Changing from detection and reaction to prediction and prevention
How digital transformation is revolutionising microbiological quality assurance
Microbiological quality assurance in the beverage and brewing industry today is based mostly on conventional methods, with the possibilities of digitisation viewed as ahead of their time. Uptake of the current digital transformation would allow users to utilise information that is already available today to gain a better understanding on past microbiological events, make production more efficient, and have the potential to avoid future contamination issues.
Digital transformation usually involves the implementation of technologies such as artificial intelligence, big data, the Internet of Things (IoT) and other digital solutions. These technologies enable companies and organisations to collect, analyse and use large amounts of data to make better decisions. The goal of digital transformation is to increase efficiency and productivity, drive innovation and create new opportunities to meet the demands of a rapidly changing world.
"Predictive diagnostics" has long since arrived as a decision-making aid for human medical issues. Not without controversy, this "foresighted" diagnosis refers to the analysis of medical data in order to use Machine Learning to make predictions about the future state of health or disease risks of a patient (or a population). The aim is to detect diseases at an early stage and thus enable preventive treatment. Translated to the food industry, this involves the bundling of microbiological expertise, genomics, bioinformatics and data science, as well as the integration of metadata in order to maintain and improve the health of your company.
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Microbiological diagnostics in beverage production make an important contribution to safeguarding against serious quality defects or even product recalls. Classical microbiological diagnostics usually require well-trained employees with adept experience in the field. Nowadays, however, it is no longer feasible due to the long-term commitment required; it is therefore necessary to adopt a new approach.
Experts agree that digital transformation holds enormous potential for quality optimisation and testing in the food industry. Given the amount of dynamism in food production, data-based findings will become necessary in the future to understand relationships, draw conclusions, learn from them and make an assessment or prediction about them. Data is the raw material of the future, and this raw material is constantly increasing. The correct handling of the flood of data obtained within the company already forms the basis for tomorrow's decisions. This much is already clear today: paper means 100% data loss.
bioMérieux is the world's leading provider of microbiological laboratory diagnostics solutions for the food and pharmaceutical industries. The French family-owned company has been developing and distributing sales for more than 60 years of microbiological test systems and associated software solutions. With its Augmented Diagnostic Approach, bioMérieux is also doing pioneering work in this area.
Augmented Diagnostics Approach in the Beverage and Brewing Industry
In order to provide a reliable foundation and to educate decision-makers and actions, quality-assuring diagnostics must not only obtain relevant data, but primarily reliable data. Data must be collected in a standardised and consistent manner to ensure that it is comparable and has not been distorted by unexpected influences. This is where diagnostics with a high degree of automation, which deliver objective results and are copied to laboratory information systems, score points.
The analysis of the flood of data obtained and the faster and more accurate interpretation of sometimes complex amount of data are also important focuses. Analysing the collected data can help identify the root cause of a problem and plan preventive corrective actions before a contamination occurs. Suitable assistance systems can also increase the efficiency of the quality system itself. However, the long-term goal of the Augmented Diagnostic Ecosystem is to allow users to benefit from the data. This means learning from experience and data through AI systems, recognising patterns and correlations, making quick and correct decisions, and preventing emerging problems. To put it plainly: to scratch yourself before it itches.
How good is your data?
Classical microbiological methods can only be standardised to a limited extent, and the susceptibility to errors is generally quite high. In addition, cultural methods only ever offer a "diagnostic window", so it is always possible that problematic spoilers or pathogens remain undetected. Microbiology is considered complicated and always requires a deep understanding of the underlying structures in order to manage them effectively.
As already mentioned, the loadability of the data is the basis of Augmented Diagnostics. In order to be fit for tomorrow, laboratory processes must be set up today in such a way that random human errors are avoided.
Here, for example, are two of our laboratory systems for the beverage industry:
D-COUNT® is used to detect or exclude bacteria and yeasts in fruit juices or their precursors. We deliberately avoid cultural enrichment media as far as possible, which at best serve as an artificial model of the food you produce. We focus on the milieu in which the spoilers or pathogen grow in "real life" – namely your products.
