Saturday, December 25, 2010

Seasons Greetings from

Seasons Greetings from the staff at and Microbiology Consultants, LLC.

We hope you and all your coworkers, family, and friends have a lovely holiday season filled with joy and meaning. Best wishes for a healthy, peaceful and prosperous New Year.

Wednesday, December 22, 2010

Immunochromatographic strip test for detection of genus Cronobacter

This just in from the December 2010 issue of Biosensors and Bioelectronics. Researchers at the Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Czech Republic, have published a paper that describes a novel method for the rapid detection of Enterobacter sakazakii, now known as Cronobacter sakazakii. Here is the abstract:

Members of the genus Cronobacter are opportunistic pathogens formerly known as Enterobacter sakazakii, which induce severe meningitis and sepsis in neonates and infants, with a high fatality rate. In this work, a simple and rapid immunochromatographic strip test for the detection of this pathogen was developed. Following the shortened bacteria cultivation and isolation of DNA, a specific gene sequence targeting 16S rRNA from Cronobacter spp. was amplified by PCR using 5'-end labelled specific primers. The PCR product, amplicon labelled with digoxigenin on one side and biotin on the other side, was directly added to the immunochromatographic strip test, composed of nitrocellulose membrane with bound antibody against digoxigenin in the test line. The visualization was mediated by colloidal carbon conjugated to neutravidin, and the appearance of grey/black line was indicative of the presence of specific amplicon. Colour intensity of the test line in pathogen-positive assay was visually distinguishable from that of negative sample within 10min. The visual detection limit of PCR product was 8ng. The specificity of the developed method was confirmed by standard microbiological techniques. Whole detection procedure with the incorporated immunostrip was applied to analysis of infant formulae samples, contaminated with less than 10 cells of Cronobacter spp. per 10g. The results from immunochromatographic test indicated the absolute agreement with those from standard microbiological methods. Moreover, the developed procedure considerably reduced the total analysis time to 16h whereas the reference microbiological method needs 6-7 days.

Tuesday, December 21, 2010

MIT Researchers Reconstruct Evolution of 3 Billion-Year-Old Microbes

Computational biologists at the Massachusetts Institute of Technology (MIT) have developed a mathematical model that is capable of using modern genomes to mimic the evolution of ancient microbes. Lawrence David and Eric Alm have traced the evolution of microbes back billions of years using modern genomes in an effort to identify points of change through history.

The Cambrian Explosion, which occurred approximately 580 million years ago, was a period of rapid change on Earth where new life forms came about and contributed to the modern diversity of animals. Paleontologists are able to understand and archive the evolution of life from the Cambrian Explosion until now because of fossils, but recording the evolution of life before the Cambrian Explosion has been difficult due to the fact that soft Precambrian cells hardly left "fossil imprints" behind.

But now, Alm and David have created a mathematical model that paints the picture of life more clearly over the 3 billion year period before the Cambrian Explosion. To do this, they used 100 modern genomes because all living organisms "inherit their genomes from ancestral genomes." All of the possible ways that genes evolve was combined with the mathematical model, such as the fact that new gene families can be born and inherited, duplicated in the same genome, lost, or swapped or horizontally transferred between organisms.

With the 100 modern genomes, researchers were able to trace thousands of genes back to their very first moment on Earth and were able to tell which ancient microbes carried these genes. According to the results, the genome of all life experienced an expansion between 3.3 and 2.8 billion years ago where 27 percent of all existing gene families were born. Alm and David are calling this period of time the Archean Expansion.

"What is really remarkable about these findings is that they prove that the histories of very ancient events are recorded in the shared DNA of living organisms," said Alm. "And now that we are beginning to understand how to decode that history, I have hope that we can reconstruct some of the earliest events in the evolution of life in great detail."

At first, Alm and David believed that the emergence of oxygen was the cause of the Archean Expansion since the new genes they've found are related to oxygen, and oxygen was not available on Earth until around 2.5 billion years ago when it started accumulating and killing off anaerobic life forms during the Great Oxidation Event. But when investigating further, they found that oxygen-utilizing genes didn't exist until the end of the Archean Expansion, which is when geochemists dated the Great Oxidation Event.

After eliminating that possibility, Alm and David now believe they've identified the beginnings of modern electron transport, which is the biochemical process that moves electrons around within cell membranes. The process is necessary for breathing, and is used by plants and some microbes during photosynthesis. It is believed that during the Great Oxide Event, a type of photosynthesis called oxygenic photosynthesis generated the oxygen we breathe today. Ultimately, electron transport's evolution through the Archean Expansion would be responsible for photosynthesis and respiration.

"Our results can't say if the development of electron transport directly caused the Archean Expansion," said David. "Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems."

Micro- and nanocantilever devices and systems for biomolecule detection

I recently came across a review article on the use of micro and nanocantilevers as a rapid way of detecting the presence of a variety of microorganisms. A microcantilever is a device that can act as a physical, chemical or biological sensor by detecting changes in cantilever bending or vibrational frequency. It is the miniaturized counterpart of a diving board that moves up and down at a regular interval based on mass. The mass changes when contaminants land on the devices, causing them to vibrate at a different "resonant frequency, " which can be quickly detected. The authors are from the Korea Institute of Science and Technology. Their abstract is provided below:

Micro- and nanocantilever devices and systems for biomolecule detection. Hwang KS, Lee SM, Kim SK, Lee JH, Kim TS. Annu Rev Anal Chem (Palo Alto Calif). 2009; 2:77-98.

