Hostname: page-component-586b7cd67f-t8hqh Total loading time: 0 Render date: 2024-11-28T00:47:06.107Z Has data issue: false hasContentIssue false
  • English
  • Français

Microbial Disruption Indices to Detect Colonization With Multidrug-Resistant Organisms

Published online by Cambridge University Press:  13 September 2017

Rafael Araos ,
Veronica Montgomery ,
Juan A. Ugalde ,
Graham M. Snyder  and
Erika M. C. D’Agata
Rafael Araos*
Affiliation:
Genomics and Resistant Microbes (GeRM) Group, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
Veronica Montgomery
Affiliation:
Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
Juan A. Ugalde
Affiliation:
Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
Graham M. Snyder
Affiliation:
Department of Medicine, Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA
Erika M. C. D’Agata*
Affiliation:
Rhode Island Hospital, Brown University, Providence, Rhode Island
*
Address correspondence to Rafael Araos, MD, MMSc, Genomics and Resistant Microbes (GeRM) Group, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Avenida Vitacura 5951, Santiago, Chile ([email protected]) or Erika M. C. D’Agata, Division of Infectious Diseases, Rhode Island Hospital, 593 Eddy Street, Aldrich 7, Providence, Rhode Island ([email protected]).
Address correspondence to Rafael Araos, MD, MMSc, Genomics and Resistant Microbes (GeRM) Group, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Avenida Vitacura 5951, Santiago, Chile ([email protected]) or Erika M. C. D’Agata, Division of Infectious Diseases, Rhode Island Hospital, 593 Eddy Street, Aldrich 7, Providence, Rhode Island ([email protected]).
Get access Rights & Permissions [Opens in a new window]

Abstract

OBJECTIVE

To characterize the microbial disruption indices of hospitalized patients to predict colonization with multidrug-resistant organisms (MDROs).

DESIGN

A cross-sectional survey of the fecal microbiome was conducted in a tertiary referral, acute-care hospital in Boston, Massachusetts.

PARTICIPANTS

The study population consisted of adult patients hospitalized in general medical/surgical wards.

METHODS

Rectal swabs were obtained from patients within 48 hours of hospital admission and screened for MDRO colonization using conventional culture techniques. The V4 region of the 16S rRNA gene was sequenced to assess the fecal microbiome. Microbial diversity and composition, as well as the functional potential of the microbial communities present in fecal samples, were compared between patients with and without MDRO colonization.

RESULTS

A total of 44 patients were included in the study, of whom 11 (25%) were colonized with at least 1 MDRO. Reduced microbial diversity and high abundance of metabolic pathways associated with multidrug-resistance mechanisms characterized the fecal microbiome of patients colonized with MDRO at hospital admission.

CONCLUSIONS

Our data suggest that microbial disruption indices may be key to predicting MDRO colonization and could provide novel infection control approaches.

Infect Control Hosp Epidemiol 2017;38:1312–1318

Type
Original Articles
Information
Infection Control & Hospital Epidemiology , Volume 38 , Issue 11 , November 2017 , pp. 1312 - 1318
Copyright
© 2017 by The Society for Healthcare Epidemiology of America. All rights reserved 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

PREVIOUS PRESENTATION: These data were presented in part as a poster at IDWeek 2016 on October 29, 2016, in New Orleans, Louisiana, poster #2229.

