The New “Cold” War

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A guest blog from Steve Connell, a SARS-COV2 Testing Laboratory Lead about the topic on every news platform: COVID.

March 17, 2021

By Steve Connell

Less than a year ago now, an insidious sneak attack was launched by Nature. Don’t get me wrong, this is not the first of these “unprovoked” attacks on our existence. These attacks are legion in number, this is the nature of Nature, (definitely revisiting that concept!).

What seems like an epoch ago, someone said of SARS-CoV2 (CoVid19), “…it’s just like a bad cold for most folks…..”, to a large extent true, further, some individuals are wholly asymptomatic. However, in the UK this virus has claimed the lives of >120,000 and counting (yep, sometimes one needs to see that as an actual number!)

So, you see, this is a new invader much more pernicious and insidious than we could have imagined. We all fear the infectious disease that claims the lives of most of the people it infects, like the group of diseases generically known as the Viral Haemorrhagic Fever infections, or VHFs, (Ebola is a notable example). However, these, whilst deadly, are not that successful in spreading and replicating, primarily because they kill a high proportion of those they infect. They are successful in their ability to cause human infection, just not so good at ensuring successful spread.

Conversely, SARS-CoV2 (CoVid19), does not kill a high proportion of those it infects, <1% is a small percentage but still a big number in reality. In Scotland, this figure is 4,236 deaths or 0.077% of the total population and 2% of those who have been infected (the known number of positives in the population currently stands at 3.8% in Scotland remember this is known, tested positive cases, NOT the actual number of positives circulating in the community, this is likely to be significantly higher by at least a third). So, it is evident that SARS-CoV2 is a very successful spreader that kills a small percentage but that small percentage turns into a big number when we talk about population(s).

In conflicts of this nature there is a silent escalation in the capability to become successful as a spreader (or from the virus point of view getting genes into the next generation). In the conventional “Cold War” terminology this capability would be centred on advances in technology, implements of combat and amassing forces to utilise these. At critical mass, the combatants enter a war of non-engagement, espionage and a race for, theoretical, supremacy without the heat of engagement.

SARS-CoV2 entered the human arena in 2019 (so far as we know) after spending a not insignificant amount of time amassing mechanisms of insidious attack, on a virgin population (us), in another mammalian incubators, probably bats (not picking on bats unfairly, strains of coronavirus >95% similar to SARS-CoV2 have been isolated from bat colonies). This should not be surprising in the aftermath of other viral infections that have acclimatised in other hosts before going on to infect humans (influenza being a prominent example). This process enables the virus to test multiple versions of itself against immune system challenges, closely related to humans, until it ultimately fails, or in this case, creates a version of itself that can successfully invade mammals and subsequently humans.

We should not anthropomorphosise a virus, as if this process is a directed, targeted intention to infect humans; this process is random, non-directed and scatter gun in the approach. Many, many copies of slightly different virus are produced in live infection, most are unsuccessful. Just as in the Darwinian caveat from Origin of Species, organisms existing under selective pressures will create more offspring than can realistically survive, but some will and these will pass on those inherited characteristics that made them successful, and the cycle goes again. This is why we see variant(s), there are currently >1000 known variants from the originally isolated SARS-CoV2 strain, some are successful Wuhan, Kent, Brazil, South African strains and some have appeared and disappeared. Why are these so highly mutable? Well primarily it is due to the nature of the heritable material that makes up the genome of the virus. Our own information carrying material is DNA, the SARS-CoV2 genome is made from RNA a much less stable information carrying material, prone to non-directed, random mutation, frequently termed as highly mutable.

This mutability is the main weapon developed by the virus in this Cold War, (that, and the human propensity to be social creatures!) only we are now developing our own “molecular weapons” to combat this pernicious, insidious and very successful virus.

In effect, like in a conventional Cold War, we have entered into a molecular level arms race with this foe. The outcome is yet unknown, but next time we can look at the implication(s) of this “Molecular Arms Race”.

One year on: reflecting on our first year in our head office

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After a year of set-backs for some, our Managing Director, Jennifer, celebrates our successes on the first anniversary of our offices and chemistry building.

