The genomic sequencing service offers you a very flexible and varied service that will meet your objectives.

From complete genome sequencing of bacteria and viruses to complex research projects, including bioinformatics analyzes if necessary, our turnkey service will meet your needs.

Distributed in 3 laboratories according to the desired expertise, this service has four high-throughput sequencers with advanced technologies, such as MiSeq and iSeq100 from Illumina, the S5 Prime from Ion Torrent and the MinION from Nanopore.

Depending on the nature of your project, we invite you to contact the following appropriate managers who will be able to discuss with you the direction of your project and the available options :

 

Targeted pathogens Contact Email
E.coli and enterobacteria (Salmonella, Yersinia, Klebsiella, Enterobacter, Citrobacter, etc.) Ghyslaine Vanier ghyslaine.vanier@umontreal.ca
A. pleuropneumoniae, Glaesserella  (Haemophilus) parasuis, S. suis and other swine bacterial pathogens Sonia Lacouture sonia.lacouture@umontreal.ca
All other bacterial or viral sequencing (on demand) and metagenomics (e.g. microbial, microbiome, RNAseq, Ampliseq…) Chantale Provost chantale.provost@umontreal.ca

 

 


Service


Sequencing service


The service offered involves several devices and/or analyzes such as:

    • MiSeq (Illumina)
    • iSeq100 (Illumina)
    • S5 Prime (Ion Torrent)
    • MinION (Nanopore)
    • Bioanalyzer
      • Device to check the quality and quantity of libraries, DNA and RNA
    • QIAxcel
      • Device to check the quality and quantity of libraries, as well as DNA and RNA gel analysis
    • Microbiome 16S
      • Most used kit: QIAseq 16S / ITS Screening Panel, which allows 6 amplicons to be separated into 3 pools which, together, can cover the entire 16S ribosomal gene. In addition, the QIAseq 16S / ITS screening panel contains primers for ITS to amplify fungal DNA.
    • MicroRNA
      • Sequencing of the small fragments of cellular RNA, which prevent the production of a particular protein by binding to and destroying the messenger RNA
    • AmpliSeq
      • Sequencing of a pre-amplification of a certain number of targeted genes or predefined gene region
    • RNA-Seq
      • Random sequencing of the transcriptome
    • Metagenomics (virome)
      • Sequencing of the total genetic content of a sample, then comparison of the sequences obtained with microorganism databases
    • De novo
      • Assembly of genomic sequences without reference
    • Re-sequencing
      • Assembly of genomic sequences with a reference

Bioinformatics analyzes


We can provide a complete bioinformatic analysis service. This service mainly uses two analysis programs, CLC Genomic Workbench and Geneious Prime. Several analysis options are available such as:

    • Genome assembly
      • De novo
          • Assembly of genetic sequences without reference
      • Re-sequencing
          • Assembly of genetic sequences with reference
      • Annotations
          • Identification of gene locations and all coding regions of a genome
      • Plasmids
    • MLST / cgMLST
      • Multi-focus sequence typing (MLST): typing of several loci allowing the characterization of isolates of microbial species using the DNA sequences of internal fragments of several household genes
      • Determination of O:H serotype, and determination of phylogenetic group of E.coli
    • PFGE
      • Pulsed field gel electrophoresis: Type of DNA fingerprint for a bacterial isolate
    • Antimicrobial resistance genes
      • Portion of DNA encoding the survival of an organism when exposed to antibiotics
      • Point mutations known to generate antimicrobial resistance
    • Genes coding for virulence factors
      • Portion of coding DNA of an infectious agent, which contributes to its pathogenic nature when infecting host
    • Phylogenetic trees
      • Schematic tree showing the relationships between the organisms compared
    • Genetic alignments
      • Comparison of the genetic sequences of several viral strains or different organisms
    • Metagenomic analyzes
      • 4 different databases:
          • Kraken Metagenomics by BaseSpace Labs
          • Microbial Genome Database by CLC Genomic Workbench
          • NCBI reference by Taxonomic Profiling Index – CLC Genomic Workbench
          • Nucleotide (GenBank) by NCBI

 


The VHTSL Publications


 

Xie J, Vereecke N, Theuns S, Oh D, Vanderheijden N, Trus I, Sauer J, Vyt P, Bonckaert C, Lalonde C, Provost C, Gagnon CA, Nauwynck H. Comparison of primary virus isolation in pulmonary alveolar macrophages and four different continuous cell lines for type 1 and type 2 porcine reproductive and respiratory syndrome virus. Vaccines. 2021. Jun 3; 9(6):594

 

Morice P, Allano M, Provost C, Fairbrother J-H, Gagnon CA, Sauvé F. Whole genome sequencing of methicillin-resistant and methicillin-sensitive Staplylococcus aureus isolated from 4 horses in a veterinary teaching hospital and its ambulatory service. Can J Vet Res. 2021. 85(3):218-223

 

de Lagarde M, Vanier G, Arsenault J, Fairbrother JM. High Risk Clone: A Proposal of Criteria Adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig Population. Antibiotics. 2021. 10(3), 244.

