Skip to main content

Advertisement

SpringerLink
Log in

Pyrosequencing reveals the complex polymicrobial nature of invasive pyogenic infections: microbial constituents of empyema, liver abscess, and intracerebral abscess

  • Article
  • Published:
European Journal of Clinical Microbiology & Infectious Diseases Aims and scope Submit manuscript

Abstract

The polymicrobial nature of invasive pyogenic infections may be underestimated by routine culture practices, due to the fastidious nature of many organisms and the loss of viability during transport or from prior antibacterials. Pyrosequencing was performed on brain and liver abscesses and pleural fluid and compared to routine culture data. Forty-seven invasive pyogenic infection samples from 44 patients [6 intracerebral abscess (ICA), 21 pyogenic liver abscess (PLA), and 18 pleural fluid (PF) samples] were assayed. Pyrosequencing identified an etiologic microorganism in 100 % of samples versus 45 % by culture, p <0.01. Pyrosequencing was also more likely than traditional cultures to classify infections as polymicrobial, 91 % versus 17 %, p <0.001. The median number of genera identified by pyrosequencing compared to culture was 1 [interquartile range (IQR) 1–3] versus 0 (IQR 0–1) for ICA, 7 (IQR 1–15) versus 1 (IQR 0–1) for PLA, and 15 (IQR 9–19) versus 0 (IQR 0–1) for PF. Where organisms were cultured, they typically represented the numerically dominant species identified by pyrosequencing. Complex microbial communities are involved in invasive pyogenic infection of the lung, liver, and brain. Defining the polymicrobial nature of invasive pyogenic infections is the first step towards appreciating the clinical and diagnostic implications of these complex communities.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Laupland KB, Ross T, Church DL et al (2006) Population-based surveillance of invasive pyogenic streptococcal infection in a large Canadian region. Clin Microbiol Infect 12:224–230

    Article  PubMed  CAS  Google Scholar 

  2. Xiao F, Tseng MY, Teng LJ et al (2005) Brain abscess: clinical experience and analysis of prognostic factors. Surg Neurol 63:442–449, discussion 449–50

    Article  PubMed  Google Scholar 

  3. Roche M, Humphreys H, Smyth E et al (2003) A twelve-year review of central nervous system bacterial abscesses; presentation and aetiology. Clin Microbiol Infect 9:803–809

    Article  PubMed  CAS  Google Scholar 

  4. Chen SC, Tsai SJ, Chen CH et al (2008) Predictors of mortality in patients with pyogenic liver abscess. Neth J Med 66:196–203

    PubMed  CAS  Google Scholar 

  5. Kaplan GG, Gregson DB, Laupland KB (2004) Population-based study of the epidemiology of and the risk factors for pyogenic liver abscess. Clin Gastroenterol Hepatol 2:1032–1038

    Article  PubMed  Google Scholar 

  6. Alvarez Pérez JA, González JJ, Baldonedo RF et al (2001) Clinical course, treatment, and multivariate analysis of risk factors for pyogenic liver abscess. Am J Surg 181:177–186

    Article  PubMed  Google Scholar 

  7. Rahman NM, Chapman SJ, Davies RJ (2006) The approach to the patient with a parapneumonic effusion. Clin Chest Med 27:253–266

    Article  PubMed  Google Scholar 

  8. Wolcott RD, Gontcharova V, Sun Y et al (2009) Bacterial diversity in surgical site infections: not just aerobic cocci any more. J Wound Care 18:317–323

    PubMed  CAS  Google Scholar 

  9. Dowd SE, Sun Y, Secor PR et al (2008) Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol 8:43

    Article  PubMed  Google Scholar 

  10. Dowd SE, Wolcott RD, Sun Y et al (2008) Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS One 3:e3326

    Article  PubMed  Google Scholar 

  11. Al Masalma M, Armougom F, Scheld WM et al (2009) The expansion of the microbiological spectrum of brain abscesses with use of multiple 16S ribosomal DNA sequencing. Clin Infect Dis 48:1169–1178

    Article  PubMed  Google Scholar 

  12. Al Masalma M, Lonjon M, Richet H et al (2012) Metagenomic analysis of brain abscesses identifies specific bacterial associations. Clin Infect Dis 54:202–210

    Article  PubMed  Google Scholar 

  13. Sibley CD, Rabin H, Surette MG (2006) Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol 1:53–61

    Article  PubMed  CAS  Google Scholar 

  14. Sibley CD, Parkins MD, Rabin HR et al (2008) A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci U S A 105:15070–15075

