A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing

2014 ◽  
Vol 21 ◽  
pp. 54-57 ◽  
Author(s):  
Vartul Sangal ◽  
Andreas Burkovski ◽  
Alison C. Hunt ◽  
Becky Edwards ◽  
Jochen Blom ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Basis ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome

scholarly journals Whole-genome sequencing to investigate a possible genetic basis of perosomus elumbis in a calf resulting from a consanguineous mating

2021 ◽  
Vol 5 (Supplement_S1) ◽  
pp. S1-S5
Author(s):  
Alexa M Barber ◽  
Alyssa Helms ◽  
Riley Thompson ◽  
Brian K Whitlock ◽  
David J Steffen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Basis ◽  
Whole Genome

scholarly journals Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

2019 ◽  
Vol 24 (2) ◽  
Author(s):  
Anja Berger ◽  
Alexandra Dangel ◽  
Tilmann Schober ◽  
Birgit Schmidbauer ◽  
Regina Konrad ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome ◽  
Next Generation ◽  
Insect Bites ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

scholarly journals Whole-Genome Sequencing Uncovers the Genetic Basis of Chronic Mountain Sickness in Andean Highlanders

2013 ◽  
Vol 93 (3) ◽  
pp. 452-462 ◽  
Author(s):  
Dan Zhou ◽  
Nitin Udpa ◽  
Roy Ronen ◽  
Tsering Stobdan ◽  
Junbin Liang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Basis ◽  
Whole Genome ◽  
Chronic Mountain Sickness ◽  
Mountain Sickness

scholarly journals Assessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011-2019

2020 ◽  
Author(s):  
Justine Schaeffer ◽  
Steliana Huhulescu ◽  
Anna Stoeger ◽  
Franz Allerberger ◽  
Werner Ruppitsch
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Diphtheria Toxin ◽  
Corynebacterium Diphtheriae ◽  
Toxin Gene ◽  
Whole Genome ◽  
Skin Infections ◽  
Antimicrobial Resistance Genes

Background: Diphtheria is a vaccine preventable disease with a high potential for re-emergence. One of its causative agent is Corynebacterium diphtheriae, some strains producing the diphtheria toxin. From 2011 to 2019, 57 clinical C. diphtheriae strains were isolated in Austria, either from the respiratory track or from skin infections. Objectives: The aim of the study was to investigate the genetic diversity of these C. diphtheriae isolates using whole genome sequencing. Methods: Isolates were characterized by genome wide comparison using single nucleotide polymorphism or core genome multilocus sequence typing, and by searching sequence data for antimicrobial resistance genes and genes involved in diphtheria toxin production. Results: Genetic diversity between the isolates was high, with no clear distribution over time or place. C. belfantii isolates were separated from other strains, and were strongly associated with respiratory infections (OR = 57). Two clusters, limited in time and space, were identified. Almost 40% of strains carried resistance genes against tetracycline or sulfonamides, mostly from skin infections. Microbiological tests showed that 55% of isolates were resistant to penicillin, but did not carry genes conferring β-lactam resistance. Diphtheria toxin gene with no non-synonymous mutation was found in three isolates only. Conclusion: This study showed that sequencing can provide valuable information complementing routine microbiological and epidemiological investigations. It allowed us to identify unknown clusters, evaluate antimicrobial resistances more broadly and support toxigenicity results obtained by PCR. For these reasons, C. diphtheriae surveillance could strongly benefit from the routine implementation of whole genome sequencing.

scholarly journals Defining the genetic basis of early onset hereditary spastic paraplegia using whole genome sequencing

Neurogenetics ◽  
2016 ◽  
Vol 17 (4) ◽  
pp. 265-270 ◽  
Author(s):  
Kishore R Kumar ◽  
G.M. Wali ◽  
Mahesh Kamate ◽  
Gautam Wali ◽  
André E Minoche ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Hereditary Spastic Paraplegia ◽  
Early Onset ◽  
Genetic Basis ◽  
Whole Genome ◽  
Spastic Paraplegia

scholarly journals Genetic Basis of Pancreas Cancer Development and Progression: Insights from Whole-Exome and Whole-Genome Sequencing