March 15, 2021

By Jennifer Newton

A year after the pandemic hit the UK, stories are popping up everywhere to mark the anniversary that our normal lives changed. Of course, the pandemic has affected us, but we mark the 15th March 2021 for a positive reason. It is now a year since we moved into our new head offices and custom-built chemistry lab at Unit 5 Mill road Industrial Estate.

In November 2019, it became apparent the unit we were operating out of at 42 Mill Road Industrial Estate was not fit for our growth aspirations. Space was getting tight in the offices as well as the chemistry lab. Will and I were pondering what to do to find more space when serendipity struck and a building which had lay empty for over eight years had a new “for rent” sign up. We acted fast over the Christmas holidays getting in touch with the estate agents and getting access to see inside.

Chemistry lab before

What we found was plenty of usable space, but a lot of work was going to be required to get the building back into tip top shape. The clincher on whether this new building would work, was if we could get a direct line of communication with the micro lab 200 meters away. It just so happened this single-story building had a “folly tower”, basically a two story tower with nothing in it, but a proud place to display a sign. This tower was high enough for us to get the line of site and a seamless communication link which allows both buildings to work in real time with each other.

Chemistry lab after

After frantic negotiations with the owners, we gained entry on the 31st January 2020 and hit the ground running, replacing flooring, carpeting and lights. We laid new drainage and repaired broken ones. We altered the office layout and added two more rooms. We installed new boilers and instated benchwork and tons of electrical points for the chemistry lab. We even had to replace the cat cabling to bring the infrastructure up to current standards.

Our contractors worked tirelessly, as did Will answering the endless questions on where, how and when things needed doing. Then on the 15th March we moved in – no time to spare before the country went into lockdown. Had we delayed even a day, the outcome would have been very different; caught between an unfinished building and an unsuitable one (with no lease). Luck was certainly on our side. If we had not moved when we did, working under the Covid regulations would have been very different with social distancing near impossible to maintain.

Kitchen before
Kitchen after

So, a year on instead of having to decrease our activities we have managed to expand our services with new accredited methods in the chemistry lab, increase the number of technical and customer services personnel and a brand-new Communications Manager to boot. As the offices and the chemistry lab grew so did the micro lab, and we had to rent more warehouse space and a dedicated workshop for our maintenance department. We are now investigating the possibility to move our media production lab to the Unit 5 site (which has loads of surrounding land) to accommodate their continued growth in animal by-product, CSPO (Control of Salmonella Order), food and water testing. Looking back over the year I am proud of what we have accomplished during what can only be described as dark times. As the world returns to normal, I see us attaining even more lofty goals based on the evidence of what we accomplished last year.

The story of Mary Mallon, the first asymptomatic carrier in history

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The real story of Typhoid Mary.

March 9, 2021

By Antonio Baena Marin

Due to the COVID-19 global pandemic we are currently facing, everyone is probably quite familiar with the terminology “asymptomatic carrier” and what that means, but back in the early 20th century this concept was unknown even for healthcare workers.    

That brings me to the story of Mary Mallon, the first known asymptomatic carrier of Salmonella typhi in history. Salmonella typhi is an enterobacteria that is spread by eating or drinking food or water contaminated with the faeces of an infected person. She infected at least 51 people with typhoid fever, three of whom died, while working as cook in the US.

Mary was born in 1869 in Ireland and as many other, she emigrated to the US in 1884 at the age of 15. She had worked in different domestic position until she became a cook. She worked as a cook for wealthy families from 1900 to 1907 in the New York city area, seven of which contracted the disease. No one suspected from Mary (not even Mary!) until August 1906, when she started to work for a wealthy banker´s family. She went along with the family to Oyster Bay, where they rented a house to spend the summer holidays. 6 of the 11 members of the family were infected while vacationing there.

