Genomic characterization of a novel virulent phage infecting Shigella fiexneri and isolated from sewage

Lu, Haiquan; Yan, Peihan; Xiong, Wenbin; Wang, Jingwei; Liu, Xinchun

doi:10.1016/j.virusres.2020.197983

Cited by 25 publications

(15 citation statements)

References 35 publications

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“…The burst size of most reported phages, including Autographiviridae phages, was at dozens to hundreds of PFU/cell ( Baudoux et al, 2012 ; Huang et al, 2013 ; Merabishvili et al, 2014 ; Qin et al, 2017 ; Anand et al, 2018 ; Lu et al, 2020 ). A literature review found Stenotrophomonas phage IME13 of the Myoviridae family and Cronobacter phage vB_CtuP_B1 of genus Kayfunavirus in subfamily Studiervirinae of family Autographiviridae had especially prominently high burst size of 3,000 ( Fan et al, 2012 ) and 4,006 PFU/cell ( Zeng et al, 2021 ), respectively, which were the highest reported burst sizes of dsDNA phages.…”

Section: Discussionmentioning

confidence: 99%

“…A few phages infect bacteria at the genus level, and a few phages infect bacteria of different genera, such as phage vB_EcoM_APEC ( Deng et al, 2021 ). The burst size of most of the reported phages, including phages of family Autographiviridae, was dozens to hundreds of PFU/cell ( Baudoux et al, 2012 ; Huang et al, 2013 ; Merabishvili et al, 2014 ; Qin et al, 2017 ; Anand et al, 2018 ; Lu et al, 2020 ). A literature review found that the biggest burst size of the reported dsDNA phages is Cronobacter phage vB_CtuP_B1 of the Autographiviridae family, which has a particularly high burst size of 4,006 PFU/cell ( Zeng et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

Pan

Sun

et al. 2022

Front. Microbiol.

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A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35–45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

Pan

Sun

et al. 2022

Front. Microbiol.

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“…Globally, scientists have invested efforts in diagnosis and treatment of COVID-19. The breadth of the current research on COVID-19 focuses more on its clinical characteristics [ 2 ], likelihood of survival [ 3 ], genomic characterization of the virus [ 4 ] and drug and therapeutic options [ 5 ]. Additionally, growing incidences of anxiety, pain, insomnia and distress have been reported widely across nations [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

COVID-19 and psychological distress: Lessons for India

Verma¹,

Aggarwal

Nanjundappa

et al. 2021

PLoS ONE

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Purpose The COVID-19 pandemic has undoubtedly altered the routine of life and caused unanticipated changes resulting in severe psychological responses and mental health crisis. The study aimed to identify psycho-social factors that predicted distress among Indian population during the spread of novel Coronavirus. Method An online survey was conducted to assess the predictors of distress. A global logistic regression model was built, by identifying significant factors from individual logistic regression models built on various groups of independent variables. The prediction capability of the model was compared with the random forest classifier. Results The respondents (N = 1060) who are more likely to be distressed, are in the age group of 21-35 years, are females (OR = 1.425), those working on site (OR = 1.592), have pre-existing medical conditions (OR = 1.682), do not have health insurance policy covering COVID-19 (OR = 1.884), have perceived seriousness of COVID-19 (OR = 1.239), have lack of trust in government (OR = 1.246) and whose basic needs’ fulfillment are unsatisfactory (OR = 1.592). The ones who are less likely to be distressed, have higher social support and psychological capital. Random forest classifier correctly classified 2.3% and 17.1% of people under lower and higher distress respectively, with respect to logistic regression. Conclusions This study confirms the prevalence of high distress experienced by Indians at the time of COVID-19 and provides pragmatic implications for psychological health at macro and micro levels during an epidemiological crisis.

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“…This suggests that phage IME268 possessed a bifunctional protein that play a role both as a helicase and primase to complete the unwinding and catalytic synthesis of DNA. 40 …”

Section: Resultsmentioning

confidence: 99%

Characterization and Genomic Analysis of a Novel Drexlervirial Bacteriophage IME268 with Lytic Activity Against Klebsiella pneumoniae

Nazir¹,

Qi²,

Shi³

et al. 2022

IDR

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Introduction Klebsiella pneumoniae , a multidrug resistant bacterium, that causes nosocomial infections including septicemia, pneumonia etc. Bacteriophages are potential antimicrobial agents for the treatment of antibiotic resistant bacteria. Methods and Results In this study, a novel bacteriophage IME268 was isolated from hospital sewage against clinical multi-drug resistant Klebsiella pneumoniae . Transmission electron microscopy and genomic characterization of this phage exhibited it belongs to the Webervirus genus, Drexlerviridae family. Phage IME268 possessed a double-stranded DNA genome composed of 49,552bp with a GC content of 50.5%. The phage genome encodes 77 open reading frames, out of 44 are hypothetical proteins while 33 had assigned putative functions. No tRNA, virulence related or antibiotic resistance genes were found in phage genome. Comparative genomic analysis showed that phage IME268 has 95% identity with 87% query cover with other phages in NCBI database. Multiplicity of infection, one step growth curve and host range of phage were also measured. Conclusion According to findings, Phage IME268 is a promising biological agent that infects Klebsiella pneumoniae and can be used in future phage therapies.

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Genomic characterization of a novel virulent phage infecting Shigella fiexneri and isolated from sewage

Cited by 25 publications

References 35 publications

First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

COVID-19 and psychological distress: Lessons for India

Characterization and Genomic Analysis of a Novel Drexlervirial Bacteriophage IME268 with Lytic Activity Against Klebsiella pneumoniae

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