Next-Generation Sequencing

The LMM houses both second and third generation sequencers in a spacious room with dedicated space for DNA/RNA isolation and quantification.

In addition, the following equipment are readily available:

  • PacBio Sequel systems both for fulfilling in-house and third-party sequencing requirements. More information here.
  • Several thermal cyclers (PCR) and qPCR devices (Applied Biosystem and BioRad)
  • Bioanalyzer (Agilent)
  • Lab Chip (Perkin Elmer)
  • Zephyr G3 (Perkin Elmer)
  • MiSeq (Illumina Inc.)
  • MinION (Oxford Nanopore)

The LMM can provide instruments for quantity and quality control and a Zephyr G3 NGS automatic sample handling system robot that facilitates high-throughput library preparation.

Publications

Read our relevant publications related to NGS.

Xavier BB, Mysara M, Bolzan M, Ribeiro-Gonçalves B, Alako BTF, Harrison P, Lammens C, Kumar-Singh S, Goossens H, Carriço JA, Cochrane G, Malhotra-Kumar S. BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology. iScience (Cell Press), 2020.

Xavier BB, Lammens C, Ruhal R, Butaye P, Kumar-Singh S, Goossens H, Malhotra-Kumar S. Identification of a novel plasmid-mediated colistin resistant gene mcr-2 in E. coli, Belgium, June 2016. Euro surveillance. 2016.

Xavier BB, Lammens C, Butaye P, Goossens H, Malhotra-Kumar S. 2016. Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms. Journal of Antimicrobial Chemotherapy.

Malhotra-Kumar S, Xavier BB, Das AJ, Lammens C, Butaye P, Goossens H. 2016. Colistin resistance gene mcr-1 harboured on a multidrug-resistant plasmid. The Lancet Infectious Diseases.

Sabirova JS, Xavier BB, Coppens J, Lammens C, Wagner T, Pournaras S, Goossens H, Malhotra-Kumar S. 2016. Whole-genome typing and characterisation of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole genome mapping and sequencing. Journal of Antimicrobial Chemotherapy.

Xavier BB, Gesuele R, Lammens C, Abdessalam C, Goossens H, Schrenzel J, Harbarth S, Malhotra-Kumar S. 2019. Potential in vivo transfer of a blaCTX-M14-harboring plasmid established using long-read sequencing. Journal of Microbiological Methods.

Xavier BB, Vervoort J, Stewardson A, Adriaenssens N, Coenen S, Harbarth S, Goossens H, Malhotra-Kumar S. 2014. Complete genome sequences of nitrofurantoin-sensitive and -resistant Escherichia coli ST540 and ST2747 strains. Genome Announc. 2(2): e00239-.

Vervoort J, Xavier BB, Stewardson A, Adriaenssens N, Coenen S, Harbarth S, Goossens H, Malhotra-Kumar S. 2015. Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota. Journal of Antimicrobial Chemotherapy. March 12, 2015.

Hotterbeekx, A, Xavier BB, Bielen K, Lammens C, Moons P, Schepens T, Goossens H, Malhotra-Kumar S (2016). The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis. Scientific Reports, 6, 36507.

Vervoort J, Xavier BB, Stewardson A, Adriaenssens N, Coenen S, Harbarth S, Goossens H, Malhotra-Kumar S. An in vitro deletion in ribE encoding lumazine synthase contributes to nitrofurantoin resistance in Escherichia coli. Antimicrobial Agents Chemotherapy, 2014 Sep.

Sabirova J, Xavier BB, Hernalsteens J-P, de Greve H, Ieven M, Goossens H, Malhotra-Kumar S. 2014. Complete genome sequences of two prolific biofilm-forming Staphylococcus aureus isolates belonging to USA300 and EMRSA-15 clonal lineages. Genome Announcements. 2(3): e00610-14.

Xavier BB, Miao VP, Jonsson ZO, Andresson OS. 2012. Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny. Fungal Biology 116: 802-814.

Julia S, Hernalsteens J-P, de Backer S, Xavier BB, Moons P, Turlej-Rogacka A, De Greve H., Goossens H, Malhotra-Kumar S. 2015. Fatty acid kinase A is an important determinant of biofilm formation in Staphylococcus aureus USA300 BMC genomics.

Tomislav K, Strateva T, Xavier BB, Proevska J, Lammens C, Markova B, Goossens H, Malhotra-Kumar S. 2016. Detection, and characterisation of two NDM-1 producing Klebsiella pneumoniae strains from Bulgaria. Journal of Antimicrobial Chemotherapy.

Coppens J, Xavier BB, Vanjari L, De Backer S, Lammens C, Vemu L, Goossens H, Malhotra-Kumar S. Novel composite SCCmec type III element in ST239 MRSA isolated from an Indian hospital. Journal of Antimicrobial Chemotherapy. 2018 Oct 4.

Matheeussen V, Xavier BB, Mermans I, De Weerdt A, Lammens C, Goossens H, Jansens H, Malhotra-Kumar S. 2019. Emergence of colistin resistance during treatment of recurrent pneumonia caused by Carbapenemase Producing Klebsiella pneumoniae. Diagnostic Microbiology and Infectious Disease.

Daniele Armaleo; Olaf Mueller; François Lutzoni; Ólafur Andrésson; Guillaume Blanc; Helge B Bode; Frank R Collart; Francesco Dal Grande; Fred Dietrich; Igor V Grigoriev; Suzanne Joneson; Alan Kuo; Peter E Larsen; John M Logsdon Jr; David Lopez; Francis Martin; Susan P May; Tami R McDonald; Sabeeha S Merchant; Vivian Miao; Emmanuelle Morin; Ryoko Oono; Matteo Pellegrini; Nimrod Rubinstein; Maria Virginia Sanchez-Puerta; Elizabeth Savelkoul; Imke Schmitt; Jason C Slot; Darren Soanes; Péter Szövényi; Nick Talbot; Claire Veneault-Fourrey; Xavier BB. 2019. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics.

Coppens J, Xavier BB, Loens K, Lammens C, Matheeussen V, Ieven M, Goossens H, Malhotra-Kumar S, 2019. Remarkable Genome Stability among emm1 Group A Streptococcus in Belgium over 19 Years. Genome Biology and Evolution.