Genomic and Transcriptomic Analysis of Bovine Pasteurella multocida Serogroup A Strain Reveals Insights Into Virulence Attenuation

Pasteurella multocida is one of the primary pathogens of bovine respiratory disease (BRD), and causes huge losses in the cattle industry. The Pm3 strain was a natural isolate, which is a strong form of pathogen and is sensitive to fluoroquinolones antibiotics. A high fluoroquinolone resistant strain, Pm64 (MIC = 64 μg/mL), was formed after continuous induction with subinhibitory concentration (1/2 MIC) of enrofloxacin, with the enhanced growth characteristics and large attenuation of pathogenicity in mice. This study reports the whole genome sequence and the transcription profile by RNA-Seq of strain Pm3/Pm64. The results showed an ineffective difference between the two strains at the genome level. However, 32 genes could be recognized in the gene islands (GIs) of Pm64, in which 24 genes were added and 8 genes were lost. Those genes are involved in DNA binding, trehalose metabolism, material transportation, capsule synthesis, prophage, amino acid metabolism, and other functions. In Pm3 strain, 558 up-regulated and 568 down-regulated genes were found compared to Pm64 strain, from which 20 virulence factor-related differentially expressed genes (DEGs) were screened. Mainly differentially transcribed genes were associated with capsular polysaccharide (CPS), lipopolysaccharide (LPS), lipooligosaccharide (LOS). Iron utilization, and biofilm composition. We speculated that the main mechanism of virulence attenuation after the formation of resistance of Pm64 comes from the change of the expression profile of these genes. This report elucidated the toxicity targets of P. multocida serogroup A which provide fundamental information toward the understanding of the pathogenic mechanism and to decreasing antimicrobial drugs resistance.

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Reduced virulence and enhanced host adaption during antibiotics therapy: A story of a within-host carbapenem-resistant Klebsiella pneumoniae sequence type 11 evolution in a fatal scrotal abscess patient

10.1101/2021.05.06.443049 ◽

2021 ◽

Author(s):

Meiping Ye ◽

Chunjie Liao ◽

Mengya Shang ◽

Danyang Zou ◽

Jingmin Yan ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Binding Site ◽

Biofilm Formation ◽

Capsular Polysaccharide ◽

Human Life ◽

Sequence Type ◽

Genomic Diversity ◽

Rna Seq ◽

Carbapenem Resistant ◽

Virulence Attenuation

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and become a major threat to human life. The sequence type (ST) 11 CRKP is a dominant clone in Asia, especially China, but how this clone evolves in vivo, then adapts to host and facilitates dissemination remain largely unknown. We analyzed the genomic dynamics of 4 ST11-CRKP isolates sequencially isolated from the urine of a patient with initial fatal scrotal abscess and finally recovered without effective medication. Genomic differences were identified and their implications for pathogenesis and host adaptation were investigated. The related transcriptional pathways were further explored by RNA-Seq. Genomic analysis identified 4-24 mutations and 94%-100% were synonymous or intergenic. The mutation rate of ST11-CRKP was 2.1×10-6-1.7×10-5 substitutions/site/year over 47 days of antibiotics therapy. During this period, CRKP underwent several adaptive changes including tigecycline resistance and virulence attenuation. Tigecycline resistance was caused by ramR ribosomal binding site (RBS) deletion, which has been described by us previously. In this study, we demonstrated that mutations associated with acyltransferase (act) and ompK26 caused the virulence attenuation of ST11-CRKP. act deletion reduced the production of capsular polysaccharide and enhanced biofilm formation. RNA-Seq analysis revealed that act influenced the expression of ldhA, bglX, mtnK and metE which likely participate in capsular synthesis and biofilm formation. ompK26 affected the virulence by its overexpression caused by the deletion of upstream repressor binding site. Our finding suggested that the broad genomic diversity, high evolutionary capacity and rapid within-host adaptability of ST11-CRKP might contribute to the worldwide dissemination of this clone.

