Pasteurella multocida Genome sequencing and assembly
The gel diffusion precipitin test (GDPT) and restriction endonuclease analysis (REA) have commonly been used in serotyping and genotyping of Pasteurella multocida. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis has become the gold standard for other organisms, offering higher resolution than previously available methods. This study compared WGS to REA and GDPT on 163 isolates of P. multocida to determine if WGS produced more precise results and could be used in place of REA and/or GDPT. The isolates used represented the sixteen reference serovars, isolates with REA profiles matching the fowl cholera vaccine strain, and isolates from ten different animal species. Isolates originated from across the United States and from Chile. This study found that identical REA profiles clustered together in the phylogenetic tree. It was also discovered that REA profiles that differed by only a few bands also had fewer SNP differences than REA profiles with more differences, as expected. The GDPT results were diverse but it was common to see a single serotype show up repeatedly within clusters. Several errors were found when examining the REA profiles. WGS was able to confirm these errors and compensate for the subjectivity in analysis of REA. Also, results of WGS and SNP analysis more closely correlated with the epidemiological data than GDPT. From the data produced in this study WGS and SNP analysis was superior to REA and GDPT and highlighted some of the issues present in the older tests.
| Main Author: | |
|---|---|
| Format: | Dataset biblioteca |
| Published: |
2017
|
| Subjects: | Genetics, Pasteurella multocida, eBacteria, genome sequencing and assembly, |
| Online Access: | https://figshare.com/articles/dataset/Pasteurella_multocida_Genome_sequencing_and_assembly/25081670 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | The gel diffusion precipitin test (GDPT) and restriction endonuclease analysis (REA) have commonly been used in serotyping and genotyping of Pasteurella multocida. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis has become the gold standard for other organisms, offering higher resolution than previously available methods. This study compared WGS to REA and GDPT on 163 isolates of P. multocida to determine if WGS produced more precise results and could be used in place of REA and/or GDPT. The isolates used represented the sixteen reference serovars, isolates with REA profiles matching the fowl cholera vaccine strain, and isolates from ten different animal species. Isolates originated from across the United States and from Chile. This study found that identical REA profiles clustered together in the phylogenetic tree. It was also discovered that REA profiles that differed by only a few bands also had fewer SNP differences than REA profiles with more differences, as expected. The GDPT results were diverse but it was common to see a single serotype show up repeatedly within clusters. Several errors were found when examining the REA profiles. WGS was able to confirm these errors and compensate for the subjectivity in analysis of REA. Also, results of WGS and SNP analysis more closely correlated with the epidemiological data than GDPT. From the data produced in this study WGS and SNP analysis was superior to REA and GDPT and highlighted some of the issues present in the older tests. |
|---|