Background: The 2022-2023 cholera outbreak in Malawi, the deadliest in the country's history, led to the unexpected identification of Aeromonas caviae in patients presenting with cholera-like symptoms. While A. caviae has been reported in similar cases across Africa, no population genomic studies have been conducted in cholera-endemic regions like Malawi. This study characterizes the genetic and antimicrobial resistance (AMR) profiles of A. caviae to improve diagnosis and treatment strategies.
Methods: We analyzed A. caviae isolates from suspected cholera cases using microbiological phenotypic isolation, whole-genome sequencing, and bioinformatics tools such as Bactopia and KmerFinder. Sequence quality checks were performed with FastQC, and low-quality reads were trimmed using Trimmomatic.
Results: A. caviae was identified in 7.4% (5/68) of cases, underscoring the need for broader pathogen screening in cholera outbreaks. AMR profiling revealed resistance genes for tetracyclines (tetA, tetE, tetC), aminoglycosides (aac(3)-Iid, aadA1), beta-lactams (blaOXA-427, blaMOX-5, blaCTX-M-15), and sulfonamides (sul1, dfrA15). Virulence factors linked to motility (motX, pomA2), adhesion (mshE, tapB), and secretion systems (exeA, hcp) suggest strong pathogenic potential.
Conclusion: A. caviae played a significant role in misdiagnosed cholera cases. The presence of tetracycline resistance genes is alarming, as this antibiotic is a frontline treatment for cholera. These findings highlight the need for improved diagnostic approaches and alternative treatment strategies to prevent treatment failures.