Molecular Characterization of a Prophage of Salmonella enterica Serotype Typhimurium DT104

Abstract

Isolates of the Salmonella enterica serotype Typhimurium definitive phage type (DT104) were found to contain the same prophage (designated phage ST104). The complete sequence of the DNA genome of prophage ST104 was determined. The entire DNA sequence consisted of 41,391 bp, including 64 open reading frames, and exhibited high similarity to P22 and to phage type conversion phage ST64T.Recently, Salmonella enterica serotype Typhimurium multidrug-resistant strain definitive phage type 104 (DT104) has emerged and spread over many countries (4,9,14,15). The organism has a core pattern of resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline. Previously, we used fluorescent amplified-fragment length polymorphism fingerprinting (FAFLP) analysis for molecular epidemiological investigation of serotype Typhimurium (13). Among 120 isolates from cattle, there were 17 FAFLP profiles that formed four distinct clusters (A to D). The isolates belonging to cluster A, in which all of the isolates of DT104 were included, have become increasingly common since 1992 in the northernmost island of Japan. The sequence of a polymorphic marker that is common to the strains of FAFLP cluster A has homology with the segment of the eae gene of phage P22. In this study, we isolated prophage ST104, which is common to isolates of DT104, and determined the whole sequence of this phage. The genomic architecture is similar to that of P22, and a number of regions are very similar to those of P22.Isolation of prophage common to serotype Typhimurium DT104. Forty-two serotype Typhimurium strains, including the 12 isolates of DT104 used in this study, were described previously (13). To investigate whether lysogenic prophages are present in serotype Typhimurium, we cultured the strains in the presence of mitomycin C at a concentration of 0.5 g/ml as previously described (17). Thirty-four out of 42 strains released phages that produced plaques on lawns of serotype Typhimurium strain LT2. To characterize the isolated phages, the restriction patterns of their DNAs were compared. Endonuclease digestion with EcoRI revealed five DNA types, designated a1, a2, b, c, and d (Fig. 1). All of the phages isolated from strains that belong to FAFLP cluster A (13), including 12 isolates of DT104, show the same restriction pattern, type a1 (Fig. 1). We have named this phage ST104. The restriction patterns of the prophages from strains NET25 and NET26, both of which belong to FAFLP cluster B, are similar to that of ST104; however, an additional EcoRI site was observed (Fig. 1). Therefore, the DNA type of these phages was designated a2. The restriction patterns of the phages isolated from strains belonging to FAFLP cluster B or C are different from those of ST104. No phage was detected in the two strains that belong to FAFLP cluster D. Schicklmaier et al. (10) suggested that prophage restriction patterns in natural isolates of serotype Typhimurium could serve as markers for the epidemiologic classification of pathogenic strains. Our resul...

Prophage Sequences Defining Hot Spots of Genome Variation inSalmonella entericaSerovar Typhimurium Can Be Used To Discriminate between Field Isolates

“…Prophage 1/ST104, also known as PDT17 (21), previously has been described as a resident prophage in S. enterica serovar Typhimurium DT104 (23). Interestingly, a prophage 1-like element also was detected in the nontypeable S. enterica serovar Typhimurium isolates H20004467 and H19992292 (DT170), although only the former was confirmed by multiplex PCR.…”

“…Detailed bioinformatic analysis of the microarray data revealed that the majority of these regions of variation corresponded to prophage-like elements within the genome of S. enterica serovar Typhimurium DT104 (NCTC 13348). The prophage in DT104 (NCTC 13348) included prophage 1 (also called ST104 [23]; hereafter it is referred to as prophage 1/ST104) (genome coordinates 365588.406646); prophage 2 (genome coordinates 1079201.1124674), which is related to the GIFSY-2 phage (17); prophage 3 (genome coordinates 1954176. 1995367); prophage 4 (genome coordinates 2109720.2149064); and prophage 5 (genome coordinates 2797168.2845750) ( Fig.…”

Genetic Relationships of Phage Types and Single Nucleotide Polymorphism Typing of Salmonella enterica Serovar Typhimurium

“…It was first reported in the 1960s and then emerged in an MDR form in the early 1980s in Britain (48). MDR DT104 isolates carry genes for multidrug resistance on 43-kb Salmonella genomic island 1 (SGI1), which encodes 44 open reading frames (28), and a prophage, ST104 (15,46), which carries two putative toxin genes (artAB) encoding an ADP-ribosyl transferase toxin homologue (41). In addition, Matiasovicova et al (24) found previously that all MDR DT104 isolates carry a deletion that includes the genes for the utilization of allantoin.…”

Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Isolates from Cattle in Hokkaido, Japan: Evidence of Clonal Replacement and Characterization of the Disseminated Clone

“…After BLASTN analysis through GenBank, these 25 fragments were divided into five groups showing sequence similarity to either the S. enterica serovar Newport SL254 plasmid pSN254 (n ϭ 14), S. Typhimurium plasmid pU302L (n ϭ 4), S. Typhimurium DT104 bacteriophage ST104 (n ϭ 2), S. Typhimurium DT64 bacteriophage STB64B (n ϭ 3), or avian pathogenic E. coli (APEC) strain O1 (n ϭ 2) (see Table S2). The presence of four DNA fragments (SN-11, PU302-2, ST104-1, and ST64B-1) showing high sequence similarities to portions of pSN254 (38), pU302L (7), ST104 (35), and STB64 (21), respectively, was tested in 29 isolates, including 21 representative isolates of the 21 PFGE profiles assigned to cluster VII by PCR. Fragments SN-11 and PU302L-2 were present in almost all of the representative isolates of cluster VII but were absent in those of the other clusters ( Table 4).…”