scholarly journals Vibrio vulnificus Bacteriophage SSP002 as a Possible Biocontrol Agent

2013 ◽  
Vol 80 (2) ◽  
pp. 515-524 ◽  
Author(s):  
Hyun Sung Lee ◽  
Slae Choi ◽  
Hakdong Shin ◽  
Ju-Hoon Lee ◽  
Sang Ho Choi
Keyword(s):  
Vibrio Vulnificus ◽  
Burst Size ◽  
Genomic Analysis ◽  
The Yellow Sea ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Growth Curve Analysis ◽  
Range Analysis ◽  
Content Type ◽  
One Step

ABSTRACTA novelVibrio vulnificus-infecting bacteriophage, SSP002, belonging to theSiphoviridaefamily, was isolated from the coastal area of the Yellow Sea of South Korea. Host range analysis revealed that the growth inhibition of phage SSP002 is relatively specific toV. vulnificusstrains from both clinical and environmental samples. In addition, a one-step growth curve analysis and a bacteriophage stability test revealed a latent period of 65 min, a burst size of 23 ± 2 PFU, as well as broad temperature (20°C to 60°C) and pH stability (pH 3 to 12) ranges. A Tn5random transposon mutation ofV. vulnificusand partial DNA sequencing of the inserted Tn5regions revealed that theflhA,flhB,fliF, andfleQmutants are resistant to SSP002 phage infection, suggesting that the flagellum may be the host receptor for infection. The subsequent construction of specific gene-inactivated mutants (flhA,flhB,fliF, andfleQ) and complementation experiments substantiated this. Previously, the genome of phage SSP002 was completely sequenced and analyzed. Comparative genomic analysis of phage SSP002 andVibrio parahaemolyticusphage vB_VpaS_MAR10 showed differences among their tail-related genes, supporting different host ranges at the species level, even though their genome sequences are highly similar. An additional mouse survival test showed that the administration of phage SSP002 at a multiplicity of infection of 1,000 significantly protects mice from infection byV. vulnificusfor up to 2 months, suggesting that this phage may be a good candidate for the development of biocontrol agents againstV. vulnificusinfection.

scholarly journals Draft Genome Sequence of Vibrio vulnificus 86573B, a Bacterium Isolated from Diseased Tilapia in Taiwan

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Shu-Ting Cho ◽  
Yi-Ming Tsai ◽  
Chun-Yao Chen ◽  
Chih-Horng Kuo
Keyword(s):  
Genome Sequence ◽  
Vibrio Vulnificus ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Content Type

Vibrio vulnificus 86573B is a biotype 1 strain isolated from a moribund tilapia collected in Kaohsiung, Taiwan, during an outbreak early in 1997. Here, we report the draft genome sequence of this bacterium to facilitate the investigation of its biology and future comparative genomic analysis.

scholarly journals Characterization and Comparative Genomic Analysis of a Novel Bacteriophage, SFP10, Simultaneously Inhibiting both Salmonella enterica and Escherichia coli O157:H7

2011 ◽  
Vol 78 (1) ◽  
pp. 58-69 ◽  
Author(s):  
Minjung Park ◽  
Ju-Hoon Lee ◽  
Hakdong Shin ◽  
Minsik Kim ◽  
Jeongjoon Choi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Salmonella Enterica ◽  
Burst Size ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Tail Fiber ◽  
Content Type ◽  
E Coli ◽  
Development Of Resistance

