Jon Kallay - Senior Technology and Market Development Manager Microbial Solutions, Charles River; Tony Cundell - Principal Consultant, Microbiological Consulting, LLC; Jeanne Moldenhauer - Chief Science Officer of C-Polar Technologies, Chief Science Officer, Excellent Pharma Consulting; Mark Hallworth - Life Science GMP Advisor, Particle Measuring Systems; Danielle DeCesaro - Senior Associate Product Manager, Rapid Micro Biosystems; Briana Nunez - Lead Researcher – Microbiology, Sievers Instruments; Dr. Tim Sandle, PhD - Head of GxP Compliance and Quality Risk Management, Bio Products Laboratory Limited; Eric C. Arakel - Global Product Manager, Sterility Testing and Microbial Air Monitoring, Sartorius; Meg Provenzano - Product Manager – Bio-detection, Sievers Instruments
Comparing last year to this year – in general - have there been any significant or interesting developments in microbiology tools and technologies?
Jon Kallay, Senior Technology and Market Development Manager Microbial Solutions | Charles River: I have heard rumors of game-changing technologies since I first started as a microbiologist. The interesting technologies are those that are found to be viable in the manufacturing environment for widespread use. But those technologies pose a business risk – why invest if you can’t guarantee their acceptance for use?
Rapid Microbial Methods are a great example of this development. Rapid technologies, such as Celsis® instruments, allow laboratories to detect microbial contamination in half the time compared to traditional sterility tests, allowing medicine to get to patients faster. Different rapid methods have been around for decades, but rarely used for final product release.
USP Chapter <1223> was published four years ago. With that publication, manufacturers had a road map to gain regulatory acceptance for using a rapid method. Finally, in the past year, multiple companies have presented on validating and using those rapid methods for final product release. This year the flood gates are open, it seems every manufacturer is looking for a way to speed up their laboratory process.
Tony Cundell, Principal Consultant, Microbiological Consulting, LLC: Industry collaborations such as the PEMM/Biophorum, NIST, and the Kilmer Consortia have been active promoting modern microbiological methods. These industry groups have different emphasis’ with the PEMM consortium promoting biofluorescence particle monitoring of air in aseptic processing areas and pharmaceutical –grade water monitoring, the NIST consortium working on the characterization of reference stains of microorganisms beyond the colony-forming unit as standard for the new nucleic acid-based technologies, and the Kilmer consortium working on overcoming the barriers to the implementation of Rapid Microbial Methods in the pharmaceutical industry. All these activities will be useful going forward.
The USP continues to work on the simplification of microbiological method validation and writing modern microbiological methods as general test chapters. For example, an in-process revision of a genomic-based mycoplasma-testing chapter will be published in the Pharmacopeial Forum in September 2022. Same day mycoplasma testing will allow biopharmaceutical companies to aggressively monitor starting material, cell cultures, in-process intermediates, and finished products for mycoplasma contamination.
Jeanne Moldenhauer, Chief Science Officer of C-Polar Technologies; Chief Science Officer, Excellent Pharma Consulting: On the scientific development side, there has been an increase in new products that utilize cationic or anionic polymerization for the inactivation of microorganisms and viruses. It is resulting in many new “self-sanitizing or self-sterilizing” items to utilize in your facilities, e.g., air filters, disinfectants, gowning materials, and protective wear.
Mark Hallworth, Life Science GMP Advisor, Particle Measuring Systems: Possibly the most significant recent development is one that has yet to manifest itself, that is the release of the final version of EU GMP Annex 1. This new regulation includes many factors that will require new ways of performing, recording, reporting, and analyzing the environmental conditions of our cleanrooms. It will require us to demonstrate risk-based control over potential contaminating events. During this period preceding its official release, there have been many upgrades to equipment across the pharmaceutical manufacturing industry that will be better suited to meet the demands of the new regulation. For example, at Particle Measuring Systems, we have extended our single-use microbial sampling technology for continuous use up to four hours. The basis of this sampling method is traditional microbiology so there are no new paradigms in how the data is interpreted, but by using single-use technology (sterile sealed impactor and media devices), we can now continuously monitor a process quantitatively, using active air microbial sampling for extended periods of time. This is a major shift away from settle plates and negates the need to implement and interpret remote monitoring.
