Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel bastille-like group of phages in the subfamily Spounavirinae

Abstract

BackgroundSpounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype.ResultsIn this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents.ConclusionsWe confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1757-0) contains supplementary material, which is available to authorized users.

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

“…Phage-encoded antibiotic resistance genes F Enault et al potentially conferring trimethoprim resistance is more likely to be involved in nucleotide metabolism in phages (Asare et al, 2015b). β-Lactamases were closely inspected, as several reports have suggested their presence on phages (Quiros et al, 2014;Asare et al, 2015a), sometimes with atypical length.…”

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

“…Ninety-six of these could be rejected as non-significant because the target ARG was poorly covered (<40%), too highly divergent (<30% identity), or else had homology to enzymes likely to serve non-ARG functions in phages. On the latter, homology with di-hydrofolate reductase was rejected without further consideration, as this enzyme potentially conferring trimethoprim resistance is more likely to be involved in nucleotide metabolism in phages (Asare et al 2015b). Beta-lactamases were also further considered, as genes with homology to beta-lactamases likely play different roles in phages (Asare et al 2015a, Quiros et al 2014, particularly when of atypical length.…”

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

“…Moreover, BLASTN has also been used to determine relationships between phages at larger phylogenetic distances [17,18], although the meaning of a similarity search hit in the absence of a true-shared ancestry remains unclear. Most of the newer programs that calculate phylogenetic relationships between genome sequences, including CLANS [20], GEGENEES [21], and mVISTA [22], are based upon sequence similarity analyses such as provided by BLASTN [19]. Complete and near-complete viral genome and protein homologies will be the focus of the Bacterial and Archaeal Viruses Subcommittee's attention in 2016 to develop clearer parameters for the molecular definition of genera, subfamilies, and families.…”