Genome Sequences of 38 Bacteriophages Infecting Escherichia coli, Isolated from Raw Sewage (original) (raw)
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Complete genome equences of Microbacterium bacteriophages Danno, Otwor and Scumberland isolated in Clarksville, Tennessee. , 2021
This paper reports the genome sequences of bacteriophages isolated from soil samples using Microbacterium foliorum. Phages Danno and Otwor (cluster EE) have genomes of 17,452 bp and 17,454 bp, respectively, and 25 predicted genes. The phage Scumberland (cluster EC) has a genome of 53,276 bp with 92 predicted genes.
PloS one, 2014
The T1-like bacteriophages vB_EcoS_AHP24, AHS24, AHP42 and AKS96 of the family Siphoviridae were shown to lyse common phage types of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7), but not non-O157 E. coli. All contained circularly permuted genomes of 45.7-46.8 kb (43.8-44 mol% G+C) encoding 74-81 open reading frames and 1 arginyl-tRNA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the structural proteins were identical among the four phages. Further proteomic analysis identified seven structural proteins responsible for tail fiber, tail tape measure protein, major capsid, portal protein as well as major and minor tail proteins. Bioinformatic analyses on the proteins revealed that genomes of AHP24, AHS24, AHP42 and AKS96 did not encode for bacterial virulence factors, integration-related proteins or antibiotic resistance determinants. All four phages were highly lytic to STEC O157:H7 with considerable potential as biocontrol agents. Comparati...
Microbiology, 2013
Bacteriophages are considered as promising biological agents for the control of infectious diseases. Sequencing of their genomes can ascertain the absence of antibiotic resistance, toxin or virulence genes. The anti-O157 : H7 coliphage, PhaxI, was isolated from a sewage sample in Iran. Morphological studies by transmission electron microscopy showed that it has an icosahedral capsid of 85-86 nm and a contractile tail of 115¾15 nm. PhaxI contains dsDNA composed of 156 628 nt with a G+C content of 44.5 mol% that encodes 209 putative proteins. In MS analysis of phage particles, 92 structural proteins were identified. PhaxI lyses Escherichia coli O157 : H7 in Luria-Bertani medium and milk, has an eclipse period of 20 min and a latent period of 40 min, and has a burst size of about 420 particles per cell. PhaxI is a member of the genus 'Viunalikevirus' of the family Myoviridae and is specific for E. coli O157 : H7.
Viruses, 2019
Phages infecting members of the opportunistic human pathogen, Salmonella enterica, are widespread in natural environments and offer a potential source of agents that could be used for controlling populations of this bacterium; yet, relatively little is known about these phages. Here we describe the isolation and characterization of 45 phages of Salmonella enterica from disparate geographic locations within British Columbia, Canada. Host-range profiling revealed host-specific patterns of susceptibility and resistance, with several phages identified that have a broad-host range (i.e., able to lyse >40% of bacterial hosts tested). One phage in particular, SE13, is able to lyse 51 out of the 61 Salmonella strains tested. Comparative genomic analyses also revealed an abundance of sequence diversity in the sequenced phages. Alignment of the genomes grouped the phages into 12 clusters with three singletons. Phages within certain clusters exhibited extraordinarily high genome homology (&...
Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica
2019
Background: Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica . A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should provide a broader understanding of Salmonella biology and virulence and contribute to the practical applications of phages as vectors and antibacterial agents. Results: Comparative analysis of the full genome sequences of 142 prophages of Salmonella enterica subsp. enterica retrieved from public databases revealed an extensive variation in genome sizes (6.4- 358.7 kb) and guanine plus cytosine (GC) content (35.5-65.4%) and a linear correlation between the genome size and the number of open reading frames (ORFs). We used three approaches to compare the phage genomes. The NUCmer/MUMmer genome alignment tool was used to evaluate ...
Genome Sequences of 12 Phages That Infect Klebsiella pneumoniae
Microbiology Resource Announcements
Klebsiella pneumoniae is a pathogen responsible for significant proportions of nosocomial and health care-associated infections and is known to acquire multiple antibiotic resistance genes. Here, we announce the full genome sequences of 12 K. pneumoniae bacteriophages from samples collected in wastewater treatment facilities across the western United States.
