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Dangerous Experiments

Dangerous Experiments is the LabSpaces spot for guest bloggers. The purpose of the blog is to give new and old bloggers a space to experiment with blogging. If you'd like to contribute to this experiment, send us an e-mail or contact us on twitter at either @LSBlogs or @LabSpaces.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Monday, May 16, 2011

Our co-guest blogger of the week is Melissa Hughes.  Her scientific interest is one that is quite unique and fairly new compared to other scientific disciplines: food microbiology and food safety.  She received her M.S. degree in food science/microbiology back in 2009, and is currently employed at a private food and environmental testing laboratory in the San Francisco Bay Area. On top of being a food microbiologist and overseeing the quality operations in the lab, she also organizes and helps teach various food safety training workshops throughout the year.


I would bet money that right now you are thinking, “What in the world does a food microbiologist do?” Don’t worry, I get asked that a lot…and then it typically leads to a discussion about a story heard on the news regarding some food-related outbreak or a product recall.

Food microbiology is quite simply the study of those microorganisms (both beneficial and harmful) that impact food and beverage products. It encompasses two major areas: general microbiology and food safety/quality. A proper understanding of microorganisms (especially bacteria, yeasts, molds, and parasites) and those factors that impact growth, survival and pathogenesis provide the foundation to this field of study. More specifically, the organisms of interest for food microbiologists are those that:

1)     Have health benefits or are essential to the production of certain foods (like the probiotic organism Lactobacillus acidophilus in yogurt).

2)     Result in the deterioration or spoilage of foods, causing unpleasant odors, tastes and textures (such as Botrytis cinerea growth on stored strawberries or grapes).

3)     Are a concern for consumer health and safety, and their presence in food products can cause “food poisoning” and perhaps death for certain at-risk populations (such as Salmonella in eggs or E. coli O157:H7 in ground beef).

We really do live in a microbial world, and there are ample opportunities “from farm to fork” for food products to be contaminated. On farms, many organisms are naturally present in the intestines, hides, feathers and feces of healthy animals raised for food. For crops, contamination can occur in many ways. A few examples are irrigation water, poorly composted manure, human workers, wild animals, insects, and obviously the soil itself are all sources of microorganisms. What about food processing environments? Humans (again), facility design, contaminated ingredients, inadequate or no treatments to inhibit microorganisms, bad cleaning/sanitation programs, poor packaging, etc. all contribute as well. Even in the kitchen, poor hygiene, improper cleaning, cross-contamination of raw and ready-to-eat foods (like using the same cutting board and utensils for raw chicken and salad), not using a thermometer when cooking, and keeping the refrigerator above 40°F are all poor food safety practices that are actually still very common among consumers.

To help ensure that products made in the U.S. or imported in from other countries are safe for human consumption, microbiological testing of ingredients and/or the finished product is a practice that is becoming more common, and is even required for certain products. Many have “test and hold” procedures where the product is not released into commerce until they get results back from the lab. Larger food companies often have their own laboratories, but smaller companies typically use third-party testing labs (like the one I work for)…and each have their pro’s and con’s. We have clients that range from very large food companies with multiple products, to local organic farms to restaurants to even producers of pet food!

So what is a typical day like in a food microbiology lab? The samples are received, inspected, and verified against a chain of custody form, and are logged in to the system. Once in the lab, they are processed and enriched in some type of selective enrichment broth. This allows for the growth of the target microorganism, and incubation temperature and duration vary depending on the organism. Then there is the initial screening test. Some common rapid technologies utilize gene amplification and detection by real-time PCR, or enzyme-linked fluorescent immunoassay. Those that are found to be presumptive positive for the microorganism in question are plated on selective media, and further confirmed using immunological, biochemical, and molecular methods. Final results are sent to the client in the form of an electronic certificate of analysis as soon as possible, and obviously this is all strictly confidential. Since our lab is A2LA accredited, we must adhere to standardized testing protocols all the time and have lots of quality control checks in place.

Some common microbiological tests include aerobic plate counts, yeasts, molds, lactic acid bacteria, coliforms, generic Escherichia coli, Staphylococcus aureus, Bacillus cereus, Salmonella, E. coli O157:H7, Listeria spp., L. monocytogenes…just to name a few. At times, our lab smells quite interesting with all of the different food products being incubated in their enrichment broths!

There are limitations to food microbiological testing though. Were the samples collected properly at the food company? Were enough samples taken to be representative of a certain batch or lot? Is management responding properly to test results, and do they even understand what the results mean? Also, the turnaround time for negative or presumptive positive results for most bacteria are typically around 2-3 days, and confirmed positives can take 5-8 days. Because of the potential negative impact towards product quality and human health, there is a drive to develop even more affordable testing technologies that can get results out faster without sacrificing sensitivity and specificity.

