Advanced Molecular Biology in Microbial Identification: Improving Precision and Efficiency

Highlights

• Introduction
• Importance of microbial identification in the food and beverage industry
• Recent innovations in the industry

Microbial identification is the process of detecting the specific types of microorganisms in a sample, such as bacteria, viruses, fungi, or protozoa. This procedure involves analyzing morphological, biochemical, and genetic traits of microorganisms to classify and differentiate them. Techniques like microscopy, culture methods, and advanced molecular biology tools such as DNA sequencing and mass spectrometry are commonly used for microbial assessment. This process is essential in microbiology, medicine, food testing, and environmental science, assisting in disease diagnosis, research, and the implementation of targeted control measures.

Innovations in molecular biology, genomics, and other advanced techniques have transformed the microbial identification industry. Techniques such as next-generation sequencing, polymerase chain reaction (PCR), and mass spectrometry enhance the precision, speed, and efficiency of microbial identification. These advancements improve identification accuracy and enable high-throughput analysis, meeting the increasing demand for rapid and comprehensive identification solutions.

Use of microbial genetics for better food safety practices

Microbes have been used since ancient times to produce fermented foods such as dairy, bread, and beverages. In modern times, microbes are integrated to improve food quality and increase food production, but rapid multiplication of other microbial species leads to food spoilage.  Advanced identification methods assist food manufacturers in monitoring microbial contamination throughout the supply chain, ensuring the continued safety of products. Techniques such as whole genome sequencing offer comprehensive insights into microbial genetics, enabling detailed tracking of contaminants. Food microbiology labs use a variety of products to rapidly confirm and differentiate microbes at the genus, species, and serotype levels. These products include biochemical reagents, identification panels, latex tests, and agglutinating sera. 

 

However, regular microbial testing throughout the food supply chain is essential for monitoring contamination at various stages, from production to processing and distribution. By identifying sources of contamination, food manufacturers implement targeted interventions to minimize risks, thereby enhancing overall food hygiene and safety. Microbial identification supports research into the survival mechanisms of pathogens in food environments, leading to the development of improved preservation techniques and food safety practices. Understanding microbial behavior helps in designing strategies to prevent contamination and spoilage.

The NOVA algorithm's success in identifying unknown bacterial isolates

Researchers at the University of Basel have developed the latest algorithm called Novel Organism Verification and Analysis (NOVA) to assess bacterial isolates that cannot be characterized using conventional identification methods. Since 2014, the team has been collecting and analyzing patient samples with unknown bacterial isolates and has discovered over thirty new bacterial species, some of which are linked to clinically significant infections.

In this study, researchers led by Daniel Goldenberger, PhD, analyzed 61 unknown microbial pathogens found in blood or tissue samples from patients with various medical conditions. Conventional laboratory methods, such as mass spectrometry and partial bacterial genome sequencing, had been unsuccessful in characterizing these isolates.

Bruker’s MS-based microbial identification kit

In January 2021, Bruker Corporation received US FDA clearance and launched the MBT Sepsityper Kit US IVD in the US. This kit allows for the rapid detection of microorganisms from positive blood samples with the help of the MALDI Biotyper CA System. The MBT Sepsityper Kit US IVD enables the accelerated identification of various microbes from positive cultures. Microorganisms are first harvested and processed, then analyzed using the MALDI Biotyper CA System, which utilizes proteomic fingerprinting via mass spectrometry. The kit features a reference library that comprises 425 various gram-positive and gram-negative bacterial species, groups, and yeasts, including Candida auris, an emerging pathogen associated with hospital-acquired yeast infections.

The MBT Sepsityper Kit workflow usually completes the identification process in under 30 minutes from the sampling of a positive blood culture. This reduces the time-to-result (TTR) by up to 24 hours compared to traditional methods involving additional agar plate culturing and an additional 8–12 hours for biochemical identification following agar plate culturing.

The U.S. Food and Drug Administration (FDA) and bioMérieux have teamed up to enhance microbial detection tools

In February 2024, bioMérieux, a global leader in in-vitro diagnostics for 60 years, partnered with the US FDA, Regulatory Science (ORS), Offices of Applied Research and Safety Assessment (OARSA), and Center for Food Safety and Applied Nutrition (CFSAN). This collaboration aims to develop advanced tools to address food-borne pathogens, establishing the platform for numerous innovative projects to enhance detection and microbial characterization systems for pathogens that contaminate food.

To conclude, innovations in microbial identification, such as advanced molecular techniques and rapid diagnostic tools, have significantly improved the accuracy and speed of detecting microorganisms. These advancements enhance food safety by enabling precise tracking of contaminants and supporting research into pathogen survival mechanisms. However, technological innovations in these methods are expected to optimize public health protection.

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