Colavecchio Anna, D'Souza Yasmin, Tompkins Elizabeth, Jeukens Julie, Freschi Luca, Emond-Rheault Jean-Guillaume, Kukavica-Ibrulj Irena, Boyle Brian, Bekal Sadjia, Tamber Sandeep, Levesque Roger C, Goodridge Lawrence D
Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-BellevueQC, Canada.
Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec CityQC, Canada.
Front Microbiol. 2017 Jul 10;8:1283. doi: 10.3389/fmicb.2017.01283. eCollection 2017.
is a bacterial species that is a major cause of illness in humans and food-producing animals. exhibits considerable inter-serovar diversity, as evidenced by the large number of host adapted serovars that have been identified. The development of methods to assess genome diversity in will help to further define the limits of diversity in this foodborne pathogen. Thus, we evaluated a PCR assay, which targets prophage integrase genes, as a rapid method to investigate genome diversity. To evaluate the PCR prophage integrase assay, 49 isolates of were selected, including 19 clinical isolates from clonal serovars (Enteritidis and Heidelberg) that commonly cause human illness, and 30 isolates from food-associated serovars that rarely cause human illness. The number of integrase genes identified by the PCR assay was compared to the number of integrase genes within intact prophages identified by whole genome sequencing and phage finding program PHASTER. The PCR assay identified a total of 147 prophage integrase genes within the 49 genomes (79 integrase genes in the food-associated isolates, 50 integrase genes in . Enteritidis, and 18 integrase genes in . Heidelberg). In comparison, whole genome sequencing and PHASTER identified a total of 75 prophage integrase genes within 102 intact prophages in the 49 genomes (44 integrase genes in the food-associated isolates, 21 integrase genes in . Enteritidis, and 9 integrase genes in . Heidelberg). Collectively, both the PCR assay and PHASTER identified the presence of a large diversity of prophage integrase genes in the food-associated isolates compared to the clinical isolates, thus indicating a high degree of diversity in the food-associated isolates, and confirming the clonal nature of . Enteritidis and . Heidelberg. Moreover, PHASTER revealed a diversity of 29 different types of prophages and 23 different integrase genes within the food-associated isolates, but only identified four different phages and integrase genes within clonal isolates of Enteritidis and Heidelberg. These results demonstrate the potential usefulness of PCR based detection of prophage integrase genes as a rapid indicator of genome diversity in .
是一种细菌，是人类和食用动物患病的主要原因。表现出相当大的血清型间多样性，大量已鉴定的宿主适应性血清型证明了这一点。评估该细菌基因组多样性方法的发展将有助于进一步界定这种食源性病原体的多样性极限。因此，我们评估了一种针对前噬菌体整合酶基因的PCR检测方法，作为研究该细菌基因组多样性的快速方法。为了评估PCR前噬菌体整合酶检测方法，选择了49株该细菌分离株，包括19株来自通常导致人类疾病的克隆血清型（肠炎沙门氏菌和海德堡沙门氏菌）的临床分离株，以及30株来自很少导致人类疾病的与食物相关的该细菌血清型的分离株。将PCR检测方法鉴定的整合酶基因数量与通过全基因组测序和噬菌体发现程序PHASTER鉴定的完整前噬菌体中的整合酶基因数量进行比较。PCR检测方法在49个该细菌基因组中总共鉴定出147个前噬菌体整合酶基因（在与食物相关的该细菌分离株中有79个整合酶基因，在肠炎沙门氏菌中有50个整合酶基因，在海德堡沙门氏菌中有18个整合酶基因）。相比之下，全基因组测序和PHASTER在49个该细菌基因组的102个完整前噬菌体中总共鉴定出75个前噬菌体整合酶基因（在与食物相关的该细菌分离株中有44个整合酶基因，在肠炎沙门氏菌中有21个整合酶基因，在海德堡沙门氏菌中有9个整合酶基因）。总体而言，与临床分离株相比，PCR检测方法和PHASTER都鉴定出与食物相关的分离株中存在大量不同的前噬菌体整合酶基因，从而表明与食物相关的分离株具有高度多样性，并证实了肠炎沙门氏菌和海德堡沙门氏菌的克隆性质。此外，PHASTER揭示了与食物相关的分离株中有29种不同类型的前噬菌体和23种不同的整合酶基因，但在肠炎沙门氏菌和海德堡沙门氏菌的克隆分离株中仅鉴定出四种不同的噬菌体和整合酶基因。这些结果证明了基于PCR检测前噬菌体整合酶基因作为该细菌基因组多样性快速指标的潜在有用性。
