scholarly journals Whole Genome Analysis Detects the Emergence of a Single Salmonella enterica Serovar Chester Clone in Japan’s Kanto Region

2021 ◽  
Vol 12 ◽  
Author(s):  
Naoshi Ando ◽  
Tsuyoshi Sekizuka ◽  
Eiji Yokoyama ◽  
Yoshiyuki Aihara ◽  
Noriko Konishi ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Selection Pressure ◽  
Minimum Spanning Tree ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Whole Genome Analysis ◽  
Japanese Strain ◽  
Contaminated Food ◽  
Geographical Distances ◽  
Kanto Region

In Japan’s Kanto region, the number of Salmonella enterica serovar Chester infections increased temporarily between 2014 and 2016. Concurrently with this temporal increase in the Kanto region, S. Chester isolates belonging to one clonal group were causing repetitive outbreaks in Europe. A recent study reported that the European outbreaks were associated with travelers who had been exposed to contaminated food in Morocco, possibly seafood. Because Japan imports a large amount of seafood from Morocco, we aimed to establish whether the temporal increase in S. Chester infections in the Kanto region was associated with imported Moroccan seafood. Short sequence reads from the whole-genome sequencing of 47 S. Chester isolates from people in the Kanto region (2014–2016), and the additional genome sequences from 58 isolates from the European outbreaks, were analyzed. The reads were compared with the complete genome sequence from a S. Chester reference strain, and 347 single nucleotide polymorphisms (SNPs) were identified. These SNPs were used in this study. Cluster and Bayesian cluster analyses showed that the Japanese and European isolates fell into two different clusters. Therefore, ΦPT and IAS values were calculated to evaluate genetic differences between these clusters. The results revealed that the Japanese and European isolates were genetically distinct populations. Our root-to-tip analysis showed that the Japanese isolates originating from one clone had accumulated mutations, suggesting that an emergence of this organism occurred. A minimum spanning tree analysis demonstrated no correlation between genetic and geographical distances in the Japanese isolates, suggesting that the emergence of the serovar in the Kanto region did not involve person-to-person contact; rather, it occurred through food consumption. The dN/dS ratio indicated that the Japanese strain has evolved under positive selection pressure. Generally, a population of bacterial clones in a reservoir faces negative selection pressure. Therefore, the Japanese strain must have existed outside of any reservoir during its emergence. In conclusion, S. Chester isolates originating from one clone probably emerged in the Kanto region via the consumption of contaminated foods other than imported Moroccan seafood. The emerging strain may have not established a reservoir for survival in the food supply chain resulting in its disappearance after 2017.

scholarly journals Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Indiana C629, a Carbapenem-Resistant Bacterium Isolated from Chicken Carcass in China

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Wei Wang ◽  
Feng Liu ◽  
Zixin Peng ◽  
Fengqin Li ◽  
Aiguo Ma
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
Carbapenem Resistance ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Carbapenem Resistant ◽  
Chicken Carcass ◽  
Plasmid Genes

The carbapenem-resistant Salmonella enterica subsp. enterica serovar Indiana strain C629 was isolated from a chicken carcass collected from a slaughterhouse in Qingdao, China. The complete genome sequence of C629 contains a circular 4,791,723-bp chromosome and a circular 210,106-bp plasmid. Genes involved in carbapenem resistance of this bacterium were identified by whole-genome analysis.

scholarly journals Whole Genome Analysis of a Single Scottish Deerhound Dog Family Provides Independent Corroboration That a SGK3 Coding Variant Leads to Hairlessness

2019 ◽  
Vol 10 (1) ◽  
pp. 293-297 ◽  
Author(s):  
Heidi G. Parker ◽  
D. Thad Whitaker ◽  
Alexander C. Harris ◽  
Elaine A. Ostrander
Keyword(s):  
Domestic Dog ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Canis Lupus Familiaris ◽  
Coding Region ◽  
Whole Genome Analysis ◽  
Mixed Litter ◽  
Single Base Pair ◽  
Sparse Hair ◽  
Gene Expression Levels