Danielle DeCesaro; Senior Associate Product Manager, Rapid Micro Biosystems: There have been recent significant changes in the area of industrial microbiology. As one manufacturing area advances, others have to adapt to keep up. This is the case with manufacturing Pharma 4.0™ where digitization of data and the introduction of robotics, to reduce the frequency of human interactions and errors, has elicited the need for change. The industry trend is also moving to the use of isolator technology for manufacturing processes, often in a modular format to accelerate bringing the facility on-line. Interest in real-time viable air sampling has significantly increased as have the introduction of robotic systems performing bioburden testing from sample to filtration, incubation, and colony counting in a closed environment. Several groups are working to define validation strategies to comply with changing regulatory needs. Underpinning Pharma 4.0™ is the ability to create, transfer, and capture data streams from analytical instruments in the QC laboratory that can then be analyzed remotely. Most of the automated systems recently available in QC Microbiology have addressed this requirement to some degree and are designed to be compliant to the needs of 21CFR Part 11. This is a time of evolution for the microbiology lab that has traditionally been slow to evolve.
Briana Nunez, Lead Researcher – Microbiology, Sievers Instruments: Within microbiology detection, there have been advances in the speed, ease-of-use, and efficiency of testing technologies. For both endotoxin testing and microbial analysis, instrument manufacturers like Sievers are developing products that enable significant efficiency gains in QC Micro labs – from drastic reductions in hands-on time for endotoxin testing, to rapid microbial detection methods. These new technologies introduce automation and speed to help manufacturers reduce risk and make it easier to ensure product quality.
Dr. Tim Sandle, PhD, Head of GxP Compliance and Quality Risk Management, Bio Products Laboratory Limited: One of the most interesting developments is with artificial intelligence, or more precisely, machine learning. This technology holds great promise for improving the accuracy of microbial identifications. The success of this technology rests with the computational power of the algorithm and how well it learns from its errors – this may sound counterintuitive, but algorithms improve by assessing their mistakes more than their successes.
A further application of identification technology is with drug research, especially in assessing candidate antimicrobial compounds. Anything we can harness in the battle against resistant organisms will be a benefit.
Technology is also advancing in the area of microbiological predictive modeling and risk analysis. Here computational analysis is aiding biotechnology and with harvesting microbial metabolites of interest.
Another area that could be see growth is the combination approach of a rapid microfluidic assay and an efficient cell filtration process. Some trials have been undertaken that have the potential to integrate rapid tests directly into pharmaceutical microbiological screening workflows. The aim here is to reduce end-product testing by assessing microbial bioburden in real time.
Has the pandemic and associated supply chain issues affected the delivery of microbiology tools and technologies to industry? How have you responded to this situation?
Cundell: The COVID-19 global pandemic and trade disruptions between the United States and China have created supply chain issues. Early in the pandemic there were serious shortages of gloves and masks. The surge in demand for disinfectants and hand sanitizers to combat the virus has led to shortage of these materials in the pharmaceutical industry. This was magnified by the over emphasis of disinfection in combating a respiratory virus, spread largely by airborne aerosols and droplets and not contact with surfaces. It was viewed as cheaper and simpler to apply a disinfectant than increase the number of air changes per hour in building. The well-intended FDA policy of providing temporary registration to foreign manufacturers to making alcohol hand sanitizers has led to hundreds of recalls of methanol adulterated hand sanitizers mainly from Mexico. A classic example of an unintended consequence.
In addition, my colleagues in industry report spot shortages of microbiological media, disposable laboratory items, tubing, syringes, sterile diluents, and single-use disposable processing equipment.
Responses to this situation include establishing standing orders with primary suppliers to lock in your supply, identifying and qualifying alternate suppliers to reduce risk, managing the usage of supplies more carefully, and air freighting supplies from company sites in one region to another region of the world.
Moldenhauer: It is more important today to really plan for the laboratory needs and not let your supplies get too low. The old days of calling and getting the supplies the next day is not guaranteed any more.
