scholarly journals De Novo Sequencing Provides Insights Into the Pathogenicity of Foodborne Vibrio parahaemolyticus

2021 ◽  
Vol 11 ◽  
Author(s):  
Jianfei Liu ◽  
Kewei Qin ◽  
Chenglin Wu ◽  
Kaifei Fu ◽  
Xiaojie Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Vibrio Parahaemolyticus ◽  
De Novo ◽  
Genomic Analysis ◽  
Pathogenicity Test ◽  
Evolutionary Potential ◽  
Gastrointestinal Infections ◽  
Functional Region ◽  
Genomic Change ◽  
The Difference

Vibrio parahaemolyticus is a common pathogenic marine bacterium that causes gastrointestinal infections and other health complications, which could be life-threatening to immunocompromised patients. For the past two decades, the pathogenicity of environmental V. parahaemolyticus has increased greatly, and the genomic change behind this phenomenon still needs an in-depth exploration. To investigate the difference in pathogenicity at the genomic level, three strains with different hemolysin expression and biofilm formation capacity were screened out of 69 environmental V. parahaemolyticus strains. Subsequently, 16S rDNA analysis, de novo sequencing, pathogenicity test, and antibiotic resistance assays were performed. Comparative genome-scale interpretation showed that various functional region differences in pathogenicity of the selected V. parahaemolyticus strains were due to dissimilarities in the distribution of key genetic elements and in the secretory system compositions. Furthermore, the genomic analysis-based hypothesis of distinct pathogenic effects was verified by the survival rate of mouse models infected with different V. parahaemolyticus strains. Antibiotic resistance results also presented the multi-directional evolutionary potential in environmental V. parahaemolyticus, in agreement with the phylogenetic analysis results. Our study provides a theoretical basis for better understanding of the increasing pathogenicity of environmental V. parahaemolyticus at the genome level. Further, it has a key referential value for the exploration of pathogenicity and prevention of environmental V. parahaemolyticus in the future.

scholarly journals Pan-genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia

2019 ◽  
Author(s):  
Bryan Naidenov ◽  
Karyn Willyerd ◽  
Alexander Lim ◽  
Nathanial J Torres ◽  
William L. Johnson ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
De Novo ◽  
Binary Classification ◽  
Genomic Analysis ◽  
Machine Learning Algorithms ◽  
Emerging Pathogens ◽  
Phenotypic Resistance ◽  
Elizabethkingia Meningoseptica ◽  
Long Read ◽  
Or Gene

AbstractThe Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and Elizabethkingia meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84 respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75 and 0.54 respectively.

Antibiotic Resistance in the Shellfish Pathogen Vibrio parahaemolyticus Isolated from the Coastal Water and Sediment of Georgia and South Carolina, USA

2008 ◽  
Vol 71 (12) ◽  
pp. 2552-2558 ◽  
Author(s):  
CRAIG BAKER-AUSTIN ◽  
J. V. McARTHUR ◽  
R. CARY TUCKFIELD ◽  
MICHAEL NAJARRO ◽  
ANGELA H. LINDELL ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
South Carolina ◽  
Vibrio Parahaemolyticus ◽  
Atlantic Coast ◽  
Sample Type ◽  
Gastrointestinal Infections ◽  
Water And Sediment ◽  
Virulent Strains ◽  
Antibiotic Susceptibility Patterns ◽  
Current Guidelines

Vibrio parahaemolyticus is a gram-negative pathogen commonly encountered in estuarine and marine environments, and a common cause of seafood-related gastrointestinal infections. We isolated 350 V. parahaemolyticus strains from water and sediment at three locations along the Atlantic coast of Georgia and South Carolina during various seasons. These isolates were tested for susceptibility to 24 antibiotics. Isolate virulence was determined through PCR of tdh and trh genes. The breadth of resistance to antibiotics was unexpectedly high, with 24% isolates demonstrating resistance to 10 or more agents. A significant fraction of isolates were resistant to diverse β-lactams, aminoglycosides, and other classes of antibiotics. Fifteen of the 350 strains possessed virulence genes, with no apparent correlation between virulence and site, sample type, or season of isolation. Antibiotic resistance was slightly reduced among the virulent strains. This study represents one of the largest surveys to date of the virulence and antibiotic resistance in environmental V. parahaemolyticus strains. The observed antibiotic susceptibility patterns suggest that current guidelines for the antibiotic treatment of non-cholerae Vibrio should be reevaluated and extended.

