneda Pastor A. 2012. Pyogenic liver abscess: clinical presentation and predictors of unfavorable outcome. Gastroenterol. Hepatol. 35, 229–235.
Malik A.A., Bari S.U., Rouf K.A., and Wani K.A. 2010. Pyogenic liver abscess: Changing patterns in approach. World J. Gastrointest. Surg. 2, 395–401.
Mignard S. and Flandrois J.P. 2006. 16S rRNA sequencing in routine bacterial identification: a 30-month experiment. J. Microbiol. Methods 67, 574–581.
Ochsner A., DeBakey M., and Murray S. 1938. Pyogenic abscess of the liver: II. An analysis of forty-seven cases with review of the literature. Am. J. Surg. 40, 292–319.
Padhye A.A., Smith G., McLaughlin D., Standard P.G., and Kaufman L. 1992. Comparative evaluation of a chemiluminescent DNA probe and an exoantigen test for rapid identification of Histoplasma capsulatum. J. Clin. Microbiol. 30, 3108–3111.
Patel J.B. 2001. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol. Diagn. 6, 313–321.
Petrosino J.F., Highlander S., Luna R.A., Gibbs R.A., and Versalovic J. 2009. Metagenomic pyrosequencing and microbial identification. Clin. Chem. 55, 856–866.
Petti C.A., Polage C.R., and Schreckenberger P. 2005. The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods. J. Clin. Microbiol. 43, 6123–6125.
Quince C., Lanzen A., Davenport R.J., and Turnbaugh P.J. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38.
Rousée J.M., Bermond D., Piémont Y., Tournoud C., Heller R., Kehrli P., Harlay M.L., Monteil H., and Jaulhac B. 2002. Dialister pneumosintes associated with human brain abscesses. J. Clin. Microbiol. 40, 3871–3873.
Salipante S.J., Sengupta D.J., Rosenthal C., Costa G., Spangler J., Sims E.H., Jacobs M.A., Miller S.I., Hoogestraat D.R., Cookson B.T., and et al. 2013. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS ONE 8, e65226.
Siu L.K., Fung C.P., Chang F.Y., Lee N., Yeh K.M., Koh T.H., and Ip M. 2011. Molecular typing and virulence analysis of serotype K1 Klebsiella pneumoniae strains isolated from liver abscess patients and stool samples from noninfectious subjects in Hong Kong, Singapore, and Taiwan. J. Clin. Microbiol. 49, 3761–3765.
Stein M., Schirotzek I., Preuss M., Scharbrodt W., Oertel M. 2011. Brainstem abscess caused by Haemophilus influenza and Peptostreptococcus species. J. Clin. Neurosci. 18, 425–428.
Woo P.C., Lau S.K., Teng J.L., Tse H., and Yuen K.Y. 2008. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin. Microbiol. Infect. 14, 908–934.
Yu S.C., Ho S.S., Lau W.Y., Yeung D.T., Yuen E.H., Lee P.S., and Metreweli C. 2004. Treatment of pyogenic liver abscess: prospective randomized comparison of catheter drainage and needle aspiration. Hepatology 39, 932–938.
Zibari G.B., Maguire S., Aultman D.F., McMillan R.W., and Mc-Donald J.C. 2000. Pyogenic liver abscess. Surg. Infect. (Larchmt) 1, 15–21.
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Song, Y.G., Shim, S.G., Kim, K.M. et al. Profiling of the bacteria responsible for pyogenic liver abscess by 16S rRNA gene pyrosequencing. J Microbiol. 52, 504–509 (2014). https://doi.org/10.1007/s12275-014-4241-7
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DOI: https://doi.org/10.1007/s12275-014-4241-7