Food microbiological testing is definitely an important piece of the food safety puzzle, but is certainly not the only piece. Everyone involved in the food supply, from farmers to food processors to legislators all have a role to play in food safety. There is no doubt that there are many difficult challenges ahead for the food industry…not to mention how we are going to provide food for a world population that is approaching 7 billion people. Collaboration among all of the different sectors (industry, academia, government, and consumers), improved technologies and proper education in food safety and basic microbiology concepts are all important steps to take in reaching the ultimate goal: a safe global food supply.

Side note: Some of you may be aware of the new Food Safety Modernization Act (FSMA), signed into law by President Obama in January of this year. This is the largest change to U.S. Food Law since the enactment of the Food, Drug & Cosmetic Act in 1938. Most notably, it will impact recall authority, facility registration, product traceability, the safety of imported foods, and even food laboratories. Everything in the FSMA will take many years to implement, and even the FDA is not sure how they are going to do all of it…but I am optimistic that we are on the right track.

Another side note: Interested in some consumer-friendly food safety websites? Check out, and Fight BAC! by the Partnership for Food Safety Education (PFSE). Want information on pathogenic bacteria transmitted through food and foodborne illness? Please check out CDC FoodNet and Emerging Infectious Diseases (January 2011). For more information on the latest product recalls, please visit the FDA’s website on recalls and market withdrawals.

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Hi Melissa,

Nice article. I've done some work with food samples. I don't understand how the method "Wash and Boil" has become the standard. We find that the DNA is so dirty that the qPCR results are usually way off. I've been to IAFP and FERN conferences and it is surprising how the scientists don't question many of the methods they use or know how to interpret the results.

I'd like to see more food micro labs doing pathogen testing get more up to speed with the molecular techniques. I know time is of the essence but if they need to wait 5 days anyway for a culture positive result, why not take the extra 20 minutes to make clean DNA for testing?

I wonder, what is the philosophy of the FDA and public health labs when it comes to rapid testing and molecular techniques?

Brian Krueger, PhD
Columbia University Medical Center
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Jade said:

I wonder, what is the philosophy of the FDA and public health labs when it comes to rapid testing and molecular techniques?

It would be really sad if the standards lagged that far behind current technology.  I had a similar question though, what are the standard techniques for doing this? PCR assays, cultures?


Melissa Hughes
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Most major and profitable food micro labs these days are up to speed on using commercial rapid tests and molecular techniques…and are much better than they used to be.

Real-time qPCR assays, ELISA/ELFA, IMS, lateral flow assays, gene sequencing etc. are all very common now…and are big business. Some of the companies that make these rapid technologies are DuPont, bioMerieux, Bio-Rad, BioControl, Neogen, etc…and the list goes on. Many of these companies have been making these products for years, and many are fast, reliable, less labor-intensive, are comparable if not better than traditional culture methods, are “official” methods, and the consumables are often not too expensive.

Typically, food micro labs have to follow certain standardized or “official” methods when testing for microorganisms and/or their toxins for food clients…we can’t just use any method (unless for in-house or contract research purposes). A few common protocols followed in the U.S. for food are the FDA Bacteriological Analytical Manual (BAM), AOAC Official Methods of Analysis (OMA), the AOAC Research Institute (RI), and the Compendium of Methods for the Microbiological Examination of Foods (CMMEF) of the American Public Health Association. Some of the methods have been around a long time (traditional micro) and they still serve their purpose…while others included are very new (rapid tests and molecular techniques). Each have their place and come with their own pro’s and con’s.

It is difficult, expensive and very time-consuming to get new methods approved to be included among this group, especially AOAC or so I’ve heard. There is a peer-review process, and the procedures are carried out in an interlaboratory study with multiple types of products and the results compared back to the traditional culture methods. Despite this, new commercial rapid test types are continually being added and there is a wide assortment to choose from. These companies (like the ones mentioned before) really strive to get their tests approved by these groups, because it is good marketing obviously, and any accredited and reputable lab these days is going to require it.

I agree with you Jade on how many food scientists in my area do not fully understand all of the little details with these rapid technologies. A lot of these commercial tests are very simple to use and straightforward…but interpreting the results and fully understanding them, as you know, is a whole different story. This is where proper education comes in. Of course, it always comes back to this for just about any issue! A lot of food science programs at universities do not require courses in molecular biology/biotechnology (they are optional). With time I bet that will change though. We are fortunate in my lab to have several PhD’s with a biotech/molecular background who really know their stuff and train our technicians who work in that area.