Hallworth: Supply Chain issues have definitely had an influence on availability of parts for the production of instrumentation. This delayed both the manufacturing of existing instruments, and the engineering of new products. As part of the Spectris group, we were fortunately able to leverage our relationships with our other operating companies to mitigate the effect. Instituting long term supply contracts and stocking larger quantities of parts helped ensure availability and allowed us to keep delivering products to our customers.
DeCesaro: We have seen a ripple effect from the pandemic that has had an impact on all industries including Microbiology. It is no secret that there have been many challenges within supply chains, ranging from product availability to extended lead times. The surge from COVID research has contributed to supply disruption, primarily due to an increase in demand and a limit on raw materials and resources including labor shortages.
In response to this situation, we are focusing on a few key areas: increasing safety stock levels on long lead items, engaging in more frequent communication with customers (internal/external) on the extended lead times, and solidifying alternate sources to avoid single streams.
Eric C. Arakel – Global Product Manager, Sterility Testing and Microbial Air Monitoring, Sartorius: The pandemic has without question been a period of turmoil. We have faced challenges at several stages: raw material shortages - polymers/resins for instance, bottlenecks at sterilization sites due to an increased demand in single-use technologies, personnel staffing shortages due to illnesses, disruptions in freight services, reprioritization of manufacturing lines internally and at suppliers - the list is long.
Our forecasts couldn’t have prepared us for the immense surge in demand. We’ve had to qualify second suppliers in record time, simultaneously validate multiple sterilization vendors to ensure seamless access to irradiation slots, increase the number of work shifts and hire new personnel, implement manufacturing technology upgrades to make processes more efficient, renegotiate supply contracts and help suppliers network with other pre-approved vendors. We may not have always got it right, and we’ve had our fair share of run-ins with Murphy’s law, but, we have always tried our very best to cater to all our customers’ needs.
By all appearances, we have exited the pandemic tunnel. We aren’t in the clear though. The war in Ukraine has had an additional impact on several technology sectors, electronics being one of them. Inflation is on the rise and prices of components have skyrocketed. To avoid the dominoes toppling and a subsequent increase in the cost of therapeutics, we are trying our hardest to limit passing these cost increments on to our customers. Uncertain times do call for creative measures.
Nunez: Many companies have seen disturbances in their production due to supply chain issues arising from the pandemic. Longer lead times, more time spent sourcing alternate materials, and increased financial commitments to secure parts have potentially reduced the overall growth of certain companies producing microbiology tools and instruments. Our company has invested in improving our relationship with vendors and committing to purchasing larger quantities to reduce the potential of long lead times making materials unobtainable.
Sandle: The biggest impact from the pandemic was with swabs used for environmental monitoring. Several studies across the past decade have shown the superior recovery from flocked swabs compared to plain swabs. The problem was that many COVID-19 test kits required flocked swabs, leading to a shortfall in the marketplace.
This impacted cleanroom monitoring. To a degree some locations can be switched to contact plates, but these cannot be used for critical swabs like filling needles. Returning to plain swabs would have been a retrograde step, so supplies had to be carefully controlled.
The pandemic also impacted on cleanroom clothing, especially masks. A number of vendors were offering masks with a lower bacterial filter efficiency; these had to be avoided, otherwise the risk of operator derived contamination could increase (including oral bacteria like Streptococci).
Some firms also had shortfalls of reagents. Plus, getting disinfectants was not always straightforward. We had to qualify some different biocides in order to have sufficient disinfectants to maintain cleanroom controls.
As microbiology detection and control efforts become more comprehensive, detailed, and labor intensive, what are some strategies pharmaceutical companies can implement to analyze, store and leverage the data being collected?
Kallay: So much data is generated from a typical environmental monitoring program. Recent drafts of Annex 1 even include enhancements to a site’s program, such as periodically repeating EMPQs. For a robust EMPQ, a site must ID most of their recoveries to track and trend what’s most common in the environment. One way is to use Accugenix® tracking and trending. Simple spreadsheets are not capable of storing all this data in a useful way.
My suggestion: leverage all your resources, including business partners like your equipment and service vendors. They developed the technology like your Identification, rapid method, or LIMS systems. They have the SMEs on that technology. They’re motivated to get you up and running using those systems, so they should stand by them with IQOQ and validation support. They’re also open to feedback which can lead to new features to support your site.