Recent research trends in biosensing have been geared toward developing bioanalytical devices that are label free, small in size, and portable and that can operate in a rapid manner. The performance of these devices has been dramatically improved through the advent of new materials and micro-/nanofabrication technologies. This is especially true for micro-/nanosized cantilever sensors, which undergo a change in mechanical properties upon the specific binding of biomolecules. In this review, we introduce the basic principles of cantilever biosensors in static and dynamic modes. We also summarize a range of approaches to cantilever design, fabrication, and instrumentation according to their applications. More specifically, we describe cantilever-based detections of proteins, DNA molecules, bacteria, and viruses and discuss current challenges related to the targets' biophysical characteristics.

Monday, December 13, 2010

DNA Sequencing Matches Cholera Strain in Haiti with Bacteria from South Asia

A team of researchers from Harvard Medical School, Brigham and Women's Hospital, and Massachusetts General Hospital, with others from the United States and Haiti, has determined that the strain of cholera erupting in Haiti matches bacterial samples from South Asia and not those from Latin America. These findings, which appeared in the New England Journal of Medicine, conclude that the cholera bacterial strain introduced into Haiti probably came from an infected human, contaminated food or other item from outside of Latin America.

To identify the probable origin of the cholera strain in Haiti, scientists used a third-generation, single-molecule DNA sequencing method developed by Pacific Biosciences. They determined the genome sequences of two Haitian cholera samples and three cholera samples from elsewhere around the world. Based on advanced imaging technology, the method enables researchers to observe a natural enzyme synthesizing a strand of DNA in real time. As such, the technology actually tracks and documents nature at work, a rapid approach compared to other sequencing technologies. The method allowed a comprehensive analysis and comparison of critical DNA features among the various cholera samples, which included single nucleotide variations, insertions and deletions of particular portions of the genome, and structural variations. The analysis showed a close relationship between the Haitian samples and the seventh pandemic variant strains isolated in Bangladesh in 2002 and 2008.

Genetic changes occur quickly, within hours in the lab and probably weeks within the environment, through natural modes of DNA swapping and mutation among bacteria. Their evolution is based, in part, on the acquisition, loss, and alteration of mobile genetic elements, including DNA from the CTX bacterial virus, which bears the genes encoding the cholera toxin, and other genetic sequences that may make a particular strain more adapted to a given ecosystem. The resulting heterogeneity has been used to categorize strains of the seventh pandemic and to understand their transmission around the globe.

Wednesday, December 8, 2010

UTHealth professor to receive service award from American Society for Microbiology

Known nationally for her research into single-cell organisms that affect oral health, Millicent "Mimi" Goldschmidt, Ph.D., a professor of microbiology and molecular genetics at The University of Texas Health Science Center at Houston (UTHealth), has been selected to receive the 2011 American Society for Microbiology (ASM) Founders Distinguished Service Award. The award will be presented at the ASM General Meeting Awards Banquet and Dinner in New Orleans on May 22.

"Dr. Goldschmidt has furthered the understanding of the basic microbiology of the mouth," said Larry R. Kaiser, M.D., president of UTHealth. "She has done an exemplary job of serving her professional community, her scientific community and her teaching community." Microbiology is the study of cells that are invisible to the naked eye. These tiny cells include bacteria, viruses and fungi. Goldschmidt studies microbes involved with dental decay, gum disease and oral cancer, as well as rapid methods of detection (biosensors, microarrays and nanoparticles).

Before joining the UTHealth faculty in the early 1970s, Goldschmidt was the coordinator of the protocol to plan the biological tests that would be employed in the lunar receiving laboratory on the first returned moon rocks. She was also instrumental in developing isolation protocols for Apollo astronauts returning from the moon, which ensured that infectious organisms would be detected and contained.

When she started her professional career in Texas five decades ago, Goldschmidt said there were really no rapid methods to detect microorganisms. Her research contributed to the development of rapid immunological and biosensor types of detection methods to pinpoint salmonellae, E. coli and oral microbes. She consults and lectures nationally and internationally on biosensors, microarrays and nanoparticles.

Sunday, November 28, 2010

A mobile phone app that detects STDs!

This just in from the UK-based newspaper, The Guardian. People will soon be able to tell if they have an STD by urinating on a small computer chip and inserting it into a mobile phone or computer, doctors and scientists in Britain claim. The small devices, similar to pregnancy testing kits, will reportedly be able to give people a home diagnosis within minutes. Millions of pounds have been poured into the project to combat an STD epidemic in Britain, where infections reached a record 482,696 last year. The research has been given the thumbs up by Professor Noel Gill, the head of HIV and STIs at the British government's Health Protection Agency, who said he hoped the application of new technology would reduce infections among young people. The HPA would coordinate large-scale evaluations of the technology within a network of collaborating STI clinics.

"Your mobile phone can be your mobile doctor. It diagnoses whether you've got one of a range of STIs, such as chlamydia or gonorrhea and tells you where to go next to get treatment," Dr Tariq Sadiq, the sexual health expert from the University of London who is leading the project. The developers of the rapid testing devices - which include experts in microbiology and phone operators like O2 - expected them to be sold for a pound each in vending machines in nightclubs, pharmacies and supermarkets.

