Bacterial landscape of bloodstream infections in neutropenic patients via high throughput sequencing

PLoS ONE

Volumn 10, Issue 8, 2015, Pages

  Gyarmati, Peter ^a,b   Kjellander, Christian ^a   Aust, Carl ^b   Kalin, Mats ^a   Öhrmalm, Lars ^b   Giske, Christian G ^a,b  

^a KAROLINSKA INSTITUTE   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; C REACTIVE PROTEIN; ANTINEOPLASTIC AGENT; BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ACTINOBACTERIA; ADULT; ARTICLE; BACTERIAL INFECTION; BACTERIUM DETECTION; BACTEROIDETES; BLOOD CULTURE; BLOODSTREAM INFECTION; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; FEBRILE NEUTROPENIA; FEMALE; FIRMICUTES; FUSOBACTERIA; GENE AMPLIFICATION; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOCOMPROMISED PATIENT; LEUKOCYTE COUNT; MALE; MICROBIAL DIVERSITY; MORTALITY; NEUTROPHIL COUNT; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; RETROSPECTIVE STUDY; AGED; BACTEREMIA; BACTERIUM; BACTERIUM IDENTIFICATION; CLASSIFICATION; COMPLICATION; DNA SEQUENCE; GENETICS; HEMATOLOGIC NEOPLASMS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MIDDLE AGED; MOLECULAR TYPING; NEUTROPENIA; PROCEDURES;

ADULT; AGED; ANTINEOPLASTIC AGENTS; BACTEREMIA; BACTERIA; BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; DNA, RIBOSOMAL; FEMALE; HEMATOLOGIC NEOPLASMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; MOLECULAR TYPING; NEUTROPENIA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84942893153     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0135756     Document Type: Article

References (55)

