Stool and sputum microbiome during quinolone prophylaxis of spontaneous bacterial peritonitis: an exploratory study

Marcus M Mücke; Sabrina Rüschenbaum; Amelie Mayer; Victoria T Mücke; Katharina M Schwarzkopf; Stefan Zeuzem; Jan Kehrmann; René Scholtysik; Christian M Lange

doi:10.1186/s13099-020-00389-y

Stool and sputum microbiome during quinolone prophylaxis of spontaneous bacterial peritonitis: an exploratory study

Gut Pathog. 2020 Oct 30:12:51. doi: 10.1186/s13099-020-00389-y. eCollection 2020.

Authors

Affiliations

¹ Present Address: Department of Internal Medicine 1, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
² Present Address: Department for Gastroenterology and Hepatology, University Hospital Essen and University of Duisburg-Essen, Essen, Germany.
³ Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
⁴ Institute of Cell Biology, University Hospital Essen and University of Duisburg-Essen, Essen, Germany.

^# Contributed equally.

Abstract

Introduction: Quinolone prophylaxis is recommended for patients with advanced cirrhosis at high risk of spontaneous bacterial peritonitis (SBP) or with prior SBP. Yet, the impact of long-term antibiotic prophylaxis on the microbiome of these patients is poorly characterized.

Methods: Patients with liver cirrhosis receiving long-term quinolone prophylaxis to prevent SBP were prospectively included and sputum and stool samples were obtained at baseline, 1, 4 and 12 weeks thereafter. Both bacterial DNA and RNA were assessed with 16S rRNA sequencing. Relative abundance, alpha and beta diversity were calculated and correlated with clinical outcome.

Results: Overall, 35 stool and 19 sputum samples were obtained from 11 patients. Two patients died (day 9 and 12) all others were followed for 180 days. Reduction of Shannon diversity and bacterial richness was insignificant after initiation of quinolone prophylaxis (p > 0.05). Gut microbiota were significantly different between patients (p < 0.001) but non-significantly altered between the different time points before and after initiation of antibiotic prophylaxis (p > 0.05). A high relative abundance of Enterobacteriaceae > 20% during quinolone prophylaxis was found in three patients. Specific clinical scenarios (development of secondary infections during antibiotic prophylaxis or the detection of multidrug-resistant Enterobacteriaceae) characterized these patients. Sputum microbiota were not significantly altered in individuals during prophylaxis.

Conclusion: The present exploratory study with small sample size showed that inter-individual differences in diversity of gut microbiota were high at baseline, yet quinolone prophylaxis had only a moderate impact. High relative abundances of Enterobacteriaceae during follow-up might indicate failure of or non-adherence to quinolone prophylaxis. However, our results may not be clinically significant given the limitations of the study and therefore future studies are needed to further investigate this phenomenon.

Keywords: Bacterial abundance; Enterobacteriaceae; Infections; Multidrug-resistance; Quinolones.