Genetic Diversity and Population Structure of  Rattus rattus and Rattus tanezumi in Sporadic  Leptospirosis Areas of Central Java, Indonesia

Raisha Nuranindita; Derico Hitipeuw; Martini; Mursid Raharjo; Ni Kadek Dita Cahyani; Fauzi Muh Muh

Raisha Nuranindita Public Health Genomics Lab, Faculty of Public Health, Universitas Diponegoro, Semarang, Indonesia
Derico Hitipeuw Department of Environmental Health, Faculty of Public Health, Universitas Diponegoro, Semarang, Indonesia
Martini Department of Public Health, Faculty of Public Health, Universitas Diponegoro, Semarang, Indonesia
Mursid Raharjo Department of Environmental Health, Faculty of Public Health, Universitas Diponegoro, Semarang, Indonesia
Ni Kadek Dita Cahyani Department of Biology, Faculty of Science and Mathematics, Diponegoro University, Semarang, Indonesia
Fauzi Muh Muh Department of Epidemiology and Tropical Diseases, Faculty of Public Health, Universitas Diponegoro, Semarang, Indonesia

Keywords: R. rattus, R. tanezumi, population structure, haplotype, genetic diversity

Abstract

Introduction: Rattus rattus and Rattus tanezumi are important vectors of leptospirosis, a zoonotic disease of public health concern in Indonesia. This study investigated the genetic diversity and population structure of these two rat species in Purworejo Regency, Central Java, an area that experienced a leptospirosis outbreak in 2023 with the highest case fatality rate in the province.
Method: Rats were trapped in two villages with contrasting ecological settings: Dadirejo (hilly terrain with plantations) and Kutoarjo (densely populated urban area). Mitochondrial cytochrome b gene sequences were analyzed to assess phylogenetic relationships, genetic diversity, and population structure.
Results: Phylogenetic analysis revealed distinct evolutionary lineages for R. rattus and R. tanezumi, with R. tanezumi exhibiting greater intraspecific genetic diversity. Haplotype and nucleotide diversity indices indicated higher genetic variation in R. tanezumi compared to R. rattus. Analysis of molecular variance (AMOVA) showed strong genetic differentiation among R. rattus populations (FST = 0.973), suggesting limited gene flow and potential multiple introduction events. In contrast, R. tanezumi displayed greater connectivity among central
Java populations but substantial differentiation from Jakarta and Sulawesi populations. These distinct genetic profiles may influence the spatial heterogeneity of leptospirosis cases across Purworejo’s sub-districts. The higher genetic diversity in R. tanezumi could enhance its adaptability and reservoir potential, while the genetic isolation of R. rattus populations may lead to location-specific pathogen strains.
Conclusion: These findings underscore the importance of considering rat population genetics in understanding leptospirosis transmission dynamics and designing effective control strategies.

How to cite this article:
Nuranindita R, Hitipeuw D, Martini, Raharjo M, Cahyani N K D, Muh F. Genetic Diversity and Population Structure of Rattus rattus and Rattus tanezumi in Sporadic Leptospirosis Areas of Central Java, Indonesia. J Commun Dis.
2025;57(3):78-88.

DOI: https://doi.org/10.24321/0019.5138.202571

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