    Article  PubMed  CAS  Google Scholar 

  15. Sibley CD, Grinwis ME, Field TR et al (2010) McKay agar enables routine quantification of the ‘Streptococcus milleri’ group in cystic fibrosis patients. J Med Microbiol 59:534–540

    Article  PubMed  Google Scholar 

  16. Sibley CD, Grinwis ME, Field TR et al (2011) Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PLoS One 6:e22702

    Article  PubMed  CAS  Google Scholar 

  17. Clinical and Laboratory Standards Institute (CLSI) (2007)Methods for antimicrobial susceptibility testing of anaerobic bacteria; Approved Standard—Seventh edition. CLSI, Wayne, PA

  18. Clinical and Laboratory Standards Institute (CLSI) (2008) Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; Approved Guideline. CLSI, Wayne, PA

  19. Clinical and Laboratory Standards Institute (CLSI) (2011)Performance standards for antimicrobial susceptibility testing; Twenty-first informational supplement. CLSI, Wayne, PA

  20. Dowd SE, Sun Y, Wolcott RD et al (2008) Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis 5:459–472

    Article  PubMed  CAS  Google Scholar 

  21. Dowd SE, Callaway TR, Wolcott RD et al (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8:125

    Article  PubMed  Google Scholar 

  22. Gontcharova V, Youn E, Wolcott RD et al (2010) Black box chimera check (B2C2): a Windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. Open Microbiol J 4:47–52

    Article  PubMed  CAS  Google Scholar 

  23. Dowd SE, Zaragoza J, Rodriguez JR et al (2005) Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST). BMC Bioinformatics 6:93

    Article  PubMed  Google Scholar 

  24. Cole JR, Wang Q, Cardenas E et al (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145

    Article  PubMed  CAS  Google Scholar 

  25. Mandell GL (2009) Mandell, Douglas, and Bennett’s principles and practices of infectious diseases, 7th edn. Elsevier, Philadelphia

    Google Scholar 

  26. Light RW (1995) A new classification of parapneumonic effusions and empyema. Chest 108:299–301

    Article  PubMed  CAS  Google Scholar 

  27. Laupland KB, Gregson DB, Zygun DA et al (2004) Severe bloodstream infections: a population-based assessment. Crit Care Med 32:992–997

    Article  PubMed  Google Scholar 

  28. Fajardo A, Martínez-Martín N, Mercadillo M et al (2008) The neglected intrinsic resistome of bacterial pathogens. PLoS One 3:e1619

    Article  PubMed  Google Scholar 

  29. European Committee on Antimicrobial Susceptibility Testing (EUCAST) (2008) EUCAST Expert rules in antimicrobial susceptibility testing, version 1, April 2008. Available online at: http://www.srga.org/eucastwt/EUCAST%20Expert%20rules%20final%20April_20080407.pdf. Accessed 15 Nov 2011

  30. Laupland KB, Parkins MD, Ross T et al (2007) Population-based laboratory surveillance for tribe Proteeae isolates in a large Canadian health region. Clin Microbiol Infect 13:683–688

    Article  PubMed  CAS  Google Scholar 

  31. DiBaise JK, Zhang H, Crowell MD et al (2008) Gut microbiota and its possible relationship with obesity. Mayo Clin Proc 83:460–469

    Article  PubMed  Google Scholar 

  32. Hattori M (2010) Genetic analysis of intestinal microbiome by metagenomics. Nihon Rinsho 68(Suppl 8):506–510

    PubMed  Google Scholar 

  33. Wolcott RD, Gontcharova V, Sun Y et al (2009) Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches. BMC Microbiol 9:226

    Article  PubMed  Google Scholar 

  34. Gontcharova V, Youn E, Sun Y et al (2010) A comparison of bacterial composition in diabetic ulcers and contralateral intact skin. Open Microbiol J 4:8–19

    Article  PubMed  Google Scholar 

  35. Smith DM, Snow DE, Rees E et al (2010) Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing. BMC Med Genomics 3:41

    Article  PubMed  Google Scholar 

  36. Erb-Downward JR, Thompson DL, Han MK et al (2011) Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One 6:e16384

    Article  PubMed  CAS  Google Scholar 

  37. Duan K, Dammel C, Stein J et al (2003) Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication. Mol Microbiol 50:1477–1491

    Article  PubMed  CAS  Google Scholar 

  38. Sibley CD, Duan K, Fischer C et al (2008) Discerning the complexity of community interactions using a Drosophila model of polymicrobial infections. PLoS Pathog 4:e1000184