References

REFERENCES

1. Laxminarayan, R, Duse, A, Wattal, C, et al. Antibiotic resistance—the need for global solutions. Lancet Infect Dis 2013;13:1057–1098.CrossRefGoogle ScholarPubMed
2. Olesen, SW, Alm, EJ. Dysbiosis is not an answer. Nat Microbiol 2016;1:1–2.Google Scholar
3. Taur, Y, Xavier, JB, Lipuma, L, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 2012;55:905–914.CrossRefGoogle ScholarPubMed
4. Araos, R, Tai, AK, Snyder, GM, Blaser, MJ, D’Agata, EMC. Predominance of Lactobacillus spp. among patients who do not acquire multidrug-resistant organisms. Clin Infect Dis 2016;63:937–943.Google Scholar
5. Halpin, AL, McDonald, LC. Editorial commentary: the dawning of microbiome remediation for addressing antibiotic resistance. Clin Infect Dis 2016;62:1487–1488.Google Scholar
6. Halpin, AL, de Man, TJB, Kraft, CS, et al. Intestinal microbiome disruption in patients in a long-term acute care hospital: a case for development of microbiome disruption indices to improve infection prevention. Am J Infect Control 2016;44:830–836.CrossRefGoogle Scholar
7. Andersen, H, Connolly, N, Bangar, H, Staat, MPH M, Mortensen, J, Deburger, B. Use of shotgun metagenome sequencing to detect fecal colonization with multi-drug resistant. J Clin Microbiol 2016;54:1804–1813.CrossRefGoogle Scholar
8. Charlson, M, Szatrowski, TP, Peterson, J, Gold, G. Validation of a combined comorbidity index. J Clin Epidemiol 1994;47:1245–1251.Google Scholar
9. Mitchell, SL, Shaffer, ML, Kiely, DK, Givens, JL, D’Agata, E. The study of pathogen resistance and antimicrobial use in dementia: study design and methodology. Arch Gerontol Geriatr 2014;56:16–22.Google Scholar
10. Snyder, GM, Agata EMCD. Diagnostic accuracy of surveillance cultures to detect gastrointestinal colonization with multidrug-resistant gram-negative bacteria. Am J Infect Control 2012;40:474–476.CrossRefGoogle ScholarPubMed
11. Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial susceptibility testing. Supplement M100-S21; 2011.Google Scholar
12. Caporaso, JG, Lauber, CL, Walters, WA, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012;6:1621–1624.Google Scholar
13. Caporaso, JG, Kuczynski, J, Stombaugh, J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335–336.CrossRefGoogle ScholarPubMed
14. Magurran, A. Introduction: measurement of (biological) diversity. In: Measuring Biological Diversity. Hoboken, NJ: Wiley-Blackwell; 2004:1–17.Google Scholar
15. Lozupone, C, Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. App Environ Microbiol 2005;71:8228–8235.Google Scholar
16. Vázquez-baeza, Y, Pirrung, M, Gonzalez, A, Knight, R. EMPeror: a tool for visualizing high-throughput microbial community data. GigaScience 2013;2:16.Google Scholar
17. Segata, N, Izard, J, Waldron, L, et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011;12:R60.Google Scholar
18. Langille, MG, Zaneveld, J, Caporaso, JG, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 2013;31:814–821.Google Scholar
19. Kanehisa, M, Sato, Y, Kawashima, M, Furumichi, M, Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016;44:D457–D462.CrossRefGoogle ScholarPubMed
20. Taur, Y, Jenq, RR, Perales, M, et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood 2014;124:1174–1182.Google Scholar
21. Seekatz, AM, Rao, K, Santhosh, K, Young, VB. Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection. Genome Med 2016;8:47.CrossRefGoogle ScholarPubMed
22. Ubeda, C, Bucci, V, Caballero, S, et al. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect Immun 2013;81:965–973.CrossRefGoogle ScholarPubMed
23. Pamer, EG. Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens. Science 2016;352:535–538.CrossRefGoogle ScholarPubMed
24. Bilinski, J, Grzesiowski, P, Sorensen, N, et al. Fecal microbiota transplantation in patients with blood disorders inhibits gut colonization with antibiotic-resistant bacteria: results of a prospective, single-center study. Clin Infect Dis 2017. doi: 10.1093/cid/cix252.Google Scholar
25. Richmond, GE, Evans, LP, Anderson, MJ, et al. The Acinetobacter baumannii two-component system ADeRS regulates genes required for multidrug efflux, biofilm formation, and virulence in a strain-specific manner. mBio 2016;7:e00852–16; doi: 10.1128/mBio.00852-16.Google Scholar
26. Lubelski, J, Konings, WN, Driessen, AJM. Distribution and physiology of ABC-type transporters contributing to multidrug resistance in bacteria. Microbiol Mol Biol Rev 2007;71:463–476.Google Scholar
27. Ham, JS, Lee, SG, Jeong, SG, et al. Powerful usage of phylogenetically diverse Staphylococcus aureus control strains for detecting multidrug resistance genes in transcriptomics studies. Mol Cells 2010;30:71–76.Google Scholar
28. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207–214.Google Scholar
29. Zhernakova, A, Kurilshikov, A, Bonder, MJ, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 2016;352:565–569.CrossRefGoogle ScholarPubMed
30. Blaser, MJ. Antibiotic use and its consequences for the normal microbiome. Science 2016;352:544–545.Google Scholar
31. Lloyd-Price, J, Abu-Ali, G, Huttenhower, C. The healthy human microbiome. Genome Med 2016;8:51.CrossRefGoogle ScholarPubMed