scholarly journals Genomic analysis of high copy-number sequences for the targeted detection of Listeria species using a flow-through surveillance system

2021 ◽  
Author(s):  
Beatriz Quiñones ◽  
Jaszemyn C. Yambao ◽  
Veronica S. De Guzman ◽  
Bertram G. Lee ◽  
David L. Medin
Keyword(s):  
Foodborne Pathogen ◽  
Genomic Analysis ◽  
Dna Aptamer ◽  
Comparative Genomic ◽  
Number Sequences ◽  
Flow Through ◽  
Genomic Regions ◽  
Mechanical Lysis ◽  
Targeted Detection ◽  
Validation Experiments

AbstractThe bacterial foodborne pathogen Listeria monocytogenes has been implicated in fresh produce outbreaks with a significant economic impact. Given that L. monocytogenes is widespread in the environment, food production facilities constantly monitor for the presence of Listeria species. To develop a surveillance platform for food processing facilities, this study conducted a comparative genomic analysis for the identification of conserved high copy sequences in the ribosomal RNA of Listeria species. Simulated folding was performed to assess RNA accessibility in the identified genomic regions targeted for detection, and the developed singleplex assay accurately detected cell amounts lower than 5 cells, while no signals were detected for non-targeted bacteria. The singleplex assay was subsequently tested with a flow-through system, consisting of a DNA aptamer-capture step, followed by sample concentration and mechanical lysis for the detection of Listeria species. Validation experiments indicated the continuous flow-through system accurately detected Listeria species at low cell concentrations.

scholarly journals Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus

2020 ◽  
Vol 8 (3) ◽  
pp. 366
Author(s):  
Jarred Yasuhara-Bell ◽  
Mohammad Arif ◽  
Grethel Y. Busot ◽  
Rachel Mann ◽  
Brendan Rodoni ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
The United States ◽  
Grass Species ◽  
Comparative Genomic ◽  
Underrepresented Populations ◽  
System A ◽  
Genome Wide ◽  
The Family ◽  
Study Support ◽  
Genomic Regions

Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.

scholarly journals A database for risk assessment and comparative genomic analysis of foodborne Vibrio parahaemolyticus in China

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Rui Pang ◽  
Yanping Li ◽  
Moutong Chen ◽  
Haiyan Zeng ◽  
Tao Lei ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Foodborne Pathogens ◽  
Vibrio Parahaemolyticus ◽  
Foodborne Pathogen ◽  
Genomic Analysis ◽  
Food Samples ◽  
Comparative Genomic ◽  
Genome Database ◽  
Scientific Database ◽  
Need To Evaluate

Abstract Vibrio parahaemolyticus is a major foodborne pathogen worldwide. The increasing number of cases of V. parahaemolyticus infections in China indicates an urgent need to evaluate the prevalence and genetic diversity of this pathogenic bacterium. In this paper, we introduce the Foodborne Vibrio parahaemolyticus genome database (FVPGD), the first scientific database of foodborne V. parahaemolyticus distribution and genomic data in China, based on our previous investigations of V. parahaemolyticus contamination in different kinds of food samples across China from 2011 to 2016. The dataset includes records of 2,499 food samples and 643 V. parahaemolyticus strains from supermarkets and marketplaces distributed over 39 cities in China; 268 whole-genome sequences have been deposited in this database. A spatial view on the risk situations of V. parahaemolyticus contamination in different food types is provided. Additionally, the database provides a functional interface of sequence BLAST, core genome multilocus sequence typing, and phylogenetic analysis. The database will become a powerful tool for risk assessment and outbreak investigations of foodborne pathogens in China.

scholarly journals A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence

2020 ◽  
Vol 33 (2) ◽  
pp. 173-188 ◽  
Author(s):  
Nathan A. Wyatt ◽  
Jonathan K. Richards ◽  
Robert S. Brueggeman ◽  
Timothy L. Friesen
Keyword(s):  
Genomic Analysis ◽  
Effector Proteins ◽  
Comparative Genomic ◽  
Pyrenophora Teres ◽  
Structural Variations ◽  
Evolution Of Virulence ◽  
Reference Quality ◽  
Genomic Characterization ◽  
Genomic Regions ◽  
Subtelomeric Regions

Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high-quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison, resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes, examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions, consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in subtelomeric regions of chromosomes, with 10 of the 14 accessory region QTL localizing to subtelomeric regions. Comparative analysis of the subtelomeric regions of P. teres f. teres chromosomes revealed translocation events in which homology was detected between nonhomologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the subtelomeric accessory genomic compartments not only harbor most of the known virulence loci but, also, that these regions have the capacity to rapidly evolve.

