scholarly journals PHIDA: A High Throughput Turbidimetric Data Analytic Tool to Compare Host Range Profiles of Bacteriophages Isolated Using Different Enrichment Methods

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2120
Author(s):  
Carlos E. Martinez-Soto ◽  
Stevan Cucić ◽  
Janet T. Lin ◽  
Sarah Kirst ◽  
El Sayed Mahmoud ◽  
...  
Keyword(s):  
Host Range ◽  
High Throughput ◽  
Lytic Bacteriophage ◽  
Analytic Tool ◽  
Enrichment Technique ◽  
High Throughput Method ◽  
Host Range Determination ◽  
Range Determination ◽  
Enrichment Techniques ◽  
Enrichment Methods

Bacteriophages are viruses that infect bacteria and are present in niches where bacteria thrive. In recent years, the suggested application areas of lytic bacteriophage have been expanded to include therapy, biocontrol, detection, sanitation, and remediation. However, phage application is constrained by the phage’s host range—the range of bacterial hosts sensitive to the phage and the degree of infection. Even though phage isolation and enrichment techniques are straightforward protocols, the correlation between the enrichment technique and host range profile has not been evaluated. Agar-based methods such as spotting assay and efficiency of plaquing (EOP) are the most used methods to determine the phage host range. These methods, aside from being labor intensive, can lead to subjective and incomplete results as they rely on qualitative observations of the lysis/plaques, do not reflect the lytic activity in liquid culture, and can overestimate the host range. In this study, phages against three bacterial genera were isolated using three different enrichment methods. Host range profiles of the isolated phages were quantitatively determined using a high throughput turbidimetric protocol and the data were analyzed with an accessible analytic tool “PHIDA”. Using this tool, the host ranges of 9 Listeria, 14 Salmonella, and 20 Pseudomonas phages isolated with different enrichment methods were quantitatively compared. A high variability in the host range index (HRi) ranging from 0.86–0.63, 0.07–0.24, and 0.00–0.67 for Listeria, Salmonella, and Pseudomonas phages, respectively, was observed. Overall, no direct correlation was found between the phage host range breadth and the enrichment method in any of the three target bacterial genera. The high throughput method and analytics tool developed in this study can be easily adapted to any phage study and can provide a consensus for phage host range determination.

scholarly journals A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000

2009 ◽  
Vol 22 (1) ◽  
pp. 52-62 ◽  
Author(s):  
Nalvo F. Almeida ◽  
Shuangchun Yan ◽  
Magdalen Lindeberg ◽  
David J. Studholme ◽  
David J. Schneider ◽  
...  
Keyword(s):  
Host Range ◽  
Host Specificity ◽  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Tomato Dc3000 ◽  
Type Iii ◽  
Host Range Determination ◽  
Range Determination

Diverse gene products including phytotoxins, pathogen-associated molecular patterns, and type III secreted effectors influence interactions between Pseudomonas syringae strains and plants, with additional yet uncharacterized factors likely contributing as well. Of particular interest are those interactions governing pathogen-host specificity. Comparative genomics of closely related pathogens with different host specificity represents an excellent approach for identification of genes contributing to host-range determination. A draft genome sequence of Pseudomonas syringae pv. tomato T1, which is pathogenic on tomato but nonpathogenic on Arabidopsis thaliana, was obtained for this purpose and compared with the genome of the closely related A. thaliana and tomato model pathogen P. syringae pv. tomato DC3000. Although the overall genetic content of each of the two genomes appears to be highly similar, the repertoire of effectors was found to diverge significantly. Several P. syringae pv. tomato T1 effectors absent from strain DC3000 were confirmed to be translocated into plants, with the well-studied effector AvrRpt2 representing a likely candidate for host-range determination. However, the presence of avrRpt2 was not found sufficient to explain A. thaliana resistance to P. syringae pv. tomato T1, suggesting that other effectors and possibly type III secretion system–independent factors also play a role in this interaction.

scholarly journals Characterization and genomic analysis of two Staphylococcus aureus bacteriophages isolated from poultry/livestock farms

2013 ◽  
Vol 94 (11) ◽  
pp. 2569-2576 ◽  
Author(s):  
Hyunjin Yoon ◽  
Jiae Yun ◽  
Jeong-A Lim ◽  
Eunjung Roh ◽  
Kyu-Seok Jung ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Host Range ◽  
Genomic Analysis ◽  
Enzyme Treatment ◽  
Comparative Genomic ◽  
The Family ◽  
Phage Dna ◽  
Host Range Determination ◽  
Range Determination ◽  
Livestock Farms