scholarly journals Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease

2019 ◽  
Author(s):  
Han Ming Gan ◽  
Christopher M. Austin
Keyword(s):  
Genome Assembly ◽  
Vibrio Parahaemolyticus ◽  
De Novo ◽  
Genomic Analysis ◽  
Binary Toxin ◽  
Comparative Genomic ◽  
Chromosome 2 ◽  
Toxin Genes ◽  
Long Reads ◽  
Long Read

AbstractBackgroundVibrio parahaemolyticus MVP1 was isolated from a Malaysian aquaculture farm affected with shrimp acute hepatopancreatic necrosis disease (AHPND). Its genome was previously sequenced on the Illumina MiSeq platform and assembled de novo producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood.MethodsThe genome of Vibrio parahaemolyticus MVP1 was sequenced on the Nanopore MinION device to obtain long reads that can span longer repeats and improve genome contiguity. De novo genome assembly was subsequently performed using long-read only assembler (Flye) followed by genome polishing as well as hybrid assembler (Unicycler).ResultsLong-read only assembly produced three complete circular MVP1 contigs consisting of chromosome 1, chromosome 2 and the pVa plasmid that pirABvp binary toxin genes. Polishing of the long read assembly with Illumina short reads was necessary to remove indel errors. The complete assembly of the pVa plasmid could not be achieved using Illumina reads due to the presence of identical repetitive elements flanking the binary toxin genes leading to multiple contigs. Whereas these regions were fully spanned by the Nanopore long reads resulting in a single contig. In addition, alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed the presence of a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of all publicly available V. parahaemolyticus genomes revealed the presence of a single AinS-family quorum-sensing system in this species that can be targeted for future microbial management.ConclusionsWe generated the first chromosome-scale genome assembly of a Malaysian pirABVp-bearing V. parahaemolyticus isolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features of V. parahaemolyticus MVP1 that may be associated with host colonization and pathogenicity.

scholarly journals Comparative Genomic Analysis Using Microarray Demonstrates a Strong Correlation between the Presence of the 80-Kilobase Pathogenicity Island and Pathogenicity in Kanagawa Phenomenon-Positive Vibrio parahaemolyticus Strains

2008 ◽  
Vol 76 (3) ◽  
pp. 1016-1023 ◽  
Author(s):  
Kaori Izutsu ◽  
Ken Kurokawa ◽  
Kosuke Tashiro ◽  
Satoru Kuhara ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Genomic Analysis ◽  
Pathogenicity Island ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Genetic Event ◽  
Thermostable Direct Hemolysin ◽  
The Difference ◽  
Pandemic Strains ◽  
Almost All

ABSTRACTVibrio parahaemolyticusis a gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Almost all of the clinicalV. parahaemolyticusisolates exhibit beta-type hemolysis on Wagatsuma agar, known as the Kanagawa phenomenon (KP). KP is induced by the thermostable direct hemolysin produced by the organism and has been considered a crucial marker to distinguish pathogenic strains from nonpathogenic ones. Since 1996, so-called “pandemic clones,” the majority of which belong to serotype O3:K6, have caused worldwide outbreaks of gastroenteritis. In this study, we used a DNA microarray constructed based on the genome sequence of a pandemicV. parahaemolyticusstrain, RIMD2210633, to examine the genomic composition of 22 strains ofV. parahaemolyticus, including both pathogenic (pandemic and nonpandemic) and nonpathogenic strains. More than 86% of the RIMD2210633 genes were conserved in all of the strains tested. Many variably present genes formed gene clusters on the genome of RIMD2210633 and were probably acquired through lateral gene transfer. At least 65 genes over 11 loci were specifically present in the pandemic strains compared with any of the nonpandemic strains, suggesting that the difference between pandemic and nonpandemic strains is not due to a simple genetic event. Only the genes in the 80-kb pathogenicity island (Vp-PAI) on chromosome II, including twotdhgenes and a set of genes for the type III secretion system, were detected only in the KP-positive pathogenic strains. These results strongly suggest that acquisition of this Vp-PAI was crucial for the emergence ofV. parahaemolyticusstrains that are pathogenic for humans.

