scholarly journals Whole-Genome Sequencing of Two Bartonella bacilliformis Strains

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Yolanda Guillen ◽  
Maria Casadellà ◽  
Ruth García-de-la-Guarda ◽  
Abraham Espinoza-Culupú ◽  
Roger Paredes ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Acute Phase ◽  
Causative Agent ◽  
Genome Assembly ◽  
Whole Genome ◽  
Bartonella Bacilliformis

Bartonella bacilliformis is the causative agent of Carrion’s disease, a highly endemic human bartonellosis in Peru. We performed a whole-genome assembly of two B. bacilliformis strains isolated from the blood of infected patients in the acute phase of Carrion’s disease from the Cusco and Piura regions in Peru.

scholarly journals Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12446
Author(s):  
Darlene D. Wagner ◽  
Heather A. Carleton ◽  
Eija Trees ◽  
Lee S. Katz
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
Enteric Bacteria ◽  
Quality Metrics ◽  
Read Length ◽  
Snp Analysis ◽  
Whole Genome ◽  
Insert Size ◽  
E Coli

Background Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks. Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon WGS data quality. Methods Raw, unprocessed WGS reads from Escherichia coli, Salmonella enterica, and Shigella sonnei outbreak clusters were characterized for four quality metrics: PHRED score, read length, library insert size, and ambiguous nucleotide composition. PHRED scores were strongly correlated with improved SNPs analysis results in E. coli and S. enterica clusters. Results Assembly quality showed only moderate correlations with PHRED scores and library insert size, and then only for Salmonella. To improve SNP analyses and assemblies, we compared seven read-healing pipelines to improve these four quality metrics and to see how well they improved SNP analysis and genome assembly. The most effective read healing pipelines for SNPs analysis incorporated quality-based trimming, fixed-width trimming, or both. The Lyve-SET SNPs pipeline showed a more marked improvement than the CFSAN SNP Pipeline, but the latter performed better on raw, unhealed reads. For genome assembly, SPAdes enabled significant improvements in healed E. coli reads only, while Skesa yielded no significant improvements on healed reads. Conclusions PHRED scores will continue to be a crucial quality metric albeit not of equal impact across all types of analyses for all enteric bacteria. While trimming-based read healing performed well for SNPs analyses, different read healing approaches are likely needed for genome assembly or other, emerging WGS analysis methodologies.

scholarly journals Genomic Dissection of an Icelandic Epidemic of Respiratory Disease in Horses and Associated Zoonotic Cases

mBio ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Sigríður Björnsdóttir ◽  
Simon R. Harris ◽  
Vilhjálmur Svansson ◽  
Eggert Gunnarsson ◽  
Ólöf G. Sigurðardóttir ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Respiratory Disease ◽  
Genome Sequencing ◽  
Causative Agent ◽  
Opportunistic Pathogen ◽  
Whole Genome ◽  
National Scale ◽  
Horse Population ◽  
Viral Pathogen ◽  
First Time

ABSTRACT Iceland is free of the major infectious diseases of horses. However, in 2010 an epidemic of respiratory disease of unknown cause spread through the country’s native horse population of 77,000. Microbiological investigations ruled out known viral agents but identified the opportunistic pathogen Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) in diseased animals. We sequenced the genomes of 257 isolates of S. zooepidemicus to differentiate epidemic from endemic strains. We found that although multiple endemic clones of S. zooepidemicus were present, one particular clone, sequence type 209 (ST209), was likely to have been responsible for the epidemic. Concurrent with the epidemic, ST209 was also recovered from a human case of septicemia, highlighting the pathogenic potential of this strain. Epidemiological investigation revealed that the incursion of this strain into one training yard during February 2010 provided a nidus for the infection of multiple horses that then transmitted the strain to farms throughout Iceland. This study represents the first time that whole-genome sequencing has been used to investigate an epidemic on a national scale to identify the likely causative agent and the link to an associated zoonotic infection. Our data highlight the importance of national biosecurity to protect vulnerable populations of animals and also demonstrate the potential impact of S. zooepidemicus transmission to other animals, including humans. IMPORTANCE An epidemic of respiratory disease affected almost the entire native Icelandic horse population of 77,000 animals in 2010, resulting in a self-imposed ban on the export of horses and significant economic costs to associated industries. Although the speed of transmission suggested that a viral pathogen was responsible, only the presence of the opportunistic pathogen Streptococcus zooepidemicus was consistent with the observed clinical signs. We applied genomic sequencing to differentiate epidemic from endemic strains and to shed light on the rapid transmission of the epidemic strain throughout Iceland. We further highlight the ability of epidemic and endemic strains of S. zooepidemicus to infect other animals, including humans. This study represents the first time that whole-genome sequencing has been used to elucidate an outbreak on a national scale and identify the likely causative agent. An epidemic of respiratory disease affected almost the entire native Icelandic horse population of 77,000 animals in 2010, resulting in a self-imposed ban on the export of horses and significant economic costs to associated industries. Although the speed of transmission suggested that a viral pathogen was responsible, only the presence of the opportunistic pathogen Streptococcus zooepidemicus was consistent with the observed clinical signs. We applied genomic sequencing to differentiate epidemic from endemic strains and to shed light on the rapid transmission of the epidemic strain throughout Iceland. We further highlight the ability of epidemic and endemic strains of S. zooepidemicus to infect other animals, including humans. This study represents the first time that whole-genome sequencing has been used to elucidate an outbreak on a national scale and identify the likely causative agent.