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148 Multiple Dysregulated Novel Pathways and Genes in Aleutian Mink Disease Revealed by Selection Signatures and Gene Network Analyses Using Whole-genome Sequence Data

Journal of Animal Science ◽

10.1093/jas/skab235.137 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 76-76

Author(s):

Seyed Milad Vahedi ◽

Karim Karimi ◽

Siavash Salek Ardestani ◽

Younes Miar

Keyword(s):

Sequence Data ◽

American Mink ◽

Enrichment Analysis ◽

Whole Genome Sequence ◽

Fixation Index ◽

Pathway Enrichment Analysis ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Network Analyses ◽

Genome Level

Abstract Aleutian disease (AD) is a chronic persistent infection in domestic mink caused by Aleutian mink disease virus (AMDV). Female mink’s fertility and pelt quality depression are the main reasons for the AD’s negative economic impacts on the mink industry. A total number of 79 American mink from the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada) were classified based on the results of counter immunoelectrophoresis (CIEP) tests into two groups of positive (n = 48) and negative (n = 31). Whole-genome sequences comprising 4,176 scaffolds and 8,039,737 single nucleotide polymorphisms (SNPs) were used to trace the selection footprints for response to AMDV infection at the genome level. Window-based fixation index (Fst) and nucleotide diversity (θπ) statistics were estimated to compare positive and negative animals’ genomes. The overlapped top 1% genomic windows between two statistics were considered as potential regions underlying selection pressures. A total of 98 genomic regions harboring 33 candidate genes were detected as selective signals. Most of the identified genes were involved in the development and functions of immune system (PPP3CA, SMAP2, TNFRSF21, SKIL, and AKIRIN2), musculoskeletal system (COL9A2, PPP1R9A, ANK2, AKAP9, and STRIT1), nervous system (ASCL1, ZFP69B, SLC25A27, MCF2, and SLC7A14), reproductive system (CAMK2D, GJB7, SSMEM1, C6orf163), liver (PAH and DPYD), and lung (SLC35A1). Gene-expression network analysis showed the interactions among 27 identified genes. Moreover, pathway enrichment analysis of the constructed genes network revealed significant oxytocin (KEGG: hsa04921) and GnRH signaling (KEGG: hsa04912) pathways, which are likely to be impaired by AMDV leading to dams’ fecundity reduction. These results provided a perspective to the genetic architecture of response to AD in American mink and novel insight into the pathogenesis of AMDV.

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Reference transcriptome assembly and annotation for perennial ryegrass

Genome ◽

10.1139/gen-2017-0077 ◽

2017 ◽

Vol 60 (12) ◽

pp. 1086-1088 ◽

Cited By ~ 4

Author(s):

Hiroshi Shinozuka ◽

Noel O.I. Cogan ◽

German C. Spangenberg ◽

John W. Forster

Keyword(s):

Perennial Ryegrass ◽

Transcriptome Assembly ◽

Genotyping By Sequencing ◽

Whole Genome Sequence ◽

Grass Species ◽

Rna Seq ◽

Pasture Grass ◽

Tissue Samples ◽

Genome Sequence Assembly ◽

Transcriptome Resource

RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931 547 255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data generated a final filtered reference set of 48 713 contigs and scaffolds. The transcriptome resource will support whole genome sequence assembly, comparative genomics, implementation of genotyping-by-sequencing (GBS) methods based on transcript sampling, and identification of candidate genes for multiple biological functions.

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Development of a Rapid, Efficient, Intelligent and Cost-Saving Tool to Diagnose Pasteurella Multocida by Using Whole Genome Sequence and Genotypes of Pasteurella Multocida From Different Hosts

10.21203/rs.3.rs-104569/v1 ◽

2020 ◽

Author(s):

Zhong Peng ◽

Junyang Liu ◽

Wan Liang ◽

Fei Wang ◽

Li Wang ◽

...

