Dynamics of the surgical microbiota along the cardiothoracic surgery pathway

Frontiers in Microbiology

Volumn 5, Issue DEC, 2014, Pages

  Sara, Romano Bertrand ^a,b   Frapier, Jean Marc ^b   Calvet, Brigitte ^b   Colson, Pascal ^b   Albat, Bernard ^b   Sylvie, Parer ^a,b   Estelle, Jumas Bilak ^a,b  

^a UNIVERSITÉ MONTPELLIER 2   (France)

^b MONTPELLIER UNIVERSITY HOSPITAL   (France)

Author keywords

Dysbiosis; Microbial diversity; Pathobiome; Propionibacterium; Proteobacteria; Staphylococcus; Surgical wound; Temporal temperature gel electrophoresis

Indexed keywords

RNA 16S;

ACTINOBACTERIA; ANTISEPSIS; ARTICLE; BACTEROIDETES; CLINICAL ARTICLE; CORONARY ARTERY BYPASS GRAFT; CYANOBACTERIUM; DNA EXTRACTION; DNA FINGERPRINTING; DYNAMICS; ENZYME CHEMISTRY; FIRMICUTES; FUSOBACTERIA; GEL ELECTROPHORESIS; GENE AMPLIFICATION; GRAM NEGATIVE BACTERIUM; HUMAN; HUMAN TISSUE; MICROBIAL DIVERSITY; MICROFLORA; NONHUMAN; POLYMERASE CHAIN REACTION; PREVALENCE; PROPIONIBACTERIUM; PROTEOBACTERIA; SKIN FLORA; STAPHYLOCOCCUS; SURGICAL WOUND; TAXONOMY; THORAX SURGERY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CYANOBACTERIA; FIRMICUTES; FUSOBACTERIA; NEGIBACTERIA; OTUS; PROPIONIBACTERIUM; PROTEOBACTERIA; STAPHYLOCOCCUS;

EID: 84920653494     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00787     Document Type: Article

References (59)