    Article  PubMed  Google Scholar 

  39. Shinzato T, Saito A (1994) A mechanism of pathogenicity of “Streptococcus milleri group” in pulmonary infection: synergy with an anaerobe. J Med Microbiol 40:118–123

    Article  PubMed  CAS  Google Scholar 

  40. Wade BH, Kasper DL, Mandell GL (1983) Interactions of Bacteroides fragilis and phagocytes: studies with whole organisms, purified capsular polysaccharide and clindamycin-treated bacteria. J Antimicrob Chemother 12(Suppl C):51–62

    PubMed  CAS  Google Scholar 

  41. Rotstein OD, Pruett TL, Simmons RL (1985) Mechanisms of microbial synergy in polymicrobial surgical infections. Rev Infect Dis 7:151–170

    Article  PubMed  CAS  Google Scholar 

  42. Edwards R (1997) Resistance to beta-lactam antibiotics in Bacteroides spp. J Med Microbiol 46:979–986

    Article  PubMed  CAS  Google Scholar 

  43. Brook I (2004) Beta-lactamase-producing bacteria in mixed infections. Clin Microbiol Infect 10:777–784

    Article  PubMed  CAS  Google Scholar 

  44. Brook I (2002) Microbiology of polymicrobial abscesses and implications for therapy. J Antimicrob Chemother 50:805–810

    Article  PubMed  CAS  Google Scholar 

  45. Prasad KN, Mishra AM, Gupta D et al (2006) Analysis of microbial etiology and mortality in patients with brain abscess. J Infect 53:221–227

    Article  PubMed  Google Scholar 

  46. Jansson AK, Enblad P, Sjölin J (2004) Efficacy and safety of cefotaxime in combination with metronidazole for empirical treatment of brain abscess in clinical practice: a retrospective study of 66 consecutive cases. Eur J Clin Microbiol Infect Dis 23:7–14

    Article  PubMed  CAS  Google Scholar 

  47. Carpenter J, Stapleton S, Holliman R (2007) Retrospective analysis of 49 cases of brain abscess and review of the literature. Eur J Clin Microbiol Infect Dis 26:1–11

    Article  PubMed  CAS  Google Scholar 

  48. Moore-Gillon JC, Eykyn SJ, Phillips I (1981) Microbiology of pyogenic liver abscess. Br Med J (Clin Res Ed) 283:819–821

    Article  CAS  Google Scholar 

  49. Corredoira J, Casariego E, Moreno C et al (1998) Prospective study of Streptococcus milleri hepatic abscess. Eur J Clin Microbiol Infect Dis 17:556–560

    PubMed  CAS  Google Scholar 

  50. Maskell NA, Davies CW, Nunn AJ et al (2005) U.K. controlled trial of intrapleural streptokinase for pleural infection. N Engl J Med 352:865–874

    Article  PubMed  CAS  Google Scholar 

  51. Ahmed RA, Marrie TJ, Huang JQ (2006) Thoracic empyema in patients with community-acquired pneumonia. Am J Med 119:877–883

    Article  PubMed  Google Scholar 

  52. Rahimian J, Wilson T, Oram V et al (2004) Pyogenic liver abscess: recent trends in etiology and mortality. Clin Infect Dis 39:1654–1659

    Article  PubMed  Google Scholar 

  53. Chan KS, Chen CM, Cheng KC et al (2005) Pyogenic liver abscess: a retrospective analysis of 107 patients during a 3-year period. Jpn J Infect Dis 58:366–368

    PubMed  Google Scholar 

  54. Sabbaj J (1984) Anaerobes in liver abscess. Rev Infect Dis 6(Suppl 1):S152–S156

    Article  PubMed  Google Scholar 

  55. Zaura E, Keijser BJ, Huse SM et al (2009) Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol 9:259

    Article  PubMed  Google Scholar 

  56. Charlson ES, Bittinger K, Haas AR et al (2011) Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 184:957–963

    Article  PubMed  Google Scholar 

  57. Charlson ES, Chen J, Custers-Allen R et al (2010) Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One 5:e15216

    Article  PubMed  CAS  Google Scholar 

  58. Ruiz-Hernández JJ, León-Mazorra M, Conde-Martel A et al (2007) Pyogenic liver abscesses: mortality-related factors. Eur J Gastroenterol Hepatol 19:853–858

    Article  PubMed  Google Scholar 

  59. Zibari GB, Maguire S, Aultman DF et al (2000) Pyogenic liver abscess. Surg Infect (Larchmt) 1:15–21

    Article  CAS  Google Scholar 

  60. Lipsky BA (2007) Empirical therapy for diabetic foot infections: are there clinical clues to guide antibiotic selection? Clin Microbiol Infect 13:351–353

