Search results for: cattle manure

Authors: Shagufta Jabeen, Faez J. Firdaus Abdullah, Zunita Zakaria, Nurulfiza M. Isa, Yung C. Tan, Wai Y. Yee, Abdul R. Omar

Abstract:

Pasteurella multocida (PM) is an important veterinary opportunistic pathogen particularly associated with septicemic pasteurellosis, pneumonic pasteurellosis and hemorrhagic septicemia in cattle and buffaloes. P. multocida serotype A has been reported to cause fatal pneumonia and septicemia. Pasteurella multocida subspecies multocida of serotype A Malaysian isolate PMTB2.1 was first isolated from buffaloes died of septicemia. In this study, the genome of P. multocida strain PMTB2.1 was sequenced using third-generation sequencing technology, PacBio RS2 system and analyzed bioinformatically via de novo analysis followed by in-depth analysis based on comparative genomics. Bioinformatics analysis based on de novo assembly of PacBio raw reads generated 3 contigs followed by gap filling of aligned contigs with PCR sequencing, generated a single contiguous circular chromosome with a genomic size of 2,315,138 bp and a GC content of approximately 40.32% (Accession number CP007205). The PMTB2.1 genome comprised of 2,176 protein-coding sequences, 6 rRNA operons and 56 tRNA and 4 ncRNAs sequences. The comparative genome sequence analysis of PMTB2.1 with nine complete genomes which include Actinobacillus pleuropneumoniae, Haemophilus parasuis, Escherichia coli and five P. multocida complete genome sequences including, PM70, PM36950, PMHN06, PM3480, PMHB01 and PMTB2.1 was carried out based on OrthoMCL analysis and Venn diagram. The analysis showed that 282 CDs (13%) are unique to PMTB2.1and 1,125 CDs with orthologs in all. This reflects overall close relationship of these bacteria and supports the classification in the Gamma subdivision of the Proteobacteria. In addition, genomic distance analysis among all nine genomes indicated that PMTB2.1 is closely related with other five Pasteurella species with genomic distance less than 0.13. Synteny analysis shows subtle differences in genetic structures among different P.multocida indicating the dynamics of frequent gene transfer events among different P. multocida strains. However, PM3480 and PM70 exhibited exceptionally large structural variation since they were swine and chicken isolates. Furthermore, genomic structure of PMTB2.1 is more resembling that of PM36950 with a genomic size difference of approximately 34,380 kb (smaller than PM36950) and strain-specific Integrative and Conjugative Elements (ICE) which was found only in PM36950 is absent in PMTB2.1. Meanwhile, two intact prophages sequences of approximately 62 kb were found to be present only in PMTB2.1. One of phage is similar to transposable phage SfMu. The phylogenomic tree was constructed and rooted with E. coli, A. pleuropneumoniae and H. parasuis based on OrthoMCL analysis. The genomes of P. multocida strain PMTB2.1 were clustered with bovine isolates of P. multocida strain PM36950 and PMHB01 and were separated from avian isolate PM70 and swine isolates PM3480 and PMHN06 and are distant from Actinobacillus and Haemophilus. Previous studies based on Single Nucleotide Polymorphism (SNPs) and Multilocus Sequence Typing (MLST) unable to show a clear phylogenetic relatedness between Pasteurella multocida and the different host. In conclusion, this study has provided insight on the genomic structure of PMTB2.1 in terms of potential genes that can function as virulence factors for future study in elucidating the mechanisms behind the ability of the bacteria in causing diseases in susceptible animals.

Keywords: comparative genomics, DNA sequencing, phage, phylogenomics

Procedia PDF Downloads 183

Authors: Kedar Baral

Abstract:

This study was carried out in Mustang, Kaski, Tanahun, Baitadi, and Jhapa districts of Nepal. The study explored the spatial and temporal pattern of HWC, socio economic factors associated with it, impacts of conflict on life / livelihood of people and survival of wildlife species, and impact of climate change and forest fire onHWC. Study also evaluated people’s attitude towards wildlife conservation and assessed relevant policies and programs. Questionnaire survey was carried out with the 250 respondents, and both socio-demographic and HWC related information werecollected. Secondary information were collected from Divisional Forest Offices and Annapurna Conservation Area Project.HWC events were grouped by season /months/sites (forest type, distances from forest, and settlement), and the coordinates of the events were exported to ArcGIS. Collected data were analyzed using descriptive statistics in Excel and R Program. A total of 1465 events were recorded in 5 districts during 2015 and 2019. Out of that, livestock killing, crop damage, human attack, and cattle shed damage events were 70 %, 12%, 11%, and 7%, respectively. Among 151 human attack cases, 23 people were killed, and 128 were injured. Elephant in Terai, common leopard and monkey in Middle Mountain, and snow leopard in high mountains were found as major problematic animals. Common leopard attacks were found more in the autumn, evening, and on human settlement area. Whereas elephant attacks were found higher in winter, day time, and on farmland. Poor people farmers were found highly victimized, and they were losing 26% of their income due to crop raiding and livestock depredation. On the other hand, people are killing many wildlife in revenge, and this number is increasing every year. Based on the people's perception, climate change is causing increased temperature and forest fire events and decreased water sources within the forest. Due to the scarcity of food and water within forests, wildlife are compelled to dwell at human settlement area, hence HWC events are increasing. Nevertheless, more than half of the respondents were found positive about conserving entire wildlife species. Forests outside PAs are under the community forestry (CF) system, which restored the forest, improved the habitat, and increased the wildlife.However, CF policies and programs were found to be more focused on forest management with least priority on wildlife conservation and HWC mitigation. Compensation / relief scheme of government for wildlife damage was found some how effective to manage HWC, but the lengthy process, being applicable to the damage of few wildlife species and highly increasing events made it necessary to revisit. Based on these facts, the study suggest to carry out awareness generation activities to the poor farmers, linking the property of people with the insurance scheme, conducting habitat management activities within CF, promoting the unpalatable crops, improvement of shed house of livestock, simplifying compensation scheme and establishing a fund at the district level and incorporating the wildlife conservation and HWCmitigation programs in CF. Finally, the study suggests to carry out rigorous researches to understand the impacts of current forest management practices on forest, biodiversity, wildlife, and HWC.

Keywords: community forest, conflict mitigation, wildlife conservation, climate change

Procedia PDF Downloads 114