2012 ◽  
Vol 18 (16) ◽  
pp. 4257-4265 ◽  
Author(s):  
Christine A. Iacobuzio-Donahue ◽  
Victor E. Velculescu ◽  
Christopher L. Wolfgang ◽  
Ralph H. Hruban
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Basis ◽  
Pancreas Cancer ◽  
Cancer Development ◽  
Whole Genome ◽  
Whole Exome

scholarly journals Analisis Gen Tox Corynebacterium Diphtheriae Penyebab Difteri di Beberapa Wilayah Indonesia

2021 ◽  
Vol 49 (1) ◽  
pp. 63-70
Author(s):  
Dwi Febriyana ◽  
Sunarno Sunarno ◽  
Yudi Hartoyo ◽  
Sundari Nursofiah ◽  
Tati Febrianti ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dna Sequences ◽  
Agar Medium ◽  
Corynebacterium Diphtheriae ◽  
Silent Mutation ◽  
Data Conversion ◽  
Whole Genome ◽  
Gene Sequences ◽  
Mutation Site

Diphtheria is a vaccine-preventable disease. The clinical features and complications of diphtheria are associated with toxins produced by the causative bacteria. Diphtheria toxin synthesis is encoded by tox gene. This study aimed to provide an overview of the DNA sequences of the tox gene of Corynebacterium diphtheriae causing diphtheria in several region of Indonesia. A total of 65 Corynebacterium diphtheriae isolated from several provinces in Indonesia (2010-2017) were used as samples. Isolates recultured on blood agar medium (BA), incubated at 37 0 C overnight. DNA extraction conducted using the QiaAmp DNA Mini Kit. The DNA sequencing was carried out using the Whole Genome Sequencing (WGS) approach. The data conversion and analysis conducted using U-gene and BioEdit programs. Examination of 65 isolate C. diphtheriae with 1683 bp of tox gene sequences showed that there are 3 patterns of gene sequences with 3 mutation site. All mutations were silent mutation. The mutation sites were also not commonly used as 3’end binding site of the PCR primer. We concluded that tox gene of C. diphtheriae that causes diphtheria in some provinces in Indonesia have limited variations and these variations do not encode amino acid changes. This indicates that the vaccines used in Indonesia are still in accordance with the variations in circulating bacteria and PCR can be used for screening and predicting the toxigenicity of diphtheria-causing bacteria. Keywords: C. diphtheriae, gene tox, diphtheria, Indonesia Abstrak Difteri merupakan salah satu penyakit yang dapat dicegah dengan imunisasi (PD3I). Gambaran klinis dan komplikasi difteri dikaitkan dengan toksin yang diproduksi oleh bakteri penyebab. Sintesis toksin difteri dikode oleh gen tox. Penelitian ini bertujuan untuk memberikan gambaran sekuens DNA gen tox Corynebacterium diphtheriae penyebab difteri di beberapa wilayah Indonesia. Sebanyak 65 isolat C. diphtheriae tersimpan milik Badan Litbangkes yang diisolasi dari beberapa wilayah Indonesia tahun 2010- 2017 dijadikan sebagai sampel. Rekultur dilakukan pada medium agar darah (BA), diinkubasi pada suhu 37 o C selama sehari semalam. Ekstraksi DNA menggunakan kit QiaAmp DNA Minikit. Sekuensing DNA dilakukan dengan pendekatan Whole Genome Sequencing (WGS). Konversi dan analisis data menggunakan program U-gene dan BioEdit.Pemeriksaan 65 isolat C. diphtheriae dengan 1683 bp sekuens gen tox menunjukkan ada 3 pola sekuens gen dengan 3 lokasi mutasi. Seluruh mutasi bersifat silent mutation. Lokasi mutasi juga bukan merupakan tempat penempelan ujung 3’ primer PCR yang umum digunakan. Berdasarkan hasil penelitian dapat disimpulkan bahwa variasi gen tox yang ditemukan pada C. diphtheriae penyebab difteri di Indonesia memiliki variasi yang terbatas dan mutasi yang ada tidak mengkode perubahan asam amino. Hal ini mengindikasikan bahwa vaksin yang digunakan di Indonesia masih sesuai dengan variasi bakteri yang bersirkulasi. Hasil penelitian juga mengindikasikan bahwa PCR dapat digunakan untuk skrining dan memprediksi toksigenisitas bakteri penyebab difteri. Kata kunci : C. diphtheriae, gen tox, difteri, Indonesia

