Microbiome signatures in neonatal central line associated bloodstream infections

Autoři: Mohan Pammi aff001;  Santosh Thapa aff002;  Miriam Balderas aff002;  Jessica K. Runge aff002;  Alamelu Venkatachalam aff002;  Ruth Ann Luna aff002
Působiště autorů: Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas, United States of America aff001;  Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, United States of America aff002;  Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0227967


Neonates are at high risk for central line associated bloodstream infections (CLABSI). Biofilm formation is universal on indwelling catheters but why some biofilms seed the bloodstream to cause CLABSI is not clearly understood. With the objective to test the hypothesis that catheter biofilm microbiome in neonates with CLABSI differs than those without infection, we prospectively enrolled neonates (n = 30) with infected and uninfected indwelling central catheters. Catheters were collected at the time of removal, along with blood samples and skin swabs at the catheter insertion sites. Microbiomes of catheter biofilms, skin swabs and blood were evaluated by profiling the V4 region of the bacterial 16S rRNA gene using Illumina MiSeq sequencing platform. The microbial DNA load was higher from catheter biofilms of CLABSI patients without differences in alpha diversity when compared to that of the non-CLABSI neonates. Proteus and unclassified Staphylococcaceae were more abundant in infected catheter biofilms while Bradyrhizobium, Cloacibacterium, and Sphingomonas were more abundant in the uninfected catheters. A blood microbiome was detected in uninfected samples. The blood microbiome in CLABSI neonates clustered separately from the uninfected blood samples in beta diversity plots. We found that the microbiome signature in catheter biofilm and blood of neonates with CLABSI is different than the microbiomes of non-CLABSI neonates.

Klíčová slova:

Bacterial biofilms – Biofilms – Blood – Catheters – Microbiome – Neonates – Skin infections – Staphylococcal infection


1. CDC. National HealthCare Safety Network Report. 2011.

2. Payne NR, Carpenter JH, Badger GJ, Horbar JD, Rogowski J. Marginal increase in cost and excess length of stay associated with nosocomial bloodstream infections in surviving very low birth weight infants. Pediatrics. 2004;114(2):348–55. Epub 2004/08/03. doi: 114/2/348 [pii]. doi: 10.1542/peds.114.2.348 15286215.

3. Wagner M, Bonhoeffer J, Erb TO, Glanzmann R, Hacker FM, Paulussen M, et al. Prospective study on central venous line associated bloodstream infections. Archives of disease in childhood. 2011;96(9):827–31. Epub 2011/06/07. doi: 10.1136/adc.2010.208595 21642273.

4. Mahieu LM, De Dooy JJ, De Muynck AO, Van Melckebeke G, Ieven MM, Van Reempts PJ. Microbiology and risk factors for catheter exit-site and -hub colonization in neonatal intensive care unit patients. Infect Control Hosp Epidemiol. 2001;22(6):357–62. Epub 2001/08/25. doi: ICHE6828 [pii] doi: 10.1086/501913 [doi]. 11519913.

5. Sitges-Serra A, Puig P, Linares J, Perez JL, Farrero N, Jaurrieta E, et al. Hub colonization as the initial step in an outbreak of catheter-related sepsis due to coagulase negative staphylococci during parenteral nutrition. JPEN J Parenter Enteral Nutr. 1984;8(6):668–72. Epub 1984/11/01. doi: 10.1177/0148607184008006668 6441008.

6. Hocevar SN, Edwards JR, Horan TC, Morrell GC, Iwamoto M, Lessa FC. Device-associated infections among neonatal intensive care unit patients: incidence and associated pathogens reported to the National Healthcare Safety Network, 2006–2008. Infect Control Hosp Epidemiol. 2012;33(12):1200–6. Epub 2012/11/13. doi: 10.1086/668425 23143356.

7. Ramage G, Saville SP, Thomas DP, Lopez-Ribot JL. Candida biofilms: an update. Eukaryot Cell. 2005;4(4):633–8. Epub 2005/04/12. doi: 4/4/633 [pii] doi: 10.1128/EC.4.4.633-638.2005 [doi]. 15821123.

8. NIH. SBIR/STTR STUDY AND CONTROL OF MICROBIAL BIOFILMS. In: NIH, editor. Release Date: April 21, 1999 ed1999.

9. Anaissie E, Samonis G, Kontoyiannis D, Costerton J, Sabharwal U, Bodey G, et al. Role of catheter colonization and infrequent hematogenous seeding in catheter-related infections. Eur J Clin Microbiol Infect Dis. 1995;14(2):134–7. Epub 1995/02/01. doi: 10.1007/bf02111873 7758480.

10. Raad I, Costerton W, Sabharwal U, Sacilowski M, Anaissie E, Bodey GP. Ultrastructural analysis of indwelling vascular catheters: a quantitative relationship between luminal colonization and duration of placement. J Infect Dis. 1993;168(2):400–7. Epub 1993/08/01. doi: 10.1093/infdis/168.2.400 8335977.

