Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis

Amirhossein Shamsaddini, Patrick M. Gillevet, Chathur Acharya, Andrew Fagan, Edith Gavis, Masoumeh Sikaroodi, Sara McGeorge, Alexander Khoruts, Somaya Albhaisi, Michael Fuchs, Richard K. Sterling, Jasmohan S. Bajaj

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Background and aims: Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes. Methods: In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning. Results: A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs. Conclusions: Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.

Original languageEnglish (US)
Pages (from-to)508-521.e7
Issue number2
StatePublished - Aug 1 2021
Externally publishedYes

Bibliographical note

Funding Information:
Funding This work was partly supported by VA merit review 2I0CX00176, NCATS R21TR002024, and R21TR003095.

Publisher Copyright:
© 2021 AGA Institute


  • Ascites
  • Hepatic Encephalopathy
  • Infections
  • Machine Learning
  • Rifaximin


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