Evaluation of bloodstream infections, clostridium difficile infections, and gut microbiota in pediatric oncology patients

PLoS ONE

Volumn 13, Issue 1, 2018, Pages

  Nycz, Bryan T ^a   Dominguez, Samuel R ^a   Friedman, Deborah ^b   Hilden, Joanne M ^b   Ir, Diana ^a   Robertson, Charles E ^a   Frank, Daniel N ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b CHILDREN S HOSPITAL COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL PROTEIN; BACTERIAL RNA; BACTERIAL TOXIN; TOXB PROTEIN, CLOSTRIDIUM DIFFICILE;

ARTICLE; BACTERIUM COLONY; BLOODSTREAM INFECTION; CHILD; CHILDHOOD CANCER; CLINICAL ARTICLE; CLOSTRIDIUM DIFFICILE INFECTION; COHORT ANALYSIS; CONTROLLED STUDY; DYSBIOSIS; FECES ANALYSIS; FEMALE; HOSPITAL ADMISSION; HUMAN; INTESTINE FLORA; MALE; MEDICAL HISTORY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; POPULATION ABUNDANCE; PREDICTION; SPECIES COMPOSITION; ADOLESCENT; BACTEREMIA; BACTERIAL GENE; BIODIVERSITY; CLOSTRIDIUM INFECTION; COMPLICATION; CROSS-SECTIONAL STUDY; FECES; GENETICS; MICROBIOLOGY; NEOPLASM; PEPTOCLOSTRIDIUM DIFFICILE; PREDICTIVE VALUE; PRESCHOOL CHILD; YOUNG ADULT;

ADOLESCENT; BACTEREMIA; BACTERIAL PROTEINS; BACTERIAL TOXINS; BIODIVERSITY; CHILD; CHILD, PRESCHOOL; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM INFECTIONS; COHORT STUDIES; CROSS-SECTIONAL STUDIES; FECES; FEMALE; GASTROINTESTINAL MICROBIOME; GENES, BACTERIAL; HUMANS; MALE; NEOPLASMS; PREDICTIVE VALUE OF TESTS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; YOUNG ADULT;

EID: 85040449548     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0191232     Document Type: Article

References (62)

