Molecular detection and phylogenetic characterization of pathogenic Leptospira in commensal rats from Indonesian fishing ports

Abstract

Background: Leptospirosis is a zoonotic disease caused by the pathogenic Leptospira. The presence of commensal rats in seaport areas poses a potential risk of transmission of leptospirosis. Aim: This study aimed to investigate the prevalence and molecular characteristics of pathogenic Leptospira in rats captured from three fishing ports in West Java, Indonesia: Kejawanan (Cirebon), Karangsong (Indramayu), and Palabuhanratu (Sukabumi). Methods: Rat trapping was conducted using single live traps from July to August 2025, followed by species identification based on morphological characteristics. Pathogenic Leptospira was detected using PCR targeting the lipL32 gene. Positive samples were sequenced for species confirmation and phylogenetic analysis. Results: A total of 114 rats, consisting of Rattus norvegicus (85.1%) and Rattus tanezumi (14.9%), were captured, with an overall trap success rate of 7.13%. PCR results revealed that 47.4% of rats were positive for pathogenic Leptospira, with the highest prevalence in Kejawanan (75%), followed by Palabuhanratu (48.8%) and Karangsong (30%). Phylogenetic analysis demonstrated that the detected Leptospira clustered within L. interrogans and L. kirschneri. Conclusion: These findings confirm the circulation of pathogenic Leptospira among commensal rats in fishing port environments and highlight their role as reservoirs with potential zoonotic risk. Strengthening surveillance and rodent control is important for reducing the risk of leptospirosis transmission in port areas.