Typhoid fever was seen as a disease of crowded cities, associated with poverty and lack of basic sanitation. The landlord, concerned that the outbreak would prevent him from renting the summer house again, hired a sanitary engineer in order to investigate the source of the outbreak to determine the cause. Everything tested from the house (plumbing, faucets, cesspool, etc…) came up negative, narrowing down to Mary Mallon, the cook that has worked for the family during the outbreak. He unsuccessfully tried to obtain samples in order to prove his theory. Consequently, he gathered information about all the infections while Mary was working for the different families she had worked, providing enough evidence to notify the New York City Health Department. This organization determined in March 1907 that she was a public health threat and was forced to quarantine in a Hospital. After 3 years, Mary was released of the quarantine with the only condition of not working as a cook anymore, but she never abided to the rule.

In 1915 Mary, using a fake surname (Brown), started again to work as a cook in  Sloane Hospital for Women in Manhattan, where she infected 25 people, and 2 died. Since this episode she was stigmatized as “Typhoid Mary” and she became the centre of jokes.

After that episode, Mary was confined again to North Brother Island, where she spent the rest of her life in isolation, until she died of pneumonia at the age of 69.

Nowadays, the expression “Typhoid Mary” is used to defined anyone that spread a disease or brings bad luck.  Her story has inspired theatre plays, documentaries, books, etc.

References:

https://www.pbs.org/wgbh/nova/article/typhoid-mary-villain-or-victim/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959940/

https://www.nhs.uk/conditions/typhoid-fever/

Salmonella enterica Time-lapse

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There are many different types of Salmonella and they don’t all look the same. This is a short and sweet insight into what our microbiologists do each day in the form of a time-lapse. Enjoy!

March 2, 2021

By Michael Beavitt

Salmonella enterica subsp. enterica is one of the best-known food-poisoning culprits. While many associate it with undercooked chicken meat, in fact a large number of cases stem from the consumption of contaminated meat in general, as well as eggs and egg-containing products, and even sometimes fresh vegetables and fruit.

While a number of pathogenic varieties of Salmonella enterica exist, the most common are the Typhimurium and Enteritidis serovars. They account for the vast majority of food poisoning cases in the UK and can cause some pretty nasty symptoms.

Once they get into the body, they can trick the macrophage immune cells into “eating” them, before escaping the deadly digestive enzymes and hitching a ride to a multitude of organs and infectable sites. They can also trigger debilitating immune over-reactions, as well as producing large quantities of toxins.

Shown is a 48-hour time lapse of Salmonella enterica growing on XLD agar, which is used in our lab in the early confirmation stages of salmonella detection. One change that’s obvious is that the agar turns from orange/red to pink– this is due to the fermentation of xylose sugar and the decarboxylation of lysine (the “X” and “L” in XLD), turning the previously pH neutral surroundings alkaline. The pink colour comes from the indicator phenol red, which changes colour depending on the pH of the surrounding media. 

It’s important to note that not all Salmonella species look like this – some ferment other sugars to produce acid, turning the agar a bright yellow colour.

The other change of note is the formation of black spots in the centres of the colonies – Salmonella enterica species commonly produce H2S, a black precipitate, from sources of iron and sulphur. This allows you to quickly tell typical Salmonella species apart from other unwanted background flora that might still grow on the media.

Due to the various ways different Salmonella serovars grow on the XLD (and other selective agars used) it requires experienced microbiologists to interpret the plates as having or not having Salmonella present, and thus verifying if a food product is safe or not safe to eat.

Oysters: Dealing with Norovirus

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“If seven in 10 oysters have norovirus, should we still be eating them?”

February 23, 2021

By Jennifer Newton

It’s not often that I get enough time to ponder the specifics of food poisoning from molluscs. But, in the midst of feeling unwell after eating oysters, I found myself doing just that: wondering about the main contributors to food poisoning from oysters (in between trips to the bathroom, that is). A quick google search came up with “Nearly 200 ill in UK after eating oysters”, February 2020. But this is February 2021, so did I also fall ill to the same pathogen?

In the aforementioned article, the culprit was identified as the norovirus. The norovirus symptoms include:

  • Nausea.
  • Vomiting.
  • Stomach pain or cramps.
  • Watery or loose diarrhoea.
  • Feeling ill.
  • Low-grade fever.
  • Muscle pain.

