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This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact

Medicine --- Public health & preventive medicine --- microbial genomics --- whole genome sequencing --- epidemiology --- antimicrobial resistance (AMR) --- public health laboratory surveillance

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Pathogenic Escherichia coli strains cause a large number of diseases in humans, including diarrhea, hemorrhagic colitis, hemolytic uremic syndrome, urinary tract infections, and neonatal meningitis, while in animals they cause diseases such as calf scours and mastitis in cattle, post-weaning diarrhea and edema disease in pigs, and peritonitis and airsacculitis in chickens. The different E. coli pathotypes are characterized by the presence of specific sets of virulence-related genes. Therefore, it is not surprising that pathogenic E. coli constitutes a genetically heterogeneous family of bacteria, and they are continuing to evolve. Rapid and accurate molecular methods are critically needed to detect and trace pathogenic E. coli in food and animals. They are also needed for epidemiological investigations to enhance food safety, as well as animal and human health and to minimize the size and geographical extent of outbreaks. The serotype of E. coli strains has traditionally been determined using antisera raised against the >180 different O- (somatic) and 53 H- (flagellar) antigens. However, there are many problems associated with serotyping, including: it is labor-intensive and time consuming; cross reactivity of the antisera with different serogroups occurs; antisera are available only in specialized laboratories; and many strains are non-typeable. Molecular serotyping targeting O-group-specific genes within the E. coli O-antigen gene clusters and genes that are involved in encoding for the different flagellar types offers an improved approach for determining the E. coli O- and H-groups. Furthermore, molecular serotyping can be coupled with determination of specific sets of virulence genes carried by the strain offering the possibility to determine O-group, pathotype, and the pathogenic potential simultaneously. Sequencing of the O-antigen gene clusters of all of the known O-groups of E. coli is now complete, and the sequences have been deposited in the GenBank database. The sequence information has revealed that some E. coli serogroups have identical sequences while others have point mutations or insertion sequences and type as different serogroups in serological reactions. There are also a number of other ambiguities in serotyping that need to be resolved. Furthermore, new E. coli O-groups are being identified. Therefore, there is an essential need to resolve these issues and to revise the E. coli serotype nomenclature based on these findings. There are emerging technologies that can potentially be applied for molecular serotyping and detection and characterization of E. coli. On a related topic, the genome sequence of thousands of E. coli strains have been deposited in GenBank, and this information is revealing unique markers such as CRISPR (clustered regularly interspaced short palindromic repeats) and virulence gene markers that could be used to identify E. coli pathotypes. Whole genome sequencing now provides the opportunity to study the role of horizontal gene transfer in the evolution and emergence of pathogenic E. coli strains. Whole genome sequencing approaches are being investigated for genotyping and outbreak investigation for regulatory and public health needs; however, there is a need for establishing bioinformatics pipelines able to handle large amounts of data as we move toward the use of genetic approaches for non-culture-based detection and characterization of E. coli and for outbreak investigations.

whole genome sequencing --- detection --- pathogenic E. coli --- E. coli characterization --- Molecular serotyping --- Genetic Markers --- subtyping --- outbreak investigation --- Shiga toxin-producing E. coli --- virulence genes

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PacBio’s single-molecule real-time (SMRT) sequencing technology offers important advantages over the short-read DNA sequencing technologies that currently dominate the market. This includes exceptionally long read lengths (20 kb or more), unparalleled consensus accuracy, and the ability to sequence native, non-amplified DNA molecules. From fungi to insects to humans, long reads are now used to create highly accurate reference genomes by de novo assembly of genomic DNA and to obtain a comprehensive view of transcriptomes through the sequencing of full-length cDNAs. Besides reducing biases, sequencing native DNA also permits the direct measurement of DNA base modifications. Therefore, SMRT sequencing has become an attractive technology in many fields, such as agriculture, basic science, and medical research. The boundaries of SMRT sequencing are continuously being pushed by developments in bioinformatics and sample preparation. This book contains a collection of articles showcasing the latest developments and the breadth of applications enabled by SMRT sequencing technology.

n/a --- Cladobotryum protrusum --- allele-specific analysis --- low-input DNA --- full length RNAseq --- de novo genome assembly --- de novo assembly --- human reference genome --- Tricoplusia ni --- PacBio single molecule real-time sequencing --- secondary metabolite --- protein isoforms --- bone marrow cell subpopulations --- DNA methylation --- mycoparasite --- human whole-genome sequencing --- GRCh38 --- SMRT sequencing --- cytochrome P450 enzyme (CYP) --- mRNA isoforms --- next generation sequencing --- cobweb disease --- Swedish population --- mosquito --- long-read SMRT sequencing --- whole genome sequencing --- terpenoid --- insect genome --- optical mapping --- Gloeostereum incarnatum --- population sequencing --- statistical methods --- gene expression --- single molecule real-time sequencing --- PacBio

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This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact

Science: general issues --- Medical microbiology & virology --- Microbiology (non-medical) --- Methicillin resistant Staphylococcus aureus (MRSA) --- Methicillin susceptible S. aureus (MSSA) --- MRSA protracted outbreaks --- Whole-genome sequencing --- evolution --- Molecular Epidemiology --- antimicrobial resistance --- Point of Care Testing --- staphylococcal mobile genetic elements --- staphylococcal cassette chromosome mec (SCCmec)

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This compilation of articles elaborates on plant virus diseases that are among the most recent epidemiological concerns. The chapters explore several paradigms in plant virus epidemiology, outbreaks, epidemics, and pandemics paralleling zoonotic viruses and that can be consequential to global food security. There is evidence that the local, regional, national, and global trade of agricultural products has aided the global dispersal of plant virus diseases. Expanding farmlands into pristine natural areas has created opportunities for viruses in native landscapes to invade crops, while the movement of food and food products disseminates viruses, creating epidemics or pandemics. Moreover, plant virus outbreaks not only directly impact food supply, but also incidentally affect human health.

Research & information: general --- sugar beet --- rhizomania --- RNAseq --- virus --- necrovirus --- helper virus --- Aphis gossypii --- Cucumis melo --- cucurbit viruses --- disease progress curve --- insect trapping --- logistic model --- Spearman correlation --- temporal dynamics --- Bunyavirale --- RNA virus --- emerging virus --- virus evolution --- plant virus --- cophylogeny --- hallmark genes --- common bean --- Phaseolus vulgaris --- cytorhabdovirus --- whitefly --- Bemisia tabaci --- vector --- virus transmission --- ToTV --- emerging disease --- prevalence --- whole-genome sequencing --- phylogeny --- tomato torrado virus --- sGFP --- plant pathology --- infectious clone --- plant-virus interaction --- pandemics --- epidemics --- global --- disease --- threat --- food insecurity --- crop losses --- crop failure --- indigenous viruses --- introduced crops --- new encounter --- spillover --- developing countries --- domestication centers --- sub–Saharan Africa --- Potyviruses --- whole genome sequencing --- epidemiology --- virus resistance --- virus host interactions --- plant viruses --- viral vectors --- plant diseases --- virus spread --- biopharming --- vaccines --- viruses --- Nicotiana benthamiana --- COVID-19 --- plant-based biologics production --- n/a --- sub-Saharan Africa