Tasmin Rizwana, Hasan Nur A, Grim Christopher J, Grant Ar'Quette, Choi Seon Young, Alam M Samiul, Bell Rebecca, Cavanaugh Christopher, Balan Kannan V, Babu Uma S, Parveen Salina
Agriculture, Food and Resource Sciences, University of Maryland, Eastern Shore, Princess Anne, Maryland, United States of America.
University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America.
PLoS One. 2017 May 8;12(5):e0176938. doi: 10.1371/journal.pone.0176938. eCollection 2017.
Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B) and Kentucky (SK222_32B) recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes. Phylogenetic analysis employing homologous alignment of a 1,185 non-duplicated protein-coding gene in the Salmonella core genome demonstrated fully resolved bifurcating patterns with varying levels of diversity that separated ST221_31B and SK222_32B genomes into distinct monophyletic serovar clades. Single nucleotide polymorphism (SNP) analysis identified 2,432 (ST19) SNPs within 13 Typhimurium genomes including ST221_31B representing Sequence Type ST19 and 650 (ST152) SNPs were detected within 13 Kentucky genomes including SK222_32B representing Sequence Type ST152. In addition to serovar-specific conserved coding sequences, the genomes of ST221_31B and SK222_32B harbor several genomic regions with significant genetic differences. These included phage and phage-like elements, carbon utilization or transport operons, fimbriae operons, putative membrane associated protein-encoding genes, antibiotic resistance genes, siderophore operons, and numerous hypothetical protein-encoding genes. Phenotype microarray results demonstrated that ST221_31B is capable of utilizing certain carbon compounds more efficiently as compared to SK222_3B; namely, 1,2-propanediol, M-inositol, L-threonine, α-D-lactose, D-tagatose, adonitol, formic acid, acetoacetic acid, and L-tartaric acid. ST221_31B survived for 48 h in macrophages, while SK222_32B was mostly eliminated. Further, a 3-fold growth of ST221_31B was observed at 24 hours post-infection in chicken granulosa cells while SK222_32B was unable to replicate in these cells. These results suggest that Salmonella Typhimurium can survive host defenses better and could be more invasive than Salmonella Kentucky and provide some insights into the genomic determinants responsible for these differences.
鼠伤寒沙门氏菌是美国人类非伤寒性肠胃炎的主要病因。肯塔基沙门氏菌是从商业加工的家禽胴体中最常分离出的血清型之一。本研究使用全基因组测序、表型特征分析和细胞内杀伤试验，比较了从商业加工的鸡胴体中分离出的两株肠炎沙门氏菌菌株，即鼠伤寒沙门氏菌（ST221_31B）和肯塔基沙门氏菌（SK222_32B）的基因型和表型特性。使用Illumina MiSeq平台对两株沙门氏菌基因组进行测序。通过对沙门氏菌核心基因组中1185个非重复蛋白质编码基因进行同源比对的系统发育分析显示，具有不同多样性水平的完全解析的分支模式将ST221_31B和SK222_32B基因组分为不同的单系血清型分支。单核苷酸多态性（SNP）分析在13个鼠伤寒沙门氏菌基因组（包括代表序列型ST19的ST221_31B）中鉴定出2432个（ST19）SNP，在13个肯塔基沙门氏菌基因组（包括代表序列型ST152的SK222_32B）中检测到650个（ST152）SNP。除了血清型特异性保守编码序列外，ST221_31B和SK222_32B的基因组还含有几个具有显著遗传差异的基因组区域。这些区域包括噬菌体和类噬菌体元件、碳利用或转运操纵子、菌毛操纵子、假定的膜相关蛋白编码基因、抗生素抗性基因、铁载体操纵子以及许多假定的蛋白质编码基因。表型微阵列结果表明，与SK222_3B相比，ST221_31B能够更有效地利用某些碳化合物；即1,2 - 丙二醇、肌醇、L - 苏氨酸、α - D - 乳糖、D - 塔格糖、阿东糖醇、甲酸、乙酰乙酸和L - 酒石酸。ST221_31B在巨噬细胞中存活48小时，而SK222_32B大多被清除。此外，在感染鸡颗粒细胞24小时后观察到ST221_31B有3倍的生长，而SK222_32B在这些细胞中无法复制。这些结果表明，鼠伤寒沙门氏菌比肯塔基沙门氏菌能更好地抵御宿主防御，并且可能更具侵袭性，同时也为造成这些差异的基因组决定因素提供了一些见解。