The breeds of domestic dog, Canis lupus familiaris, display a range of coat types with variation in color, texture, length, curl, and growth pattern. One trait of interest is that of partial or full hairlessness, which is found in a small number of breeds. While the standard for some breeds, such as the Xoloitzcuintli, requires sparse hair on their extremities, others are entirely bald, including the American Hairless Terrier. We identified a small, rare family of Scottish Deerhounds in which coated parents produced a mixed litter of coated and hairless offspring. To identify the underlying variant, we performed whole genome sequencing of the dam and five offspring, comparing single nucleotide polymorphisms and small insertions/deletions against an established catalog of 91 million canine variants. Of 325 homozygous alternative alleles found in both hairless dogs, 56 displayed the expected pattern of segregation and only a single, high impact variant within a coding region was observed: a single base pair insertion in exon two of SGK3 leading to a potential frameshift, thus verifying recently published findings. In addition, we observed that gene expression levels between coated and hairless dogs are similar, suggesting a mechanism other than non-sense mediated decay is responsible for the phenotype.

scholarly journals Salmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa

2017 ◽  
Author(s):  
Philip M. Ashton ◽  
Sian V. Owen ◽  
Lukeki Kaindama ◽  
Will P. M. Rowe ◽  
Chris Lane ◽  
...  
Keyword(s):  
Public Health ◽  
Salmonella Enterica ◽  
Selection Pressure ◽  
Invasive Disease ◽  
Sequence Type ◽  
Whole Genome ◽  
Serovar Typhimurium ◽  
Lineage 2 ◽  
Sub Saharan ◽  
The Uk

AbstractThe ST313 sequence type of Salmonella enterica serovar Typhimurium causes invasive non-typhoidal salmonellosis amongst immunocompromised people in sub-Saharan Africa (sSA). Previously, two distinct phylogenetic lineages of ST313 have been described which have rarely been found outside sSA. Following the introduction of routine whole genome sequencing of Salmonella enterica by Public Health England in 2014, we have discovered that 2.7% (79/2888) of S. Typhimurium from patients in England and Wales are ST313. Of these isolates, 59/72 originated from stool and 13/72 were from extra-intestinal sites. The isolation of ST313 from extra-intestinal sites was significantly associated with travel to Africa (OR 12 [95% CI: 3,53]). Phylogenetic analysis revealed previously unsampled diversity of ST313, and distinguished UK-linked isolates causing gastroenteritis from African-associated isolates causing invasive disease. Bayesian evolutionary investigation suggested that the two African lineages diverged from their most recent common ancestors independently, circa 1796 and 1903. The majority of genome degradation of African ST313 lineage 2 is conserved in the UK ST313 lineages and only 10/44 pseudogenes were lineage 2-specific. The African lineages carried a characteristic prophage and antibiotic resistance gene repertoire, suggesting a strong selection pressure for these horizontally-acquired genetic elements in the sSA setting. We identified an ST313 isolate associated with travel to Kenya that carried a chromosomally-located blaCTX-M-15, demonstrating the continual evolution of this sequence type in Africa in response to selection pressure exerted by antibiotic usage.The S. Typhimurium ST313 sequence type has been primarily associated with invasive disease in Africa. Here, we highlight the power of routine whole-genome-sequencing by public health agencies to make epidemiologically-significant deductions that would be missed by conventional microbiological methods. The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. We speculate that the niche specialization of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.

scholarly journals Whole genome analysis of four Bangladeshi individuals

2020 ◽  
Author(s):  
Salim Khan ◽  
Shahina Akter ◽  
Barna Goswami ◽  
Ahashan Habib ◽  
Tanjina Akhtar Banu ◽  
...  
Keyword(s):  
Pilot Study ◽  
Cardiovascular Diseases ◽  
Genome Sequencing ◽  
Biological Pathways ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide Variants ◽  
Whole Genome Analysis ◽  
Single Nucleotide ◽  
Comprehensive Method

AbstractWhole-genome sequencing (WGS) is a comprehensive method for analysing entire genomes and this has been instrumental in characterizing the single nucleotide polymorphisms associated with different diseases including cancer, diabetes, cardiovascular diseases and many others. In this paper we undertake a pilot study for sequencing four Bangladeshi individuals and profiling their single nucleotide variants. Our findings shed possible light on specific biological pathways effected by such variants in this population.

