Serological Surveillance of Zoonotic Pathogens in Rats in Markets in Bogor, Indonesia.

Background: Rats are a major carrier of several pathogens, including zoonotic pathogens that can cause fatal diseases in humans. Indonesia has one of the fastest growing populations, with high infestation of rats in urban areas. Therefore, this study aims to assess the seropositivity of zoonotic pathogens in rats from four markets in Bogor, Indonesia. Materials and Methods: A total of 80 brown rats (Rattus norvegicus) were captured from the markets and screened for the presence of some zoonotic pathogens, specifically hantavirus, Leptospira spp., Orientia tsutsugamushi, tick-borne encephalitis virus (TBEV), and lymphocytic choriomeningitis virus (LCMV) antibodies, using indirect fluorescence assay or enzyme-linked immunosorbent assay. Results: Among the 80 rats, 40% were seropositive for hantavirus, 36.3% for Leptospira spp., 11.3% for O. tsutsugamushi, 6.3% for TBEV, and 0% for LCMV. Conclusion: Overall, these results indicate that rats in Bogor pose a potential zoonotic risk to humans.

Comparative genomic analysis of Leptospira spp. isolated from Rattus norvegicus in Indonesia.

Leptospirosis is one of the most prevalent zoonotic diseases caused by pathogenic spirochetes of Leptospira spp. The disease has become a public health concern in urban localities in the tropics, where rats serve as significant reservoir animals for leptospirosis transmission. In Indonesia, the occurrence of leptospirosis is underestimated, and information on the causative Leptospira genotypes and serotypes is limited. This study reports the isolation of Leptospira spp. from rats captured in urban areas of Bogor, Indonesia. Serogroups and genotypes, sequence types (STs), or multiple-locus variable-number tandem repeat analysis (MLVA) types using 11 loci, were determined for the isolates. Furthermore, whole genome sequencing (WGS) was performed on 11 Indonesian isolates and 24 isolates from other Asian countries. Ninety small mammals, including 80 Rattus norvegicus and ten Suncus murinus, were captured and, 25 Leptospira spp. were isolated solely from R. norvegicus (31.3%). The isolates were identified as Leptospira borgpetersenii serogroup Javanica with ST 143 (four strains) and Leptospira interrogans serogroup Bataviae with the same MLVA type as isolates from other Asian countries (19); the serogroup of the two L. interrogans with ST252 could not be identified. The core genome SNP-based phylogenetic tree revealed that Indonesian isolates were genetically related to L. borgpetersenii serogroup Javanica strains widely distributed in Asian countries but formed a different cluster from other strains. The phylogenetic tree of L. interrogans serogroup Bataviae isolates from Indonesia, the Philippines, Taiwan, and Vietnam revealed that isolates were grouped into five clusters based on their geographic locations. This study discovered a high carriage rate of Leptospira spp. among R. norvegicus in Bogor, Indonesia, indicating a potential risk of rat-borne leptospirosis in the area. Besides L. borgpetersenii serogroup Javanica, WGS on L. interrogans serogroup Bataviae illustrated the geographical structuring of genetic diversity in Leptospira spp.

Antimicrobial resistance in Escherichia coli isolated from brown rats and house shrews in markets, Bogor, Indonesia.

The prevalence of antimicrobial resistance (AMR) in small mammals dwelling in the city was used as an indicator of AMR bacteria in the environment. We captured 87 small mammals (79 brown rats and 8 house shrews) in four markets, Bogor, Indonesia in October 2019, and we obtained 20 AMR Escherichia coli (E. coil) from 18 brown rats and two house shrews. Of these, eight isolates were determined to be multi-drug resistant (MDR) E. coli, suggesting the potential contamination of AMR E. coli in the markets in Bogor, Indonesia, and that mammals, including humans, are at risk of infection with AMR E. coli from environment.