Staphylococcus aureus is one of the most important pathogens, causing various diseases in humans and animals. As methicillin-resistant S. aureus (MRSA) has become increasingly prevalent, controlling this pathogen with standard antibiotic treatment has become challenging. Bacteriophages (phages) have attracted interest as alternative antibacterial agents to control MRSA. In this study, we isolated six S. aureus phages from soils of poultry/livestock farms. Based on the results of host range determination with 150 S. aureus strains and restriction enzyme treatment of phage DNA, two phages, designated SP5 and SP6, were selected for further characterization and genome sequencing. Both SP5 and SP6 were classified as members of the family Siphoviridae. The genome of SP5 comprises 43 305 bp and contains 63 ORFs, while the SP6 genome comprises 42 902 bp and contains 61 ORFs. Although they have different host spectra, the phage genomes exhibit high nucleotide similarity to each other. Adsorption assay results suggested that the host range determinants of the two phages are involved in both adsorption and infection. Comparative genomic analyses of the two phages provided evidence that the lysogenic/lytic control module and tail proteins may be important for host specificity.

scholarly journals Genomic and functional characterization of five novel Salmonella-targeting bacteriophages

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Marta Kuźmińska-Bajor ◽  
Paulina Śliwka ◽  
Maciej Ugorski ◽  
Paweł Korzeniowski ◽  
Aneta Skaradzińska ◽  
...  
Keyword(s):  
Life Cycle ◽  
Host Range ◽  
Salmonella Enterica ◽  
Function Analysis ◽  
Functional Characterization ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Wide Range ◽  
Host Range Determination ◽  
Range Determination

Abstract Background The host-unrestricted, non-typhoidal Salmonella enterica serovar Enteritidis (S. Enteritidis) and the serovar Typhimurium (S. Typhimurium) are major causative agents of food-borne gastroenteritis, and the host-restricted Salmonella enterica serovar Gallinarum (S. Gallinarum) is responsible for fowl typhoid. Increasing drug resistance in Salmonella contributes to the reduction of effective therapeutic and/or preventive options. Bacteriophages appear to be promising antibacterial tools, able to combat infectious diseases caused by a wide range of Salmonella strains belonging to both host-unrestricted and host-restricted Salmonella serovars. Methods In this study, five novel lytic Salmonella phages, named UPWr_S1-5, were isolated and characterized, including host range determination by plaque formation, morphology visualization with transmission electron microscopy, and establishment of physiological parameters. Moreover, phage genomes were sequenced, annotated and analyzed, and their genomes were compared with reference Salmonella phages by use of average nucleotide identity, phylogeny, dot plot, single nucleotide variation and protein function analysis. Results It was found that UPWr_S1-5 phages belong to the genus Jerseyvirus within the Siphoviridae family. All UPWr_S phages were found to efficiently infect various Salmonella serovars. Host range determination revealed differences in host infection profiles and exhibited ability to infect Salmonella enterica serovars such as Enteritidis, Gallinarum, Senftenberg, Stanley and Chester. The lytic life cycle of UPWr_S phages was confirmed using the mitomycin C test assay. Genomic analysis revealed that genomes of UPWr_S phages are composed of 51 core and 19 accessory genes, with 33 of all predicted genes having assigned functions. UPWr_S genome organization comparison revealed 3 kinds of genomes and mosaic structure. UPWr_S phages showed very high sequence similarity to each other, with more than 95% average nucleotide identity. Conclusions Five novel UPWr_S1-5 bacteriophages were isolated and characterized. They exhibit host lysis range within 5 different serovars and are efficient in lysis of both host-unrestricted and host-restricted Salmonella serovars. Therefore, because of their ability to infect various Salmonella serovars and lytic life cycle, UPWr_S1-5 phages can be considered as useful tools in biological control of salmonellosis.

scholarly journals Field Damage to Yellow Starthistle Infected by Synchytrium solstitiale, and Greenhouse Maintenance and Host Range of the Fungus

Plant Disease ◽  
2011 ◽  
Vol 95 (8) ◽  
pp. 907-912
Author(s):  
F. M. Eskandari ◽  
W. L. Bruckart ◽  
T. L. Widmer
Keyword(s):  
United States ◽  
Biological Control ◽  
Host Range ◽  
Leaf Tissue ◽  
The United States ◽  
Carthamus Tinctorius ◽  
Yellow Starthistle ◽  
Potted Plants ◽  
Host Range Determination ◽  
Range Determination

