Ask the Experts: Microbial Identification Testing Updates

Microbial identification and organism typing provides the food industry with a way to identify organisms and sub-species of those organisms. Laboratories specializing in this type of testing offer food companies a way to determine which harmful organisms may be present in their production plant ecology and a particular ingredient or product that is out of specification. Additionally, this testing provides a way to confirm the presence of beneficial organisms in a product.

The options for microbial identification include a low-cost, quick identification of a single organism or using a typing method to distinguish one organism from another. Next Generation Sequencing (NGS) also enhances a lab’s ability to identify multiple organisms in a mixture or to more finely distinguish one organism from another.

But what do these new techniques mean to the world of microbiology?

To shed some light on our current and new microbial identification offerings, I sat down with Dr. Sarita Raengpradub, our Director of Microbiology Research & Development, and Dr. Tim Freier, our Division Vice President of Scientific Affairs and Microbiology. Dr. Raengpradub and Dr. Freier have worked hard over the past few years to improve Mérieux NutriSciences’ microbial identification and typing services offerings.

Q: What is MALDI-TOF MS, and what role does it play in the microbial identification space?

Dr. Raengpradub: Instead of sequencing select regions of the ribosomal RNA gene, Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) utilizes the ribosomal protein spectra to identify the organism. While ribosomal RNA gene sequencing, offered at our Food Science Center, is considered the gold standard for microbial identifications, MALDI-TOF MS is rapidly growing in acceptance for use within the food industry. The advantage of this technology is that it offers a much faster time to receive a result than sequencing and is less labor intensive, which frees up our technicians to work on other projects for our clients.

Q: How have you worked to lessen the negative impact to clients of discontinuing the DiversiLab technology?

Dr. Raengpradub: DiversiLab has been an important service for Mérieux NutriSciences and the Food Science Center. Customers utilize molecular subtyping to learn more about their microbial isolates, and the results answer the question, “Are these isolates the same or different?” That answer may lend greater insight into their finished food product, ingredients, production process, and environment.

When we learned that DiversiLab was being discontinued by the manufacturer, I researched and presented different options to key technical people within the company. The team decided to implement Hygiena’s RiboPrinter System. The system fits our operational needs, but more importantly, it also provides high discriminatory power, which means it can do a better job of resolving or discriminating between strains. The ribotyping option gives customers a basic option for subspecies and strain level comparison, but if they want ultimate strain resolution, we will also offer Whole Genome Sequencing (WGS).

Dr. Freier: Unfortunately, the change will be difficult for clients with many years of DiversiLab data because it is impossible to convert this data into RiboPrinter data directly. However, if there are physical isolates in frozen storage, it will be possible to re-type these isolates using the RiboPrinter system. Also, since the vendor will no longer support the DiversiLab software, we are developing a way to move DiversiLab data into our new BioNumerics software at a client’s request to ensure this data is preserved.

Q: What are your roles in the NGS in the food industry?

Dr. Freier: Dr. Raengpradub and I have actively participated in global working groups to share knowledge and methods with our colleagues in France and Italy. We are working with several key global clients to provide these services worldwide. In addition, I have met with several of our clients to share information on the powerful scientific potential of this new technology and the considerations of the complex regulatory and liability environments that come with the use of NGS.

Dr. Raengpradub: I am excited to add NGS to our North American capabilities. A single NGS run generates many millions of sequencing reads. Then the next step, called bioinformatics, is to decipher and piece together all of that sequence information into something meaningful.

The Microbiology Research & Development (R&D) team works on a few NGS applications but will start with Whole Genome Sequencing (WGS). WGS is the process of sequencing the entire DNA content of a bacterial isolate. The R&D team is working on validating both parts of the WGS method: sequencing (wet lab) and bioinformatics (dry lab). We also lead the piece I call “operational readiness,” which includes: writing the methods, obtaining approval from the Microbiology Technical Team, costing out the method, working on the LIMS code, and training our Food Science Center Operations team. The R&D team will also support Product Management, Marketing, and Operations with the service launch.

Q: How will Mérieux NutriSciences’ technical consultants utilize the new microbial identification service to aid in quality investigations?

Dr. Freier: The new identification and strain tracking capabilities will give our consultants improved tools to investigate pathogen contamination events and solve quality, spoilage, or shelf-life issues. For example, some spoilage organisms can be difficult to culture and identify. These new technologies will increase our ability to identify these problem microorganisms that can sometimes be difficult to differentiate when using conventional cultural techniques.

Q: What tips do you have for clients who want to take advantage of these new technologies but find them a bit overwhelming?

Dr. Freier: Please reach out to us. We’re happy to answer questions and find the right solution(s) for a customer’s questions and needs. NGS and WGS can provide very powerful information, which may seem daunting, but we have technical experts on the Mérieux NutriSciences team who can help ease you into it.

To address our client’s needs for this important testing type, Mérieux NutriSciences began offering biochemical assays decades ago and has now implemented the Vitek 2 Compact system. As demand grew, we incorporated more sophisticated methods by adding the DiversiLab system and gene sequencing using the Sanger method. Today, given the changing technology in the field, we’re investing in new, state-of-the-art techniques that will provide faster, more definitive answers to our clients’ identification and microbial typing questions. We are incorporating a fast and inexpensive identification technique called MALDI-TOF MS, a long-valued typing tool called Riboprinter ™ and NGS, which can be used for identification and typing.

Do you need help identifying the organisms lurking in your facility? Are you looking for results from a reputable and reliable lab? Mérieux NutriSciences offers comprehensive microbial identification services using Vitek-MS, Riboprinter, and Next Generation Sequencing. Our dedicated microbial identification team can work with you to determine which services will best meet your identification needs. Learn more about microbial identification with our latest video, “What is Micro Identification?” and download our sell sheet today to get started!