Investigation Of Pathogens And Diversity Of Bacterial Communities Of Rodent Natural Focal Diseases In Western And Eastern Regions

BackgroundRodents are widely diverse in nature,accounting for about 43%of mammalian species.They are the main host animals for tick,flea,mite and other vector organisms,and have close contact with humans and livestock.They can carry various natural pathogen related diseases.The western and eastern regions of China have complex habitats and rich species resources,which are suitable for rodent reproduction and survival.pestis,hemorrhagic fever with renal syndrome and other natural foci diseases transmitted by rodents have occurred in the two regions for many times.Therefore,in this study,two regions with large differences in climate,terrain and altitude between Huzhu Prefecture in Qinghai Province and Rizhao Prefecture in Shandong Province were selected from the east and west to investigate the pathogen related to natural foci diseases of rodents.The 16s rRNA gene high-throughput sequencing technology was used to explore the diversity and differences of bacteria carried by rodents in the two regions,and to find potential pathogenic bacteria.Objectives1.Understand the species,composition,distribution,density,and other characteristics of rodents in Huzhu and Rizhao regions;2.To explore the infection status and differences of seven natural foci disease related pathogens in rodents in the two regions,including Bartonella,phagocyte anamorpha,Borrelia burgdorferi,Leptospira,Rickettsia proboschii,Francisella tularensis,and Hantavirus;3.Clarify the composition and differences of bacterial colonies carried by rodents in the eastern and western regions of the same latitude in China,and explore potential pathogenic genera.Results1.Sample collectionThis survey collected 58 rodents and 1 insectivorous animal(shrew)from the Huzhu area,belonging to three families,three genera,and six species;Among them,the composition ratio of Mus musculus was the highest(42.37%),followed by Long tailed Hamster(28.81%)and brown rat(20.34%),followed by Rattus flavipectus(3.39%),Grey Hamster(3.39%)and Shrew(1.69%);22 female mice,35 male mice,2 of unknown gender,with a male to female ratio of 1:1.6;The mouse density is 5.29%,the mite infection rate of the mouse body is 1.69%,and the mite index is 0.24;The local advantageous vegetation is birch,while the advantageous crops are rapeseed,soybean,and astragalus.38 rodents were collected from the Rizhao area,belonging to one family,two genera,and three species;Among them,Apodemus agrarius had the highest proportion(57.89%),followed by Mus musculus(28.95%),and finally brown rat(13.16%);15 females and 23 males,with a ratio of 1:1.5;The mouse density is 3.80%,and the local dominant vegetation is poplar,with the dominant crops being wheat,corn,and peanuts.2.Analysis of ecological indicators of rodent communitiesBy comparing the ecological indicators of rodent communities in the two regions and each survey point,it is found that the species diversity of rodents in Huzhu area is more abundant than that in Rizhao area.The richness index(5.0000),diversity index(1.9883)and balance index(1.2354)of Beishan National Forest Park in Huzhu District are the highest,while the ecological dominance index(0.8000)of Haizi Village,Wufeng Township is the highest.The species richness index(3.0000)of Xiaoyuzi Village and Xiaochenjia Village in Rizhao is the same,but the diversity index(0.8487),balance index(0.7725)and ecological dominance index(0.5213)of Xiaoyuzi Village are higher than that of Xiaochenjia Village.3.Investigation of Pathogens Related to Natural Focal Diseases in RodentsRT qPCR showed that rodents were infected with Bartonella.The infection rate in Huzhu area was 11.86%,among which brown rat,Hamster and Mus musculus were infected with Bartonella,with the infection rates of 25.00%,1 1.76%and 8.00%,respectively.No Bartonella infection was detected in other mice;The infection rate of male mice was 14.29%,while that of female mice was 9.09%;Compared to other survey points,the Bartonella infection rate(5.88%)in Beishan National Forest Park in Huzhu Prefecture is the lowest,but there is no statistically significant difference in Bartonella infection rate between different genders and mouse species(P>0.05).The