Finally- make sure all that environmental data works for you. It’s “easy” to collect thousands of data points just to store the results. However, investigating trends, even if they don’t amount to alert or action levels, can prevent those alerts and actions in the future. Acting on this data early to prevent microbial failures shows regulators you embody a culture of continuous improvement.
Cundell: The instrumentation used with modern microbiological methods is more automated and computerized than the manual methods they replace. Tools to take advantage of this automation and increase in data generation include bar coding test samples, downloading data to databases for control charting, increase graphic presentation of results, standard report generation, and the interfacing standalone instruments to LIMS and Quality Management Systems.
Hallworth: There have been new/alternative Microbiological methods available for routine usage on the market for some time now; however, most testing is still performed with traditional methods. The fundamental difficulty for analytical methods is still the same: local experts must decide which method will deliver scientifically sound and quality data, and how this data can be converted into valuable information. Only when you have the right scientific information are you enabled to make well-informed decisions on the process (CAPA). A very good example of software that ties data together from different angles, and enables actionable information, is PharmaIntegrity software from Particle Measuring Systems, which combines total particle environmental monitoring data with the full set of microbiological data, enabling a 360° view of your environment.
DeCesaro: Automated testing and digitization are critical to easing the labor requirements of more comprehensive and detailed microbiology detection and control. With cloud technologies such as AWS, Google Cloud, and others, the additional analysis and access to data is enriched. Leveraging the data into established processes will always be more company policy specific, but with data integrity and automation providing the assurance that the test result for a location is accurate, information can quickly be accessed via dashboard and quick decision making is enriched.
As process efficiency and product performance data becomes readily accessible through Pharma 4.0™, the capability of decentralized decision-making through automation is adopted. A strategy that we recommend is implementing automation instruments, like the Growth Direct® System, that are proven to connect into LIMS platforms and have the flexibility necessary to pull large amounts of data into various formats based on the outputs the company needs.
Meg Provenzano, Product Manager – Bio-detection, Sievers Instruments: The pandemic has amplified the need for digital solutions for microbiological testing. Having the majority of the workforce working from home required creative solutions for signing off on data, thus many customers looked to suppliers for software solutions. Sievers DataShare Elite allows users to bring in all their Sievers TOC and conductivity data - whether from a single site, or from multiple sites worldwide - into one platform. Digital signatures allow users to sign off on data from the lab, an office, or from home. Audit trail data can be brought into the software too, allowing QC Managers to easily review audit trail data.
Sandle: Automation is set to be the big growth area. Examples include the development of robotic endotoxin testing (there have been different concepts across the past twenty years and now technology has improved considerably). This would not only sabe time, it will also improve assay performance.
To me the biggest gain will be from automated agar plate incubation and reading. The technology that is coming through also provides the advantage of enabling earlier reads and all reads have a greater accuracy than can be obtained by human vision. The types of technology used include blue light excitation. Considerable labor saving arises through high-throughput plate incubation and rapid reading.
Other technologies that will see labor saving are those that step away from conventional microbiological media and assess samples in real time, such as through cytometry or epi-fluorescence.
Specifically, what types of microbiology technologies or services are pharmaceutical companies currently most interested in? Are there any conclusions you can infer from this observation?
Kallay: Automation! Almost every laboratory team I’ve spoken to in the past year has expressed some concern about labor shortage. There are too many laboratories to manage, and not enough microbiologists to work them. There are lots of repetitive tasks in the laboratory that can burn out employees quickly, like pipetting, sample filtration, and plate counting.
Any machine that can perform those tests eases the burden on the lab. Automated Endotoxin testing systems that exist today, such as Endosafe® testing systems, can pipette and plate large number of samples, taking that out of the analysts’ hands. Automated enumeration systems that can count microbial colonies on a variety of microbial test plates are in development. These systems have a bright future in streamlining the laboratory workflow.
Data integrity goes together with automation. Systems that objectively analyze results have a distinct advantage over manual reads. Small, clear colonies on white filters can be easy for an analyst to overlook, allowing a contamination event to remain unseen in the environment. Differentiating turbid vs non-turbid sterility containers can be nerve wracking. Automated, objective tests systems don’t have to struggle with those decisions.
