AnCo3, a New Member of the Emerging Family of Phage-Like Plasmids.

A phage-like plasmid isolated from a clinical isolate of Salmonella enterica serovar Derby has strong nucleotide sequence identity to the phage-like plasmids pSTM_phi isolated from Salmonella enterica serovar Typhimurium L495, AnCo1 and AnCo2 from Escherichia coli 243 and Escherichia coli 244, and the virulent Salmonella-specific SSU5 bacteriophage.

GENOME ANNOUNCEMENT

There are nine reported members of an emerging family of phage-like plasmids. They span different bacterial species, such as Escherichia coli, Klebsiella pneumonaie, Yersinia pestis, Salmonella enterica serovar Typhi, Salmonella enterica serovar Typhimurium, and Acinetobacter baumanii (1–7). These phage-like plasmids exist extrachromosomally and are characterized by double-stranded DNA genomes ranging from approximately 106 kb to 122 kb that contain structural bacteriophage genes as well as plasmid DNA.

A clinical isolate of Salmonella enterica serovar Derby was found to contain a phage-like plasmid. We performed whole-genome sequencing of the S. Derby isolate to determine the nature of the phage-like plasmid.

Whole-genome sequencing was performed at the EcoGenomics analysis platform (Ibis; Université Laval, Québec, Canada) on an Illumina MiSeq platform with 300-bp paired-end libraries and 30× coverage. The raw reads were assembled using the A5 pipeline (8). PHASTER (9) and PhiSpy (10) identified prophage regions. RAST (11) annotated the phage-like plasmid, while HostPhinder1.1 (12) and tRNAscan (13) identified the host range of the phage-like plasmid and tRNA genes, respectively.

The complete sequence of the phage-like plasmid from S. Derby, designated AnCo3, is 105,994 bp and has a G+C content of 46.4%. It also harbors 130 coding sequences (CDSs) and a tRNA for asparagine. Its host range is suggested to include S. enterica and E. coli.

Genomic analysis revealed that AnCo3 has strong nucleotide sequence identity to phage-like plasmid pSTM_phi (accession no. KP763470.1). AnCo3 shares 114 CDSs of 130 CDSs with pSTM_Phi, of which 96 CDSs have >95% nucleotide sequence identity and 18 CDSs have >75% nucleotide sequence identity. The bacteriophage genes of AnCo3 have >90% nucleotide sequence identity to pSTM_Phi, with the exception of a phage tail fiber with 71% nucleotide sequence identity. AnCo3 phage genes include an integrase, major capsid protein, tail fiber proteins, tail proteins, tail assembly proteins, a phage portal protein, the large subunit of the terminase, a holin, and an endolysin gene.

AnCo3 also has nucleotide sequence identity to the virulent Salmonella-specific bacteriophage SSU5 (GenBank accession no. JQ965645). In total, AnCo3 shares 97 CDSs out of 130 CDSs to SSU5 with >67% nucleotide sequence identity. The bacteriophage genes of AnCo3 have >73% nucleotide sequence identity to those of SSU5.

Nucleotide sequence identity was also detected to phage-like plasmids that infect E. coli, AnCo1 (accession no. KY515224) and AnCo2 (accession no. KY515225). AnCo3 shares 84 CDSs of 134 CDSs and 132 CDSs to AnCo1 and AnCo2, respectively, with >68% nucleotide sequence identity.

In conclusion, we present a novel phage-like plasmid isolated from a clinical S. Derby isolate. This is the 10th documented report of a phage-like plasmid; hence, we suggest that phage-like plasmids may represent a new genus of phages.

Accession number(s).

The complete genome sequence of AnCo3 has been deposited in GenBank under the accession number KY515226.