scholarly journals A comparative genomic analysis of the barley pathogen Pyrenophora teres f. teres identifies sub-telomeric regions as drivers of virulence

2019 ◽  
Author(s):  
Nathan A. Wyatt ◽  
Jonathan K. Richards ◽  
Robert S. Brueggeman ◽  
Timothy L. Friesen
Keyword(s):  
Genomic Analysis ◽  
Effector Proteins ◽  
Comparative Genomic ◽  
Pyrenophora Teres ◽  
Structural Variations ◽  
Evolution Of Virulence ◽  
Reference Quality ◽  
Genomic Characterization ◽  
Genomic Regions

AbstractPyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in sub-telomeric regions of chromosomes with 10 of the 14 accessory region QTL localizing to sub-telomeric regions. Comparative analysis of the sub-telomeric regions of P. teres f. teres chromosomes revealed translocation events where homology was detected between non-homologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the sub-telomeric accessory genomic compartments not only harbor most of the known virulence loci, but also that these regions have the capacity to rapidly evolve.

scholarly journals Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs

2019 ◽  
Author(s):  
Rachel C. Williams ◽  
Marina B. Blanco ◽  
Jelmer W. Poelstra ◽  
Kelsie E. Hunnicutt ◽  
Aaron A. Comeault ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genomic Analysis ◽  
Population Level ◽  
Comparative Genomic ◽  
Effective Population ◽  
High Coverage ◽  
Genome Wide ◽  
Conservation Concern ◽  
Genomic Regions ◽  
Dwarf Lemur

AbstractMadagascar’s biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar’s dwarf lemurs (genus Cheirogaleus), the only obligate hibernating primate. We here apply comparative genomic approaches to generate the first genome-wide estimates of genetic diversity within dwarf lemurs. We generate a reference genome for the fat-tailed dwarf lemur, Cheirogaleus medius, and use this resource to facilitate analyses of high-coverage (~30x) genome sequences for wild-caught individuals representing species: C. sp. cf. medius, C. major, C. crossleyi and C. sibreei. This study represents the largest contribution to date of novel genomic resources for Madagascar’s lemurs. We find concordant phylogenetic relationships among the four lineages of Cheirogaleus across most of the genome, and yet detect a number of discordant genomic regions consistent with ancient admixture. We hypothesized that these regions could have resulted from adaptive introgression related to hibernation, indeed finding that genes associated with hibernation are present, though most significantly, that gene ontology categories relating to transcription are over-represented. We estimate levels of heterozygosity and find particularly low levels in an individual sampled from an isolated population of C. medius that we refer to as C. sp. cf. medius. Results are consistent with a recent decline in effective population size, which is evident across species. Our study highlights the power of comparative genomic analysis for identifying species and populations of conservation concern, as well as for illuminating possible mechanisms of adaptive phenotypic evolution.

Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis

2007 ◽  
Vol 32 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Daisuke Ikeda ◽  
Yosuke Ono ◽  
Phil Snell ◽  
Yvonne J. K. Edwards ◽  
Greg Elgar ◽  
...  
Keyword(s):  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Genomic Analysis ◽  
Divergent Evolution ◽  
Comparative Genomic ◽  
Chain Gene ◽  
Takifugu Rubripes ◽  
Genome Database ◽  
Genomic Regions ◽  
Syntenic Analysis

Myosin heavy chain genes ( MYHs) are the most important functional domains of myosins, which are highly conserved throughout evolution. The human genome contains 15 MYHs, whereas the corresponding number in teleost appears to be much higher. Although teleosts comprise more than one-half of all vertebrate species, our knowledge of MYHs in teleosts is rather limited. A comprehensive analysis of the torafugu ( Takifugu rubripes) genome database enabled us to detect at least 28 MYHs, almost twice as many as in humans. RT-PCR revealed that at least 16 torafugu MYH representatives (5 fast skeletal, 3 cardiac, 2 slow skeletal, 1 superfast, 2 smooth, and 3 nonmuscle types) are actually transcribed. Among these, MYH M743-2 and MYH M5 of fast and slow skeletal types, respectively, are expressed during development of torafugu embryos. Syntenic analysis reveals that torafugu fast skeletal MYHs are distributed across five genomic regions, three of which form clusters. Interestingly, while human fast skeletal MYHs form one cluster, its syntenic region in torafugu is duplicated, although each locus contains just a single MYH in torafugu. The results of the syntenic analysis were further confirmed by corresponding analysis of MYHs based on databases from Tetraodon, zebrafish, and medaka genomes. Phylogenetic analysis suggests that fast skeletal MYHs evolved independently in teleosts and tetrapods after fast skeletal MYHs had diverged from four ancestral MYHs.

