Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1

Abstract

In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of an estimated 390,000 people each year. The disease is predominantly caused by a recently described sequence type of Salmonella Typhimurium: ST313, which has a distinctive set of prophage sequences. We have thoroughly characterized the ST313-associated prophages both genetically and experimentally. ST313 representative strain D23580 contains five full-length prophages: BTP1, Gifsy-2D23580, ST64BD23580, Gifsy-1D23580, and BTP5. We show that common S. Typhimurium prophages Gifsy-2, Gifsy-1, and ST64B are inactivated in ST313 by mutations. Prophage BTP1 was found to be a functional novel phage, and the first isolate of the proposed new species “Salmonella virus BTP1”, belonging to the P22virus genus. Surprisingly, ∼109 BTP1 virus particles per ml were detected in the supernatant of non-induced, stationary-phase cultures of strain D23580, representing the highest spontaneously induced phage titer so far reported for a bacterial prophage. High spontaneous induction is shown to be an intrinsic property of prophage BTP1, and indicates the phage-mediated lysis of around 0.2% of the lysogenic population. The fact that BTP1 is highly conserved in ST313 poses interesting questions about the potential fitness costs and benefits of novel prophages in epidemic S. Typhimurium ST313.

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

“…BTP1 that was reported to be specific to the ST313 strains associated with epidemics of invasive NTS disease in sub-Saharan Africa 30 , was also present in strain SO7676-03, a strain in clade β5 (DT56 complex) adapted to circulation in wild bird (Passerine) species 12 . The mTmV phage of strain SO4698-09, that carries the sopE virulence gene in some monophasic S. Typhimurium ST34 isolates 18 , was absent from all other S. Typhimurium reference strains.…”

Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia

“…It is worth notice that Phaster only detected ST64T in ST313 and ST2936 isolates. The ST64T prophage shared a 22kb identical segment with BTP1 prophage carried by invasive African Typhimurium ST313 [10].…”

“…Recently, a new type of invasive non-typhoidal Salmonella (iNTS) causing highly fatal bloodstream infection has emerged in sub-Saharan Africa (SSA). iNTS disease is caused by two distinct lineages of S. Typhimurium ST313, both carrying MDR-encoding Tn21 elements on plasmid pSLT [9] and the prophages, BTP1 and BTP5 [10]. The acquisition of the cat chloramphenicol resistance gene by lineage 2 is thought to have played an important role in the clonal replacement of lineage 1, which occurred in Malawi and elsewhere in 2003 [9].…”

Salmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa

“…which supports the hypothesized enhanced virulence of ST313 includes the detection 84 of novel prophages BTP1 and BTP5 (15) including the reported BTP1 phage-encoded 85 putative virulence gene, st313-td (16). A number of phenotypic characteristics which 86 distinguish ST313 from gastroenteritis-associated ST19 strains have also been 87 described including a reduction in motility, flagellin expression, stationary-phase 88 catalase activity and biofilm formation (17)(18)(19).…”

“…Pathogenicity Island (SPI) repertoire was conserved in the ST313 isolates in this study 220 and in 3 ST19 gastroenteritis isolates ( Figure 2B). The African ST313 lineages carry 221 two prophages, BTP1 and BTP5, that are absent from ST19 strains (15). The entire 222 BTP1 and BTP5 prophages were found in most ST313 isolates that belonged to 223…”