Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages

Abstract

Ochrobactrum and Brucella are closely related bacteria that populate different habitats and differ in their pathogenic properties. Only little is known about mobile genetic elements in these genera which might be important for survival and virulence. Previous studies on Brucella lysogeny indicated that active phages are rare in this genus. To gain insight into the presence and nature of prophages in Ochrobactrum, temperate phages were isolated from various species and characterized in detail. In silico analyses disclosed numerous prophages in published Ochrobactrum genomes. Induction experiments showed that Ochrobactrum prophages can be induced by various stress factors and that some strains released phage particles even under non-induced conditions. Sixty percent of lysates prepared from 125 strains revealed lytic activity. The host range and DNA similarities of 19 phages belonging to the families Myoviridae, Siphoviridae, or Podoviridae were determined suggesting that they are highly diverse. Some phages showed relationship to the temperate Brucella inopinata phage BiPB01. The genomic sequences of the myovirus POA1180 (41,655 bp) and podovirus POI1126 (60,065 bp) were analyzed. Phage POA1180 is very similar to a prophage recently identified in a Brucella strain isolated from an exotic frog. The POA1180 genome contains genes which may confer resistance to chromate and the ability to take up sulfate. Phage POI1126 is related to podoviruses of Sinorhizobium meliloti (PCB5), Erwinia pyrifoliae (Pep14), and Burkholderia cenocepacia (BcepIL02) and almost identical to an unnamed plasmid of the Ochrobactrum intermedium strain LMG 3301. Further experiments revealed that the POI1126 prophage indeed replicates as an extrachromosomal element. The data demonstrate for the first time that active prophages are common in Ochrobactrum and suggest that atypical brucellae also may be a reservoir for temperate phages.

Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp.

“…POC9, in which the prophage regions were indicated manually) was applied. This enabled us to significantly extend the knowledge in this field since, in the previous works by Jackel et al [21,42,43] a total of 66 Ochrobactrum (pro)phages were indicated, while in our analysis, 277 prophages were identified within 104 out of the 113 analyzed genomes ( Supplementary Table S2). Moreover, by applying the vConTACT v2 tool [44], we compared vB_OspM_OC, vB_OspP_OH, and all identified Ochrobactrum prophages with the ProcaryoticViralRefSeq85-Merged database resources and the 12,817 bacteriophages present in the NCBI Genome database (as of 10 July 2019).…”

“…The second phage, POI1126, originating from O. intermedium POI1126, exhibited similarities to the Sinorhizobium meliloti phage PCB5, the Erwinia pyrifoliae phage PEp14, and the Burkholderia cenocepacia phages DC1, Bcep22, and BcepIL02. Interestingly, the POI1126 phage genome was nearly identical to the unnamed plasmid of the O. intermedium strain LMG 3301, which suggests that this phage appears in a plasmid-like form in both strains [21].…”

“…In 2017, the first two active lysogenic phages of Ochrobactrum spp. were described: a myovirus POA1180 and a podovirus POI1126 [21]. These phages were isolated together with a set of other viruses identified during an extensive screening of 125 Ochrobactrum isolates [21].…”

“…were described: a myovirus POA1180 and a podovirus POI1126 [21]. These phages were isolated together with a set of other viruses identified during an extensive screening of 125 Ochrobactrum isolates [21]. The performed induction experiment was successful for 60% of strains and resulted in identification of the morphologically diverse Caudovirales representatives.…”

Prediction, Diversity, and Genomic Analysis of Temperate Phages Induced From Shiga Toxin-Producing Escherichia coli Strains

“…A previous study demonstrated that the induction of Stx prophages was closely associated with the production of Stx and the transfer of stx genes among susceptible strains (Krüger et al, 2018). Although there is increasing interest in the prediction and functions of prophages found in different bacterial species, such as Ochrobactrum and Brucella (Hammerl et al, 2016;Jäckel et al, 2017), related information with respect to prophages in STEC genomes is lacking. In this study, the 40 complete whole-genome sequences of STEC strains generated by next-generation sequencing (NGS) technology and obtained from the NCBI database were used to understand the presence of different prophages within STEC genomes.…”