Scientific Reports, 2016
A large scale analysis presented in this article focuses on biological and physiological variety of bacteriophages. A collection of 83 bacteriophages, isolated from urban sewage and able to propagate in cells of different bacterial hosts, has been obtained (60 infecting Escherichia coli, 10 infecting Pseudomonas aeruginosa, 4 infecting Salmonella enterica, 3 infecting Staphylococcus sciuri, and 6 infecting Enterococcus faecalis). High biological diversity of the collection is indicated by its characteristics, both morphological (electron microscopic analyses) and biological (host range, plaque size and morphology, growth at various temperatures, thermal inactivation, sensitivity to low and high pH, sensitivity to osmotic stress, survivability upon treatment with organic solvents and detergents), and further supported by hierarchical cluster analysis. By the end of the research no larger collection of phages from a single environmental source investigated by these means had been foun...
Complete Genome Sequence of Bacteriophage Loca, Isolated on a Microbacterium foliorum Culture
Microbiology resource announcements, 2022
Microbacteriophage Loca was extracted from a shopping cart handle swab sample in Stephenville, TX, and isolated on a Microbacterium foliorum NRRL-24224 culture. The 17,475-bp double-stranded DNA genome contains 25 predicted protein-coding genes and has .96% nucleotide identity to bacteriophages Quaker and Livingwater. M icrobacterium bacteriophages are genetically diverse and composed of several types of genomic architectures containing multiple genes of unknown function (1). To expand our knowledge of the diversity of microbacteriophages isolated from central and north Texas (2-4), we report the genome sequence of microbacteriophage Loca, collected from a swab sample of a shopping cart handle in Stephenville, TX (global positioning system [GPS] coordinates, 32.206238 N, 98.23701 W). The sample was submerged in peptone-yeast extract-calcium (PYCa) liquid medium and incubated while shaking for 2 h at 220 rpm and 29°C. The supernatant was filtered through a 0.22-mm filter and incubated with the bacterial host strain Microbacterium foliorum NRRL B-24224 in PYCa liquid medium for 6 days at 29°C (5, 6). The bacteria were pelleted and the supernatant passed through 0.22-mm filters. The filtrates were 10-fold serially diluted in phage buffer (10 mM Tris [pH 7.5], 10 mM MgSO 4 , 68 mM NaCl, 1 mM CaCl 2 , 10% glycerol) and incubated with M. foliorum in a soft agar overlay on PYCa agar plates for 48 h at 29°C. Bacteriophage replication formed clear, circular plaques approximately 5 mm in diameter within the soft agar overlay. Loca was isolated by two rounds of picking a single, well-separated plaque, followed by 10-fold serial dilution of the bacteriophage sample and plating it with M. foliorum as before. High-titer lysates were prepared by flooding "webbed" plates with phage buffer overnight at 4°C, as described in Phage Discovery Guide (5). Negative-staining transmission electron microscopy showed that Loca exhibited Siphoviridae morphology (Fig. 1), and ImageJ v1.53m (7) was used to measure an approximate tail length of 105 nm and capsid diameter of 40 nm (n = 9). Genomic DNA was extracted from the high-titer lysate using a modified zinc chloride precipitation method (5, 8). The Pittsburgh Bacteriophage Institute prepared sequencing libraries using the NEBNext Ultra II DNA library prep kit (New England Biolabs, Ipswich, MA) and sequenced them using an Illumina MiSeq instrument to produce 20,276 single-end 150-bp reads. The raw reads were assembled using Newbler v2.9 to generate a single contig with 75Â coverage that was checked for completeness and genomic termini using Consed v29 (9, 10). The 17,475-bp double-stranded DNA genome contains 9-nucleotide 39 singlestranded cohesive ends (59-CCCGCCCCA-39) and 68.7% G1C content. A BLASTn (11) query of the sequence against the nonredundant/nucleotide (nr/nt) database returned .96% nucleotide sequence identity to the cluster EE bacteriophages Quaker (GenBank accession number MH371111) and Livingwater (MT498040) (1). Auto-annotation with GLIMMER v3.02 (12) and GeneMark v2.5p (13) was manually refined using Phamerator (14), PECAAN, and DNA Master v5.23.3 (http://phagesdb.org/DNAMaster/). No tRNA genes were identified using Aragorn v1.1 (15) or tRNAscan-SE v2.0 (16). Putative functions for 18 of