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.

凝胶扩散免疫沉淀试验（GDPT）及限制性内切酶分析（REA）在巴氏杆菌（Pasteurella multocida）的血清型和基因型鉴定中已被广泛应用。全基因组测序（WGS）和单核苷酸多态性（SNP）分析已成为其他生物的金标准，其分辨率高于以往的方法。本研究将WGS与REA和GDPT在163株巴氏杆菌分离株中进行了比较，以确定WGS是否能够产生更精确的结果，并能否替代REA和/或GDPT。所使用的分离株代表了十六种参考血清型、REA谱与禽霍乱疫苗株相匹配的分离株，以及来自十个不同动物种类的分离株。分离株来源于美国各地以及智利。该研究发现在系统发育树上具有相同REA谱的分离株聚集在一起。此外，还发现仅相差几个条带的REA谱与相差更多的REA谱相比，具有更少的SNP差异，这与预期相符。GDPT的结果多样，但常见到单个血清型在簇内反复出现。在检查REA谱时发现了一些错误。WGS能够确认这些错误，并补偿REA分析中的主观性。此外，WGS和SNP分析的结果与流行病学数据的相关性比GDPT更紧密。从本研究产生的数据来看，WGS和SNP分析优于REA和GDPT，并突显了旧测试中存在的一些问题。