Cundell: There has been an increased interest in automated plate readers as a response to data integrity questions and a shortage of lab personnel. However, there is yet to be a consensus on the reliability of these plate readers and what needs to be done to qualify them for routine use.
Another area of interest is in moving modern microbiological methods from the laboratory to the factory floor. For example, in an aseptic processing area you can make a significant improvement in environmental control using biofluorescent particle counters in critical areas. These counters improve clean room practices and detect loss of environmental control in real time and will significantly contribute to sterility assurance.
In gene and cell therapy production and pandemic vaccine manufacture there is an intense interest in rapid sterility/microbial contamination detection using modern microbiological methods in place of a growth-based compendial sterility test with an incubation time of at least 14 days, which is not suitable for short-lived or high demand products.
Moldenhauer: In many ways, companies have become more skeptical of rapid microbiological methods. It is not a lack of interest in them, but a frustration with the performance of the methods and the original claims of how the system benefits the laboratory. Unfortunately, when you implement the systems, you may not see the benefits or reduced time to release or other claims, it may not instantly result in the benefit. We often find out that other systems also need to be updated to realize all of the benefits.
Hallworth: Particle Measuring Systems often fields requests for, and provides solutions to meet, changing regulations. One way we do this is with Advisory Services that deliver customized and comprehensive risk assessments using air and surface environmental monitoring to demonstrate control over clean manufacturing areas. The control processes that result from these risk assessments are fully documented and traceable per existing and upcoming regulations.
There are also more requests from the industry for faster and more accessible data. This shift toward real-time, easily accessible data gives a better reflection of the conditions, as they occur, in controlled environments. The combination of enhanced traditional technologies, and their applications, will provide new insights and will control the risks to processes in a manner that is proven and tangible to finished product quality.
DeCesaro: Rapid microbiological methods frequently utilize some form of lab instrumentation. In smaller phases of the method’s development, the instrument is a stand-alone piece. We are seeing an overall rise in connection to Pharma 4.0™, as many pieces of process analytical technology as possible are desired within the pharmaceutical plant. These methods can include ATP bioluminescence, autofluorescence, biosensors, molecule detection, flow-cytometry, etc. There are many methods of interest to pharmaceutical companies, but the overall trend is accurate and rapid microbial results with the flexibility to fit the established process boundaries and integrate into LIMS systems without human error.
The focus of the pharmaceutical industry is the safe production and release of life-saving medications. This singular goal, paired with desired efficiencies in manufacturing processes, supply chain, and pandemic-altered workforce have demonstrated that combining automated technologies and data integrity to enable a streamlined process is crucial as the industry evolves.
Nunez: Rapid Microbial Detection Methods, or RMMs, have been an interest within the industry for a multitude of reasons. RMMs are technologies that allow pharmaceutical companies to receive microbiology results faster than compendial culture plates. RMMs reduce the risk to patients and allow companies to release products sooner. In the event that contamination is detected, investigations and corrective actions can be implemented sooner allowing for a more consistent manufacturing process.
Provenzano: In addition to more efficient microbiology technologies, firms are also interested in evaluating technologies that offer sustainable solutions. Take the Bacterial Endotoxin Test, for example. With endotoxin testing there’s a lot of debate out there on horseshoe crab (HSC) sustainability. Many firms are looking for a solution that reduces the amount of HSC blood consumed. There are alternative methods out there, but these require lengthy validation work. The Sievers Eclipse offers users the opportunity to use less HSC reagent, up to 90% less in fact, while using an FDA approved reagent and with no need for lengthy alternative method validations.
Sandle: It is increasingly common to hire in decontamination experts for cleanrooms, especially coming out of shutdowns and maintenance periods. Using a sporicidal vapor is often more effective than operator-led manual disinfection methods.
In terms of services, contracting out seems to be more common again (this has always been cyclical). This seems particularly so in areas like raw materials microbial enumeration and specific organism testing. Larger laboratories see ordering in smaller stocks of specific agars time consuming and costly.
Another area for outsourcing is with genotypic identification testing. Few laboratories will adopt this type of technology (such as riboprinting or PCR), mostly due to time-to-result and cost per test. However, genotypic testing is often useful for contaminant matching (to work out the origin) and where the unfortunate events of sterile manufacturing occur – sterility test failures or media fill positives.