Yep, I had all of them. So, looking pretty likely that I was being affected by the same pathogen that brought 200 people to their knees only a year previous. How did I get there? Well, I ate some raw oysters for Valentine’s day, and just over a 24 hours later I was feeling very poorly, which is the typical incubation period of the sickness (one to two days). And I felt unwell for just over a day, which is also in line with its classic diagnosis of lasting 1 to 3 days. The good news is; according to the CDC, people have temporary immunity from re-infection for up to 2 to 3 years.

Based on electron microscopic (EM) imagery, this three-dimensional (3D) illustration provides a graphical representation of a single norovirus virion, set against a beige background. The different colours represent different regions of the organism’s outer protein shell, or capsid.
Image by CDC

This led me to another line of questioning: I ate the oysters raw, but would I have been safe if I cooked them? Quick steaming oysters will not kill norovirus and other pathogens, according to the U.S. Centers for Disease and Prevention. To be safe, seafood must be cooked to an internal temperature of at least 145 degrees Fahrenheit (63°C). Other common sources of norovirus besides oysters include:

  • contaminated foods
  • shellfish
  • ready-to-eat foods, such as salads, ice, cookies, fruit, and sandwiches, that a worker with a norovirus infection has handled
  • any food that contains particles of the faeces or vomit of a person with norovirus

Norovirus is thought to be the most common cause of acute gastroenteritis (diarrhoea and vomiting illness) around the world. It spreads easily through food and drink and can have a big impact on people’s health. It was originally called the Norwalk virus, after the town of Norwalk, OH, where the first confirmed outbreak happened in 1972.

Can we test for norovirus?

Several methods have been developed to extract and test for total norovirus contamination (infectious and non-infectious virus particles) in foods; however, there are no internationally recognized standard methods to date. Despite improvements in our ability to extract viruses from foods, the analysis of rinses and extracts leaves much to be desired. Additionally, the method used to detect norovirus is based on PCR (Polymerase Chain Reaction) which can be costly and not normally a viable option to producers as a screening test.

“If seven in 10 oysters have norovirus, should we still be eating them?” Of course, there is a risk from eating oysters – they are harvested from the wild, after all. But the oyster itself is not the culprit, rather the water in which it is raised. All the oysters sold in the UK are purified for 42 hours, which largely nullifies any danger. But, to be completely safe, you can always cook oysters – or easier still, just zap them in a microwave, which would kill any residual traces of the virus.

So, should we still be eating oysters? Of course: they are good for you, and tasty, too!

Comparing Fat Testing Methods of Milk and Milk Products

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If you’ve ever wondered what methods we use to test for fats in milk and milk products, this post is for you!

February 16, 2021

By Jennifer Newton

There are so many methods to choose from when testing the fat content of milk and milk products. This might be because historically, many unscrupulous farmers watered down their milk and scooped off cream to increase their volumes, so they could make more money whilst the consumer got short-changed. Nowadays, most commercial transactions of selling milk are based on the fat content (who wants to be paying for water?). So, faster and cheaper testing methods are constantly being developed to determine the actual fat content of milk.


The question remains; “what is the best test method for fat content in milk and milk products?” The answer depends on what information you require for your decision. It can be confusing, but first determine your goal. Are you monitoring your herd’s average production? Are you selling an average season production, negotiating a crucial delivery or exporting to an important market?

If it is one of the latter, you want the test method to be recognised internationally and you want a laboratory with ISO 17025 accreditation to be doing your analysis. Those laboratories will have had their testing audited and their results assessed, and they will be using internationally recognised methods.


Whilst the most common laboratory-based method in use today are the Gerber Method in Europe and the Babcock Method in the US, there is agreement amongst experts that the ultimate precision method for determination of milk fat content is the Röse-Gottlieb (Bogomolov et al., 2017). The Babcock and Gerber method are very similar methodologies, and it has been found that the Gerber method measures consistently but only slightly higher than the Röse-Gottlieb method (Crocker et al., 2009).


If you need an accredited test for fat content in milk, cream or ice cream or would like some more information feel free to contact us.