ABSTRACTSalmonella entericaandEscherichia coliO157:H7 are major food-borne pathogens causing serious illness. Phage SFP10, which revealed effective infection of bothS. entericaandE. coliO157:H7, was isolated and characterized. SFP10 contains a 158-kb double-stranded DNA genome belonging to the Vi01 phage-like familyMyoviridae.In vitroadsorption assays showed that the adsorption constant rates to bothSalmonella entericaserovar Typhimurium andE. coliO157:H7 were 2.50 × 10−8ml/min and 1.91 × 10−8ml/min, respectively. One-step growth analysis revealed that SFP10 has a shorter latent period (25 min) and a larger burst size (>200 PFU) than ordinaryMyoviridaephages, suggesting effective host infection and lytic activity. However, differential development of resistance to SFP10 inS.Typhimurium andE. coliO157:H7 was observed; bacteriophage-insensitive mutant (BIM) frequencies of 1.19 × 10−2CFU/ml forS.Typhimurium and 4.58 × 10−5CFU/ml forE. coliO157:H7 were found, indicating that SFP10 should be active and stable for control ofE. coliO157:H7 with minimal emergence of SFP10-resistant pathogens but may not be forS.Typhimurium. Specific mutation ofrfaLinS.Typhimurium andE. coliO157:H7 revealed the O antigen as an SFP10 receptor for both bacteria. Genome sequence analysis of SFP10 and its comparative analysis with homologousSalmonellaVi01 andShigellaphiSboM-AG3 phages revealed that their tail fiber and tail spike genes share low sequence identity, implying that the genes are major host specificity determinants. This is the first report identifying specific infection and inhibition ofSalmonellaTyphimurium andE. coliO157:H7 by a single bacteriophage.

scholarly journals Biological Characteristics and Genomic Analysis of Aeromonas Hydrophila Phage BUCT551 Isolated From Aquatic Sewage

2021 ◽  
Author(s):  
Hongbo Qin ◽  
Shiting He ◽  
Xuling Xu ◽  
Xiaoping An ◽  
Ke Liu ◽  
...  
Keyword(s):  
Aeromonas Hydrophila ◽  
Burst Size ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
Range Analysis ◽  
Transmission Electron ◽  
Blastn Analysis ◽  
One Step ◽  
Ph Range ◽  
The One

Abstract Aeromonas hydrophila is a common opportunistic pathogen in aquaculture and is ubiquitous in aquatic environment. Whereby its accessibility, variety and host specificity, phage is increasingly considered as a promising complementary medicine for antibiotics. However, a small amount of A. hydrophila phages have been characterized, which suggests the significance to isolate and characterize novel A. hydrophila phages. In this study, we isolated a novel Aeromonas hydrophila phage using A. hydrophila strain A18 as an indicator and designated it as BUCT551, and it was identified as Myoviridae phage by transmission electron microscopy (TEM). The whole genome sequencing of the phage BUCT551 revealed that it has a linear DNA genome of 613,82 bp. BLASTn analysis showed that phage BUCT551 shared 86.75% homology with A. hydrophila phage LAh_7 (Genebank ID: MK838113.1). The one-step growth curve demonstrated that phage BUCT551 had a latent period of 20 min and the burst size of 32 pfu/cell at its optimal MOI of 0.1. The phage BUCT551 had a survival pH range from 5 to 10 and tolerant temperature from 0℃ to 40℃. Host range analysis shown that the phage was able to lyse not only A. hydrophila, but also A. veronii.

scholarly journals Characterization of the Escherichia coli Virulent Myophage ST32

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 616 ◽  
Author(s):  
Honghui Liu ◽  
Hany Geagea ◽  
Geneviève Rousseau ◽  
Simon Labrie ◽  
Denise Tremblay ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Tree ◽  
Biological Control Agent ◽  
Burst Size ◽  
Gc Content ◽  
Genomic Analysis ◽  
Coli Strain ◽  
Comparative Genomic ◽  
Wastewater Sample ◽  
Range Analysis

The virulent phage ST32 that infects the Escherichia coli strain ST130 was isolated from a wastewater sample in China and analyzed. Morphological observations showed that phage ST32 belongs to the Myoviridae family, as it has an icosahedral capsid and long contractile tail. Host range analysis showed that it exhibits a broad range of hosts including non-pathogenic and pathogenic E. coli strains. Interestingly, phage ST32 had a much larger burst size when amplified at 20 °C as compared to 30 °C or 37 °C. Its double-stranded DNA genome was sequenced and found to contain 53,092 bp with a GC content of 44.14%. Seventy-nine open reading frames (ORFs) were identified and annotated as well as a tRNA-Arg. Only nineteen ORFs were assigned putative functions. A phylogenetic tree using the large terminase subunit revealed a close relatedness with four unclassified Myoviridae phages. A comparative genomic analysis of these phages showed that the Enterobacteria phage phiEcoM-GJ1 is the closest relative to ST32 and shares the same new branch in the phylogenetic tree. Still, these two phages share only 47 of 79 ORFs with more than 90% identity. Phage ST32 has unique characteristics that make it a potential biological control agent under specific conditions.

