Laboratory for Molecular Typing

Welcome to the home page for the Cornell University Laboratory for Molecular Typing

The Laboratory for Molecular Typing (LMT) is a fee-for-service facility within the New York State College of Agriculture and Life Sciences at Cornell University. The LMT, established in 1996 by Professor Carl A. Batt is currently under the direction of Professor Martin Wiedmann. While we follow PulseNet’s standard protocols, we are not a member of the Centers for Disease Control and Prevention (CDC) PulseNet system.

The lab offers a wide variety of technologies to identify and characterize microorganisms to the genus, species, and subspecies level. Services are strictly confidential. We do not submit isolates or patterns to the CDC.

Discounts are available for educational institutions and companies within New York State. Researchers within Cornell University should contact the lab regarding pricing options. 

Services and fees: Pulsed Field Gel Electrophoresis (PFGE)

PFGE Typing uses the Centers for Disease Control and Prevention (CDC) PulseNet Protocol and BioNumerics Analysis Software to produce high quality, reproducible genetic fingerprints for pathogenic organisms, but our numbering system is separate from CDC PulseNet’s. We can provide electronic files if you want to submit our results to the CDC for comparison.

Pulsed Field Gel Electrophoresis (PFGE): PFGE typing does not provide species identification. If you are interested in species identification, please contact us to discuss the most suitable technology to address your needs.

Fees:  All fees listed are cost per isolate. Effective April 1, 2023.

Pricing is based on our standard testing agreement. A 20% mark-up will be added for testing covered by specialized agreements.

ServiceWithin NYOutside of NY
PFGE Typing
(per enzyme per isolate)

Turn-around time:

For up to eight isolates, turn-around time is ten business days. For turn-around times on larger isolate sets or for faster turn-around times (additional fees apply) please contact us at shelley.clark [at] (shelley[dot]clark[at]cornell[dot]edu).

Services and fees: Whole Genome Sequencing

Whole Genome Sequencing: Our standard whole genome sequence analysis service includes short read trimming and quality control, followed by de novo genome assembly and quality control. Depending on the species, we can perform in silico MLST typing and serotyping. For orders of multiple WGS sequences that our clients wish to compare, we also perform SNP identification. These analyses are highly scalable and can be effectively carried out for hundreds of genomes at a time. We use the identified SNPs to visualize the genetic relationships among analyzed isolates by constructing phylogenetic trees.

Additionally, we can prepare an individualized plan of analyses to fit your requirements. These analyses can include a high quality whole genome annotation, detection of presence/absence of genes of interest (e.g. antimicrobial resistance, virulence, metabolic pathway genes) and analysis of their variability. Additional fees apply for these analyses.

Fees:  All fees listed are cost per isolate.

Pricing is based on our standard testing agreement. A 20% mark-up will be added for testing covered by specialized agreements.

Fees Schedule: NY CustomersOut of state customers
Single isolate  $1,500  $1,750
Two to nine isolates  $1,000  $1,175
Ten or more isolates  $550   $650

The LMT offers additional subtyping services for select food borne pathogens, including MLST. Please contact Shelley Clark (shelley.clark [at] (shelley[dot]clark[at]cornell[dot]edu) ) for more information. 

Turn-around time:

Dependent on number of isolates submitted. Generally, (for up to 24 isolates) results for Salmonella and Listeria are ready in approximately three weeks. Other bacterial pathogens will be ready in approximately four weeks.

We also offer WGS for fungi. Results are reported in approximately four weeks. For pricing information for fungi, please contact mw16 [at] (Dr. Wiedmann).

Should you require faster turnaround times, have larger isolate sets, or need more information, please contact mw16 [at] (Dr. Wiedmann) for more information.

How do I submit a request for Molecular Typing?

Submit a paper copy of the submission form. The form MUST accompany isolates shipped to the lab for typing.

  • Send isolates on a plate or agar slant.  
  • All isolates must be pure cultures.  
  • If the culture you are sending requires special culturing conditions (i.e. unusual media, temperature, etc) please notify us before shipment so that proper arrangements can be made.


Ship isolates in accordance with Biohazard shipping regulations to:

Laboratory for Molecular Typing
ATTN: Shelley Clark
352 Stocking Hall
Cornell University
Ithaca, NY 14853

Contact Information

Shelley Clark, Technician
Email:  shelley.clark [at] (shelley[dot]clark[at]cornell[dot]edu)
Phone: (607) 255-1266

Martin Wiedmann, Director
Email: ribo [at] (ribo[at]cornell[dot]edu)
Phone: (607) 254-2838