Molecular surveillance of zoonotic pathogens from wild rodents in the Republic of Korea

Abstract

Background: Rodents are recognized as major reservoirs of numerous zoonotic pathogens and are involved in the transmission and maintenance of infectious diseases. Furthermore, despite their importance, diseases transmitted by rodents have been neglected. To date, there have been limited epidemiological studies on rodents, and information regarding their involvement in infectious diseases in the Republic of Korea (ROK) is still scarce.

Methodology/principal findings: We investigated rodent-borne pathogens using nested PCR/RT-PCR from 156 rodents including 151 Apodemus agrarius and 5 Rattus norvegicus from 27 regions in eight provinces across the ROK between March 2019 and November 2020. Spleen, kidney, and blood samples were used to detect Anaplasma phagocytophilum, Bartonella spp., Borrelia burgdorferi sensu lato group, Coxiella burnetii, Leptospira interrogans, and severe fever with thrombocytopenia syndrome virus (SFTSV). Of the 156 rodents, 73 (46.8%) were infected with Bartonella spp., 25 (16.0%) with C. burnetii, 24 (15.4%) with L. interrogans, 21 (13.5%) with A. phagocytophilum, 9 (5.8%) with SFTSV, and 5 (3.2%) with Borrelia afzelii. Co-infections with two and three pathogens were detected in 33 (21.1%) and 11 rodents (7.1%), respectively. A. phagocytophilum was detected in all regions, showing a widespread occurrence in the ROK. The infection rates of Bartonella spp. were 83.3% for B. grahamii and 16.7% for B. taylorii.

Conclusions/significance: To the best of our knowledge, this is the first report of C. burnetii and SFTSV infections in rodents in the ROK. This study also provides the first description of various rodent-borne pathogens through an extensive epidemiological survey in the ROK. These results suggest that rodents harbor various pathogens that pose a potential threat to public health in the ROK. Our findings provide useful information on the occurrence and distribution of zoonotic pathogens disseminated among rodents and emphasize the urgent need for rapid diagnosis, prevention, and control strategies for these zoonotic diseases.

Fig 1. Maps showing the regions where rodent-borne pathogens were detected in the Republic of Korea.

The word symbol is indicated differently according to each pathogen. Maps were created using NGII [https://www.data.go.kr/data/15062309/fileData.do] and are Korea Open Government License Type 1, which can be freely used without any permission.

Fig 2. Phylogenetic tree inferred by maximum-likelihood analysis using the K2 + G model of the 16S rRNA gene sequence of Anaplasma phagocytophilum.

The numbers at the nodes are bootstrap values expressed as a percentage of 1,000 replicates. The scale bar indicates nucleotide substitution per site. Samples sequenced from Apodemus agrarius are shown in filled circles.

Fig 3. Phylogenetic analysis based on the ITS region of Bartonella spp. (maximum-likelihood analysis using the Tamura 3-parameter + G + I model with 1,000 replicates).

The scale bar indicates nucleotide substitution per site. Sequences determined from A. agrarius are indicated in filled circles.

Fig 4. Maximum-likelihood phylogenetic tree using the Tamura-Nei model based on the ospA gene of Borrelia spp. Bootstrap values were calculated with 1,000 replicates of the alignment.

The scale bar indicates nucleotide substitution per site. Sequences obtained from A. agrarius are symbolized in filled circles.

Fig 5. Maximum-likelihood phylogenetic tree from the IS1111 gene of Coxiella burnetii.

The evolutionary analysis was inferred using the Kimura 2-parameter model. Bootstrap values (1,000 replicates) are indicated in each node. The scale bar indicates nucleotide substitution per site. Sequences determined from A. agrarius are highlighted in filled circles.

Fig 6. Phylogenetic analysis based on the rpoB gene of Leptospira interrogans.

The tree was inferred in MEGA X using maximum-likelihood and Kimura 2-parameter with 1,000 replicates. The scale bar implies nucleotide substitution per site. The box of dash lines indicates L. interrogans. Sequences obtained from A. agrarius are shown in filled circles.

Fig 7. Phylogenetic tree of the severe fever with thrombocytopenia syndrome virus based on the analysis of partial sequences of small segments.

Maximum-likelihood analysis was used to construct the Kimura 2-parameter model (1,000 bootstrap replicates). The scale bar implies nucleotide substitution per site. Sequences identified from A. agrarius are indicated in filled circles.