Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance

Asha Rani, Ravi Ranjan, Halvor S. McGee, Kalista E. Andropolis, Dipti V. Panchal, Zahraa Hajjiri, Daniel Brennan, Patricia W. Finn, David L. Perkins

Research output: Contribution to journalArticle

Abstract

Recent studies have established that a complex community of microbes colonize the human urinary tract; however, their role in kidney transplant patients treated with prophylactic antibiotics remains poorly investigated. Our aim was to investigate the urinary microbiome of kidney transplant recipients. Urine samples from 21 patients after kidney transplantation and 8 healthy controls were collected. All patients received prophylactic treatment with the antibiotic combination trimethoprim-sulfamethoxazole. Metagenomic DNA was isolated from urine samples, sequenced using shotgun sequencing approach on Illumina HiSeq 2000 platform, and analyzed for microbial taxonomic and functional annotations. Our results demonstrate that the urine microbiome of kidney transplants was markedly different at all taxonomic levels from phyla to species, had decreased microbial diversity, and increased abundance of potentially pathogenic species compared with healthy controls. Specifically, at the phylum level, we detected a significant decrease in Actinobacteria and increase in Firmicutes due to increases in Enterococcus faecalis. In addition, there was an increase in the Proteobacteria due to increases in Escherichia coli. Analysis of predicted functions of the urinary metagenome revealed increased abundance of enzymes in the folate pathway including dihydrofolate synthase that are not inhibited by trimethoprim-sulfamethoxazole, but can augment folate metabolism. This report characterizes the urinary microbiome of kidney transplants using shotgun metagenomics approach. Our results indicate that the urinary microbiota may be modified in the context of prophylactic antibiotics, indicating that a therapeutic intervention may shift the urinary microbiota to select bacterial species with increased resistance to antibiotics. The evaluation and development of optimal prophylactic regimens that do not promote antibiotic resistance is an important future goal.

Original languageEnglish (US)
Pages (from-to)59-70
Number of pages12
JournalTranslational Research
Volume181
DOIs
StatePublished - Mar 1 2017
Externally publishedYes

Fingerprint

Dysbiosis
Transplants
Microbiota
Microbial Drug Resistance
Anti-Bacterial Agents
Kidney
Metagenomics
Sulfamethoxazole Drug Combination Trimethoprim
Firearms
Urine
Folic Acid
Metagenome
Proteobacteria
Actinobacteria
Enterococcus faecalis
Urinary Tract
Metabolism
Kidney Transplantation
Escherichia coli
DNA

ASJC Scopus subject areas

  • Public Health, Environmental and Occupational Health
  • Biochemistry, medical

Cite this

Rani, A., Ranjan, R., McGee, H. S., Andropolis, K. E., Panchal, D. V., Hajjiri, Z., ... Perkins, D. L. (2017). Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance. Translational Research, 181, 59-70. https://doi.org/10.1016/j.trsl.2016.08.008

Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance. / Rani, Asha; Ranjan, Ravi; McGee, Halvor S.; Andropolis, Kalista E.; Panchal, Dipti V.; Hajjiri, Zahraa; Brennan, Daniel; Finn, Patricia W.; Perkins, David L.

In: Translational Research, Vol. 181, 01.03.2017, p. 59-70.

Research output: Contribution to journalArticle

Rani, A, Ranjan, R, McGee, HS, Andropolis, KE, Panchal, DV, Hajjiri, Z, Brennan, D, Finn, PW & Perkins, DL 2017, 'Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance', Translational Research, vol. 181, pp. 59-70. https://doi.org/10.1016/j.trsl.2016.08.008
Rani, Asha ; Ranjan, Ravi ; McGee, Halvor S. ; Andropolis, Kalista E. ; Panchal, Dipti V. ; Hajjiri, Zahraa ; Brennan, Daniel ; Finn, Patricia W. ; Perkins, David L. / Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance. In: Translational Research. 2017 ; Vol. 181. pp. 59-70.
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