Keyword(s):

Cost Saving ◽

Host Species ◽

Pasteurella Multocida ◽

Epidemiological Studies ◽

Whole Genome Sequence ◽

Clinical Settings ◽

Whole Genome ◽

Genome Sequences ◽

Host Tropism ◽

Tropism Prediction

Abstract Background: Different typing systems including capsular genotyping, lipopolysaccharide (LPS) genotyping, multilocus sequence typing (MLST), and virulence genotyping based on the detection of different virulence factor-encoding gene (VFG) profiles have been applied to characterize Pasteurella multocida strains from different host species. However, these methods require much time and effort in laboratories. Particularly, relying on one of these methods is difficult to address the biology of P. multocida from host species. Recently, we found that assigning P. multocida strains according to the combination of their capsular, LPS, and MLST genotypes (marked as capsular genotype: LPS genotype: MLST genotype) could help address the biological characteristics of P. multocida circulation in multiple hosts. However, it is still lack of a rapid, efficient, intelligent and cost-saving tool to diagnose P. multocida according to this system. Results: We have developed an intelligent genotyping and host tropism prediction tool PmGT for P. multocida strains according to their whole genome sequences by using machine learning and web 2.0 technologies. By using this tool, the capsular genotypes, LPS genotypes, and MLST genotypes as well as the main VFGs of P. multocida isolates in different host species were determined based on whole genome sequences. The results revealed a closer association between the genotypes and pasteurellosis rather than between genotypes and host species. Finally, we also used PmGT to predict the host species of P. multocida strains with the same capsular: lipopolysaccharide: MLST genotypes. Conclusions: With the advent of high-quality, inexpensive DNA sequencing, this platform represents a more efficient and cost-saving tool for P. multocida diagnosis in both epidemiological studies and clinical settings.

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Erratum for Petruzzi et al., “Capsular Polysaccharide Interferes with Biofilm Formation by Pasteurella multocida Serogroup A”

mBio ◽

10.1128/mbio.00176-18 ◽

2018 ◽

Vol 9 (1) ◽

Author(s):

Briana Petruzzi ◽

Robert E. Briggs ◽

Fred M. Tatum ◽

W. Edward Swords ◽

Cristina De Castro ◽

...

Keyword(s):

Biofilm Formation ◽

Pasteurella Multocida ◽

Capsular Polysaccharide

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Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Plants ◽

10.3390/plants9091176 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1176

Author(s):

Ivan Tsers ◽

Vladimir Gorshkov ◽

Natalia Gogoleva ◽

Olga Parfirova ◽

Olga Petrova ◽

...

Keyword(s):

Gene Expression ◽

Plant Cell Wall ◽

Soft Rot ◽

Regulatory Elements ◽

Plant Responses ◽

Gene Promoters ◽

Rna Seq ◽

Induced Plant Responses ◽

Regulatory Systems ◽

Genome Level

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular “players” in plant–Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by “missed” genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease’s development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters.

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Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress

Scientific Reports ◽

10.1038/s41598-020-78256-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Prasanta K. Subudhi ◽

Rama Shankar ◽

Mukesh Jain

Keyword(s):

Salt Tolerance ◽

Dna Polymorphisms ◽

Whole Genome Sequence ◽

Whole Genome ◽

Salt Tolerant ◽

Tolerance Mechanisms ◽

Rice Varieties ◽

Genome Wide ◽

Rice Genotypes ◽

Genome Level

AbstractSalinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

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Modulation of Pasteurella multocida capsular polysaccharide during growth under ironrestricted conditions and in vivo

Microbiology ◽

10.1099/13500872-140-2-263 ◽

1994 ◽

Vol 140 (2) ◽

pp. 263-270 ◽

Cited By ~ 23

Author(s):

M. Jacques ◽

M. Belanger ◽

M. S. Diarra ◽

M. Dargis ◽

F. Malouin

Keyword(s):

Pasteurella Multocida ◽

Capsular Polysaccharide

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USA300 and USA500 Clonal Lineages of Staphylococcus aureus Do Not Produce a Capsular Polysaccharide Due to Conserved Mutations in the cap5 Locus

mBio ◽

10.1128/mbio.02585-14 ◽

2015 ◽

Vol 6 (2) ◽

Cited By ~ 42

Author(s):

Susan Boyle-Vavra ◽

Xue Li ◽

Md Tauqeer Alam ◽

Timothy D. Read ◽

Julia Sieth ◽

...