scholarly journals Meeting summary: ethical aspects of whole exome and whole genome sequencing studies (WES/WGS) in rare diseases, Tel Aviv, Israel, January 2013

2013 ◽  
Vol 95 (2-3) ◽  
pp. 53-56 ◽  
Author(s):  
LUBA FARBEROV ◽  
AVITAL GILAM ◽  
OFER ISAKOV ◽  
NOAM SHOMRON
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Diseases ◽  
Genetic Basis ◽  
Diagnostic Tools ◽  
Whole Genome ◽  
Ethical Aspects ◽  
Genomic Technologies ◽  
Whole Exome ◽  
Sequencing Studies

SummaryA recent E-Rare workshop reviewed the ethical aspects of whole exome and whole genome-sequencing studies (WES and WGS, respectively) in rare diseases. Leveraging new genomic technologies, which output vast amounts of known and novel genetic variants, researchers are learning more about the genetic basis and mechanisms involved in rare diseases. In some cases, these findings are translated into diagnostic tools for the benefit of rare disease patients. Among the disclosed data, which can assist in treatment management, incidental findings await, bringing with them ethical concerns for the clinicians, researchers and patients.

scholarly journals A triple-hybrid cross reveals a new hybrid incompatibility locus between D. melanogaster and D. sechellia

2019 ◽  
Author(s):  
Jacob C. Cooper ◽  
Ping Guo ◽  
Jackson Bladen ◽  
Nitin Phadnis
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Basis ◽  
Whole Genome ◽  
Hybrid Incompatibility ◽  
Highly Dispersed ◽  
Hybrid Cross ◽  
Lethal Hybrid ◽  
Incompatibility Locus ◽  
Unknown Region

AbstractHybrid incompatibilities are the result of deleterious interactions between diverged genes in the progeny of two species. In Drosophila, crosses between female D. melanogaster and males from the D. simulans clade (D. simulans, D. mauritiana, D. sechellia) fail to produce hybrid F1 males. When attempting to rescue hybrid F1 males by depleting the incompatible allele of a previously identified hybrid incompatibility gene, we observed robust rescue in crosses of D. melanogaster to D. simulans or D. mauritiana, but no rescue in crosses to D. sechellia. To investigate the genetic basis of D. sechellia resistance to hybrid rescue, we designed a triple-hybrid cross to generate recombinant D. sechellia / D. simulans genotypes. We tested the ability of those genotypes to rescue hybrid males with D. melanogaster, and used whole genome sequencing to measure the D. sechellia / D. simulans allele frequency of viable F1 males. We found that recombinant genotypes were rescued when they contained two specific loci from D. simulans – a region containing previously identified Lethal hybrid rescue (Lhr), and an unknown region of chromosome 3L which we name Sechellia aversion to hybrid rescue (Satyr). Our results show that the genetic basis for the recent evolution of this hybrid incompatibility is simple rather than a highly dispersed effect. Further, these data suggest that fixation of differences at Lhr after the split of the D. simulans clade strengthened the hybrid incompatibility between D. sechellia and D. melanogaster.

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