 

Perez Contreras A, van der Meer F, Checkley S, Joseph T, King R, Ravi M, Peters D, Fonseca K, Gagnon CA, Provost C, Ojkic D, Abdul-Careem MF. Analysis of Whole-Genome Sequences of Infectious laryngotracheitis Virus Isolates from Poultry Flocks in Canada: Evidence of Recombination. Viruses. 2020. 12, 1302; doi:10.3390/v12111302.

 

Palomino-Tapia V, Mitevski D, Inglis T, van der Meer F, Martin E, Brash M, Provost C, Gagnon CA, Abdul-Careem MF. Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada. Viruses. 2020. Sep 28;12(10):E1096. doi: 10.3390/v12101096. PMID: 32998356.

 

Gagnon CA, Lalonde C, Provost C. Porcine reproductive and respiratory syndrome virus whole-genome sequencing efficacy with field clinical samples using a poly(A)-tail viral genome purification method. J Vet Diagn Invest. 2020. Aug 28:1040638720952411. doi: 10.1177/1040638720952411. Online ahead of print. PMID: 32856560.

 

Lalonde C, Provost C, Gagnon CA. Whole genome sequencing of porcine reproductive and respiratory syndrome virus (PRRSV) from field clinical samples improves the genomic surveillance of the virus. J Clin Microbiol. 2020. Aug 12:JCM.00097-20. doi: 10.1128/JCM.00097-20. Online ahead of print. PMID: 32817228.

 

Le Net R, Provost C, Lalonde C, Régimbald L, Vézina F, Gagnon CA, Lair S. Whole Genome Sequincing of an Avipoxvirus Associated with Infections in a Group of Aviary-Housed Snow Buntings (Plectrophenax Nivalis). J Zoo Wildl Med. 2020. Jan 9;50(4):803-812. doi: 10.1638/2018-0102. PMID: 31926510.

 

Chénier S, Desroches M, Provost C, Bournival V, St-Sauveur VG, Koszegi M, Gagnon CA. First reported outbreak of Duck atadenovirus A tracheobronchitis in 3-week-old ducklings in Québec including whole genome sequence of the virus. Can Vet J. 2019. Dec;60(12):1285-1288. PMID: 31814632.

 

Vounba P, Yaghouba K, Ndiaye C, Arsenault J, Fairbrother JM, Bada Alambédji R. Molecular characterization of Escherichia coli isolated from chickens with colibacillosis in Senegal. Foodborne Pathogens and Disease. 2018. 15 : 517-525. DOI: 10.1089/fpd.2017.2394 PMID : 29851365.

 


Our customers’ publications


 

Hassan MSH, Ojkic D, Coffin CS, Cork SC, van der Meer F, Abdul-Careem MF. Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination. Viruses. 2019 Nov 13;11(11). PMID: 31766215

Whole genome sequencing by HTS offered at a promotional price of 240$  or 250$* for a limited time.

*Contact us for more details and the price that will match your request. 

Sample type:

We have developed expertise in sequencing a wide variety of samples, such as:

  • Identification, sequencing of the entire genome of pathogens from clinical samples (feces, tissues, serum, etc.)
  • Isolated / purified viruses
  • Isolated bacterial strains
  • RNA
  • DNA
  • cDNA
  • AmpliSeq samples
  • Fixed or waxed samples
  • Other

It is important to note that the microbial load and the type of sample will greatly affect the quality of the sequencing. For more information, please contact our laboratory.


 Achievements


Sequencing of complete viral genomes


  • Swine influenza virus
  • Porcine reproductive and respiratory syndrome virus (PRRSV; arterivirus)
  • Avian poxvirus
  • Avian reovirus
  • Avian infectious bronchitis virus (IBV; coronavirus)
  • Avian infectious laryngotracheitis virus (ILTV; herpesvirus)
  • Swine epidemic diarrhea virus (PEDV; coronavirus)
  • Bacteriophages
  • Avian adenovirus
  • Turkey hemorrhagic enteritis virus (HEV; adenovirus)
  • Pig rotavirus
  • Viral strains of vaccine origin
  • Bovine viral diarrhea virus (BVDV; pestivirus)
  • Sapelovirus
  • Astrovirus
  • Porcine Hemagglutinating Encephalomyelitis Virus (PHEV; coronavirus)

 


Sequencing of whole bacterial genomes


  • Actinobacillus pleuropneumoniae
  • Actinobacillus suis
  • Bordetella bronchiseptica
  • Brachyspira hyodysenteriae
  • Escherichia coli
  • Glaesserella (Haemophilus) parasuis
  • Mycoplasma gallisepticum
  • Mycoplasma hemotropic
  • Photobacterium
  • Salmonella enterica
  • Staphylococcus aureus
  • Staphylococcus hyicus
  • Streptococcus equis
  • Streptococcus suis

 


Others


  • RNASeq of porcine cells coinfected with PRRSV and swine influenza virus
  • Metagenomics of many samples