Distribution of Gifsy-3 and of Variants of ST64B and Gifsy-1 Prophages amongst Salmonella enterica Serovar Typhimurium Isolates: Evidence that Combinations of Prophages Promote Clonality

Salmonella isolates harbour a range of resident prophages which can influence their virulence and ability to compete and survive in their environment. Phage gene profiling of a range of phage types of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) indicates a significant level of correlation of phage gene profile with phage type as well as correlation with genotypes determined by a combination of multi-locus variable-number tandem repeat (VNTR) typing and clustered regularly interspaced short palindromic repeats (CRISPR) typing. Variation in phage gene profiles appears to be partly linked to differences in composition of variants of known prophages. We therefore conducted a study of the distribution of variants of ST64B and Gifsy-1 prophages and coincidently the presence of Gifsy-3 prophage in a range of S. Typhimurium phage types and genotypes. We have discovered two variants of the DT104 variant of ST64B and at least two new variants of Gifsy-1 as well as variants of related phage genes. While there is definite correlation between phage type and the prophage profile based on ST64B and Gifsy-1 variants we find stronger correlation between the VNTR/CRISPR genotype and prophage profile. Further differentiation of some genotypes is obtained by addition of the distribution of Gifsy-3 and a sequence variant of the substituted SB26 gene from the DT104 variant of ST64B. To explain the correlation between genotype and prophage profile we propose that suites of resident prophages promote clonality possibly through superinfection exclusion systems.沙门氏菌分离株携带一系列常驻原噬菌体，这些原噬菌体可影响其毒力，以及在环境中竞争与存活的能力。针对多株鼠伤寒沙门氏菌（Salmonella enterica subsp. enterica serovar Typhimurium，S. Typhimurium）的噬菌体型开展噬菌体基因谱分析，结果显示噬菌体基因谱与噬菌体型存在显著相关性，同时与基于多位点可变数目串联重复序列（multi-locus variable-number tandem repeat，VNTR）分型和成簇规律间隔短回文重复序列（clustered regularly interspaced short palindromic repeats，CRISPR）分型联合确定的基因型亦存在显著相关性。噬菌体基因谱的差异似乎部分与已知原噬菌体变体的组成差异相关。为此，我们针对一系列S. Typhimurium的噬菌体型和基因型，开展了ST64B与Gifsy-1原噬菌体变体的分布研究，同时同步考察了Gifsy-3原噬菌体的存在情况。本研究发现了ST64B的DT104变体的两种变体，以及至少两种Gifsy-1的新型变体，同时还鉴定出相关噬菌体基因的变体。尽管基于ST64B和Gifsy-1变体的原噬菌体谱与噬菌体型存在明确相关性，但我们发现VNTR/CRISPR基因型与原噬菌体谱的相关性更强。通过结合Gifsy-3的分布以及来自ST64B的DT104变体的替换型SB26基因序列变体，可实现对部分基因型的进一步区分。为解释基因型与原噬菌体谱之间的相关性，我们提出假说：常驻原噬菌体组可能通过超感染排除系统促进克隆性。