Comparison of whole genome sequencing to restriction endonuclease analysis and gel diffusion precipitin test of Pasteurella multocida

The gel diffusion precipitin test (GDPT) and restriction endonuclease analysis (REA) have commonly been used in serotyping and further identifying isolates of Pasteurella multocida. GDPT has shown problems with repeatability and cross reactions. The hindrance with REA has been the subjectivity of the test. Whole genome sequencing (WGS) has become a new option in diagnostic testing due to reduced cost and quicker turnaround time. WGS has shown with other organisms to be a useful diagnostic tool and this study examined its use on P. multocida. This study compared WGS to REA and GDPT on 166 isolates of P. multocida to determine if WGS produced similar results and could be used in place of REA and/or GDPT. The isolates used represented the sixteen reference serotypes (1-16), isolates with REA profiles matching the fowl cholera vaccine strain, and 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 appeared closely related on the tree. The GDPT results were more diverse but it was common to see a single serotype show up repeatedly within clusters. Several errors were also found when examining the REA profiles, such as two assigned numbers for one profile or profiles misidentified. WGS was able to confirm these errors and compensate for the subjectivity in analysis of REA. It also provided epidemiological information that is not available with GDPT. From the data produced in this study it appears that WGS could be used in place or in conjunction with REA and GDPT