As far as FDA and public health labs, I personally have never been to one…and only have experience with university and private labs. From what I have heard, they are generally in support of rapid testing methods as long as they are “official” and are comparable to culture/plating methods.

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Some of the molecular tests for food testing- for example the qPCR kits by Life Tech (Applied Bio) spoonfed the researcher so much that even the results are spit out without the scientist needing to give any thought to the data. They don't know how to interpret standard curves and PCR efficiency information.

I think it is a disservice. It will be good when public health and FDA labs start hiring scientists who understand this technology.

The FDA has to make new methods official- to get them in the BAM. I think an outside lab like Silliker could do your validation for you but you still need to convince the FDA to approve it. I am not sure of the process, but from attending many public health lab conferences, I think this is the case.


Melissa Hughes
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Yeah, it is getting to the point where you just load samples into a machine and "push a button" where anyone can do it. Because they are making these technologies so simplistic, no one feels that they need to know the actual science behind it anymore...which is scary. We still use a lot of the culture/plate methods though in our lab, and use the microscope quite often. Every method we use has its purpose, and certain methods work better for certain food products. Some of them really do not work well with PCR and result in totally messed up curves.

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I think there is definitely a place for that type of diagnostic test- push a button- get a result. With human disease, for example, the less chance of human intervention causing error the better. With blood and plasma, some technologies don't even require purification of DNA.

But for this to work with food, I think the DNA must be pure because every food culture is so messy. If they started with colonies on a plate, you could skip a lot of steps, but I haven't heard fo any labs doing that, except for the Biomerieux assay (DiversaLab).

We've done a lot of work on different pathogens and foods using qPCR and the reactions are always inhibited using the current BAM method for DNA prep. I mean like 6-9 cycles late (100-1000 fold loss of detection). But it seems that labs really don't care - they are only looking at positive vs. negative. So why use qPCR then?

It doesn't make sense.


Guest Comment

I have worked in several food manufacturing plants, and one can seriously not stress enough how important food micro is! It's hard to implement proper sampling and control measures sometimes, though, especially when people just don't understand or particularly care... but the emergence of new, fast-response-type tests helps so much, and really gives good imput that one would sometimes have to wait a week or two for (like whether or not cleaning procedures are adequate, or what-have-you). I hope the implementation of the new FSMA regs go smoothly, because if what I have seen is indicative of many places, lord knows we need it.

Melissa Hughes
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@Jade: I can't speak for every lab (and I know there are some bad ones out there), but I know with us that it is much more than just looking at positive vs. negative, especially with the type of qPCR that we currently have. Only certain individuals are authorized to interpret the final results too. Yes, we do have issues with certain food products getting inhibited during a qPCR run…and in those cases we use a different method. Also, with us we typically follow AOAC OMA/RI methods. The reason qPCR is widely accepted is because you can get an idea of the results in real-time, and it really does save a lot of time and money for the lab and the client. Doing regular PCR with gels would just be way too expensive for a large number of samples. Cost of testing is so important to food companies…and it is challenging enough already to get them to do testing. I know with us because we are a small lab, we are competing against other labs like Silliker. The way that we are able to stay in business is because we are usually cheaper (and have way better customer service).

Ultimately, qPCR is just a screening step for the target organism too. The majority of the time, test results come back negative for foodborne pathogens after proper analysis. Makes sense, because most food companies who do invest in a routine testing program have things under control in regards to cGMPs, HACCP and sanitation programs. But, if there is a positive initial screen for a pathogen in a particular sample…then we obviously follow it with all of the necessary confirmation steps and purify the target DNA. We definitely don’t want to be wrong in identifying the organism.

@Xhihou: Proper sampling is so critical to food testing, and yes you are correct most people in the food industry do not understand it. It is sad when QA managers think that just one tiny grab sample is enough to be representative of an entire batch. Again, it all comes down to proper training. We actually offer a course on collecting samples aseptically at our company, and in the past it has been quite popular and very informative. On a different note, have you used a lot of the ATP swabs?

I am also curious to see where everything goes with the FSMA, and hope it all goes smoothly and is implemented well. A lot of it will depend I think on what kind of funding the FDA will get throughout this process. Two regulations have already been announced, and will go into affect by July of this year.

Joseph Bradley
United States
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Melissa, I too am fairly optimistic about the FSMA, which has great implications for the future of the lab testing industry. Although my company doesn't do food testing in particular, we have seen a big increase in demand these past few years for contract laboratory work and have had to scale up accordingly. Anywho, looking forward to where this will all take us :). 


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