I am aware of at least one RMM company that is able to control their technology via a mobile device, so this type of communication platform is certainly a viable opportunity for the industry.

Tuesday, November 23, 2010

Fung’s Double Tube Leads Way to Quicker Pathogen Detection

When government and industry were looking for a way to identify more rapidly the presence of the pathogenicClostridium perfringens bacterium in food and water, Daniel Fung of Kansas State University realized he had a potential solution on his shelf. He applied what’s known as the Fung Double Tube method that he developed decades earlier and determined that the detection time can be reduced from about a day or two down to four hours.

“In the meat industry and related food industries, the faster one can detect and enumerate live major pathogens such asC. perfringens, the faster corrective actions can be implemented or the food can be destroyed before reaching the consumers,” said Fung, a food science professor who researched the issue as a Food Safety Consortium-supported project. “The benefit of a rapid method to detect and enumerate live C. perfringens in foods in four hours is obvious.”

The Fung Double Tube method is relatively easy to implement. The system uses one large tube and one small tube. Insert the small tube into the larger tube that holds a water sample. Then add a specially melted agar – a gelatin-like product used for solidifying culture media as a thickening agent – to create a thin layer between the two tubes that will grow C. perfringens. The unit is then placed in an incubator at 42 degrees C.

“The system makes anaerobic microbiology very simple,” Fung said. “One can see a C. perfringens colony in the Double tube in about four to five hours. We can know in five to six hours how many living colonies of C. perfringens per milliliter of water there are. That is a major improvement and it’s so cheap.”

The system works well for water testing, but more research is necessary to prepare it for use in the food industry. Fung’s research team is examining how to apply it for use with ground beef so the meat won’t have to be incubated overnight before pathogen counts can be obtained.

More Accurate Diagnostic for Influenza and Respiratory Syncytial Virus Using Nanoparticle Probes

According to a paper in the November Journal of Clinical Microbiology, a new, fully automated system based on nanoparticle probes has been developed for the detection of influenza A and B, and respiratory syncytial virus (RSV) A and B. The new technology promises faster and more appropriate treatment of patients. The full reference is as follows: P. J. Jannetto, B.W. Buchan, K. A. Vaughan, J. S. Ledford, D. K. Anderson, D. C. Henley, N. B. Quigley, N. A. Ledeboer. 2010. Real-Time Detection of Influenza A, Influenza B, and Respiratory Syncytial Virus A and B in Respiratory Specimens by Use of Nanoparticle Probes. Journal of Clinical Microbiology; 48.11: 3997-4002.

"Instead of relying on insensitive but rapid influenza tests for diagnosis in the clinic, or waiting 24 hours or more for molecular results to come back, we can now provide molecular level sensitivity in less than three hours," says principal investigator Nathan A. Ledeboer of the Medical College of Wisconsin, and Dynacare Laboratories, Milwaukee.

"This will mean that hospitalized patients with influenza and RSV infections will be isolated faster, which will decrease the risk of transmission to other patients in the hospital," says Ledeboer. The faster turnaround also means that "fewer patients will be placed on empiric therapy, which will decrease costs and decrease the risk of an adverse event caused by medication." In the study, the assay, a microarray, was tested on 720 patient samples collected throughout the US.

The new technology, called Respiratory Virus Nucleic Acid Test SP" (RVNATsp), is 98 percent sensitive (meaning that 98 percent of positive results are accurate) and 96 percent specific, meaning that 96 percent of negative results are accurate). By comparison, the conventional alternative, culture, is nearly 100 percent specific, but only 70 percent sensitive.

Influenza virus infects millions annually. It is typically associated with infections of the upper respiratory tract and can cause mild to severe illness. RSV can cause severe symptoms in infants, young children, and immunocompromised individuals, and is the leading cause of hospitalization of children under five years of age. In the most vulnerable individuals, children less than six months old, people with chronic lung disease, and immunocompromised individuals, RSV can migrate from the initial site of infection in the upper airway to the smaller bronchioles of the lower airway, where it can cause life-threatening bronchiolitis or pneumonia.

Monday, November 15, 2010

A New Read on DNA Sequencing

I came across a very interesting article on gene sequencing. Biophysicist Stuart Lindsay, of the Biodesign Institute at Arizona State University, has demonstrated a technique that may lead to rapid, low cost reading of whole genomes, through recognition of the basic chemical units, the nucleotide bases that make up the DNA double helix. His group's research appears in the current issue of the journal Nature Nanotechnology.

Lindsay's technique for reading the DNA code relies on a fundamental property of matter known as quantum tunneling, which operates at the subatomic scale. According to quantum theory, elementary particles like electrons can do some very strange and counter-intuitive things, in defiance of classical laws of physics. Such sub-atomic, quantum entities possess both a particle and a wave-like nature. Part of the consequence of this is that an electron has some probability of moving from one side of a barrier to the other, regardless of the height or width of such a barrier. Remarkably, an electron can accomplish this feat, even when the potential energy of the barrier exceeds the kinetic energy of the particle. Such behavior is known as quantum tunneling, and the flow of electrons is a tunneling current. Tunneling is confined to small distances, so small that a tunnel junction should be able to read one DNA base at a time without interference from flanking bases. But the same sensitivity to distance means that vibrations of the DNA, or intervening water molecules, ruin the tunneling signal. So the Lindsay group has developed "recognition molecules" that "grab hold" of each base in turn, clutching the base against the electrodes that read out the signal. They call this new method "recognition tunneling."

