Abstract
In 2025, the Democratic Republic of Congo (DRC) faced its most severe cholera crisis in two decades. However, clinical diagnosis and rapid diagnostic tests (RDTs) are often limited to the identification of a single pathogen, ignoring the complexity of co-infections. This study evaluates the prevalence of Salmonella, Shigella, and E. coli strains in patients with diarrhea. The aim of this study was to highlight cases of enteric bacterial co-infections in diarrheal patients during an epidemic in the DRC. This was a cross-sectional observational study based on 255 stool samples analyzed between December 2025 and February 2026 using the RADIOne 5-Plex multiplex PCR panel. Prevalences are presented with 95% confidence intervals (CI). Pairwise associations were explored using 2×2 tables, prevalence ratios (PR), odds ratios (OR), and chi-square or Fisher's exact tests, depending on sample size. A matrix and a co-occurrence network weighted by the number of co-detections completed the analysis. The significance level was set at 5%. V. cholerae was detected in 207/255 patients (81.2%; 95% CI 75.9–85.8), Shigella in 118/255 (46.3%; 95% CI 40.0–52.6), ETEC in 85/255 (33.3%; 95% CI 27.6–39.5), Salmonella in 13/255 (5.1%; 95% CI 2.7–8.6), and STEC in 4/255 (1.6%; 95% CI 0.4–4.0). At least two pathogens were detected in 138/255 patients (54.1%). The Shigella–ETEC association was significant (OR 1.85; 95% CI 1.09–3.14; p=0.021). The Salmonella–STEC association was also significant (OR 21.82; 95% CI 2.81–169.66; p=0.014), but was based on only four cases of STEC and should be considered exploratory. No statistically significant association was demonstrated between cholera and any of the other four agents. These results demonstrate that diarrhea in the context of a cholera epidemic in the DRC is not monopathogenic. The high frequency of co-infections suggests saturated environmental contamination.
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