Differences in gene content among Salmonella enterica serovar typhi isolates

Abstract

We used a nonredundant microarray of the Salmonella enterica serovar Typhimurium LT2 and Typhi CT18 genomes to assess the genomic content of a diverse set of isolates of serovar Typhi. Comparative genomic hybridization revealed 13 regions of absent or divergent gene content in the eight Typhi strains examined compared to Typhi CT18. In particular, two Typhi CT18 prophage regions, STY1048 to STY1077 and STY2038 to STY2077, as well as a five-gene islet (STY3188 to STY3193) were absent or divergent in all other Typhi strains examined. Seven Typhi strains lacked most or all of the IS1 elements present in strain CT18, and three Typhi strains lacked a P4-like phage (STY4821 to STY4834). One strain was devoid of a 149-gene region (STY4521 to STY4680), which encodes numerous phage genes and the Vi antigen biosynthesis and export gene cluster, a type IV pilus, and numerous phage genes. In Typhi strain 26T25, an amplification of an entire inter-ribosomal region encompassing 31 genes has occurred. Furthermore, a 257-gene region (STY1360 to STY1639) showed an aberrant replication pattern in three Typhi isolates. Overall, these differences in gene content indicate that even within a highly clonal bacterial population the genomic reservoir is unstable.

FIG.1.

Detection of deleted regions on S. enterica serovar Typhi chromosomes. (A) Comparative genomic hybridization of eight S. enterica serovar Typhi strains versus serovar Typhi CT18. The eight plots display medians of signal ratios of the query S. enterica serovar Typhi strain over Typhi CT18. Genes are plotted in order of their position on the Typhi CT18 genome. The 13 regions containing genes deleted from other Typhi strains are indicated. The region with abberant replicative behavior in strains ST24A, 3125, and CDC1707 is marked with an “R.” The amplified segment in strain 26T25 is marked with an “A.” (B) Presence or absence of S. enterica serovar Typhi CT18 protein coding sequence homologues in other Typhi strains. Gene status is color coded: blue, present; purple, uncertain; red, absent; and gray, low signal. Only the 13 regions that harbor genes that are missing in other Typhi strains, along with some adjacent genes, are shown.