To read longer lengths of DNA, Lindsay's group is working to couple the tunneling readout to a nanopore -- a tiny hole through which DNA is dragged, one base at a time, by an electric field. Sequencing through recognition tunneling, if proven successful for whole genome reading, could represent a substantial savings in cost and hopefully, in time as well. Existing methods of DNA sequencing typically rely on cutting the full molecule into thousands of component bits, snipping apart the ladder of complementary bases and reading these fragments. Later, the pieces must be meticulously re-assembled, with the aid of massive computing power.

Lindsay stresses much work remains to be done before the application of sequencing by recognition can become a clinical reality. "Right now, we can only read two or three bases as the tunneling probe drifts over them, and some bases are more accurately identified than others," he says. However, the group expects this to improve as future generations of recognition molecules are synthesized.

Wednesday, November 10, 2010

WIll FDA develop a Guidance on RMMs?

We have a number of compendial (USP and Ph. Eur.) and technical (PDA TR#33) documents at our disposal for the validation of rapid microbiological methods. However, specific guidance is lacking at the regulatory level, as there are no comprehensive written policies from the FDA, EMA, TGA or the Japanese PMDA. During the PDA 5th Annual Global Conference on Pharmaceutical Microbiology, a question was asked to FDA panelists when the Agency would develop a clear guidance document on RMMs. Dr. David Hussong, Director, Microbiology, CDER, responded that In the next few years there will be an internal document that the agency will follow.

Friday, November 5, 2010

Automating the Micro QC Lab (Part 4)

Over the last few months, Steve Delity, President and CEO of Rapid Micro Biosystems, has provided his insights into the benefits of automation in the pharmaceutical microbiology lab. In my fourth and final blog on this subject, I asked Steve to briefly comment on the impact automation may have on validation.

Michael - Anyone who has attempted to validate a rapid solution knows the hurdles that must be overcome. Should companies be concerned that automation adds another level of complexity to the validation?

Steve – Not necessarily. In actuality, this could just be the opposite. A rapid method solution like ours or others in the market can greatly simplify the validation process, as automation could remove a number of validation performance requirements that other alternative methods might require. Additionally, automated methods that are based on compendial testing may also simplify this process. For most compendial microbiology methods, we utilize a certain sample size, media, incubation time and temperature and acceptance limits. Using a rapid method that has similar (or the same) testing elements will be straightforward to validate, since the difference is the automation. Methods that deviate and require different or additional steps may introduce variables and risk factors that will need to be addressed in the validation program.

Thursday, November 4, 2010

New Publication on Rapid Sterility Testing

In this month's American Pharmaceutical Review, Jennifer Gray and her team from Novartis describe the steps they took to select, validate, and gain regulatory acceptance for a rapid sterility test as an alternative to the pharmacopoeial method. The full paper may be viewed and downloaded in PDF format from our References Page ( under the Applications section. An excerpt from their introduction is reprinted below:

There are many reasons why the traditional sterility test, with its lengthy 14 days incubation time, should be replaced with a Rapid Sterility Test. As a consequence to the 14 days incubation time, possible product-contaminations and the respective corrective actions are delayed resulting potentially in an enlarged amount of affected product batches. Another important advantage of shorter incubation time is for example reduction in the release time for sterile products, therefore reduction of stock keeping costs and earlier market delivery. Furthermore, the use of RMMs (rapid microbiological methods) is highly supported by regulatory guidance documents, which request pharmaceutical microbiologists to use these methods.

After the decision had been made at Novartis that a rapid microbiological method for the replacement of the traditional pharmacopoeial sterility test should be validated, the appropriate method for replacement had to be chosen. From many available systems and methods on the market, an appropriate choice for a Rapid Sterility Test based on ATP- Bioluminescence of micro-colonies was made.

Wednesday, October 27, 2010

USP Discussion on RMMs and recommendations for USP Chapter 1223

The final session of this year’s PDA Global Conference on Pharmaceutical Microbiology is focused on the direction that the USP will take with the existing informational chapter 1223, Validation of Alternative Microbiological Methods. Questions were provided to the meeting attendees and here is an excerpt of some of the comments and responses:

Question: Has USP 1223 Validation of Alternative Microbiological Methods been useful or an impediment for the selection, validation and implementation of RMMs?

Response 1: Yes, the chapter has been useful as providing guidance for RMM validation.

Response 2: Yes, but we would like to have more guidance on sensitivity and limit of detection strategies. For example, methods for developing very low inoculum levels, such as 1 cell.

Response 3: The use of statistics for each validation criteria should be more clearly defined and relevant.

Response 4: Much work has been done on limit of detection for sterility testing and these methods are appropriate for use and should be incorporated into the USP guidance.

Response 5: There needs to be a good balance between specific guidance, such as acceptance criteria, and background information into the reasons why the guidance is provided. The chapter should not be a white paper.

Response 6: We need a simple benchmark on how to validate RMMs. The food industry and AOAC have addressed this 20 years ago!

Question: Do you like to see examples?

