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,
one, four and twelve 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 Inter-individual differences in alpha and beta diversity of gut microbiota were high
at baseline, yet quinolone prophylaxis had only a moderate impact on gut microbiota
diversity. High relative abundances of Enterobacteriaceae during follow-up might indicate failure of or non-adherence to quinolone prophylaxis.
Future studies are needed to further investigate this phenomenon and to tailor individual
prophylactic strategies in these patients.