11. Moretti EW, Ofstead CL, Kristy RM, Wetzler HP. Impact of central venous catheter type and methods on catheter-related colonization and bacteraemia. J Hosp Infect. 2005;61(2):139–45. Epub 2005/07/20. doi: S0195-6701(05)00126-X [pii] doi: 10.1016/j.jhin.2005.02.012 [doi]. 16026898.

12. Lepainteur M, Desroches M, Bourrel AS, Aberrane S, Fihman V, L'Heriteau F, et al. Role of the Central Venous Catheter in Bloodstream Infections Caused by Coagulase Negative Staphylococci in Very Preterm Neonates. Pediatr Infect Dis J. 2013. Epub 2013/02/23. doi: 10.1097/INF.0b013e318289de0f [doi]. 23429561.

13. Pammi M, O'Brien JL, Ajami NJ, Wong MC, Versalovic J, Petrosino JF. Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study. PLoS One. 2017;12(4):e0176669. Epub 2017/04/28. doi: 10.1371/journal.pone.0176669 28448623; PubMed Central PMCID: PMC5407830.

14. Nadkarni MA, Martin FE, Jacques NA, Hunter N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology (Reading, England). 2002;148(Pt 1):257–66. Epub 2002/01/10. doi: 10.1099/00221287-148-1-257 11782518.

15. Luna RA, Oezguen N, Balderas M, Venkatachalam A, Runge JK, Versalovic J, et al. Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder. Cellular and Molecular Gastroenterology and Hepatology. 2017;3(2):218–30. doi: 10.1016/j.jcmgh.2016.11.008 28275689

16. Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome. 2014;2(1):30. Epub 2014/01/01. doi: 10.1186/2049-2618-2-30 27367037; PubMed Central PMCID: PMC4179863.

17. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature methods. 2013;10(10):996–8. doi: 10.1038/nmeth.2604 23955772.

18. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. doi: 10.7717/peerj.2584 27781170

19. 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 research. 2013;41(Database issue):D590–6. doi: 10.1093/nar/gks1219 23193283; PubMed Central PMCID: PMC3531112.

20. Leiby JS, McCormick K, Sherrill-Mix S, Clarke EL, Kessler LR, Taylor LJ, et al. Lack of detection of a human placenta microbiome in samples from preterm and term deliveries. Microbiome. 2018;6(1):196. doi: 10.1186/s40168-018-0575-4 30376898

21. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nature methods. 2010;7(5):335–6. Epub 04/11. doi: 10.1038/nmeth.f.303 20383131.

22. Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics (Oxford, England). 2010;26(6):715–21. doi: 10.1093/bioinformatics/btq041 20130030

23. Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5(1):27. doi: 10.1186/s40168-017-0237-y 28253908

24. Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6(1):226. doi: 10.1186/s40168-018-0605-2 30558668

25. Cantey JB, Baird SD. Ending the Culture of Culture-Negative Sepsis in the Neonatal ICU. Pediatrics. 2017;140(4). Epub 2017/09/21. doi: 10.1542/peds.2017-0044 28928289.

26. Schelonka RL, Chai MK, Yoder BA, Hensley D, Brockett RM, Ascher DP. Volume of blood required to detect common neonatal pathogens. The Journal of pediatrics. 1996;129(2):275–8. Epub 1996/08/01. doi: 10.1016/s0022-3476(96)70254-8 8765627.

27. Millar M, Zhou W, Skinner R, Pizer B, Hennessy E, Wilks M, et al. Accuracy of bacterial DNA testing for central venous catheter-associated bloodstream infection in children with cancer. Health Technol Assess. 2011;15(7):1–114. Epub 2011/02/08. doi: 10.3310/hta15070 [doi]. 21294989.

28. Wolcott R, Costerton JW, Raoult D, Cutler SJ. The polymicrobial nature of biofilm infection. Clin Microbiol Infect. 2013;19(2):107–12. Epub 2012/08/29. doi: 10.1111/j.1469-0691.2012.04001.x [doi]. 22925473.

29. Pammi M, Liang R, Hicks J, Mistretta TA, Versalovic J. Biofilm extracellular DNA enhances mixed species biofilms of Staphylococcus epidermidis and Candida albicans. BMC microbiology. 2013;13:257. doi: 10.1186/1471-2180-13-257 24228850; PubMed Central PMCID: PMC3833181.

30. Nishikawa K, Takasu A, Morita K, Tsumori H, Sakamoto T. Deposits on the intraluminal surface and bacterial growth in central venous catheters. J Hosp Infect. 2010;75(1):19–22. Epub 2010/03/17. doi: S0195-6701(09)00509-X [pii] doi: 10.1016/j.jhin.2009.11.005 [doi]. 20227135.

31. Nikkari S, McLaughlin IJ, Bi W, Dodge DE, Relman DA. Does blood of healthy subjects contain bacterial ribosomal DNA? J Clin Microbiol. 2001;39(5):1956–9. Epub 2001/04/28. doi: 10.1128/JCM.39.5.1956-1959.2001 11326021; PubMed Central PMCID: PMC88056.