1. Alekseyenko, A. V., Perez-Perez, G. I., De Souza, A., Strober, B., Gao, Z., Bihan, M., et al. (2013). Community differentiation of the cutaneous microbiota in psoriasis. Microbiome 1,31. doi:10.1186/2049-2618-1-31.
2. Aujoulat, F., Jumas-Bilak, E., Masnou, A., Sallé, F., Faure, D., Segonds, C., et al. (2011). Multilocus sequence-based analysis delineates a clonal population of Agrobacterium (Rhizobium) Radiobacter (Agrobacterium tumefaciens) of human origin. J. Bacteriol.193, 2608-18. doi:10.1128/JB.00107-11.
3. Bangsgaard, B., Maria, K., Krych, L., Sørensen, D. B., Pang, W., Nielsen, D. S., et al. (2012). Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse. PloS One 7, e46231. doi:10.1371/journal.pone.0046231.
4. Bard, J. D., Deville, J. G., Summanen, P. H., and Lewinski, M. A. (2010). Roseomonas mucosa isolated from bloodstream of pediatric patient. J. Clin. Microbiol. 48, 3027-29. doi:10.1128/JCM.02349-09.
5. Beckmann, A., Doebler, K., Schaefer, E., Koetting, J., Gastmeier, P., and Graf, K. (2011). Sternal surgical site infection prevention-Is there any room for improvement?. Eur. J. Cardiothorac. Surg. 40, 347-51. doi:10.1016/j.ejcts.2010.12.016.
6. Bouza, E., Muñoz, P., Alcalá, L., Pérez, M. J., Rincón, C., Barrio, J. M., et al. (2006). Cultures of sternal wound and mediastinum taken at the end of heart surgery do not predict postsurgical mediastinitis. Diagn. Microbiol. Infect. Dis. 56, 345-49. doi:10.1016/j.diagmicrobio.2006.06.012.
7. Chaudhuri, A., Shekar, K., and Coulter, C. (2012). Post-operative deep sternal wound infections: making an early microbiological diagnosis. Eur. J. Cardiothorac Surg. 41, 1304-8. doi: 10.1093/ejcts/ezr239.
8. Cheong, H. S., Wi, Y. M., Moon, S. Y., Kang, C.-I., Son, J. S., Ko, K. S., et al. (2008). Clinical features and treatment outcomes of infections caused by Sphingomonas paucimobilis. Infect. Control Hosp. Epidemiol. 29, 990-92. doi:10.1086/591091.
9. Dekio, I., Hayashi, H., Sakamoto, M., Kitahara, M., Nishikawa, T., Suematsu, M. et al. (2005). Detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling. J. Medical. Microbiol. 54, 1231-38. doi:10.1099/jmm.0.46075-0.
10. Dethlefsen, L., McFall-Ngai, M., and Relman, D. A. (2007). An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449, 811-18. doi:10.1038/nature06245.
11. Ding, G.-C., Heuer, H., and Smalla, K. (2012). Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders. Front. Microbiol. 3, 290. doi:10.3389/fmicb.2012.00290.
12. Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J. P., and Raoult, D. (2000). 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 38, 3623-30.
13. Filsoufi, F., Aklog, L., and Adams, D. H. (2001). Minimally invasive CABG. Curr. Opin. Cardiol. 16, 306-9.
14. Filsoufi, F., Castillo, J. G., Rahmanian, P. B., Broumand, S. R., Silvay, G., Carpentier, A. et al. (2009). Epidemiology of deep sternal wound infection in cardiac surgery. J. Cardiothorac. Vasc. Anesth. 23, 488-94. doi:10.1053/j.jvca.2009.02.007.
15. Fournier, P.-E., La, M.V., Casalta, J.-P., Richet, H., Collart, F., and Raoult, D. (2008). Finegoldia magna, an early post-operative cause of infectious endocarditis: report of two cases and review of the literature. Anaerobe 14, 310-12. doi:10.1016/j.anaerobe.2008.11.001.
16. Gao, Z., Tseng, C.-H., Pei, Z., and Blaser, M. J. (2007). Molecular a nalysis of human forearm superficial skin bacterial biota. Proc. Natl. Acad. Sci. U S A. 104, 2927-32. doi:10.1073/pnas.0607077104.
17. Gårdlund, B., Bitkover, C. Y. and Vaage, J. (2002). Postoperative mediastinitis in cardiac surgery-microbiology and pathogenesis. Eur. J. Cardiothorac. Surg. 21, 825-30.
18. George, R. S., Birks, E. J., Haj-Yahia, S., Bowles, C. T., Hall, A., Khaghani, A. et al. (2006). Acinetobacter mediastinitis in a heart transplant patient. Ann. Thorac. Surg. 82, 715-16. doi:10.1016/j.athoracsur.2005.11.008.
19. Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C, et al. (2009). Topographical and temporal diversity of the human skin microbiome. Science. 324, 1190-92. doi:10.1126/science.1171700.
20. Grice, E. A., Kong, H. H., Renaud, G., Young, A. C., Bouffard, G. G., Blakesley, R. W., et al. (2008). A diversity profile of the human skin microbiota. Genome Res. 18, 1043-50. doi:10.1101/gr.075549.107.
21. Grice, E. A., and Segre, J. A. (2011). The skin microbiome. Nat. Rev. Microbiol. 9, 244-53. doi:10.1038/nrmicro2537.