Response 1: In the EU, regulators took the example in Ph. Eur. 5.1.6 as gospel and that caused many problems for companies validating RMMs. As a result, the next revision of 5.1.6 will not contain an example but will be published in PharmEuropa.

Response 2: I want to see real, practical and successful case studies of how RMMs have been validated, not theoretical examples.

Response 3: Recommendation is not to have an example but to put this information in Pharmacopeial Forum and/or reference other guidance documents that will provide examples, such as PDA Technical Report #33.

Response 4: I want to see guidance on controls based on technology platforms and applications (e.g., negative and positive controls). But don’t provide specific examples, but more suggestions on good controls that should be run.

Question: Should compendial guidance documents (JP, USP, and EP) on the validation of RMMs be harmonized?

Response: By a show of hands, many in the audience said yes.

Final summary statements from the USP based on these discussions:

We may be making this much harder than it should be. We need to go back and take a closer look at our recommendations in this chapter and provide a more “user-friendly” set of recommendations. Because there are many different processes and products that would utilize RMMs, it is really up to you, the users of RMMs, to define how to best validate these new systems. USP intends to provide better guidance on the use of alternative methods with input from stakeholders.

USP 1223 needs to be revised. There needs to be a clarification of sensitivity, limit of detection and limit of quantification, with specific validation criteria and not sole reliance on parallel testing. The use of CFUs is difficult because there is no good quantitative definition of what a CFU is. Statistical models used with validation criteria needs to be revisited. Microorganisms chosen during validation should be appropriate for the intended applications, process and product. We need to consider how to handle slow growing microorganisms, and address the use of appropriate controls.

Next, it appears that specific examples should not be included to avoid regulatory expectations that may not be appropriate. Instead, maybe we should reference PDA TR #33 and/or submit a Stimuli Article. Any reference to specific RMM technologies should not be included.

We should address the relevance of referee tests for short shelf-life products such as biologics.

We should work toward harmonizing all RMM guidance documents; however, this may be easier said than done. This is not a simple matter and could be time consuming. However, we will discuss how we can interact with other organizations to determine if our revisions can take into account other guidance documents.

Finally, we need to have more discussions with the stakeholders of RMMs more frequently than we have in the past, and we will discuss how we can seek out mechanisms to make this happen.

Japanese PMDA Perspectives on RMMs

Following the FDA presentations, Dr. Tsuguo Sasaki, Japanese PMDA, provided his views on the use of RMMs in Japan. The PMDA will work with companies in the development of RMM strategies for use in Japan. For example, in a number of cases, it may not be possible to detect microorganisms in stressed environments, such as purified water and RO test samples. Therefore, it is hoped that more rapid and continuous monitoring methods be developed for microorganism detection in pharmaceutical-grade water systems.

Regardless of the technology, the PMDA will follow a similar strategy for reviewing RMM validation submissions as the US FDA does.

FDA Perspectives on RMMs

Following comment from the Australian TGA, two FDA staff members provided their
perspectives on RMMs. CDER's Dr. David Hussong stated that RMMs are very important for meeting Quality by Design (QbD) principles, smart processing and Process Analytical Technology (PAT). CDER actively encourages the use of new technologies, and the regulatory mechanisms for implementation of RMMs are evolving. For QbD, ongoing analysis of your processes is expected, and continuous improvement strategies should be utilized, in order to facilitate defining and revision of your design space and understanding what changes in your processes are acceptable. For RMMs, current policy provides for the use of comparability protocols and a number of post-approval change strategies, including prior-approval supplements, annual reports and Special Reports.

Next, Dr. Rajesh Gupta (CBER) discussed the use of RMMs as an alternative for sterility testing for biologics. The USP sterility test has been around for decades, and for many years, the test has had a good track record for ensuring product safety. So, why would there be a need for an alternative sterility test for biologics? From a manufacturing perspective, RMMs can provide faster resolution of process problems, screening of raw materials, and implementation of corrective actions. Some biologics have a very short shelf life (e.g., less than 14 days, which is the timing for the incubation phase of the sterility test), are manufactured in small quantities, and immediately required for emergency use (e.g., pandemic vaccines).

CBER’s considerations for a RMM for biologics are viewed on a case-by-case situation depending on the product. The RMM should preferably be a non-destructive technology (the expectation is that a sterility test contaminant can be identified), or use the same/comparable technology as the current methods *i.e., growth-based. The RMM should also be shown to detect VBNC organisms. Some non-acceptable practices when validating a RMM test includes the use of 10-99 CFU of test organisms as cited in the USP and CFR. However, the expectation is that you use less than 10 CFU, and include environmental isolates and stressed organisms. Furthermore, you should look for product interference and run the existing and RMM in parallel. The FDA labs compared the MilliFlex Rapid, BACTEC FX and BacT/ALERT systems as potential RMMs for sterility testing. Dr. Gupta stated that the MiliFlex system shows promise as an alternative sterility test for filterable products, and that the other two methods were not as sensitive with regard to a lower spike of organisms and in products containing thimerosol. In these cases, modifications may need to be made to the latter two RMMs.

In summary, CBER supports the application of RMMs for sterility testing. However, because there are not many applicants coming forward, this is the reason why the FDA labs have conducted their own validation and comparability studies.

