Urinary Microbiome Characteristics in Female Patients with Acute Uncomplicated Cystitis and Recurrent Cystitis

Abstract

Traditionally, the diagnostic mainstay of recurrent urinary tract infection has been urinary culture. However, the causative uropathogen of recurrent cystitis has not been well established. Urine DNA next-generation sequencing (NGS) can provide additional information on these infections. Herein, we compared urine NGS results and urine cultures in patients with acute uncomplicated cystitis (AUC) and recurrent cystitis (RC), and evaluated the difference in microbiome patterns in the NGS results. Patients who underwent urine culture and NGS due to AUC or RC were retrospectively reviewed. All urine samples were collected via a transurethral catheter and studied utilizing a type of NGS called 16S ribosomal RNA gene amplification and sequencing. The sensitivity of urine NGS was significantly higher than that of conventional urine culture (69.0% vs. 16.7%, p < 0.05). The detection rate of urine NGS was slightly lower in the RC group than in the AUC group (67.7% vs. 72.7%). Microbiome diversity was significantly higher in the RC group compared to the AUC group (p = 0.007), and the microbiome composition was significantly different between the AUC and RC groups. In the urine NGS results, Pseudomonas, Acinetobacter, and Enterobacteriaceae were found in the AUC group, and Sphingomonas, Staphylococcus, Streptococcus, and Rothia spp. were detected in the RC group. Urine NGS can significantly increase the diagnostic sensitivity compared to traditional urine culture methods, especially in RC patients. AUC and RC patients had significant differences in bacterial diversity and patterns. Therefore, recurrent cystitis might be approached from a different perspective.

Keywords: 16S rRNA next-generation sequencing; cystitis; microbiome; urinary tract infection.

Figure 1

Diversity analysis of acute uncomplicated cystitis and recurrent cystitis, (A) Pairwise alpha diversity comparisons of urine microbiota between the two cystitis groups. Boxplot of the Shannon index shows significant differences between the two types of cystitis (** p < 0.01), (B) Principal coordinate analysis of the urine microbiota based on weighted UniFrac distances between the two cystitis groups shows significant differences in microbial composition.

Figure 2

A heatmap showing bacterial genera differentially abundant between the two cystitis groups, (A) The columns represent the samples, and the rows represent the top 100 genera based on overall abundance. The value in the heatmap represents the log2-normalized number of sequencing reads, with increasing shades of blue representing greater relative abundance, (B) The stacked bar plot shows the relative abundance of genera in each sample sorted by the order in the heatmap (left). Genera with an overall abundance of less than 1% were summed into “Others.”.

Figure 3

Comparison of bacterial taxa between acute uncomplicated cystitis and recurrent cystitis, (A) LEfSe analysis showing the bacterial taxa that were significantly different in abundance between the two cystitis groups. The taxa enriched in the acute uncomplicated cystitis group are shown in red with negative linear discriminant analysis (LDA) scores, and the recurrent cystitis group is shown in green with positive LDA scores. Only taxa passing the LDA threshold value of >2.0 are shown, (B) Boxplots showing the log2-transformed relative abundance of eight genera with LDAs above the significant threshold of 3 based on LefSe analysis between the two cystitis groups (* p < 0.05, ** p < 0.01).

Figure 4

Comparison of frequently encountered uropathogens in acute uncomplicated cystitis and recurrent cystitis, (A) Conventional urine culture, (B) Urine NGS.