Nutrition Facts: The Science Behind the Label

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All about nutritional values and how they are produced.

February 12, 2021

By Francisca Navarro Fuentes

Have you ever read the nutrition facts on your Friday nights double pepperoni frozen pizza? Did you ever wonder what those values mean, or think about how they are produced? Feed your curiosity with this post and find out about the science behind the label!

Nutrition facts are a powerful tool to help you understand the composition of a product, so that the consumer of the product is informed. Nowadays, the variety of products to choose from is endless, but knowing what is in your food can help you to pick what to buy.

By law, it is mandatory that nutrition facts are included in labels. This is controlled by Regulation (EU) No 1169/2011 [1] on the provision of food information to consumers. Therefore, nutrition declaration must include energy (KJ/Kcal), total fat and saturated fat (g), carbohydrates and sugars (g), proteins (g) and salt (g). Besides, it is optional to include values such as mono-unsaturates and polyunsaturates, polyols, starch, fibers and vitamins or minerals. The values are reported per 100g or 100mL of product, and often per portion too.

But do all products have to have a nutrition label? It may surprise you to learn that the answer is: no. There are products  exempt from this rule, such as waters, spices, salt, sweeteners, tea, food additives, gelatine, yeast and chewing gums, among others.

Most people don’t pay attention to the nutritional information and one of the reasons could be a lack of knowledge on how to interpret them. In order to help the consumer, the NHS has published a list of guidelines, summarized in Table 1.

So how are nutritional values produced?

Nutritional values are produced in analytical chemistry laboratories. A representative portion of the product arrives to the laboratory, this is then blended and homogenized into a paste (like your morning vegetable smoothy, ew!). This paste is stored in an airtight bag, ready for analysis.

Chromatography, flame photometry, spectrophotometry, high temperatures (up to 600 ºC!) and high pressures are techniques and conditions used to determine nutritional values. As you would imagine, in order to provide this information, trained chemistry analysts are required. I know, these techniques sound scary but, believe me, chemists love them! Although these machines are subject to break downs, chemists like me thrive on a broken machine’s challenge.

Now, how can you (or I), as a consumer, trust the values in the nutrition facts table? For that, a governmental body, known as United Kingdom Accreditation Service (UKAS), assesses and accredits analytical chemistry laboratories ensuring that the values obtained in laboratory A would be the same as the ones in laboratory B across the UK.

In conclusion, labels are educational as it helps to understand calories and nutrients. They regulated by Regulation (EU) No 1169/2011 and the values are generated in UKAS accredited analytical chemistry laboratories, ensuring the customer rights and accuracy of the data.

References

[1] EUR-Lex Website: https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:02011R1169-20180101 Last visited 6/2/21

[2] NHS Website: https://www.nhs.uk/live-well/eat-well/how-to-read-food-labels/#:~:text=Nutrition%20labels%20are%20often%20displayed,certain%20nutrients%2C%20such%20as%20fibre. Last visited 6/2/21

Are Coliforms and Enterobacteriaceae the same thing?

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Some interesting facts about Enteros and Coliforms

January 18, 2018

Express Micro Science

If you look up Coliforms and Enterobacteriaceae in Wikipedia and read the first two lines:

“Coliform bacteria are defined as rod-shaped Gram-negative non-spore forming and motile or non-motile bacteria which can ferment lactose with the production of acid and gas when incubated at 35–37°C. They are a commonly used indicator of sanitary quality of foods and water.”

“The Enterobacteriaceae are a large family of Gram-negative bacteria that includes, along with many harmless symbionts, many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis, Klebsiella, and Shigella. Other disease-causing bacteria in this family include Proteus, Enterobacter, Serratia, and Citrobacter.”

One might get the impression these are two completely different groups of bacteria. That may be how Wikipedia works, one person wrote one article and another wrote the other so the style is somewhat different. In any case, when testing food in a microbiology lab, there isn’t a whole lot of difference between the two.

Both Coliforms and Enterobacteriaceae (Enteros) are used as indicator organisms in microbiology.  Most of them do not cause illness but where they come from, the environments in which they grow well and the way they die is the same for most foodborne pathogens. Therefore it is a good indication that if these bacteria are high in a food the likelihood of more sinister bacteria being present increases and vice versa.