Regulatory RMM Perspectives at the PDA Global Microbiology Conference: The Australian TGA

Yesterday, I reported on the Compendial RMM session where we heard from the chairs of the USP, Ph. Eur. and the JP. Today, global regulators representing FDA, the Japanese PMDA and the Australian TGA provided their current perspectives on rapid microbiological methods.

Vivian Christ, Australian TGA first reviewed some of the policies and guidance that they follow with regard to RMMs. The TGA utilizes relevant sections in the Ph. Eur. and BP in that these compendia allow for the validation alternate methods. They also rely on the validation guidance from USP 1223, Ph. Eur. 5.1.6, PDA TR #33, and ISO 17025 (validation of non-standard methods), to name a few. From the legislative perspective, the TGA turns to the TGA GMPs, which allows for other acceptable methods as long as they are shown to be equivalent to those in the GMP guide, as well as Annex 11 (computer validation) and Annex 15 (IQ, OQ, PQ). However, unlike other regulatory agencies, such as the FDA, the TGA only “quietly” embraces new technologies but they have not come out with a formal statement or policy.

The TGA views RMMs to be used in a wide range of applications, including finished product testing and in-process testing. Validation expectations include a DQ, IQ and OQ performed by the vendor, and the PQ (jointly performed by the vendor and user) and verification of the method using actual product. Testing on potential interfering substances should be performed, and for users intending to develop a matrix testing strategy (i.e., grouping products together), a justification for doing so should be provided. Furthermore, there is the expectation that equivalence or superiority to classical method is demonstrated, as well as the computer validation of software. For a qualitative method, the validation should address specificity, sensitivity, ruggedness, robustness, and equivalence. For quantitative tests, the user should demonstrate accuracy, precision, ruggedness, robustness, equivalence sensitivity, linearity, and specificity.

Many companies have discussed implementing RMMs with the TGA but very few have actually taken the plunge and have moved forward. The TGA doesn’t really understand the reason for this. However, when companies do come in to discuss their intentions, the TGA encourages them.

TGA does have some regulatory concerns. For example, what happens if a company obtains a positive result by a RMM but not the referee test (what does this mean?). Next, do specifications need to be changed, and how will the company use the results from RMM testing, such as batch release? All of these points must be considered. From an administrative perspective, the local inspectors are starting to see RMMs but primarily for in-process testing, where there is no requirement for a formal regulatory change submission. Additionally, there is no published policy on the testing requirements for RMMs. From an economic standpoint, the TGA is considering cutting the costs associated with formal change submissions and RMMs, such as lumping many products together for a single RMM. Hopefully, we will hear more about this in the near future. In summary, the TGA hopes that more companies will move forward, validate and implement RMMs.

Tuesday, October 26, 2010

Pharmacopoiea Perspectives on RMMs Provided by USP, Ph. Eur. and JP Expert Committees

The Chairs of the USP, Ph. Eur. and JP provided their perspectives on the current and future state of rapid methods and plans for revisions to existing monographs and information chapters.

Dr. James Akers, USP Expert Committee, explained that any new United States Pharmacopoeia referee method must be very broad in application and suitable for use with the vast majority of monograph product. Furthermore, new candidate methods must not be from a patented, single-source technology. It is also critical to be clear on the distinction between QC quality control release testing versus in-process testing and monograph requirements. Therefore, companies that desire to submit a RMM for inclusion in the USP as a referee test must take these points into consideration. USP 1223 was developed to provide guidance on the implementation/validation of alternative methods, and this chapter should be used to support the use of a RMM as an alternative to a compendial test. To clarify, RMMs and alternative methods are already allowed under USP 62, as long as they are appropriately validated. Finally, the USP is looking to the industry to comment on the existing chapter 1223 in order to support future revision processes in this area. This will be discussed in further detail in a subsequent session tomorrow (check back for my blog covering this session!).

Dr. Han van Doorne, Ph. Eur. Expert Committee, stated that the General Notices section of the European Pharmacopoeia and Chapters 2.6.12 and 2.6.13 state that alternative methods may be used as long as they have been shown to be equivalent to the existing compendial methods. Chapter 2.6.27 states that automated systems may be used for the control of cellular products (e.g., for the daily observation of sterility). A separate chapter on the use of nucleic acid technologies for the detection of Mycoplasma (2.6.7) is also available, and Ph. Eur. 5.1.6 was developed to provide guidance on the validation of alternative microbiological methods. Dr. van Doorne then discussed the committee’s plans to revise Chapter 5.1.6. They would like to add more information on Process Analytical Technology (PAT), a better distinction for methods for isolation and detection, and for microbial identification. The examples at the end of the current chapter should be improved and expanded to include the validation of ID methods. However, these examples will not appear in a future revision of the chapter, but rather, it will be published as a separate white paper in PharmEuropa. The future revision of this chapter will also include updates to technologies and applications and a greater explanation of DNA-based methods. Finally, he discussed a survey that was sent to the industry asking what companies would like to see in a revision of Chapter 5.1.6. Questions included the following: what applications have been approved for use with RMMs, do you use RMMs for testing other than batch release, would you favor more validation examples, what are the strengths and weaknesses of the existing chapter, did the chapter facilitate applications to regulatory bodies, do you consider the chapter example (Annex) useful, and what compendial methods have been replaced by a RMM.