    Article  PubMed  CAS  Google Scholar 

  61. Lipsky BA, Armstrong DG, Citron DM et al (2005) Ertapenem versus piperacillin/tazobactam for diabetic foot infections (SIDESTEP): prospective, randomised, controlled, double-blinded, multicentre trial. Lancet 366:1695–1703

    Article  PubMed  CAS  Google Scholar 

  62. Solomkin J, Teppler H, Graham DR et al (2004) Treatment of polymicrobial infections: post hoc analysis of three trials comparing ertapenem and piperacillin–tazobactam. J Antimicrob Chemother 53(Suppl 2):ii51–ii57

    Article  PubMed  CAS  Google Scholar 

  63. Wacha H, Hau T, Dittmer R et al (1999) Risk factors associated with intraabdominal infections: a prospective multicenter study. Peritonitis Study Group. Langenbecks Arch Surg 384:24–32

    Article  PubMed  CAS  Google Scholar 

  64. Dupont H, Friggeri A, Touzeau J et al (2011) Enterococci increase the morbidity and mortality associated with severe intra-abdominal infections in elderly patients hospitalized in the intensive care unit. J Antimicrob Chemother 66:2379–2385

    Article  PubMed  CAS  Google Scholar 

  65. Nocker A, Richter-Heitmann T, Montijn R et al (2010) Discrimination between live and dead cellsin bacterial communities from environmental water samples analyzed by 454 pyrosequencing. Int Microbiol 13:59–65

    PubMed  CAS  Google Scholar 

  66. Castillo M, Martín-Orúe SM, Manzanilla EG et al (2006) Quantification of total bacteria, enterobacteria and lactobacilli populations in pig digesta by real-time PCR. Vet Microbiol 114:165–170

    Article  PubMed  CAS  Google Scholar 

  67. Grahn N, Olofsson M, Ellnebo-Svedlund K et al (2003) Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons. FEMS Microbiol Lett 219:87–91

    Article  PubMed  CAS  Google Scholar 

  68. Spangler R, Goddard NL, Thaler DS (2009) Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria. PLoS One 4:e7010

    Article  PubMed  Google Scholar 

  69. McGowan JE Jr (2006) Resistance in nonfermenting gram-negative bacteria: multidrug resistance to the maximum. Am J Infect Control 34:S29–S37, discussion S64–73

    Article  PubMed  Google Scholar 

  70. Boucher HW, Talbot GH, Bradley JS et al (2009) Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin Infect Dis 48:1–12

    Article  PubMed  Google Scholar 

  71. Rice LB (2006) Antimicrobial resistance in gram-positive bacteria. Am J Infect Control 34:S11–S19, discussion S64–73

    Article  PubMed  Google Scholar 

Download references

Funding

This project was performed with starter grants from both Calgary Laboratory Services and the Department of Medicine Research Development Fund from the Calgary Health Zone of Alberta Health Services.

Disclosures

C.D.S., D.L.C., S.E.D., M.G.S., and M.D.P. have no conflicts to report.

Author information

Authors and Affiliations

  1. Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive NW, Calgary Laboratory Services, Calgary, AB, T2N 4N, Canada

    C. D. Sibley, M. G. Surette & M. D. Parkins

  2. Department of Medicine, The University of Calgary, 3330 Hospital Drive NW, Calgary Laboratory Services, Calgary, AB, T2N 4N, Canada

    M. D. Parkins

  3. Department of Pathology and Laboratory Medicine, The University of Calgary, 3330 Hospital Drive NW, Calgary Laboratory Services, Calgary, AB, T2N 4N, Canada

    D. L. Church

  4. Department of Medicine, McMaster University, Hamilton, ON, Canada

    M. G. Surette

  5. Molecular Research LP (MR DNA), Shallowater, TX, USA

    S. E. Dowd

Authors
  1. C. D. Sibley
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. L. Church
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. G. Surette
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. E. Dowd
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. M. D. Parkins
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. D. Parkins.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sibley, C.D., Church, D.L., Surette, M.G. et al. Pyrosequencing reveals the complex polymicrobial nature of invasive pyogenic infections: microbial constituents of empyema, liver abscess, and intracerebral abscess. Eur J Clin Microbiol Infect Dis 31, 2679–2691 (2012). https://doi.org/10.1007/s10096-012-1614-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10096-012-1614-x

Keywords

Search

Navigation