infection rate of rodent Bartonella in Rizhao area was 34.21%.brown rat,Mus musculus and Apodemus agrarius all had Bartonella infection,with the infection rates of 100.00%,45.45%and 13.64%respectively;The infection rate of male mice was 34.78%,while that of female mice was 33.33%;The difference in Bartonella infection rates among different mouse species in the region is statistically significant(x 2=16.14,P<0.001),but there was no statistically significant difference in the infection rate of Bartonella among different genders and survey points(P>0.05).The infection rate of Bartonella in rodents in Huzhu area is lower than that in Rizhao area,and the difference between the two areas is statistically significant(χ2=7.05,P=0.008).In addition,six natural foci disease related pathogens,including Borrelia burgdorferi,Leptospira leptospira,phagocyte amoeba,Francisella tularensis,Rickettsia mornii and Hantavirus,were not detected in rodents in the two regions.4.Diversity analysis of bacterial communities carried by rodents in the two regions20 samples positive for Bartonella detected by RT qPCR were subjected to 16s rRNA gene amplicon sequencing analysis,and 18 samples were successfully amplified.A total of 5 valid specimens were obtained in Huzhu area,including 3 brown rat,1 long tailed hamster and 1 small house mouse.315028 high-quality sequences were amplified and 176 OTUs were aggregated;A total of 13 valid specimens were obtained in Rizhao,including 4 brown rat,5 Mus musculus and 4 Apodemus agrarius.954062 high-quality sequences were amplified and 736 OTUs were aggregated.After alpha and beta diversity analysis,it was found that there were statistical differences in the bacterial community diversity(P=0.0026)and bacterial community structure(P=0.001)carried by rodents in the two regions,and the bacterial community diversity in the Rizhao area was more abundant than that in the Huzhu area.In addition,there was no statistical difference in the bacterial community diversity carried by brown rat in the two regions(P=0.077),but there was a statistical difference in the bacterial community structure(P=0.034).The sequencing results of 16s rRNA gene amplifiers of rodents in the two regions showed that,except for Bartonella,which is the same pathogen with high relative abundance,the potential pathogenic bacteria with relatively high abundance in Huzhu region are Rhodococcus,Acinetobacter and Pseudomonas,while the potential pathogenic bacteria with relatively high abundance in Rizhao region are Corynebacterium,Neisseria,Acinetobacter,Pseudomonas and Streptococcus.Conclusions1.Six mouse species,including Mus musculus,Mus norvegicus,Long tailed hamster,Gray hamster,Common shrew,and Rattus flavipectus,were captured in Huzhu area,while three mouse species,Apodemus agrarius,Mus norvegicus,and Mus norvegicus,were captured in Rizhao area.There were differences in the composition of mouse species communities between the two regions.2.According to the ecological indicators of the communities in the two regions,the species diversity of rodents in Huzhu region is more abundant than that in Rizhao region.3.Rodents in the eastern and western regions all have Bartonella infection.The infection rate in Rizhao region(34.21%)is higher than that in Huzhu region(11.86%),but there is no statistical difference in the infection rate in terms of gender.In addition,neither region has detected Borrelia burgdorferi,Leptospira leptospira,Phagophagocytic aplasia,Franciscia tularensis,Rickettsia morgdorferi Six natural focus disease related pathogens,including hantavirus.4.There are statistical differences in the diversity and structure of bacterial communities carried by rodents in the two regions,and the diversity of bacterial communities in the Rizhao region is more abundant than that in the Huzhu region;The bacterial community structure carried by brown rat in the two regions was statistically different.In the analysis of microbial flora carried by rodents,Acinetobacter,Pseudomonas and other potential pathogenic bacteria with relatively high abundance were found;In addition,in Huzhu District,there are also Rhodococcus species which are harmful to local animal husbandry.In Rizhao District,there are Corynebacterium species,Neisseria species and Streptococcus species.