32. Potgieter M, Bester J, Kell DB, Pretorius E. The dormant blood microbiome in chronic, inflammatory diseases. FEMS microbiology reviews. 2015;39(4):567–91. Epub 2015/05/06. doi: 10.1093/femsre/fuv013 25940667; PubMed Central PMCID: PMC4487407.

33. Schierwagen R, Alvarez-Silva C, Madsen MSA, Kolbe CC, Meyer C, Thomas D, et al. Circulating microbiome in blood of different circulatory compartments. Gut. 2018. Epub 2018/03/28. doi: 10.1136/gutjnl-2018-316227 29581241.

34. Paisse S, Valle C, Servant F, Courtney M, Burcelin R, Amar J, et al. Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing. Transfusion. 2016;56(5):1138–47. Epub 2016/02/13. doi: 10.1111/trf.13477 26865079.

35. Xu M, Yang Y, Zhou Y, Liu Z, Liu Y, He M. Metagenomics in pooled plasma, with identification of potential emerging infectious pathogens. Transfusion. 2018;58(3):633–7. Epub 2017/12/19. doi: 10.1111/trf.14455 29250787.

36. Dinakaran V, Rathinavel A, Pushpanathan M, Sivakumar R, Gunasekaran P, Rajendhran J. Elevated levels of circulating DNA in cardiovascular disease patients: metagenomic profiling of microbiome in the circulation. PLoS One. 2014;9(8):e105221. Epub 2014/08/19. doi: 10.1371/journal.pone.0105221 25133738; PubMed Central PMCID: PMC4136842.

37. Van Leeuwen PA, Boermeester MA, Houdijk AP, Ferwerda CC, Cuesta MA, Meyer S, et al. Clinical significance of translocation. Gut. 1994;35(1 Suppl):S28–34. Epub 1994/01/01. doi: 10.1136/gut.35.1_suppl.s28 8125386; PubMed Central PMCID: PMC1378143.

38. Gorski A, Wazna E, Dabrowska BW, Dabrowska K, Switala-Jelen K, Miedzybrodzki R. Bacteriophage translocation. FEMS immunology and medical microbiology. 2006;46(3):313–9. Epub 2006/03/24. doi: 10.1111/j.1574-695X.2006.00044.x 16553803.

39. Merlini E, Bai F, Bellistri GM, Tincati C, d'Arminio Monforte A, Marchetti G. Evidence for polymicrobic flora translocating in peripheral blood of HIV-infected patients with poor immune response to antiretroviral therapy. PLoS One. 2011;6(4):e18580. Epub 2011/04/16. doi: 10.1371/journal.pone.0018580 21494598; PubMed Central PMCID: PMC3073938.

40. Frances R, Gonzalez-Navajas JM, Zapater P, Munoz C, Cano R, Pascual S, et al. Translocation of bacterial DNA from Gram-positive microorganisms is associated with a species-specific inflammatory response in serum and ascitic fluid of patients with cirrhosis. Clinical and experimental immunology. 2007;150(2):230–7. Epub 2007/09/08. doi: 10.1111/j.1365-2249.2007.03494.x 17822441; PubMed Central PMCID: PMC2219344.

41. Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Fofanova T, Nelson A, et al. Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 2017;5(1):75. Epub 2017/07/14. doi: 10.1186/s40168-017-0295-1 28701177; PubMed Central PMCID: PMC5508794.

42. Suresh GK, Edwards WH. Central line-associated bloodstream infections in neonatal intensive care: changing the mental model from inevitability to preventability. American journal of perinatology. 2012;29(1):57–64. Epub 2011/09/01. doi: 10.1055/s-0031-1286182 21879458

43. Stevens TP, Schulman J. Evidence-based approach to preventing central line-associated bloodstream infection in the NICU. Acta paediatrica (Oslo, Norway: 1992) Supplement. 2012;101(464):11–6. Epub 2012/03/21. doi: 10.1111/j.1651-2227.2011.02547.x 22404886.

44. Huskins WC. Quality improvement interventions to prevent healthcare-associated infections in neonates and children. Current opinion in pediatrics. 2012;24(1):103–12. Epub 2011/12/23. doi: 10.1097/MOP.0b013e32834ebdc3 22189394.

45. Butler-O'Hara M, D'Angio CT, Hoey H, Stevens TP. An evidence-based catheter bundle alters central venous catheter strategy in newborn infants. The Journal of pediatrics. 2012;160(6):972–7 e2. Epub 2012/01/14. doi: 10.1016/j.jpeds.2011.12.004 22240109.

46. Schulman J, Stricof R, Stevens TP, Horgan M, Gase K, Holzman IR, et al. Statewide NICU central-line-associated bloodstream infection rates decline after bundles and checklists. Pediatrics. 2011;127(3):436–44. Epub 2011/02/23. doi: 10.1542/peds.2010-2873 21339265.

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