Genetic rescue by augmenting gene flow

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Inbreeding Coefficient ◽  
Outbreeding Depression ◽  
Genetic Rescue ◽  
Evolutionary Potential ◽  
Beneficial Effects ◽  
The Difference ◽  
Inbred Populations ◽  
Harmful Effects

Inbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of outbreeding depression, there are large and consistent benefits on fitness that persist across generations in outbreeding species. Benefits are greater in species that naturally outbreed than those that inbreed, and increase with the difference in inbreeding coefficient between crossed and inbred populations in mothers and zygotes. However, benefits are similar across invertebrates, vertebrates and plants. There are also important benefits for evolutionary potential of crossing between populations.

Prognostic implication of CT-FFR based functional SYNTAX score in patients with de novo three-vessel disease

2020 ◽  
Author(s):  
Hong Yan Qiao ◽  
Jian Hua Li ◽  
U Joseph Schoepf ◽  
Richard R Bayer ◽  
Fiona C Tinnefeld ◽  
...  
Keyword(s):  
De Novo ◽  
Predictive Accuracy ◽  
Computed Tomographic Angiography ◽  
Syntax Score ◽  
Cardiac Events ◽  
Fractional Flow ◽  
Computed Tomographic ◽  
Flow Reserve ◽  
The Difference ◽  
Functional Syntax

Abstract Aims This study was aimed at investigating whether a machine learning (ML)-based coronary computed tomographic angiography (CCTA) derived fractional flow reserve (CT-FFR) SYNTAX score (SS), ‘Functional SYNTAX score’ (FSSCTA), would predict clinical outcome in patients with three-vessel coronary artery disease (CAD). Methods and results The SS based on CCTA (SSCTA) and ICA (SSICA) were retrospectively collected in 227 consecutive patients with three-vessel CAD. FSSCTA was calculated by combining the anatomical data with functional data derived from a ML-based CT-FFR assessment. The ability of each score system to predict major adverse cardiac events (MACE) was compared. The difference between revascularization strategies directed by the anatomical SS and FSSCTA was also assessed. Two hundred and twenty-seven patients were divided into two groups according to the SSCTA cut-off value of 22. After determining FSSCTA for each patient, 22.9% of patients (52/227) were reclassified to a low-risk group (FSSCTA ≤ 22). In the low- vs. intermediate-to-high (>22) FSSCTA group, MACE occurred in 3.2% (4/125) vs. 34.3% (35/102), respectively (P < 0.001). The independent predictors of MACE were FSSCTA (OR = 1.21, P = 0.001) and diabetes (OR = 2.35, P = 0.048). FSSCTA demonstrated a better predictive accuracy for MACE compared with SSCTA (AUC: 0.81 vs. 0.75, P = 0.01) and SSICA (0.81 vs. 0.75, P < 0.001). After FSSCTA was revealed, 52 patients initially referred for CABG based on SSCTA would have been changed to PCI. Conclusion Recalculating SS by incorporating lesion-specific ischaemia as determined by ML-based CT-FFR is a better predictor of MACE in patients with three-vessel CAD. Additionally, the use of FSSCTA may alter selected revascularization strategies in these patients.

scholarly journals Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2273
Author(s):  
Menelaos Kavouras ◽  
Emmanouil E. Malandrakis ◽  
Ewout Blom ◽  
Kyriaki Tsilika ◽  
Theodoros Danis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
De Novo ◽  
Close Association ◽  
Ionic Channels ◽  
Long Term Potentiation ◽  
General Term ◽  
The Difference ◽  
Common Sole

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

scholarly journals Educational Video Improves Knowledge about Outpatients’ Usage of Antibiotics in Two Public Hospitals in Indonesia

Antibiotics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 606
Author(s):  
Fauna Herawati ◽  
Rika Yulia ◽  
Bustanul Arifin ◽  
Ikhwan Frasetyo ◽  
Setiasih ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
General Hospital ◽  
Sampling Technique ◽  
Knowledge Score ◽  
Antibiotic Use ◽  
Public Hospitals ◽  
Educational Video ◽  
Inappropriate Use ◽  
Quasi Experimental ◽  
The Difference