1. Leffler DA, Lamont JT. Clostridium difficile Infection. New England Journal of Medicine. 2015; 372 (16):1539–48. https://doi.org/10.1056/NEJMra1403772 PMID: 25875259.
2. Rupnik M, Wilcox MH, Gerding DN. Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Micro. 2009; 7(7):526–36.
3. Kelly CP, Pothoulakis C, LaMont JT. Clostridium difficile colitis. The New England journal of medicine. 1994; 330(4):257–62. Epub 1994/01/27. https://doi.org/10.1056/NEJM199401273300406 PMID: 8043060.
4. Vital signs: preventing Clostridium difficile infections. MMWR Morbidity and mortality weekly report. 2012; 61(9):157–62. Epub 2012/03/09. PMID: 22398844.
5. Johnson S, Gerding DN. Clostridium difficile—associated diarrhea. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. 1998; 26(5):1027–34; quiz 35–6. Epub 1998/05/23. PMID: 9597221.
6. El Feghaly RE, Stauber JL, Tarr PI, Haslam DB. Viral co-infections are common and are associated with higher bacterial burden in children with Clostridium difficile infection. Journal of pediatric gastroenterology and nutrition. 2013; 57(6):813–6. Epub 2013/07/11. https://doi.org/10.1097/MPG. 0b013e3182a3202f PMID: 23838821.
7. Khanna S, Pardi DS, Aronson SL, Kammer PP, Orenstein R, St Sauver JL, et al. The epidemiology of community-acquired Clostridium difficile infection: a population-based study. The American journal of gastroenterology. 2012; 107(1):89–95. Epub 2011/11/24. https://doi.org/10.1038/ajg.2011.398 PMID: 22108454.
8. de Blank P, Zaoutis T, Fisher B, Troxel A, Kim J, Aplenc R. Trends in Clostridium difficile infection and risk factors for hospital acquisition of Clostridium difficile among children with cancer. The Journal of pediatrics. 2013; 163(3):699–705.e1. Epub 2013/03/13. https://doi.org/10.1016/j.jpeds.2013.01.062PMID: 23477996.
9. Dominguez SR, Dolan SA, West K, Dantes RB, Epson E, Friedman D, et al. High Colonization Rate and Prolonged Shedding of Clostridium difficile in Pediatric Oncology Patients. Clin Infect Dis. 2014; 59 (3):401–3. https://doi.org/10.1093/cid/ciu302 PMID: 24785235.
10. Kim J, Shaklee JF, Smathers S, Prasad P, Asti L, Zoltanski J, et al. Risk factors and outcomes associated with severe Clostridium difficile infection in children. Pediatr Infect Dis J. 2012; 31(2):134–8. Epub 2011/10/28. https://doi.org/10.1097/INF.0b013e3182352e2c PMID: 22031485.
11. Kim J, Smathers SA, Prasad P, Leckerman KH, Coffin S, Zaoutis T. Epidemiological features of Clostridium difficile-associated disease among inpatients at children’s hospitals in the United States, 2001–2006. Pediatrics. 2008; 122(6):1266–70. Epub 2008/12/03. https://doi.org/10.1542/peds.2008-0469PMID: 19047244.
12. Tai E, Richardson LC, Townsend J, Howard E, McDonald LC. Clostridium difficile infection among children with cancer. Pediatr Infect Dis J. 2011; 30(7):610–2. Epub 2011/01/06. https://doi.org/10.1097/INF.0b013e31820970d1 PMID: 21206395.
13. Lessa FC, Mu Y, Bamberg WM, Beldavs ZG, Dumyati GK, Dunn JR, et al. Burden of Clostridium difficile Infection in the United States. New England Journal of Medicine. 2015; 372(9):825–34. https://doi.org/10.1056/NEJMoa1408913 PMID: 25714160.
14. Shah DN, Aitken SL, Barragan LF, Bozorgui S, Goddu S, Navarro ME, et al. Economic burden of primary compared with recurrent Clostridium difficile infection in hospitalized patients: a prospective cohort study. The Journal of hospital infection. 2016; 93(3):286–9. Epub 2016/05/23. https://doi.org/10.1016/j.jhin.2016.04.004 PMID: 27209056.
15. Seekatz AM, Young VB. Clostridium difficile and the microbiota. The Journal of clinical investigation. 2014; 124(10):4182–9. Epub 2014/07/19. https://doi.org/10.1172/JCI72336 PMID: 25036699.
16. Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiological reviews. 2010; 90(3):859–904. Epub 2010/07/29. https://doi.org/10.1152/physrev.00045.2009 PMID: 20664075.
17. Yang L, Nossa CW, Pei Z. Microbial Dysbiosis and Esophageal Diseases. In: Highlander SK, Rodriguez-Valera F, White BA, editors. Encyclopedia of Metagenomics: Environmental Metagenomics. Boston, MA: Springer US; 2015. p. 379–84.
18. Frank DN, Zhu W, Sartor RB, Li E. Investigating the biological and clinical significance of human dys-bioses. Trends Microbiol. 2011; 19(9):427–34. https://doi.org/10.1016/j.tim.2011.06.005 PMID: 21775143.
19. Galloway-Pena J, Brumlow C, Shelburne S. Impact of the Microbiota on Bacterial Infections during Cancer Treatment. Trends in microbiology. 2017; 25(12):992–1004. Epub 2017/07/22. https://doi.org/10.1016/j.tim.2017.06.006 PMID: 28728967.