Dr. Tsuguo Sasaki, Japanese Pharmacopeia Expert Committee, PMDA, described two new RMM chapters that are now part of the Japanese Pharmacopoeia. These include Chapter 22 (Rapid identification of microorganisms based on molecular biological methods) and Chapter 33 (Rapid enumeration of bacteria based on a fluorescence staining method). He then provided some examples of where RMM validations were not at a level that was accepted by the Pharmacopoeia. For example, an ophthalmic manufacturer submitted a validation package for a RMM with a shortened sterility test (2 weeks for the compendial method to a 1 week incubation followed by ATP bioluminescence technology). The company validated the system using soybean casein digest medium instead of a medium that would recover more stressful or injured microbes. For this reason, the submission was not approved. Dr. Sasaki then presented data demonstrating that micro-colonies of a particular organism developed on R2A medium but not on TSA (this is one reason why the original submission was rejected). Therefore, the company would be required to go back and investigate the most appropriate media for this purpose (for a strategy that has already been approved by the FDA, EMA and MHRA, please see my earlier post describing this type of validation by Jennifer Gray at Novartis).

Rapid Method Session 2 at the PDA Global Microbiology Conference

Sara Polson, Accugenix, discussed their use of the Bruker MALDI time-of-flight mass spectrometry (TOF MS) microbial identification system. MALDI TOF MS ionizes microbial cells and the resulting particles are separated according to size and charge. The resulting spectral fingerprint can be used for microbial identification.

Kevin Luongo, Pfizer, presented an evaluation of the Millipore Milliflex Quantum Rapid Detection System. He described a method utilizing viability staining and enumeration of micro-colonies. The non-fluorescent stain is enzymatically cleaved inside the cell, liberating fluorescent marker that can be detected by the system. For most organisms evaluated, enumeration of low levels or organisms occurred within 24 hours. Part of his assessment included demonstrating that the technology is non-destructive and that staining does not impact microbial viability. This may allow subsequent testing of the micro-colonies that have developed, including microbial identification.

Michael Miller, Microbiology Consultants, LLC (yes, that’s me!), discussed a strategy and case study on false positive testing using the BioVigilant IMD-A, a real-time active air monitoring technology. Materials normally used in cleanroom and manufacturing environments were tested for their potential for eliciting a false positive response (i.e., a positive biological response when no viable microorganisms are actually present). Based on the data obtained, Dr. Miller provided strategies to minimize or eliminate the potential for observing false positives with the materials evaluated and when using the IMD-A system.

Rapid Method Session 1 at PDA Global Microbiology Conference

Jennifer Gray of Novartis Pharma AG, Switzerland, presented their strategy for validating the Millipore Milliflex Rapid as an alternative ATP bioluminescence RMM to the traditional compendial sterility test. The drivers for a rapid sterility test included the early identification of product contamination events, a reduction of through put time for sterile drug product release, and to increase the company’s level of expertise in the field of rapid microbiological methods. Novartis validated a 5-day sterility test using 22 heat-stressed cultures (7 ATCC strains and 15 environmental isolates). The cultures were also used to determine the most optimal medium to be used in the system. The FDA approved comparability protocols outlining the validation strategy for multiple products, EMA approval was obtained in February 2010 and MHRA approval was obtained in May 2010.

Amelia Tait-Kamradt, Pfizer, discussed their assessment of Pall’s new GeneDisc system. They conducted a number of studies addressing specificity, limit of detection, ruggedness, robustness, and the impact that excipients may have on the ability of the system to detect microorganisms. More information on the GeneDisc system may be found on our website on the Technology page.

Dr. Geert Verdonk of Merck presented his validation studies using the Charles River Laboratories Endosafe PTS. Dr. Verdonk explored the use of this rapid and portable endotoxin detection system as part of Merck’s PAT-RMM program. A variety of validation studies were also presented.

Monday, October 25, 2010

Dr. Ed Tidswell Discusses Viable but Non-Culturable (VBNC) Organisms

Dr. Tidswell presented an excellent overview of viable but non-culturable (VBNC) organisms and their clinical implications and risk mitigation in sterile manufacturing. Of the estimated more than 1.5 million different microbial species, less than 0.1% are known to be culturable. He stated that media fills, environmental monitoring and finished product sterility testing may actually fail to capture all microorganisms that may be present, due to the use of growth-based, conventional assays. Therefore, Dr. Tidswell recommends the adoption of rapid nongrowth based, PAT microbiology methods to ensure a risk based, integrated approach to the assurance of asepsis, and to reduce our reliance on traditional sterility testing.

FDA's Hussong Discusses Objectionable Organisms and RMMs

Dr. David Hussong, FDA CDER, reviewed the impact that B. cepacia can have on pharmaceutical product and the reasons why this organism may be considered objectionable for certain dosage forms. He stated that current test methods, including finished product testing, may not be sufficient in detecting objectionable organisms, and that it is more critical to look for these types of organisms during in-process screening using rapid methods. BlogBooster-The most productive way for mobile blogging. BlogBooster is a multi-service blog editor for iPhone, Android, WebOs and your desktop

Opening Session at PDA Global Microbiology Conference

Opening of the PDA Global Conference on Pharmaceutical Microbiology. Speaking is Dr. Mark Ott, Chief Microbiologist atNASA, on the topic of minimizing infectious disease risk while decreasing the necessary resources required during a spaceflight mission. Floating basketball-sized condensate harboring bacteria and fungi have been found on recent missions, making microbial monitoring extremely challenging!

