Laboratory Supply Shortages Are Impacting COVID-19 and Non-COVID Diagnostic Testing

Oct. 15, 2020

Diagnostic testing is an integral part of delivering good patient care and controlling the spread of infectious diseases, something the COVID-19 pandemic has demonstrated on a scale that little else could. Since early spring, shortages of SARS-CoV-2 laboratory supplies associated with the high demand for COVID-19 testing have been impacting the laboratory supply chain and forcing many clinical laboratories to pivot their efforts and redistribute resources. But reports of concerning and unprecedented supply shortages for non-COVID-19-related tests are now emerging.

What Laboratory Items Are in Short Supply?

When asked about the challenges clinical laboratories are facing, Dr. Nicole Zitterkopf, Vice President of Laboratory Service Line at Optum (the health services platform of UnitedHealth Group) in Minneapolis Minn. poignantly asked, “Where do I begin? There are multiple problems that need to be addressed here.”
 
Many laboratories still do not have reliable access to COVID-19 test kits, reagents and/or machines, with even normally well-equipped, high-complexity labs still unable to get the kits they need to run SARS-CoV-2 assays. But now there’s a new challenge. Shortages are affecting routine non-COVID-19-related laboratory procedures and diagnostic testing for a variety of other diseases including, but not limited to, sexually transmitted infections (STIs), pneumonia, cystic fibrosis, urinary tract infection (UTI), gastroenteritis and surgical site infection. 
 
“The supply chain issues that laboratories are currently experiencing are ever-changing, unpredictable and unprecedented,” Dr. Robin Patel, former ASM President and Director of the Infectious Diseases Laboratory at Mayo Clinic in Rochester, Minn. explained to Bloomberg
 
Included in the ever-changing, ever-growing list of hard-to-come-by supplies are culture and transport media, swabs, pipettes, pipette tips and collection tubes. Importantly, most of these items are used to perform a variety of laboratory procedures needed for routine patient care on a daily basis. They are multifunctional and considered indispensable, under normal circumstances.
 
Streptococcus pyogenes culture on blood agar.
Streptococcus pyogenes culture on blood agar.
Source: Micronerdbox @ Flickr / CC BY (https://creativecommons.org/licenses/by/2.0)
For example, many laboratories s are reporting shortages of blood agar, a type of enriched culture medium used to grow and identify hundreds of different types of bacteria, including streptococci, enterococci, and staphylococci; this is impacting testing for pneumonia, UTI’s, bloodstream infections, and, really, all types of bacterial infection.

Labs are also reporting shortages in Mueller Hinton (MH) media, a type of growth medium used to measure antibiotic susceptibility of many bacteria, examples of which include Neisseria gonorrhoeae, the causative agent of gonorrhea, Acinetobacter species and Enterobacteralaes, such as Klebsiella pneumoniae, resistance in which is considered an urgent threat by the United States Centers for Disease Control and Prevention (CDC). If antibiotic susceptibility of these and other bacteria cannot be tested, patients may not receive appropriate antibiotics for their infections, leading to either under-treatment (and therefore adverse outcomes, including death), or overtreatment (leading to microbiome disturbances and unneeded toxicity).
 
Others have reported that they’re about to run out of chocolate agar, fungal culture media, viral transport media, vaginal panels, chromogenic agar plates, selective agar for growing streptococci, tryptic soy broth, buffered charcoal yeast extract agar, sabouraud dextrose agar, calcofluor white stain and BD Max Enteric Bacterial Panels.

Antibiogram of Pseudomonas aeruginosa on Mueller-Hinton agar.
Antibiogram of Pseudomonas aeruginosa on Mueller-Hinton agar.
Source: Stefan Walkowski / CC BY-SA (https://creativecommons.org/licenses/by-sa/4.0)
As a result of these widespread limitations, many labs are beginning to implement resourceful (albeit less efficient, less user-friendly and less technologically advanced) workarounds, some of which may compromise patient care. Some have been forced to reach back to older protocols in order to bypass the need for out-of-stock supplies.  
 
“We’re back to Gram stain, fungal culture and Trichomonas vaginalis PCR rather than BD MAX because we can’t get any [BD MAX Panels],” one laboratory shared with ASM.

Others are beginning to restrict minimal inhibitory concentration (MIC) testing, which could lead to increases in unidentified and mistreated antibiotic resistant infections, or conversely, overuse of antibiotics.

‚ÄčOn a related note, on September 3rd, 2020, the CDC issued recommendations about what to do when testing for STIs (which is usually easily available) is not available, including, in some cases, administering antibiotics without making a specific diagnosis as to what is causing the infection. 
 
It is clear that the uncertainty and lack of supplies are significant hurdles, hindering day-to-day laboratory operations in the United States. Diagnostic testing for all kinds of diseases, not just COVID-19, are now being impacted. The downstream effects may be inadequacies in patient treatment and care, ineffective infectious disease management and containment and increases in antibacterial resistance. 

Why are Laboratory Supply Shortages Happening?

As it turns out, these shortages are direct and indirect effects of the ongoing pandemic. 
 
“Reference labs are overloaded by the sheer volume of samples they are receiving,” explained Zitterkopf. So much so, that at times, some refuse to accept new samples during surges, and if they do accept samples, turnaround times extend beyond 7 days.

Among several factors associated with the pandemic, the high demand for COVID-19 testing has led clinical testing suppliers and manufacturers to redistribute resources and personnel to concentrate on the production of COVID-19 collection, transport and diagnostic supplies. Not only have there been fewer non-COVID-19 supplies produced in recent months, but a portion of the preexisting inventory was also discarded along the way. In the early days of the pandemic, when many research laboratories were forced to shut down or curb their research, the demand for plated media fell off significantly, resulting in expired inventory which had to be destroyed.
 
It’s not surprising, then, that BDRemel and Hardy Diagnostics, are now experiencing back orders for a variety of supplies, including routine culture media. In response to these shortages, BD has created a prioritized product list that focuses production on the media and supplies that are in highest demand, and Jay Hardy, CEO of Hardy Diagnostics has stated, “You can be assured that we are doing everything possible to prevent back orders. We have implemented night shifts and are also working on weekends in order to keep up with the increasing demand. New equipment has been ordered, but the lead time for installation is about 6 months. We have always prided ourselves on ‘next day’ service, but unfortunately it may take a few days longer at the present time, and for that we apologize.”

How Do We Improve Diagnostic Testing for COVID-19 and Non-COVID Diseases?

In an effort to identify debilitating supply chain issues and alleviate strain, ASM has partnered with the Association for Supply Chain Management (ASCM) to develop an online platform that will monitor and report up-to-date laboratory shortages and demand. Analyzed data from 296 CLIA-Certified labs, is being reported and made publicly available. This data collection tool will provide a detailed overview of the most recent shortages of culture media, reagents, collection devices and consumables that are significantly impacting day-to-day, COVID-19 and non-COVID-19 testing on a national, state and regional level.

Author: Ashley Hagen, M.S.

Ashley Hagen, M.S.
Ashley Hagen is a science communications specialist at ASM.