First genome sequences of Achromobacter phages reveal new members of the N4 family.
BACKGROUND
Multi-resistant Achromobacter xylosoxidans has been recognized as an emerging pathogen causing nosocomially acquired infections during the last years. Phages as natural opponents could be an alternative to fight such infections. Bacteriophages against this opportunistic pathogen were isolated in a recent study. This study shows a molecular analysis of two podoviruses and reveals first insights into the genomic structure of Achromobacter phages so far.


METHODS
Growth curve experiments and adsorption kinetics were performed for both phages. Adsorption and propagation in cells were visualized by electron microscopy. Both phage genomes were sequenced with the PacBio RS II system based on single molecule, real-time (SMRT) technology and annotated with several bioinformatic tools. To further elucidate the evolutionary relationships between the phage genomes, a phylogenomic analysis was conducted using the genome Blast Distance Phylogeny approach (GBDP).


RESULTS
In this study, we present the first detailed analysis of genome sequences of two Achromobacter phages so far. Phages JWAlpha and JWDelta were isolated from two different waste water treatment plants in Germany. Both phages belong to the Podoviridae and contain linear, double-stranded DNA with a length of 72329 bp and 73659 bp, respectively. 92 and 89 putative open reading frames were identified for JWAlpha and JWDelta, respectively, by bioinformatic analysis with several tools. The genomes have nearly the same organization and could be divided into different clusters for transcription, replication, host interaction, head and tail structure and lysis. Detailed annotation via protein comparisons with BLASTP revealed strong similarities to N4-like phages.


CONCLUSIONS
Analysis of the genomes of Achromobacter phages JWAlpha and JWDelta and comparisons of different gene clusters with other phages revealed that they might be strongly related to other N4-like phages, especially of the Escherichia group. Although all these phages show a highly conserved genomic structure and partially strong similarities at the amino acid level, some differences could be identified. Those differences, e.g. the existence of specific genes for replication or host interaction in some N4-like phages, seem to be interesting targets for further examination of function and specific mechanisms, which might enlighten the mechanism of phage establishment in the host cell after infection.
Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany. johannes.wittmann@dsmz.de.
Johannes
J
Wittmann
Brigitte
B
Dreiseikelmann
Manfred
M
Rohde
Jan P
JP
Meier-Kolthoff
Boyke
B
Bunk
Christine
C
Rohde
D042441:Achromobacter denitrificans / Q000821:virology*; D001435:Bacteriophages / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics*; D016679:Genome, Viral; D005858:Germany; D046529:Microscopy, Electron, Transmission; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D017902:Podoviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D017422:Sequence Analysis, DNA; D014771:Virion / Q000648:ultrastructure; D053585:Virus Attachment; D014779:Virus Replication; D062065:Wastewater / Q000821:virology
D004279:DNA, Viral; D062065:Wastewater