scholarly journals Genomic Investigation of Lysogen Formation and Host Lysis Systems of the Salmonella Temperate Bacteriophage SPN9CC

2013 ◽  
Vol 80 (1) ◽  
pp. 374-384 ◽  
Author(s):  
Hakdong Shin ◽  
Ju-Hoon Lee ◽  
Hyunjin Yoon ◽  
Dong-Hyun Kang ◽  
Sangryeol Ryu
Keyword(s):  
Host Cell ◽  
Burst Size ◽  
Group Analysis ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Cell Lysis ◽  
Comparative Genomic ◽  
Phage Group ◽  
Content Type ◽  
Lysis Activity

ABSTRACTTo understand phage infection and host cell lysis mechanisms in pathogenicSalmonella, a novelSalmonella entericaserovar Typhimurium-targeting bacteriophage, SPN9CC, belonging to thePodoviridaefamily was isolated and characterized. The phage infectsS. Typhimurium via the O antigen of lipopolysaccharide (LPS) and forms clear plaques with cloudy centers due to lysogen formation. Phylogenetic analysis of phage major capsid proteins revealed that this phage is a member of the lysogen-forming P22-like phage group. However, comparative genomic analysis of SPN9CC with P22-like phages indicated that their lysogeny control regions and host cell lysis gene clusters show very low levels of identity, suggesting that lysogen formation and host cell lysis mechanisms may be diverse among phages in this group. Analysis of the expression of SPN9CC host cell lysis genes encoding holin, endolysin, and Rz/Rz1-like proteins individually or in combinations inS. Typhimurium andEscherichia colihosts revealed that collaboration of these lysis proteins is important for the lysis of both hosts and that holin is a key protein. To further investigate the role of the lysogeny control region in phage SPN9CC, a ΔcImutant (SPN9CCM) of phage SPN9CC was constructed. The mutant does not produce a cloudy center in the plaques, suggesting that this mutant phage is virulent and no longer temperate. Subsequent comparative one-step growth analysis and challenge assays revealed that SPN9CCM has shorter eclipse/latency periods and a larger burst size, as well as higher host cell lysis activity, than SPN9CC. The present work indicates the possibility of engineering temperate phages as promising biocontrol agents similar to virulent phages.

scholarly journals Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis

2018 ◽  
Vol 62 (11) ◽  
Author(s):  
Glen P. Carter ◽  
James E. Ussher ◽  
Anders Gonçalves Da Silva ◽  
Sarah L. Baines ◽  
Helen Heffernan ◽  
...  
Keyword(s):  
Neonatal Sepsis ◽  
Neonatal Intensive Care ◽  
Genomic Analysis ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Coagulase Negative Staphylococci ◽  
Content Type ◽  
Staphylococcus Capitis ◽  
Hospital Infection Control

ABSTRACT Coagulase-negative staphylococci (CoNS), such as Staphylococcus capitis, are major causes of bloodstream infections in neonatal intensive care units (NICUs). Recently, a distinct clone of S. capitis (designated S. capitis NRCS-A) has emerged as an important pathogen in NICUs internationally. Here, 122 S. capitis isolates from New Zealand (NZ) underwent whole-genome sequencing (WGS), and these data were supplemented with publicly available S. capitis sequence reads. Phylogenetic and comparative genomic analyses were performed, as were phenotypic assessments of antimicrobial resistance, biofilm formation, and plasmid segregational stability on representative isolates. A distinct lineage of S. capitis was identified in NZ associated with neonates and the NICU environment. Isolates from this lineage produced increased levels of biofilm, displayed higher levels of tolerance to chlorhexidine, and were multidrug resistant. Although similar to globally circulating NICU-associated S. capitis strains at a core-genome level, NZ NICU S. capitis isolates carried a novel stably maintained multidrug-resistant plasmid that was not present in non-NICU isolates. Neonatal blood culture isolates were indistinguishable from environmental S. capitis isolates found on fomites, such as stethoscopes and neonatal incubators, but were generally distinct from those isolates carried by NICU staff. This work implicates the NICU environment as a potential reservoir for neonatal sepsis caused by S. capitis and highlights the capacity of genomics-based tracking and surveillance to inform future hospital infection control practices aimed at containing the spread of this important neonatal pathogen.

scholarly journals Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies

2021 ◽  
Vol 10 (46) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Natsuko Tokito
Keyword(s):  
Complete Genome ◽  
Thermus Thermophilus ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Hybrid Assembly ◽  
Genome Resequencing ◽  
Short Read ◽  
Content Type ◽  
Sequencing Technologies ◽  
Long Read

Complete genome resequencing was conducted for Thermus thermophilus strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related T. thermophilus genomes.

Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Danni Wu ◽  
Hongcan Liu ◽  
Yuguang Zhou ◽  
Xiaolei Wu ◽  
Yong Nie ◽  
...  
Keyword(s):  
Type Species ◽  
Genomic Analysis ◽  
Oil Production ◽  
Gene Families ◽  
Specific Gene ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A pink, ovoid-shaped, Gram-stain-negative, strictly aerobic and motile bacterial strain, designated ROY-5-3T, was isolated from an oil production mixture from Yumen Oilfield in PR China. The strain grew at 4–42 °C (optimum, 30 °C), at pH 5–10 (optimum, 7) and with 0–5 % (w/v) NaCl (optimum, 0%). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ROY-5-3T belongs to the genus Roseomonas and shared the highest pairwise similarities with Roseomonas frigidaquae CW67T (98.1%), Roseomonas selenitidurans BU-1T (97.8%), Roseomonas tokyonensis K-20T (97.7%) and Roseomonas stagni HS-69T (97.3%). The average nucleotide identity and digital DNA–DNA hybridization values between ROY-5-3T and other related type strains of Roseomonas species were less than 84.08 and 28.60 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate ROY-5-3T shared 3265 core gene families with the four closely related type strains in Roseomonas , and the number of strain-specific gene families was 513. The major fatty acids were identified as summed feature 8 (C18 : 1 ω6c/C18 : 1 ω7c), summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and C16 : 0. Strain ROY-5-3T contained Q-10 as the main ubiquinone and the genomic DNA G+C content was 69.8 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Based on the phylogenetic, morphological, physiological, chemotaxonomic and genome analyses, strain ROY-5-3T represents a novel species of the genus Roseomonas for which the name Roseomonas oleicola sp. nov. is proposed. The type strain is ROY-5-3T (=CGMCC 1.13459T =KCTC 82484T).

scholarly journals The Complete Genome of the Atypical Enteropathogenic Escherichia coli Archetype Isolate E110019 Highlights a Role for Plasmids in Dissemination of the Type III Secreted Effector EspT

2019 ◽  
Vol 87 (10) ◽  
Author(s):  
Tracy H. Hazen ◽  
David A. Rasko
Keyword(s):  
Escherichia Coli ◽  
Complete Genome ◽  
Genomic Analysis ◽  
Host Cells ◽  
Comparative Genomic ◽  
Content Type ◽  
E Coli ◽  
Type Iii ◽  
Severe Diarrhea ◽  
Typical Epec

ABSTRACT Enteropathogenic Escherichia coli (EPEC) is a leading cause of moderate to severe diarrhea among young children in developing countries, and EPEC isolates can be subdivided into two groups. Typical EPEC (tEPEC) bacteria are characterized by the presence of both the locus of enterocyte effacement (LEE) and the plasmid-encoded bundle-forming pilus (BFP), which are involved in adherence and translocation of type III effectors into the host cells. Atypical EPEC (aEPEC) bacteria also contain the LEE but lack the BFP. In the current report, we describe the complete genome of outbreak-associated aEPEC isolate E110019, which carries four plasmids. Comparative genomic analysis demonstrated that the type III secreted effector EspT gene, an autotransporter gene, a hemolysin gene, and putative fimbrial genes are all carried on plasmids. Further investigation of 65 espT-containing E. coli genomes demonstrated that different espT alleles are associated with multiple plasmids that differ in their overall gene content from the E110019 espT-containing plasmid. EspT has been previously described with respect to its role in the ability of E110019 to invade host cells. While other type III secreted effectors of E. coli have been identified on insertion elements and prophages of the chromosome, we demonstrated in the current study that the espT gene is located on multiple unique plasmids. These findings highlight a role of plasmids in dissemination of a unique E. coli type III secreted effector that is involved in host invasion and severe diarrheal illness.

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

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