22. Hinic, V., Lang, C., Weisser, M., Straub, C., Frei, R., and Goldenberger, D. (2012). Corynebacterium tuberculostearicum: a potentially misidentified and multiresistant Corynebacterium species isolated from clinical specimens. J. Clin. Microbiol. 50, 2561-67. doi:10.1128/JCM.00386-12.
23. Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature 486, 207-14. doi:10.1038/nature11234.
24. Jacquot, A., Neveu, D., Aujoulat, F., Mercier, G., Marchandin, H., Jumas-Bilak, E., et al. (2011). Dynamics and clinical evolution of bacterial gut microflora in extremely premature patients. J. Pediatr. 158, 390-96. doi:10.1016/j.jpeds.2010.09.007.
25. Jakob, S. M., and Stanga, Z. (2010). Perioperative metabolic changes in patients undergoing cardiac surgery. Nutrition 26, 349-53. doi:10.1016/j.nut.2009.07.014
26. Jernberg, C., Löfmark, S., Edlund, C., and Jansson, J. K. (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 1, 56-66. doi:10.1038/ismej.2007.3.
27. Kovaleva, J., Degener, J. E., and van der Mei, H. C. (2014). Methylobacterium and its role in health care-associated infection. J. Clin. Microbiol. 52, 1317-21. doi:10.1128/JCM.03561-13.
28. Kuczynski, Justin, Christian L. Lauber, William A. Walters, Laura Wegener Parfrey, José C. Clemente, Dirk Gevers, et Rob Knight. 2012. « Experimental and Analytical Tools for Studying the Human Microbiome ». Nature Reviews Genetics 13 (1): 47-58. doi:10.1038/nrg3129.
29. Kühme, T., Isaksson, B., and Dahlin, L.-G. (2007). Wound contamination in cardiac surgery. A systematic quantitative and qualitative study of the bacterial growth in sternal wounds in cardiac surgery patients. APMIS. 115, 1001-7. doi:10.1111/j.1600-0463.2007.00832.x.
30. Lederberg, J., and McCray, A. (2001). 'Ome Sweet 'Omics-- A genealogical treasury of words | The Scientist Magazine®. The Scientist. http://www.the scientist.com/?articles.view/articleNo/13313/title/-Ome-Sweet--Omics---A Genealogical-Treasury-of-Words/.
31. Lee, M. J., Pottinger, P. S., Butler-Wu, S., Bumgarner, R. E., Russ, S. M., and Matsen, F. A. (2014). Propionibacterium persists in the skin despite standard surgical preparation. J. Bone Joint Surg. Am. 96, 1447-50. doi:10.2106/JBJS.M.01474.
32. Leite, D. C. A., Balieiro, F. C., Pires, C. A., Madari, B. E., Rosado, A. S., Coutinho, H. L. C., et al. (2014). Comparison of DNA extraction protocols for microbial communities from soil treated with biochar. Braz. J. Microbiol. 45, 175-83.
33. Li, W., Han, L., Yu, P., Ma, C., Wu, X., and Xu, J. (2014). Nested PCR-denaturing gradient gel electrophoresis analysis of human skin microbial diversity with age. Microbiol. Res. 169, 686-92. doi: 10.1016/j.micres.2014.02.008.
34. Lu, H., He, J., Wu, Z., Xu, W., Zhang, H., Ye, P., et al. (2013). Assessment of microbiome variation during the perioperative period in liver transplant patients: a retrospective analysis. Microb. Ecol. 65, 781-91. doi:10.1007/s00248-013-0211-6.
35. Luong, M.-L., Békal, S., Vinh, D. C., Lauzon, D., Leung, V., Al-Rawahi, G. N., et al. (2008). First report of isolation and characterization of Aurantimonas altamirensis from clinical samples. J. Clin. Microbiol. 46, 2435-37. doi:10.1128/JCM.00337-08.
36. Mangram, A. J., Horan, T. C., Pearson, M. L., Silver, L. C., and Jarvis, W. R. (1999). Guideline for prevention of surgical site infection, 1999. Hospital Infection Control Practices Advisory Committee. Infect. Control Hosp. Epidemiol. 20, 250-78; quiz 279-80. doi:10.1086/501620.
37. Morgan, X. C., and Huttenhower, C. (2012). Chapter 12: human microbiome analysis. PLoS Comput. Biol. 8, e1002808. doi:10.1371/journal.pcbi.1002808.
38. Morrow, K. M., Moss, A. G., Chadwick, N. E., and Liles, M. R. (2012). Bacterial associates of two caribbean coral species reveal species-specific distribution and geographic variability. Appl. Environm. Microbiol. 78, 6438-49. doi:10.1128/AEM.01162-12.
39. Nakatsu, C. H., Armstrong, A., Clavijo, A. P., Martin, B. R., Barnes, S., and Weaver, C. M. (2014). Fecal bacterial community changes associated with isoflavone metabolites in postmenopausal women after soy bar consumption. PloS One 9, e108924. doi:10.1371/journal.pone.0108924.
40. Neefs, J. M., Van de Peer, Y., De Rijk, P., Chapelle, S., and De Wachter, R. (1993). Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21, 3025-49.
41. Ogier, J.-C., Son, O., Gruss, A., Tailliez, P., and Delacroix-Buchet, A. (2002). Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis. Appl. Environm. Microbiol. 68, 3691-3701.