scholarly journals A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus.

2021 ◽  
Author(s):  
Klaudia Chrzastek ◽  
Chandana Tennakoon ◽  
Dagmara Bialy ◽  
Graham L Freimanis ◽  
John Flannery ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
Influenza A ◽  
Limit Of Detection ◽  
Clinical Samples ◽  
Sequence Information ◽  
Whole Genome ◽  
Random Priming ◽  
Influenza A H1n1

Background: Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. Methods: The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. Results: The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of COVID that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. Conclusions: The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.

scholarly journals Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomic rearrangements using the MinION sequencing device

2017 ◽  
Author(s):  
JR Tyson ◽  
NJ O’Neil ◽  
M Jain ◽  
HE Olsen ◽  
P Hieter ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Genomic Rearrangements ◽  
Whole Genome ◽  
C Elegans ◽  
Long Reads

ABSTRACTAdvances in 3rd generation sequencing have opened new possibilities for ‘benchtop’ whole genome sequencing. The MinION is a portable device that uses nanopore technology and can sequence long DNA molecules. MinION long reads are well suited for sequencing and de novo assembly of complex genomes with large repetitive elements. Long reads also facilitate the identification of complex genomic rearrangements such as those observed in tumor genomes. To assess the feasibility of the de novo assembly of large complex genomes using both MinION and Illumina platforms, we sequenced the genome of a Caenorhabditis elegans strain that contains a complex acetaldehyde-induced rearrangement and a biolistic bombardment-mediated insertion of a GFP containing plasmid. Using ∼5.8 gigabases of MinION sequence data, we were able to assemble a C. elegans genome containing 145 contigs (N50 contig length = 1.22 Mb) that covered >99% of the 100,286,401 bp reference genome. In contrast, using ∼8.04 gigabases of Illumina sequence data, we were able to assemble a C. elegans genome in 38,645 contigs (N50 contig length = ∼26 kb) containing 117 Mb. From the MinION genome assembly we identified the complex structures of both the acetaldehyde-induced mutation and the biolistic-mediated insertion. To date, this is the largest genome to be assembled exclusively from MinION data and is the first demonstration that the long reads of MinION sequencing can be used for whole genome assembly of large (100 Mb) genomes and the elucidation of complex genomic rearrangements.

Whole genome sequencing as a novel approach for characterising Neisseria meningitidis in Australia

2017 ◽  
Vol 38 (3) ◽  
pp. 142
Author(s):  
Shakeel Mowlaboccus
Keyword(s):  
Neisseria Meningitidis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Causative Agent ◽  
Western Australia ◽  
Meningococcal Disease ◽  
Whole Genome ◽  
Novel Approach ◽  
Routine Surveillance ◽  
Life Threatening

Neisseria meningitidis (meningococcus) is the causative agent of invasive meningococcal disease that manifests as life-threatening septicaemia and/or meningitis. This review provides a brief overview of the prevention of the disease and also highlights the importance of whole genome sequencing (WGS) in detecting outbreaks of meningococci in Australia. The use of WGS in identifying the emergence of a penicillin-resistant cluster of meningococci is Western Australia is used as an example for advocating the implementation of WGS on the routine surveillance in Australia.

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