20. van Vliet MJ, Harmsen HJ, de Bont ES, Tissing WJ. The role of intestinal microbiota in the development and severity of chemotherapy-induced mucositis. PLoS pathogens. 2010; 6(5):e1000879. Epub 2010/ 06/05. https://doi.org/10.1371/journal.ppat.1000879 PMID: 20523891.
21. Dominguez SR, Anderson LJ, Kotter CV, Littlehorn CA, Arms LE, Dowell E, et al. Comparison of Whole-Genome Sequencing and Molecular-Epidemiological Techniques for Clostridium difficile Strain Typing. Journal of the Pediatric Infectious Diseases Society. 2015. Epub 2015/09/26. https://doi.org/10.1093/jpids/piv020 PMID: 26407257.
22. Dantes R, Epson EE, Dominguez SR, Dolan S, Wang F, Hurst A, et al. Investigation of a cluster of Clostridium difficile infections in a pediatric oncology setting. American journal of infection control. 2016; 44 (2):138–45. Epub 2015/11/26. https://doi.org/10.1016/j.ajic.2015.09.004 PMID: 26601705.
23. Needell JC, Ir D, Robertson CE, Kroehl ME, Frank DN, Zipris D. Maternal treatment with short-chain fatty acids modulates the intestinal microbiota and immunity and ameliorates type 1 diabetes in the offspring. PLoS One. 2017; 12(9):e0183786. Epub 2017/09/09. https://doi.org/10.1371/journal.pone. 0183786 PMID: 28886045.
24. Needell JC, Dinarello CA, Ir D, Robertson CE, Ryan SM, Kroehl ME, et al. Implication of the intestinal microbiome as a potential surrogate marker of immune responsiveness to experimental therapies in autoimmune diabetes. PLoS One. 2017; 12(3):e0173968. Epub 2017/03/17. https://doi.org/10.1371/journal.pone.0173968 PMID: 28301545.
25. Brumbaugh DE, Arruda J, Robbins K, Ir D, Santorico SA, Robertson CE, et al. Mode of Delivery Determines Neonatal Pharyngeal Bacterial Composition and Early Intestinal Colonization. J Pediatr Gastro-enterol Nutr. 2016; 63(3):320–8. https://doi.org/10.1097/MPG.0000000000001124 PMID: 27035381.
26. Frank DN, Bales ES, Monks J, Jackman MJ, MacLean PS, Ir D, et al. Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine. PLoS One. 2015; 10(7):e0131944. https://doi.org/10.1371/journal.pone.0131944 PMID: 26147095.
27. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985; 82(20):6955–9. PMID: 2413450.
28. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991; 173(2):697–703. PMID: 1987160.
29. Frank DN. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC bioinformatics. 2009; 10:362. Epub 2009/10/31. https://doi.org/10.1186/1471-2105-10-362 PMID: 19874596.
30. Markle JGM, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, et al. Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity. Science. 2013; 339(1084):1088.
31. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998; 8(3):186–94. PMID: 9521922.
32. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27(16):2194–200. https://doi.org/10.1093/bioinformatics/btr381PMID: 21700674
33. Schloss PD, Westcott SL. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. 2011; 77(10):3219–26. https://doi.org/10.1128/AEM.02810-10 PMID: 21421784
34. Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012; 28(14):1823–9. https://doi.org/10.1093/bioinformatics/ bts252 PMID: 22556368
35. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013; 41(Data-base issue):D590–D6. https://doi.org/10.1093/nar/gks1219 PMID: 23193283
36. Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, et al. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Bioinformatics. 2013; 29(23):3100–1. https://doi.org/10.1093/bioinformatics/btt526 PMID: 24021386
37. R Development Core Team. R: A Language and Environment for Statistical Computing. 2014.
38. Magurran AE. Measuring biological diversity: John Wiley & Sons; 2013.
39. Schloss PD, Handelsman J. The last word: books as a statistical metaphor for microbial communities. Annu Rev Microbiol. 2007; 61:23–34. https://doi.org/10.1146/annurev.micro.61.011507.151712 PMID: 17439361
40. Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, et al. Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis. BMC genomics. 2016; 17(1):635. Epub 2016/08/17. https://doi.org/10.1186/s12864-016-2965-y PMID: 27527070.
41. Price V, Portwine C, Zelcer S, Ethier M-C, Gillmeister B, Silva M, et al. Clostridium difficile infection in pediatric acute myeloid leukemia: from the Canadian Infections in Acute Myeloid Leukemia Research Group. The Pediatric infectious disease journal. 2013; 32(6):610–3. https://doi.org/10.1097/INF. 0b013e31828690a4 PMID: 23838731