Changes detected in the genome sequences of Escherichia coli, Listeria monocytogenes, Vibrio parahaemolyticus, and Salmonella enterica after serial subculturing

2019 ◽  
Vol 65 (11) ◽  
pp. 842-850
Author(s):  
Nicholas Petronella ◽  
Palni Kundra ◽  
Olivia Auclair ◽  
Karine Hébert ◽  
Mary Rao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Listeria Monocytogenes ◽  
Foodborne Pathogens ◽  
Salmonella Enterica ◽  
Vibrio Parahaemolyticus ◽  
Molecular Techniques ◽  
Genomic Variation ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genomic Changes

Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS is significantly higher than that offered by other molecular techniques, and WGS readily allows infrequent differences that occur between 2 closely related strains to be found. In this investigation, WGS was used to identify the changes that occurred in the genomes of 13 strains of bacterial foodborne pathogens after 100 serial subcultures. Pure cultures of Shiga-toxin-producing Escherichia coli, Salmonella enterica, Listeria monocytogenes, and Vibrio parahaemolyticus were subcultured daily for 100 successive days. The 1st and 100th subcultures were whole-genome sequenced using short-read sequencing. Single nucleotide polymorphisms (SNPs) were identified between the 1st and final culture using 2 different approaches, and multilocus sequence typing of the whole genome was also performed to detect any changes at the allelic level. The number of observed genomic changes varied by strain, species, and the SNP caller used. This study provides insight into the genomic variation that can be detected using next-generation sequencing and analysis methods after repeated subculturing of 4 important bacterial pathogens.

scholarly journals Role of SNPs in the Biogenesis of Mature miRNAs

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Ying Wang ◽  
Jidong Ru ◽  
Xianglian Meng ◽  
Jianhua Song ◽  
Qingfeng Jiang ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Mature Mirnas ◽  
Mirna Biogenesis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Sequence Alignments ◽  
Whole Genome Analysis ◽  
Functional Snps ◽  
Mirna Sequencing

Single nucleotide polymorphisms (SNPs) play a significant role in microRNA (miRNA) generation, processing, and function and contribute to multiple phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect miRNA maturation mechanisms is important for precision medicine. The present study established an SNP-associated pre-miRNA (SNP-pre-miRNA) database, named miRSNPBase, and constructed SNP-pre-miRNA sequences. We also identified phenotypes and disease biomarker-associated isoform miRNA (isomiR) based on miRFind, which was developed in our previous study. We identified functional SNPs and isomiRs. We analyzed the biological characteristics of functional SNPs and isomiRs and studied their distribution in different ethnic groups using whole-genome analysis. Notably, we used individuals from Great Britain (GBR) as examples and identified isomiRs and isomiR-associated SNPs (iso-SNPs). We performed sequence alignments of isomiRs and miRNA sequencing data to verify the identified isomiRs and further revealed GBR ethnographic epigenetic dominant biomarkers. The SNP-pre-miRNA database consisted of 886 pre-miRNAs and 2640 SNPs. We analyzed the effects of SNP type, SNP location, and SNP-mediated free energy change during mature miRNA biogenesis and found that these factors were closely associated to mature miRNA biogenesis. Remarkably, 158 isomiRs were verified in the miRNA sequencing data for the 18 GBR samples. Our results indicated that SNPs affected the mature miRNA processing mechanism and contributed to the production of isomiRs. This mechanism may have important significance for epigenetic changes and diseases.

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