Genomic sequencing service

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…)	Marika Koszegi	marika.koszegi@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

Burgher-Pulgaron Y, Provost C, Alvarez F, Meza-Serrano E, Pesant MJ, Price CA,Gagnon CA. DUSP1 mRNA modulation during porcine circovirus type 2 and porcine reproductive and respiratory syndrome virus co-infection regulates viruses replication. Virus Res. 2024 Jan 2;339:199282. doi: 10.1016/j.virusres.2023.199282. Epub 2023 Dec 1. PMID: 37995964; PMCID: PMC10711501.

Burgher Pulgaron Y, Provost C, Pesant MJ, Gagnon CA. Porcine Circovirus Modulates Swine Influenza Virus Replication in Pig Tracheal Epithelial Cells and Porcine Alveolar Macrophages. Viruses. 2023 May 20;15(5):1207. doi: 10.3390/v15051207. PMID: 37243291; PMCID: PMC10222781.

Gagnon CA, Bournival V, Koszegi M, Nantel-Fortier N, St-Sauveur VG, Provost C, Lair S. Cross-Canada Disease Report. Quebec : Avian pathogens identification and genomic characterization: 2021 annual review of the Molecular Diagnostic Laboratory, Université de Montréal. Can Vet J. 2022 May;63(5):486-490. PMID: 35502259;

Elshafiee EA, Hassan MSH, Provost C, Gagnon CA, Ojkic D, Abdul-Careem MF. Comparative full genome sequence analysis of wild-type and chicken embryo origin vaccine-like infectious laryngotracheitis virus field isolates from Canada. Infect Genet Evol. 2022 Aug 14;104:105350. doi: 10.1016/j.meegid.2022.105350. Epub ahead of print. PMID: 35977653.

Gagnon CA, Provost C, Lair S. Coding-Complete Genome Sequence of a Falcon aviadenovirus A Strain Associated with Necrotizing Hepatitis in an American Kestrel (Falco sparverius). Microbiol Resour Announc. 2022 Mar 17:e0000922. doi: 10.1128/mra.00009-22 . Epub ahead of print. PMID: 35297683.

Bourque L, Nielsen O, Jager M, Ojkic D, Provost C, Gagnon CA, Lockerbie B, Snyman H, Stevens B, Needle D, Nakagun S, Cox S, Khodadad J, Jones MEB. In situ hybridization and virus characterization of skunk adenovirus in North America wildlife reveals multisystemic infections in a broad range of hosts. J Wildl Dis. 2022 Feb 1. doi: 10.7589/JWD-D-21-00099. Epub ahead of print. PMID: 35104340.

Savard C, Provost C, Ariel O, Morin S, Fredrickson R, Gagnon CA, Broes A, Wang L. First report and genomic characterization of a bovine-like coronavirus causing enteric infection in an odd-toed non-ruminant species (Indonesian tapir, Acrocodia indica) during an outbreak of winter dysentery in a zoo. Transbound Emerg Dis. 2021 Aug 24. doi: 10.1111/tbed.14300. Online ahead of print. PMID: 34427399

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

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