The inappropriate use or misuse of antibiotics, particularly by outpatients, increases antibiotic resistance. A lack of public knowledge about “Responsible use of antibiotics” and “How to obtain antibiotics” is a major cause of this. This study aimed to assess the effectiveness of an educational video about antibiotics and antibiotic use to increase outpatients’ knowledge shown in two public hospitals in East Java, Indonesia. A quasi-experimental research setting was used with a one-group pre-test—post-test design, carried out from November 2018 to January 2019. The study population consisted of outpatients to whom antibiotics were prescribed. Participants were selected using a purposive sampling technique; 98 outpatients at MZ General Hospital in the S regency and 96 at SG General Hospital in the L regency were included. A questionnaire was used to measure the respondents’ knowledge, and consisted of five domains, i.e., the definition of infections and antibiotics, obtaining the antibiotics, directions for use, storage instructions, and antibiotic resistance. The knowledge test score was the total score of the Guttman scale (a dichotomous “yes” or “no” answer). To determine the significance of the difference in knowledge before and after providing the educational video and in the knowledge score between hospitals, the (paired) Student’s t-test was applied. The educational videos significantly improved outpatients’ knowledge, which increased by 41% in MZ General Hospital, and by 42% in SG General Hospital. It was concluded that an educational video provides a useful method to improve the knowledge of the outpatients regarding antibiotics.

Supine Traction Versus Prone Bending Radiographs for Assessing the Curve Flexibility in Spinal Deformity

2021 ◽  
pp. 219256822097913
Author(s):  
Niek te Hennepe ◽  
Maarten Spruit ◽  
Martin H. Pouw ◽  
Marco Hinderks ◽  
Petra Heesterbeek
Keyword(s):  
Idiopathic Scoliosis ◽  
Spinal Deformity ◽  
Retrospective Cohort ◽  
De Novo ◽  
Traction Force ◽  
Degenerative Lumbar Scoliosis ◽  
Curve Correction ◽  
Subgroup Analyses ◽  
The Difference ◽  
Side Bending

Study Design: Retrospective cohort study. Objectives: No consensus exists among surgeons on which radiologic method to prefer for the assessment of curve flexibility in spinal deformity. The objective of this study was to evaluate the difference in curve correction on supine traction radiographs versus prone side bending radiographs. Methods: A retrospective analysis of idiopathic scoliosis (IS), degenerative idiopathic scoliosis (DIS) and de novo degenerative lumbar scoliosis (DNDLS) patients was performed on supine traction as well as prone bending films (when available). Age, weight, traction force, diagnosis and Cobb angles of the primary and secondary curves were extracted. Differences in curve correction (percentages) on traction versus prone bending radiographs were analyzed for the primary and secondary curve. Subgroup analyses were performed for the 3 different diagnoses. Results: In total, 170 patients were eligible for inclusion. 43 were diagnosed with IS, 58 with DIS and 69 with DNDLS. For the primary curve, greater curve correction was obtained with bending in the DNDLS group ( P < 0.001). In the DIS group, there was a trend toward more correction on bending ( P = 0.054). In de IS group no difference was found. For the secondary curve, bending showed more curve correction in the IS and DIS group ( P = 0.002 and P <0.001). No difference was found in the DNDLS group. Conclusion: Compared to traction radiographs, bending radiographs better serve the purpose of curve flexibility assessment of IS, DIS and DNDLS spinal deformity, despite the fact that patients are exposed to more radiation.

scholarly journals Draft Genome Sequence of the Shrimp Pathogen Vibrio parahaemolyticus ST17.P5-S1, Isolated in Peninsular Malaysia

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Sridevi Devadas ◽  
Subha Bhassu ◽  
Tze Chiew Christie Soo ◽  
Fatimah M. Yusoff ◽  
Mohamed Shariff
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Vibrio Parahaemolyticus ◽  
East Coast ◽  
Draft Genome ◽  
Antibiotic Resistance Genes ◽  
Peninsular Malaysia ◽  
Penaeus Vannamei ◽  
Content Type ◽  
Acute Hepatopancreatic Necrosis Disease

We sequenced the genome of Vibrio parahaemolyticus strain ST17.P5-S1, isolated from Penaeus vannamei cultured in the east coast of Peninsular Malaysia. The strain contains several antibiotic resistance genes and a plasmid encoding the Photorhabdus insect-related (Pir) toxin-like genes, pirAvp and pirBvp, associated with acute hepatopancreatic necrosis disease (AHPND).

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