1. De Naurois J, Novitzky-Basso I, Gill MJ, Marti FM, Cullen MH, Roila F, ESMO Guidelines Working Group 2010. Management of febrile neutropenia: ESMO Clinical Practice Guidelines. Ann Oncol. 21, Suppl 5:v252-6. doi: 10.1093/annonc/mdq196 PMID: 20555092
2. Hughes WT, Armstrong D, Bodey GP, Bow EJ, Brown AE, Calandra T, et al. 2002. 2002 guidelines for the use of antimicrobial agents in neutropenic patients with cancer. Clin Infect Dis. 34(6):730-51. PMID: 11850858
3. Kjellander C, Björkholm M, Cherif H, Kalin M, Giske CG 2012. Low all-cause mortality and low occurrence of antimicrobial resistance in hematological patients with bacteremia receiving no antibacterial prophylaxis: a single-center study. Eur J Haematol. 88(5):422-30. doi: 10.1111/j.1600-0609.2012. 01768.x PMID: 22335785
4. Lecuit M, Eloit M. 2014. The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening. Front Cell Infect Microbiol. 4:25. doi: 10.3389/fcimb.2014.00025 PMID: 24639952
5. Wade WG. 2013. The oral microbiome in health and disease. Pharmacol Res. 69(1):137-43. doi: 10. 1016/j.phrs.2012.11.006 PMID: 23201354
6. Ward DM, Weller R, Bateson MM. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 345:63-65. PMID: 1691827
7. Sears CL. 2005. A dynamic partnership: celebrating our gut flora. Anaerobe. 11(5):247-51. PMID: 16701579
8. Ecker DJ, Sampath R, Li H, Massire C, Matthews HE, Toleno D, et al. 2010. New technology for rapid molecular diagnosis of bloodstream infections. Expert Rev Mol Diagn. 10(4):399-415. doi: 10.1586/erm.10.24 PMID: 20465496
9. Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, et al. 2013. High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions. Nucleic Acids Res. 41:22.
10. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41(1):e1. doi: 10.1093/nar/gks808 PMID: 22933715
11. Salter S, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. 2014. Reagent contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12:78.
12. Hamady M, Knight R. 2009. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 19(7):1141-52. doi: 10.1101/gr.085464.108 PMID: 19383763
13. Mago. T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 27(21):2957-63. doi: 10.1093/bioinformatics/btr507 PMID: 21903629
14. Li W, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 22(13):1658-1659. PMID: 16731699
15. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26(19):2460-2461. doi: 10.1093/bioinformatics/btq461 PMID: 20709691
16. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403-10. PMID: 2231712
17. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37 (Database issue):D141-5. doi: 10.1093/nar/gkn879 PMID: 19004872
18. Federhen S. 2012. The NCBI Taxonomy database. Nucleic Acids Res. 40 (D1):D136-D143.
19. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Meth. 7(5):335-6.
20. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 27(16):2194-2200. doi: 10.1093/bioinformatics/btr381 PMID: 21700674
21. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb. 73(16):5261-5267.
22. Werner JJ, Koren O, Hugenholtz P, De Santis TZ, Walters WA, Caporaso JG, et al. 2012. Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys. ISME J. 6:94-103. doi: 10.1038/ismej.2011.82 PMID: 21716311
23. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments. PLOS One. 5:3.
24. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41 (D1):D590-D596.
25. Kuderer NM, Dale DC, Crawford J, Cosler LE, Lyman GH. 2006. Mortality, morbidity, and cost associated with febrile neutropenia in adult cancer patients. Cancer. 106(10):2258-66. PMID: 16575919
26. Kommedal O, Wilhelmsen MT, Skrede S, Meisal R, Jakovljev A, Gaustad P, et al. 2014. Massive parallel sequencing provides new perspectives on bacterial brain abscesses. J Clin Microbiol. 52(6):1990-7. doi: 10.1128/JCM.00346-14 PMID: 24671797
27. Ni J, Yan Q, Yu Y. 2013. How much metagenomic sequencing is enough to achieve a given goal? Sci Rep. 3:1968. doi: 10.1038/srep01968 PMID: 23752679
28. Gomila M, Bowien B, Falsen E, Moore ER, Lalucat J. 2007. Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water. Int J Syst Evol Microbiol. 57(11):2629-35.
29. Sze MA, Tsuruta M, Yang SW, Oh Y, Man SF, Hogg JC, et al. 2014. Changes in the Bacterial Microbiota in Gut, Blood, and Lungs following Acute LPS Instillation into Mice Lungs. PLOS One. 9(10):e111228. doi: 10.1371/journal.pone.0111228 PMID: 25333938
30. Jacob-Kokura S, Chan CY, Kaplan L. 2014. Bacteremia and empyema caused by Shewanella algae in a trauma patient. Ann Pharmacother. 48(1):128-36. doi: 10.1177/1060028013517630 PMID: 24396089