scholarly journals A Comparative Genomic Analysis of Diverse Clonal Types of EnterotoxigenicEscherichia coliReveals Pathovar-Specific Conservation

2010 ◽  
Vol 79 (2) ◽  
pp. 950-960 ◽  
Author(s):  
Jason W. Sahl ◽  
Hans Steinsland ◽  
Julia C. Redman ◽  
Samuel V. Angiuoli ◽  
James P. Nataro ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Middle Income ◽  
E Coli ◽  
Colonization Factor ◽  
Genomic Core ◽  
Genomic Regions

ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of theE. colirelationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETECE. coligenomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.

scholarly journals Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yoshitaka Tateishi ◽  
Yuriko Ozeki ◽  
Akihito Nishiyama ◽  
Mari Miki ◽  
Ryoji Maekura ◽  
...  
Keyword(s):  
Complex Disease ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Mycobacterium Intracellulare ◽  
Clinical Strains ◽  
Genetic Components ◽  
Genomic Regions ◽  
Insight Into

Abstract Background Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. Results In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. Conclusions Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.

scholarly journals Molecular Prediction of the O157:H-Negative Phenotype Prevalent in Australian Shiga Toxin-ProducingEscherichia coliCases Improves Concordance ofIn SilicoSerotyping with Phenotypic Motility

2018 ◽  
Vol 56 (4) ◽  
Author(s):  
Alexander P. Pintara ◽  
Christine J. D. Guglielmino ◽  
Irani U. Rathnayake ◽  
Flavia Huygens ◽  
Amy V. Jennison
Keyword(s):  
Shiga Toxin ◽  
In Silico ◽  
Antigen Processing ◽  
Severe Disease ◽  
Foodborne Pathogen ◽  
Genomic Analysis ◽  
Epidemiological Surveillance ◽  
Comparative Genomic ◽  
Content Type ◽  
Negative Phenotype

ABSTRACTShiga toxin-producingEscherichia coli(STEC) is a foodborne pathogen, and serotype O157:H7 is typically associated with severe disease. Australia is unique in its STEC epidemiology, as severe cases are typically associated with non-O157 serogroups, and locally acquired O157 isolates are H-negative/nonmotile. The H-negative phenotype and reduced severity of disease compared to that associated with H7/motile strains are distinct features of Australian O157 strains, but the molecular mechanism behind this phenotype has not been reported. Accurate characterization of the H-negative phenotype is important in epidemiological surveillance of STEC. Serotyping is moving away from phenotype-based methods, as next generation sequencing allows rapid extrapolation of serotype throughin silicodetection of the O-antigen processing genes,wzx,wzy,wzm, andwzt, and the H-antigen gene,fliC. The detection and genotyping offliCalone is unable to determine the motility of the strain. Typically, most Australian O157:H-negative strains carry an H7 genotype yet phenotypically are nonmotile; thus, many are mischaracterized as H7 strains byin silicoserotyping tools. Comparative genomic analysis of flagellar genes between Australian and international isolates was performed and an insertion at nucleotide (nt) 125 in theflgFgene was identified in H-negative isolates. Chi-square results showed that this insertion was significantly associated with the H-negative phenotype (P< 0.0001). Phylogenetic analysis was also completed and showed that the Australian H-negative isolates with the insertion inflgFrepresent a clade within the O157 serogroup, distinct from O157:H7 serotypes. This study provides a genetic target for inferring the nonmotile phenotype of Australian O157 STEC, which increases the predictive value ofin silicoserotyping.

scholarly journals Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation

2011 ◽  
Vol 77 (20) ◽  
pp. 7418-7424 ◽  
Author(s):  
Jaejoon Jung ◽  
Eugene L. Madsen ◽  
Che Ok Jeon ◽  
Woojun Park
Keyword(s):  
Metabolic Pathways ◽  
Genomic Analysis ◽  
Metal Resistance ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Content Type ◽  
Large Size ◽  
Genomic Regions ◽  
Reading Frames

ABSTRACTThe comparative genomics ofAcinetobacter oleivoransDR1 assayed withA. baylyiADP1,A. calcoaceticusPHEA-2, andA. baumanniiATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of thenagIgene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution ofAcinetobacterspecies.

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