But can these bacteria groups really be used interchangeably?

In the laboratory we use slightly different agars to grow Coliforms and Enteros, the difference being Coliforms metabolise lactose better than glucose so we use lactose as the main sugar when testing for Coliforms (Violet Red Bile Agar) and glucose for Enteros (Violet Red Bile Glucose Agar). The theory being not all Enteros can metabolize lactose but all Coliforms can metabolize glucose so the Coliform media is slightly more selective than the Entero media.

But how does this effect your test report?  If you asked for both Coliforms and Enteros on the same sample, it would depend on the sample type if any real differences in the result would ensue.

For example, dairy products primary sugar is lactose so Coliforms grow better in these products and should probably be grown up on a lactose based agar. In meat where glucose is more prevalent but always at a low level overall, the number of Coliforms and Enteros would probably be very similar. In fact most other foods glucose or sucrose, which contains glucose, is much more common so the more general VRBGA should be used to capture as many indicator bacteria as possible.

 

                              Top Facts

  1. All coliforms are enteros but not all enteros are coliforms
  2. Coliforms prefer lactose as their sugar source but can metabolize glucose
  3. Not all enteros can grow on lactose alone but most can
  4. Both coliforms and enteros are good indicator organisms for sanitation in water and food, as they come from the same places, grow well under the same conditions and are killed in similar fashion as many pathogens

 

For Coliforms, Enteros and other microbiology testing available from Express Micro Science, please click on food testing.

More information on indicator organisms will be posted soon…

Salmonella enteritidis and testing for the vaccine strain

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Why PCR testing helps with Salmonella enteritidis differentiation

January 5, 2018

Salmonella enterica subsp. enterica is a rod-shaped, facultatively anaerobic gram negative bacterium that has several subtypes called serovars, which are the primary cause of Salmonella infections in humans, also known as salmonellosis. Salmonellosis is the second most common foodborne disease after campylobacteriosis. Common symptoms are diarrhoea, fever, vomiting and abdominal cramps 12 to 72 hours after infection.

One serovar, Enteritidis, is responsible for over 40% of total recorded human infections worldwide. The primary reason is the vertical transmission or zoonosis of Salmonella enteritidis between galliformes (ground-feeding birds, such as chickens, turkeys and pheasants) and humans because of the worldwide consumption of poultry meat and associated products e.g. eggs.

Between 1981 and 1991 the numbers of Salmonella infections rose by 170% in the UK, primarily due to an epidemic of Salmonella enteritidis. An industry-led vaccination scheme began in breeding flocks in 1994 and in laying flocks in 1998. Mass vaccination has continued for breeders subscribing to the Lion Quality Code of Practice and using the Lion Mark on eggs, which account for approximately 85% of the UK market. As a result of this and other control measures, the number of cases fell eight-fold from 1.6 cases per 1000 persons per year from 1993 to 1996 to just 0.2 cases per 1000 persons per year in 2008 to 2009. The number of lab-confirmed cases dropped from 18000 in 1993 to just 459 in 2010.

There are several vaccine strains of commercial Salmonella enteritidis available on the market. However, in traditional culture techniques for detection of Salmonella, they cannot differentiate between these harmless vaccine strains and the harmful ‘field’ strains of Salmonella enteritidis that may be present. In order to differentiate the two, we have to use the technique polymerase chain reaction (PCR). PCR amplifies a copy of a small segment of DNA exponentially to generate millions of copies of a particular DNA sequence. This DNA sequence is unique to the vaccine strains of Salmonella enteritidis and the detection of it can then be used to differentiate from the field strains.

 

Express Micro Science utilises two different PCR kits that can detect and differentiate different commercial vaccine strains of Salmonella enteritidis such as Salmovac SE, Salmovac 440 Gallivac SE and AviPro SALMONELLA VAC E. For more information on the testing we can perform on poultry, please contact us.

 

 

Written by: Paul Moffat, Microbiologist and Project Manager at Express Micro Science