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GENE-UP® is a real-time PCR solution that detects specific beverage and beer spoilers, as well as pathogens with the highest precision. In addition, their risk potential for spoilage of beverages or "off-flavour" (e.g. guaiacol formation in Alicyclobacillus spp.) can be genetically determined at the same time as detection. Various fields of application can be found for the systems mentioned, but the main features are the simple workflow, ready-to-use reagents, and the objectified measurements. Routine processes can be understood intuitively, and all protocols are standardised and largely harmonised. This prevents user errors and makes results largely reproducible. In order to ensure the reliability and accuracy of laboratory tests, as well as the analysis of related data, reproducibility of measurements plays an important role.
Another component of the Augmented Diagnostics ecosystem is CONNECT-UP, a data management software. CONNECT-UP connects various laboratory systems with each other and automatically manages the entire traceability of your internal sample workflow and acts as a communication platform between your LIMS, ERP or MES.
What questions can we answer today with the help of digital technologies?
Now let's dive into specific questions that come to mind as soon as the microbiological alarm systems in the company go off:
- What is this strain?
- Has this isolate or strain ever been detected?
- Where can this bacterial strain be found in the production environment of my company?
- Is this strain also responsible for the contamination in the product?
- Did this strain already develop resistance to a particular refining agent?
If bacteria remain in a certain environment for several generations, they are able to adapt to a changed environment ("adaptation"). This occurs via genetic mechanisms, such as mutations in the genome or gene transfer between existing bacterial lineages. Those germs that are best adapted have a selection advantage and multiply faster than other bacteria in the population.
Molecular typing methods are used to detect and analyse differences and similarities between bacterial lineages or strains at the level of molecules. The detection of such sometimes minimal genetic differences between populations of bacteria, which may have occurred only in short periods of time, requires highly discriminatory typing methods. bioMérieux offers a tailor-made service package called Spoilage Mapping for root cause analysis in order to better understand and track outbreaks - together with your quality team - and to take appropriate measures to combat them. DNA sequencing is considered a key analytical method and has revolutionised the biological sciences in recent years. Whole Genome Sequencing (WGS) measures the sequence of all nucleotides (approx. 4.6 million).
In recent years, WGS has become more popular compared to other methods (e.g. 16S rRNA sequencing). Whole genome sequencing (WGS) offers a much more detailed resolution and thus enables a more precise analysis of the entire genome of a bacterium.
The sequence of nucleotides results in a characteristic code, similar to a barcode on food packaging for identification. Today, our partner laboratories are already able to analyze the entire genome within a reasonable time frame, and the costs for this analysis method have been reduced in the various times, so that they can close a diagnostic gap. Beverage producers can benefit greatly by analysing the vast amounts of data in the genetic code.
Without the help of bioinformatics, any sequence information remains of no scientific value.
The task of bioMérieux's bioinformatics team is to analyse, interpret and model biological data derived from laboratory analysis or genomic sequencing.
A key task of sequencing analysis is to identify genes that point to regulatory elements, virulence factors, resistances and other important genetic characteristics of an organism. These can indicate adaptations in your site and serve as valuable information in the fight against stubborn, recurring infections within the food company.
The comparison of genomes of different strains of a bacterial species also reveals the "degree of relatedness" within the isolates found. In this way, pathogen populations from different areas of the plant can be differentiated, networks can be modeled and migration routes of bacteria from the production environment to the product can also be reconstructed.
With the help of the genetic data of the development of these specific kits does not only include the molecular biological detection of specific pathogens or their genetic information. Essential for the design of highly sensitive tests is also the customer-specific sample material, or the environment from which the germ is to be isolated from.
In the future, advancing technologies will make it possible to independently carry out typifications of their target pathogens and thus save valuable time. However, these must also be feasible without relevant technical expertise and must be within reasonable budget.
The AI systems with the help of algorithms recognising data and patterns, and making quality assurance decisions based on them, is still a vision of the future, but by no means a utopia. bioMérieux pursues the higher goal of "augmented diagnostics" and recommends the standardisation of your data, as well as the collection and preservation of pathogens that may be relevant. By means of cryobeads, germs can be infected for years. The company laboratory itself will continue to be kept “frozen in time” and may provide valuable insights at a later date.
An Article by Konstantin Ronfeld. Business Developper Beer Industry Central Europe.
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- Poster IAFP P-2 31 ISO Distinguishable control strains.pdf
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Molecular typing of isolates of the species Pseudomonas aeruginosa from a dairy: Representation of the identified clusters and the phylogenetic Network.