42. Simon A, Ammann RA, Bode U, Fleischhack G, Wenchel HM, Schwamborn D, et al. Healthcare-associated infections in pediatric cancer patients: results of a prospective surveillance study from university hospitals in Germany and Switzerland. BMC infectious diseases. 2008; 8:70. Epub 2008/05/27. https://doi.org/10.1186/1471-2334-8-70 PMID: 18500998.
43. Gaur AH, Bundy DG, Gao C, Werner EJ, Billett AL, Hord JD, et al. Surveillance of Hospital-Acquired Central Line—Associated Bloodstream Infections in Pediatric Hematology-Oncology Patients Lessons Learned, Challenges Ahead. Infection Control & Hospital Epidemiology. 2015; 34(3):315–20. https://doi.org/10.1086/669513 PMID: 23388370
44. Rogers AE, Eisenman KM, Dolan SA, Belderson KM, Zauche JR, Tong S, et al. Risk factors for bacteremia and central line–associated blood stream infections in children with acute myelogenous leukemia: A single—institution report. Pediatric blood & cancer. 2017;64(3).
45. Rogers AEJ, Eisenman KM, Dolan SA, Belderson KM, Zauche JR, Tong S, et al. Risk factors for bacteremia and central line–associated blood stream infections in children with acute myelogenous leukemia: A single-institution report. Pediatric Blood & Cancer. 2016:n/a–n/a. https://doi.org/10.1002/pbc.26254PMID: 27616655
46. Vogtmann E, Goedert JJ. Epidemiologic studies of the human microbiome and cancer. British journal of cancer. 2016.
47. Kwa M, Plottel CS, Blaser MJ, Adams S. The Intestinal Microbiome and Estrogen Receptor—Positive Female Breast Cancer. Journal of the National Cancer Institute. 2016; 108(8):djw029.
48. Bultman SJ, editor The microbiome and its potential as a cancer preventive intervention. Seminars in oncology; 2016: Elsevier.
49. Alfano M, Canducci F, Nebuloni M, Clementi M, Montorsi F, Salonia A. The interplay of extracellular matrix and microbiome in urothelial bladder cancer. Nature Reviews Urology. 2016; 13(2):77–90. https://doi.org/10.1038/nrurol.2015.292 PMID: 26666363
50. Ohtani N, editor Microbiome and cancer. Seminars in immunopathology; 2015: Springer.
51. Schwabe RF, Jobin C. The microbiome and cancer. Nature Reviews Cancer. 2013; 13(11):800–12. https://doi.org/10.1038/nrc3610 PMID: 24132111
52. Kelly DL, Lyon DE, Yoon SL, Horgas AL. The Microbiome and Cancer: Implications for Oncology Nursing Science. Cancer Nurs. 2016; 39(3):E56–62. https://doi.org/10.1097/NCC.0000000000000286PMID: 26110573.
53. Bultman SJ. Emerging roles of the microbiome in cancer. Carcinogenesis. 2014; 35(2):249–55. https://doi.org/10.1093/carcin/bgt392 PMID: 24302613.
54. Grivennikov SI, Wang K, Mucida D, Stewart CA, Schnabl B, Jauch D, et al. Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth. Nature. 2012; 491 (7423):254–8. https://doi.org/10.1038/nature11465 PMID: 23034650
55. Son JS, Khair S, Pettet DW 3rd, Ouyang N, Tian X, Zhang Y, et al. Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice. PLoS One. 2015; 10(6): e0127985. https://doi.org/10.1371/journal.pone.0127985 PMID: 26121046.
56. Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, et al. Chemotherapy-driven dysbiosis in the intestinal microbiome. Alimentary pharmacology & therapeutics. 2015; 42(5):515–28. Epub 2015/07/07. https://doi.org/10.1111/apt.13302 PMID: 26147207.
57. Wang Y, Xue J, Zhou X, You M, Du Q, Yang X, et al. Oral microbiota distinguishes acute lymphoblastic leukemia pediatric hosts from healthy populations. PloS one. 2014; 9(7):e102116. Epub 2014/07/16. https://doi.org/10.1371/journal.pone.0102116 PMID: 25025462.
58. Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV, et al. Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection. The Journal of infectious diseases. 2015; 211(1):19–27. Epub 2014/07/25. https://doi.org/10.1093/infdis/jiu409 PMID: 25057045.
59. Kaakoush NO. Insights into the Role of Erysipelotrichaceae in the Human Host. Frontiers in Cellular and Infection Microbiology. 2015; 5(84). https://doi.org/10.3389/fcimb.2015.00084 PMID: 26636046
60. Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008; 3(4):213–23. https://doi.org/10.1016/j.chom.2008.02.015 PMID: 18407065.
61. Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PloS one. 2012; 7(6):e39743. Epub 2012/07/05. https://doi.org/10.1371/journal.pone.0039743 PMID: 22761885.
62. Wajant H, Pfizenmaier K, Scheurich P. Tumor necrosis factor signaling. Cell Death Differ. 2003; 10 (1):45–65. https://doi.org/10.1038/sj.cdd.4401189 PMID: 12655295