More Variants Coming - better or worse?

a microbiology newsletter -february, 2022

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SARS-CoV-2, Omicron is now dominant, but...

Are More Variants Coming?

How dangerous are the BA.2 and BA.3 sub-variants compared to the Omicron BA.1 that we already know?

South Africa has one of the most robust public health systems in the world, carefully monitoring their SARS-CoV-2 case load, which has been dominated these last few months by the Delta variant. In recent months, however, South Africa's case load has increased sharply due to the variant: B.1.1.529, sub-lineage BA.1.(1) First detected in a specimen collected on November 9^th 2021, the new variant was reported to the World Health Organization (WHO) on the 24^th and deemed a “variant of concern.”(3)

This variant has nearly twice as many mutations as the Delta variant, many of which are associated with transmissibility and immune evasion.(2)

The increased transmissibility of Omicron, the ability of the virus to spread between people, when compared to the already-highly-transmissible Delta variant, is of great international concern.

Now a new sub-variant of Omicron B.1.1.529 is making the news: Called BA.2. The BA.2 strain is a prevalent form of Omicron in Denmark, making up about half of the cases there. It has been found in 40 countries and is prevalent in India, Sweden, and Singapore. It is now the most prevalent variant in South Africa. In the US, it is estimated that BA.2 makes up about 5% of all Covid cases. It is believed that that the BA.2 sub-variant is no more lethal that the original BA.1 variant, although research is ongoing. Hospitalization rates so far have been reported to be the same as the original Omicron BA.1 sub-variant. However, this new omicron coronavirus sub-variant appears to be slightly more contagious. Data out of Denmark suggests that BA.2 is about 1.5 times more contagious than the original BA.1 strain of omicron.(6) BA.2 has been nicknamed the “Stealth Variant” because it is more difficult for the PCR test to identify the variant, although it can identify the virus itself without difficulty. (5)

BA.3 is another sub-lineage of Omicron that shows mutations in the in spike protein. However, they are not unique mutations, and show a combination of mutations found in the BA.1 and BA.2 spike proteins.(8)

Meanwhile, sewage wastewater continues to be monitored for the virus overall. The wastewater district in South Boston reports on January 29^th that an average of 1,328 copies of viral RNA per milliliter of water were found, which is about an 88% plummet from the Omicron peak in early January.(6)

Preventive steps remain our first and best methods of reducing the spread of SARS-CoV-2; physical distancing and avoiding crowded spaces, masking, and maintenance of an up-to-date vaccination status. Please consult your local public health professionals for further advice and recommendations to protect yourself, your family, and your community. Also, it is encouraging that early treatment protocols have been found to be of value in preventing hospitalizations.(7)

By David Cochran and Jay Hardy

Ref: 1, 2, 3, 4, 5, 6, 7, 8

Did you know that Hardy Diagnostics was the first to introduce Chromogenic Media to America in 1996?

Chromogenic media allows the microbiologist to make identifications based on colony color. The principle involves a carbohydrate molecule in the media that is bound to a colorless chromogen. When a specific bacterial enzyme cleaves the bond, the chromogen turns color, thus creating color throughout the bacterial colony.

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Interested in trying out any of our HardyCHROM plates? Contact your account rep here for free evaluation samples.

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With Candida auris on the rise...

There is an Urgent Need for More Antifungals

Globally, 13.5 million people suffer each year with life-threatening fungal infections. Every year, infections of molds and yeasts such as Aspergillus and Candida kill more than 1.5 million people; that's more than malaria and on a par with tuberculosis. Even more concerning is that new drug-resistant strains are emerging, such as Candida auris, first detected in Japan in 2009 and since then reported on every continent except Antarctica.

Currently, there are only three classes of antifungal drugs (amphotericin, azoles, and echinocandins). Candida auris, which the CDC has deemed "an urgent threat," has been known to show resistance to all three for some strains. This emerging pathogen has an alarming mortality rate of about 50%.

Any new drugs to hit the market must be toxic to the yeast cells, but not human cells, which makes drug development difficult since Candida is a eukaryote and has a nucleus, similar to our own cells.

Hopefully, pharmaceutical companies will recognize the dire need for novel drugs to combat antibiotic resistance and invest in the development of new therapeutics.

In the meantime, thankfully, there are quick and easy ways to screen for Candida auris. Hardy Diagnostics released a new chromogenic media plate several months ago that causes colonies of C. auris to fluoresce (see photo at right), thus revolutionizing the way this dangerous organism can be detected.