Finally, what long-term changes has the pandemic left on the industry in general and microbiology specifically?
Kallay: My earlier answers hint at this industry trend. Laboratories want to get microbiological results faster so they can release product to patients in need. This was incredibly important during the development of COVID vaccines and treatments. Industry leaders in these medicines have presented at conferences on the implementation and use of rapid methods to meet that goal.
It’s also not surprising that a pandemic caused by a communicable respiratory pathogen has caused the workforce to shy away from in person workplaces. With fewer people wanting to be in the lab, laboratories need automation that can do those jobs. This is great news for R&D mechanical and software engineers! Even microbiologist consultants are needed to develop these systems. As these automated activities continue to work their way into the manufacturing workflow, we may see a massive reduction in the human-caused contamination associated with cleanrooms. More good news!
Cundell: The pharmaceutical industry is now more mindful of their supply chain, recognize the need for flexibility in manufacturing and testing as the demand for COVID vaccines and antivirals surged and the demand for other drugs decreased due to reduced elective surgery and doctor visits.
The role of Contract Manufacturing Organization in the rapid development of pandemic vaccines and ant-viral drug must be acknowledged. They are a critical part of our industry.
In addition, the achievement of developing mRNA COVID vaccines, conducting extensive clinical trials with a diversity of subjects, obtaining regulatory approval, and distributing the vaccine in less than one year from the sequencing of the virus is truly remarkable in that the shortness timeline for a previous vaccine was four years. This inspiring achievement from the federal research establishment, American pharmaceutical companies, and the FDA should provide an accelerated pathway for future drug development.
Moldenhauer: One of the biggest concerns I have seen is ensuring that personnel are protected. While PPE has been used for a long time, there are now improvements in technology that can improve safety for all employees (e.g., people handling filters to remove them). The other big issue has been dealing with absences and the need for cross-training and back-ups for all individuals performing testing.
Hallworth: The industry, governments and the public now understand that reaction times in crisis can save lives, and that only having access to state-of-the-art science can enable the most effective outcomes. Traditional Microbiology stands in direct contrast to technology and regulatory realities, like Pharma 4.0, QbD and PAT. Manufacturing science can only reach its full potential with innovations in this area, as traditional microbiological methods are one of the rate-limiting steps in the quality and production cycle of modern drugs today.
DeCesaro: As with all industries, there have been challenges in employee retention, supply chains, and establishing new norms of work while continuing to provide products and support to our customers. Some positives of those new norms of work are the enablement and further acceptance of rapid microbiological technologies. As hybrid work continues, personnel will be able to plan limited days in office while ensuring the highest quality of work.
The pandemic has left many long-term changes to the industry, with one of the obvious being virtual collaboration. However, a change or shift that I see being the most impactful over the next few years is the need for laboratory automation and process optimization. Due to the shifts in the labor market and constraints on resources, microbiology laboratories have turned to laboratory automation, digitization, and workflow optimization to gain efficiencies. These efforts include adopting new technologies and challenging the industry to innovate in the microbiology space. As organizations begin to see and share the benefits in these changes, more adoption will spread throughout the industry and set the stage for the microbiology laboratory of the future.
Provenzano: The pandemic has left the pharmaceutical microbiology industry craving technological advancement. Firms want rapid results on simple platforms. The pandemic greatly increased the turnover rate in most employment areas, and QC labs can’t afford to lose analysts. It can take months to train an analyst to be proficient in some QC Micro tests - time which firms don’t have. Switching to platforms that allow an analyst to be up and running in days rather months is a huge win for firms. With instrumentation like the Sievers Eclipse, analysts can be qualified and trained in less than a week.
Sandle: Certainly, thinking more rationally about resources. The pandemic enabled the environmental monitoring program to be reviewed, looking at different types of samples and the necessity of each result. In a sense this helped to drive a more risk-centric approach to the topic.
Longer-term, I think the pandemic will help to drive the use of rapid methods, especially those that require smaller sample sizes and reagent volumes.
Another impact is with cleanroom operators. Some of them who have found contamination control concepts challenging came to a greater understanding given the hygiene requirements of the pandemic!
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