Keyword(s):

United States ◽

Staphylococcus Aureus ◽

Capsular Polysaccharide ◽

The United States ◽

Whole Genome Sequence ◽

Content Type ◽

Capsule Production ◽

Usa300 Strain

ABSTRACTThe surface capsular polysaccharide (CP) is a virulence factor that has been used as an antigen in several successful vaccines against bacterial pathogens. A vaccine has not yet been licensed againstStaphylococcus aureus, although two multicomponent vaccines that contain CP antigens are in clinical trials. In this study, we evaluated CP production in USA300 methicillin-resistantS. aureus(MRSA) isolates that have become the predominant community-associated MRSA clones in the United States. We found that all 167 USA300 MRSA and 50 USA300 methicillin-susceptibleS. aureus(MSSA) isolates were CP negative (CP−). Moreover, all 16 USA500 isolates, which have been postulated to be the progenitor lineage of USA300, were also CP−. Whole-genome sequence analysis of 146 CP−USA300 MRSA isolates revealed they all carry acap5locus with 4 conserved mutations compared with strain Newman. Genetic complementation experiments revealed that three of these mutations (in thecap5promoter,cap5Dnucleotide 994, andcap5Enucleotide 223) ablated CP production in USA300 and that Cap5E75 Asp, located in the coenzyme-binding domain, is essential for capsule production. All but three USA300 MSSA isolates had the same fourcap5mutations found in USA300 MRSA isolates. Most isolates with a USA500 pulsotype carried three of these four USA300-specific mutations, suggesting the fourth mutation occurred in the USA300 lineage. Phylogenetic analysis of thecaploci of our USA300 isolates as well as publicly available genomes from 41 other sequence types revealed that the USA300-specificcap5mutations arose sequentially inS. aureusin a common ancestor of USA300 and USA500 isolates.IMPORTANCEThe USA300 MRSA clone emerged as a community-associated pathogen in the United States nearly 20 years ago. Since then, it has rapidly disseminated and now causes health care-associated infections. This study shows that the CP-negative (CP−) phenotype has persisted among USA300 isolates and is a universal and characteristic trait of this highly successful MRSA lineage. It is important to note that a vaccine consisting solely of CP antigens would not likely demonstrate high efficacy in the U.S. population, where about half of MRSA isolates comprise USA300. Moreover, conversion of a USA300 strain to a CP-positive (CP+) phenotype is unlikelyin vivoorin vitrosince it would require the reversion of 3 mutations. We have also established that USA300 MSSA isolates and USA500 isolates are CP−and provide new insight into the evolution of the USA300 and USA500 lineages.

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Genome sequencing of the multicellular alga Astrephomene provides insights into convergent evolution of germ-soma differentiation

Scientific Reports ◽

10.1038/s41598-021-01521-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shota Yamashita ◽

Kayoko Yamamoto ◽

Ryo Matsuzaki ◽

Shigekatsu Suzuki ◽

Haruyo Yamaguchi ◽

...

Keyword(s):

Genome Sequence ◽

Convergent Evolution ◽

Tandem Duplication ◽

De Novo ◽

Molecular Genetic ◽

Somatic Cells ◽

Whole Genome Sequence ◽

Rna Seq ◽

Genome Data ◽

Genes Encoding

AbstractGerm-soma differentiation evolved independently in many eukaryotic lineages and contributed to complex multicellular organizations. However, the molecular genetic bases of such convergent evolution remain unresolved. Two multicellular volvocine green algae, Volvox and Astrephomene, exhibit convergent evolution of germ-soma differentiation. The complete genome sequence is now available for Volvox, while genome information is scarce for Astrephomene. Here, we generated the de novo whole genome sequence of Astrephomene gubernaculifera and conducted RNA-seq analysis of isolated somatic and reproductive cells. In Volvox, tandem duplication and neofunctionalization of the ancestral transcription factor gene (RLS1/rlsD) might have led to the evolution of regA, the master regulator for Volvox germ-soma differentiation. However, our genome data demonstrated that Astrephomene has not undergone tandem duplication of the RLS1/rlsD homolog or acquisition of a regA-like gene. Our RNA-seq analysis revealed the downregulation of photosynthetic and anabolic gene expression in Astrephomene somatic cells, as in Volvox. Among genes with high expression in somatic cells of Astrephomene, we identified three genes encoding putative transcription factors, which may regulate somatic cell differentiation. Thus, the convergent evolution of germ-soma differentiation in the volvocine algae may have occurred by the acquisition of different regulatory circuits that generate a similar division of labor.

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