Reference article

Phraseology

"Red Tape"

This term, which is associated with excessive government bureaucracy, originated with the Spanish administration of Charles V, King of Spain and Holy Roman Emperor in the early 16th century, who started to use red tape in an effort to modernize the administration that was running his vast empire. The red tape was used to bind the most important administrative dossiers that required immediate discussion by the Council of State, and separate them from issues that were treated in an ordinary administrative way, which were bound with ordinary string. Charles V's empire, which included most of Europe was so vast and so difficult to manage and control, that he eventually abdicated the throne and spent the remainder of his life in a monastery. This practice of using red tape to separate the important dossiers was copied by the other modern European monarchs to speed up their administrative machines.

The tradition continued through to the 17th and 18th century. In David Copperfield, Charles Dickens wrote, "Britannia, that unfortunate female, is always before me, like a trussed fowl: skewered through and through with office-pens, and bound hand and foot with red tape."

Drug resistance on the rise...

A Sinister Salmonella Strain

Salmonella Infantis

Globally, Salmonella causes illness in 93.8 million people and causes approximately 155,000 deaths each year.(1) Within the United States alone, Salmonella is responsible for 1.35 million infections, 26,000 of which are severe enough to warrant hospitalization and over 400 deaths.(2)

Infection occurs after ingesting more than 50,000 bacterial cells from contaminated food or water with symptoms appearing from 6 to 72 hours after consumption.(3) In addition, the actual morbidity rate worldwide is likely higher than reported, especially in developing countries.

Typically, the gastroenteritis will resolve itself in 5–7 days without need for treatment other than IV fluids. Antibiotics are usually contraindicated unless there is evidence of invasive disease (i.e. bacteremia) or typhoid fever, as antibiotics are unlikely to lessen the duration of illness or decrease the severity of symptoms and have the potential to increase bacterial antibiotic resistance.(3)

Typhoid fever is immediately treated with antibiotics, due to the systemic nature of the infection. Broad spectrum Fluoroquinolones (i.e. ciprofloxacin) have become the primary treatment, however resistance to this class of antimicrobials is increasing, as evidenced in studies conducted in endemic regions. Third generation cephalosporins are now often the second-line treatment for typhoid fever. Multiple Drug Resistant (MDR) strains are becoming increasingly more common, highlighting the need for better prophylactic therapeutics.(3)

Ninety-nine percent of all cases of salmonellosis are caused by S. enterica, and now a serovar of that species is causing great concern. Salmonella enterica serovar Infantis has been in the news lately for escalating anxiety levels of clinicians and the general population alike. Salmonella Infantis contains a multifaceted danger profile. Worldwide geographical distribution paired with multiple drug resistance genes are a combination befitting an infamous bacteria.(4,5,6) These characteristics of Salmonella Infantis make it challenging to investigate in the case of an outbreak.

For example, in 2019, a single outbreak of Salmonella Infantis from chicken resulted in 129 illnesses across 32 different states.(7) When the Centers for Disease Control and Prevention (CDC) launched the official investigation, 76 different chicken processing establishments showed the presence of Salmonella Infantis, which caused ambiguity as to the source of the outbreak. Further genetic analysis from 97 patients and 139 environmental samples showed that Salmonella Infantis contains resistance genes to many of the most commonly used broad-spectrum antibiotics.(7) Even with antibiotics and proper food handling, there is no guarantee of Salmonella-free chicken. The CDC estimates that one out of every twenty-five packs of chicken from the store is contaminated with Salmonella.(8)

The United States has one of the safest food supply chains globally. Still, the United States Department of Agriculture (USDA) regulatory authority begins at the slaughterhouse and does not have the labor force or authority to check all farming operations. The extensive presence of this pathogen paired with antibiotic resistance results in an alarming combination with a single solution. If you plan to eat chicken, you must store it properly -18ºC (0ºF) and thoroughly cook it to an internal temperature of 74ºC (165ºF).(8)

One monitoring method for food products is to enrich samples in Buffered peptone water (Cat. no.U142) and plate to HardyCHROM Salmonella (Cat no. G309). Hardy Diagnostics also offers SS NoPRO (Cat. no. G327) agar to screen clinical samples to assist clinicians in getting the most accurate and expedited results. This plated media is especially useful in that Proteus, which can mimic Salmonella in appearance, will be inhibited, thus eliminating many false positives. Hardy Diagnostics is here to help by providing the best microbiological solutions for the food and clinical laboratories.

Works Cited: 1, 2, 3, 4, 5, 6, 7, 8

By Isaac Adelman

Technical Services Microbiologist

Hardy Diagnostics

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