Friday, October 22, 2010

Live RMM Blog Next Week!

Remember to follow my live blog from the PDA Global Conference on Pharmaceutical Microbiology next week!

On Tuesday and Wednesday I will blog LIVE from the PDA Micro meeting during the rapid micro methods sessions. Topics will include technology updates, regulatory perspectives (from US, EU and Japanese regulators), and the current Pharmacopoeia positions by experts from the USP, Ph. Eur. and JP. BlogBooster-The most productive way for mobile blogging. BlogBooster is a multi-service blog editor for iPhone, Android, WebOs and your desktop

Monday, October 18, 2010

New Pharmaceutical Microbiology Textbok Includes RMMs

Madhu Raju Saghee, Tim Sandle and Ed Tidswell have recently published a new book entitled Microbiology and Sterility Assurance in Pharmaceuticals and Medical Devices. Chapters on rapid and alternative microbiological methods have been provided by myself and Claudio Denoya. To read the entire Table of Contents, please Click Here. Below please find a brief overview.

Injectable product manufacturing is booming because of the growth of new biopharmaceuticals and small molecule anticancer drugs. The requirements for contamination control will become even more stringent than today. Isolators or blow-fill-seal equipment have already replaced the conventional clean rooms and LAF-hoods in many production facilitities. Conventional microbiological monitoring methods, requiring 3 to 5 days of incubation will become inappropriate. Equipment is already available allowing real time, simultaneous viable and non-viable counting.

This book is a useful reference guide for the SMB (Small and Medium Business) pharmaceutical sector which does not have the resources to have access to such top-quality information in this field. This book therefore represents an unparalleled and unprecedented text in the field of pharmaceutical and medical device microbiology. Perhaps even more outstanding is the fact that this book not only covers subject matter and technical content which is established as best and expected practice, but also includes content regarded as possible, future and emerging technology or processes.

The results of 45 years of scientific and technological development are laid down in these 33 chapters. These chapters, all written by international experts, give a vivid picture of today’s pharmaceutical microbiology. The high standard of the chapters makes it an essential reference guide that should be on the shelf of everyone who is involved or interested in this field.

Wednesday, October 6, 2010

LIVE RMM BLOGGING During the PDA Global Microbiology Conference

Rapid micro methods will be the talk of the town at the upcoming PDA Global Conference on Pharmaceutical Microbiology. I will be blogging LIVE on topics related to RMMs and other relevant areas of interest. You can follow the live blog at the following online locations:

Three day Microbiology GMP and RMM Conference in Istanbul, Turkey, Dec. 13-15

To address the microbiological needs of the global pharmaceutical and biotech industries, Quality Academia is very proud to announce a comprehensive, informative and interactive 3-day training program entitled "Pharmaceutical Microbiology for the 21st Century: GMPs, Rapid Method Technologies, Regulatory Expectations and Contamination Control Strategies."

Taught by two of the most experienced and globally recognized industry leaders, Dr. Michael J. Miller and Ms. Jeanne Moldenhauer, you will discover the latest advances in pharmaceutical microbiology and significantly expand your knowledge of microbiology GMPs and strategies for successful contamination control programs.

A summary of the conference and a PDF of the entire program may be viewed by visiting

Sunday, October 3, 2010

Participants needed for online survey on RMM return on investment

In the next few weeks I will be conducting an online survey on return on investment (ROI) and rapid micro methods. Specifically, the survey will focus on the use of PCR for the rapid detection of microorganisms. I am currently identifying potential participants. If you are interested, please send an email to with your interest. I will contact you shortly thereafter with the details!

High-throughput Universal Probe Salmonella Serotyping (UPSS) by nanoPCR

A new publication from the September 2010 Journal of Microbiological Methods discusses the use of nano liter PCR to detect Salmonella. This is quite interesting opportunity in automating and miniaturizing PCR procedures. Here is the abstract:

Salmonella enterica subsp. enterica serovar identification is of great importance with respect to outbreak monitoring and case verification. Therefore rapid, sensitive and cost efficient detection of Salmonella spp is indispensable within microbiology labs. To amalgamate single tube isolate identification with Salmonella typing, we developed the high-throughput Universal Probe Salmonella Serotyping (UPSS) technique based on nano liter PCR. In comparison to the classical approach, where O- and H-antisera are applied, the UPSS relies on specific gene content amplification of Salmonella spp. by an universal TaqMan assay for all markers and identification of the specific amplicon pattern. To enable high-throughput technology we employed a chip format containing 1024 wells loaded by an automated liquid-handling system which allowed us to perform TaqMan PCR reactions in volumes of 100 nano liters per well. Herein we present proof of principle of the UPSS method by the use of a test panel of 100 previously serotyped Salmonella isolates to successfully verify the usability, accuracy and feasibility of the newly developed UPSS approach. We found that the methodology of the UPSS technology is capable of unequivocally identifying 30 Salmonella serotypes on a single chip within 3 hours but can be highly parallelized by the use of multiple PCR machines. Therefore the UPSS method offers a robust and straightforward molecular alternative for Salmonella detection and typing that saves expensive chemistry and can be easily automated.

Authors: Mertes F, Biens K, Lehrach H, Wagner M, and Dahl A. from the Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.