Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1

Bhattacharjee, Ananda S.; Motlagh, Amir Mohaghegh; Gilcrease, Eddie B.; Islam, Imdadul; Casjens, Sherwood; Goel, Ramesh

doi:10.1186/s40793-017-0290-y

Cited by 5 publications

(3 citation statements)

References 37 publications

(47 reference statements)

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“…The G7-like phages The E. coli phage N4, the prototype species of the group of N4-related viruses was a database orphan for many years (Kazmierczak et al 2002). However, over the last decade, numerous N4-like viruses that infect Gram-negative bacteria were isolated and sequenced (Faidiuk et al 2017;Golomidova et al 2007;Cai et al 2015;Patel et al 2015;Li et al 2016;Ma et al 2016;Shigehisa et al 2016;Bhattacharjee et al 2017;Katharios et al 2017;Buttimer et al 2018), and for reviews see (Chan et al 2014;Wittmann et al 2015). The N4-related sequences are also ubiquitous in human fecal metagenomes and viromes (Waller et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems

Babenko

Golomidova

Иванов

et al. 2019

Preprint

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Tailed bacteriophages (Caudovirales order) are omnipresent on our planet. Their impressive ecological and evolutionary success largely relies on the bacteriophage potential to adapt to great variety of the environmental conditions found in the Biosphere. It is believed that the adaptation of bacteriophages, including short time scale adaptation, is achieved almost exclusively via the (micro)evolution processes. In order to analyze the major mechanisms driving adaptation of phage genomes in a natural habitat we used comparative genomics of G7C-like coliphage isolates obtained during 7 years period from the feces of the horses belonging to a local population. The data suggest that even at this relatively short time scale the impact of various recombination events overwhelms the impact of the accumulation of point mutations. The access to the large pool of the genes of a complex microbial and viral community of the animal gut had major effect on the evolutionary trajectories of these phages. Thus the "real world" bacteriophage evolution mechanisms may differ significantly from those observed in the simplified laboratory model systems.

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Section: Discussionmentioning

confidence: 99%

Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems

Babenko

Golomidova

Иванов

et al. 2019

Preprint

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“…Phage KL-2146 was isolated from activated sludge obtained from a wastewater treatment plant (Salt Lake City, Utah) by infection of K. pneumoniae BAA-2146 utilizing methods in sequential filtration and centrifugation previously described (Delfan et al, 2012;Bhattacharjee et al, 2017;Hockett and Baltrus, 2017). A single plaque was thusly isolated and propagated by infection of the same hosts in liquid culture (Earnshaw et al, 1976).…”

Section: Phage Isolation Propagation and Physical Characterizationmentioning

confidence: 99%

A Klebsiella pneumoniae NDM-1+ bacteriophage: Adaptive polyvalence and disruption of heterogenous biofilms

Gilcrease

Casjens²,

Bhattacharjee³

et al. 2023

Front. Microbiol.

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Bacteriophage KL-2146 is a lytic virus isolated to infect Klebsiella pneumoniae BAA2146, a pathogen carrying the broad range antibiotic resistance gene New Delhi metallo-betalactamase-1 (NDM-1). Upon complete characterization, the virus is shown to belong to the Drexlerviridae family and is a member of the Webervirus genus located within the (formerly) T1-like cluster of phages. Its double-stranded (dsDNA) genome is 47,844 bp long and is predicted to have 74 protein-coding sequences (CDS). After challenging a variety of K. pneumoniae strains with phage KL-2146, grown on the NDM-1 positive strain BAA-2146, polyvalence was shown for a single antibiotic-sensitive strain, K. pneumoniae 13,883, with a very low initial infection efficiency in liquid culture. However, after one or more cycles of infection in K. pneumoniae 13,883, nearly 100% infection efficiency was achieved, while infection efficiency toward its original host, K. pneumoniae BAA-2146, was decreased. This change in host specificity is reversible upon re-infection of the NDM-1 positive strain (BAA-2146) using phages grown on the NDM-1 negative strain (13883). In biofilm infectivity experiments, the polyvalent nature of KL-2146 was demonstrated with the killing of both the multidrug-resistant K. pneumoniae BAA-2146 and drug-sensitive 13,883 in a multi-strain biofilm. The ability to infect an alternate, antibiotic-sensitive strain makes KL-2146 a useful model for studying phages infecting the NDM-1+ strain, K. pneumoniae BAA-2146.

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“…Despite the abundance and ubiquity of Comamonadaceae in freshwater habitats, phages infecting members of this family were rarely studied in freshwater habitats. To our knowledge, only one lytic phage that infects a strain of Rhodoferax , and three phages that infect Delftia of the family Comamonadaceae have been reported so far 26 , 27 . In this study, to obtain more freshwater phages that infect Comamonadaceae , lytic bacteriophages have been screened from Lake Soyang using the IMCC26059 strain as a host, which resulted in the successful isolation of two phages, P26059A and P26059B.…”

Section: Introductionmentioning

confidence: 99%

Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium

Moon

Kang

Kim

et al. 2018

Sci Rep

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Bacteriophages of freshwater environments have not been well studied despite their numerical dominance and ecological importance. Currently, very few phages have been isolated for many abundant freshwater bacterial groups, especially for the family Comamonadaceae that is found ubiquitously in freshwater habitats. In this study, we report two novel phages, P26059A and P26059B, that were isolated from Lake Soyang in South Korea, and lytically infected bacterial strain IMCC26059, a member of the family Comamonadaceae. Morphological observations revealed that phages P26059A and P26059B belonged to the family Siphoviridae and Podoviridae, respectively. Of 12 bacterial strains tested, the two phages infected strain IMCC26059 only, showing a very narrow host range. The genomes of the two phages were different in length and highly distinct from each other with little sequence similarity. A comparison of the phage genome sequences and freshwater viral metagenomes showed that the phage populations represented by P26059A and P26059B exist in the environment with different distribution patterns. Presence of the phages in Lake Soyang and Lake Michigan also indicated a consistent lytic infection of the Comamonadaceae bacterium, which might control the population size of this bacterial group. Taken together, although the two phages shared a host strain, they showed completely distinctive characteristics from each other in morphological, genomic, and ecological analyses. Considering the abundance of the family Comamonadaceae in freshwater habitats and the rarity of phage isolates infecting this family, the two phages and their genomes in this study would be valuable resources for freshwater virus research.

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Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1

Cited by 5 publications

References 37 publications

Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems

Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems

A Klebsiella pneumoniae NDM-1+ bacteriophage: Adaptive polyvalence and disruption of heterogenous biofilms

Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium

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