31. Myung DS, Jung YS, Kang SJ, Song YA, Park KH, Jung SI, et al. 2009. Primary Shewanella algae bacteremia mimicking Vibrio septicemia. J Korean Med Sci. 24(6):1192-4. doi: 10.3346/jkms.2009.24.6. 1192 PMID: 19949681
32. Dominguez H, Vogel BF, Gram L, Hoffmann S, Schaebel S. (1996) Shewanella alga bacteremia in two patients with lower leg ulcers. Clin Infect Dis. 22(6):1036-9. PMID: 8783706
33. Holt HM, Gahrn-Hansen B, Bruun B. 2005. Shewanella algae and Shewanella putrefaciens: clinical and microbiological characteristics. Clin Microbiol Infect. 11(5):347-52. PMID: 15819859
34. Ortega M, Marco F, Soriano A, Almela M, Martinez JA, Rovira M, et al. 2014. Epidemiology and outcome of bacteraemia in neutropenic patients in a single institution from 1991.2012. Epidemiol Infect. 30:1-7.
35. Kang CI, Kim SH, Kim HB, Park SW, Choe YJ, Oh MD, et al. 2003. Pseudomonas aeruginosa bacteremia: risk factors for mortality and influence of delayed receipt of effective antimicrobial therapy on clinical outcome. Clin Infect Dis. 37(6):745-51. PMID: 12955633
36. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H. 2000. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol. 50(4):1563-89.
37. Mulet M, Lalucat J, Garcia-Valdes E. 2010. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol. 12(6):1513-30. doi: 10.1111/j.1462-2920.2010.02181.x PMID: 20192968
38. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A, Harayama S. 2000. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology. 146:2385-2394. PMID: 11021915
39. Belkaid Y, Hand TW. 2014. Role of the microbiota in immunity and inflammation. Cell. 157(1):121-41. doi: 10.1016/j.cell.2014.03.011 PMID: 24679531
40. Beck JM, Young VB, Huffnagle GB. 2012. The microbiome of the lung. Transl Res. 160(4):258-66. doi: 10.1016/j.trsl.2012.02.005 PMID: 22683412
41. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. 2007. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 104(34):13780-5. PMID: 17699621
42. Sekirov I, Russell SL, Antunes LC, Finlay BB. 2010. Gut microbiota in health and disease. Physiol Rev. 90(3):859-904. doi: 10.1152/physrev. 00045.2009 PMID: 20664075
43. Sartor RB, Mazmanian SK. 2012. Intestinal Microbes in Inflammatory Bowel Diseases. Am J Gastroenterol Suppl. 1:15-21.
44. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. 2005. Diversity of the human intestinal microbial flora. Science. 308(5728):1635-8. PMID: 15831718
45. Schwiertz A, Taras D, Schafer K, Beijer S, Bos NA, Donus C, et al. 2010. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 18(1):190-5. doi: 10.1038/oby.2009.167 PMID: 19498350
46. Benson A, Pifer R, Behrendt CL, Hooper LV, Yarovinsky F. 2009. Gut commensal bacteria direct a protective immune response against Toxoplasma gondii. Cell Host Microbe. 6(2):187-96. doi: 10.1016/j. chom.2009.06.005 PMID: 19683684
47. Craven M, Egan CE, Dowd SE, McDonough SP, Dogan B, Denkers EY, et al. 2012. Inflammation drives dysbiosis and bacterial invasion in murine models of ileal Crohn's disease. PLOS One. 7:7.
48. Molloy MJ, Grainger JR, Bouladoux N, Hand TW, Koo LY, Naik S, et al. 2013. Intraluminal containment of commensal outgrowth in the gut during infection-induced dysbiosis. Cell Host Microbe. 14(3):318-28. doi: 10.1016/j.chom.2013.08.003 PMID: 24034617
49. Raetz M, Hwang SH, Wilhelm CL, Kirkland D, Benson A, Sturge CR, et al. 2013. Parasite-induced TH1 cells and intestinal dysbiosis cooperate in IFN-γ-dependent elimination of Paneth cells. Nat Immunol. 14(2):136-42. doi: 10.1038/ni.2508 PMID: 23263554
50. Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, et al. 2012. Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PLOS One. 7(6):e38499. doi: 10.1371/journal.pone.0038499 PMID: 22723863
51. Murillo N, Raoult D. 2013. Skin microbiota: overview and role in the skin diseases acne vulgaris and rosacea. Future Microbiol. 8(2):209-22. doi: 10.2217/fmb.12.141 PMID: 23374126
52. Grice EA, Kong HH, Renaud G, Young AC; NISC Comparative Sequencing Program, Bouffard GG, et al. 2008. A diversity profile of the human skin microbiota. Genome Res. 18(7):1043-50. doi: 10. 1101/gr.075549.107 PMID: 18502944
53. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. 2010. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. mBio. 1:3.
54. Wunderink RG, Walley KR. 2014. Update in sepsis and pulmonary infections 2013. Am J Respir Crit Care Med. 190(1):25-31. doi: 10.1164/rccm.201403-0577UP PMID: 24983219
55. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, et al. 2010. The human oral microbiome. J Bacteriol. 192(19):5002-17. doi: 10.1128/JB.00542-10 PMID: 20656903