42. Panda, S., El khader, I., Casellas, F., Vivancos, J. L., Cors, M. G., Santiago, A., et al. (2014). Short-term effect of antibiotics on human gut microbiota. PloS One 9, e95476. doi:10.1371/journal.pone.0095476.
43. Pflughoeft, K. J., and Versalovic, J. (2012). Human microbiome in health and disease. Ann. Rev. Pathol. 7, 99-122. doi:10.1146/annurev-pathol-011811-132421.
44. Pires, A. C. C., Cleary, D. F. R., Almeida, A., Cunha, A., Dealtry, S., et al. (2012). Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples. Appl. Environm. Microbiol. 78, 5520-28. doi:10.1128/AEM.00386-12.
45. Reen, F. J., Woods, D. F., Mooij, M. J., Chróinín, M. N., Mullane, D., Zhou, L., et al. (2014). Aspirated bile: a major host trigger modulating respiratory pathogen colonisation in cystic fibrosis patients. Eur. J. Clin. Microbiol. Infect. Dis. 33, 1763-71. doi:10.1007/s10096-014-2133-8.
46. Risnes, I., Abdelnoor, M., Almdahl, S. M., and Svennevig, J. L. (2010). Mediastinitis after coronary artery bypass grafting risk factors and long-term survival. Ann. Thorac. Surg. 89, 1502-9. doi:10.1016/j.athoracsur.2010.02.038.
47. Romano-Bertrand, S., Beretta, M., Jean-Pierre, H., Frapier, J.-M., Calvet, B., Parer, S., et al. (2014). Propionibacterium acnes populations involved in deep pathological samples and their dynamics along the cardiac surgical pathway. Eur. J. Clin. Microbiol. Infect. Dis. in press.
48. Romano-Bertrand, S., Parer, S., Lotthé, A., Colson, P., Albat, B., and Jumas-Bilak, E. (2012). Temporal temperature gel electrophoresis to survey pathogenic bacterial communities: the case of surgical site infections. In Gel Electrophoresis-Advanced Techniques, ed. S. Magdeldin. ISBN: 978-953-51-0457-5, InTech. DOI: 10.5772/37985.
49. Rosenthal, V. D, Richtmann, R., Singh, S., Apisarnthanarak, A., Kübler, A., Viet-Hung, N., et al. (2013). Surgical site infections, international nosocomial infection control consortium (INICC) report, data summary of 30 countries, 2005-2010. Infect. Control Hosp. Epidemiol. 34, 597-604. doi:10.1086/670626.
50. Roudière, L., Jacquot, A., Marchandin, H., Aujoulat, F., Devine, R., Zorgniotti, I., et al. (2009). Optimized PCR-temporal temperature gel electrophoresis compared to cultivation to assess diversity of gut microbiota in neonates. J. Microbiol. Methods. 79, 156-65. doi:10.1016/j.mimet.2009.08.005.
51. Rungrassamee, W., Klanchui, A., Chaiyapechara, S., Maibunkaew, S., Tangphatsornruang, S., Jiravanichpaisal, P., et al. (2013). Bacterial population in intestines of the black tiger shrimp (Penaeus monodon) under different growth stages. PloS One. 8, e60802. doi:10.1371/journal.pone.0060802.
52. Santos, T. M. A., and Bicalho, R. C. (2012). Diversity and succession of bacterial communities in the uterine fluid of postpartum metritic, endometritic and healthy dairy cows. PloS One. 7, e53048. doi:10.1371/journal.pone.0053048.
53. Schweiger, M., Stiegler, P., Scarpatetti, M., Wasler, A., Sereinigg, M., Prenner, G. et al. (2011). Case of Paracoccus yeei infection documented in a transplanted heart. Transpl. Infect. Dis. 13, 200-203. doi:10.1111/j.1399-3062.2010.00571.x.
54. Sundquist, A., Bigdeli, S., Jalili, R., Druzin, M. L., Waller, S., Pullen, K. M., et al. (2007). Bacterial flora-typing with targeted, chip-based pyrosequencing. BMC Microbiol. 7, 108. doi:10.1186/1471-2180-7-108.
55. Tammelin, A., Hambraeus, A., and Ståhle, E. (2002). Mediastinitis after cardiac surgery: improvement of bacteriological diagnosis by use of multiple tissue samples and strain typing. J. Clin. Microbiol. 40, 2936-41.
56. Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., and Gordon, J I. (2009). The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14. doi:10.1126/scitranslmed.3000322.
57. Vayssier-Taussat, M., Albina, E., Citti, C., Cosson, J.-F., Jacques, M.-A., Lebrun, M.-H., et al. (2014). Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Front. Cell. Infect. Microbiol. 4, 29. doi:10.3389/fcimb.2014.00029.
58. Wacklin, P., Tuimala, J., Nikkilä, J., Tims, S., Mäkivuokko, H., Alakulppi, N., et al. (2014). Faecal microbiota composition in adults is associated with the FUT2 gene determining the secretor status. PloS One. 9, e94863. doi:10.1371/journal.pone.0094863.
59. Zeeuwen, P. L. J. M., Boekhorst, J., van den Bogaard, E. H., de Koning, H. D., van de Kerkhof, P. M. C., Saulnier, D. M., et al. (2012). Microbiome dynamics of human epidermis following skin barrier disruption. Gen. Biol. 13, R101. doi:10.1186/gb- 2012-13-11-r101.