Yellow starthistle (YST, Centaurea solstitialis) is a major weed pest of the western United States. Synchytrium solstitiale, a pathogen of YST, caused significant damage to symptomatic (versus asymptomatic) plants in a field study in France. Before it was evaluated as a candidate for biological control of YST in the United States, protocols for pathogen maintenance under greenhouse conditions were developed. Maintenance, increase, and host range determination protocols involved incubation at 10/15°C (night/day) with an 8-h photoperiod either of potted or exhumed (i.e., roots of 4-week-old plants grown in flasks of water) plants inoculated with galled leaf tissue, or potted plants in which inoculum was wrapped within healthy leaves by a plastic wrap. The leaf-wrap protocol, used during the host range determination, always resulted in disease of YST. Several safflower (Carthamus tinctorius) cultivars and other plants related to YST became diseased following this protocol, thus raising concern about host specificity. Development of disease on nontarget species precludes proposal of S. solstitiale for biological control of YST at this time.

Serratia entomophilabacteriophages: host range determination and preliminary characterization

1997 ◽  
Vol 43 (11) ◽  
pp. 1069-1073 ◽  
Author(s):  
Maureen O'Callaghan ◽  
Trevor A. Jackson ◽  
Travis R. Glare
Keyword(s):  
Host Range ◽  
Restriction Endonuclease ◽  
Large Scale ◽  
Dna Analysis ◽  
Bacterial Pathogen ◽  
Restriction Endonuclease Analysis ◽  
Scale Production ◽  
Bacterial Isolates ◽  
Host Range Determination ◽  
Range Determination

Eight bacteriophages specific to Serratia entomophila, a commercially available bacterial pathogen of the New Zealand grass grub (Costelytra zealandica), were characterized by host range determination, morphology and restriction endonuclease patterns of DNA. Phages were originally isolated from grass grub larvae and fermenter broth where phages had disrupted large-scale production of S. entomophila. Seven of the phages (CW1–CW5, BC, and BT) had heads similar in size (approximately 60 × 60 nm) and long noncontractile tails (185 × 10 nm). Phage AgRP8 (P8) had a smaller head and a short tail structure. Restriction endonuclease analysis divided the phages into four groups: CW2, CW4, CW5, BC, and BT gave identical patterns, while CW1, CW3, and P8 each gave different patterns. Six distinct phage groups were distinguished by host range determination, after screening phages against 70 bacterial isolates: CW1, CW2/CW4, CW3, CW5, BC/BT, and P8. While confirming the indicated groupings by DNA analysis, it was possible to distinguish between some of the phages in the largest group: CW2/4 could be distinguished from CW5 and BC/BT. Screening of soil bacterial isolates of S. entomophila against nondiluted phages will aid in monitoring the establishment and persistence of strains applied for biological control of the grass grub.Key words: Serratia entomophila, bacteriophage, morphology, phage typing, host range.

scholarly journals Genes influencing phage host range in Staphylococcus aureus on a species-wide scale

2020 ◽  
Author(s):  
Abraham G Moller ◽  
Kyle Winston ◽  
Shiyu Ji ◽  
Junting Wang ◽  
Michelle N Hargita Davis ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Host Range ◽  
Genetic Basis ◽  
Host Interactions ◽  
Genome Wide ◽  
Host Range Determination ◽  
Wide Scale ◽  
Range Determination ◽  
The Impact ◽  
Sequence Types

Staphylococcus aureus is a human pathogen that causes serious diseases ranging from skin infections to septic shock. Bacteriophages ("phages") are both natural killers of S. aureus, offering therapeutic possibilities, as well as important vectors of horizontal gene transfer in the species. Here, we used high-throughput approaches to understand the genetic basis of strain-to-strain variation in sensitivity to phages, which defines the host range. We screened 259 diverse S. aureus strains covering more than 40 sequence types for sensitivity to eight phages, which were representatives of the three phage classes that infect the species. The phages were variable in host range, each infecting between 73 and 257 strains. Using genome-wide association approaches, we identified putative loci that affect host range and validated their function using USA300 transposon knockouts. In addition to rediscovering known host range determinants, we found several previously unreported genes affecting bacterial growth during phage infection, including trpA, phoR, isdB, sodM, fmtC, and relA. We used the data from our host range matrix to develop predictive models that achieved between 40 and 95% accuracy. This work illustrates the complexity of the genetic basis for phage susceptibility in S. aureus but also shows that with more data, we may be able to understand much of the variation. With a knowledge of host range determination, we can rationally design phage therapy cocktails that target the broadest host range of S. aureus strains and address basic questions regarding phage-host interactions, such as the impact of phage on S. aureus evolution.

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