Partners in Prevention: Raising the Profile of the Clinical Microbiology Laboratory in Ongoing HAI Control and Outbreaks

By Kelly M. Pyrek

This article originally appeared in the July 2022 issue of Healthcare Hygiene magazine.

The clinical microbiology laboratory (CML) plays a critical role in the surveillance, treatment, prevention and control of healthcare-acquired infections (HAI), working alongside infection preventionists and healthcare epidemiologists. The major importance of medical microbiology is that it helps in the identification, isolation, diagnosis, and treatment of pathogenic microorganisms.

For example, the diagnosis of bloodstream infections (BSIs) is one of the most critical functions of CMLs. But they also help establish an etiologic diagnosis of infections within the central nervous system, such as meningitis and encephalitis; soft tissue infections; upper and lower respiratory tract bacterial and fungal infections, including hospital-acquired and ventilator-associated pneumonias; gastrointestinal infections; bone and joint infections; urinary tract infections, including catheter-associated urinary tract infections (CAUTIs); genital infections; viral syndromes, and others.

As the American Clinical Laboratory Association (ACLA) observes, “America’s clinical laboratories serve as the foundation for early diagnosis, prevention, and personalized care for millions of patients. From routine blood tests to ground-breaking genetic and molecular diagnostics, clinical laboratories play a vital role in improving patient outcomes and quality of life while delivering better value for the health system. Clinical laboratories serve as a driving force in medical innovation. The growing demand for laboratory developed tests – clinical diagnostics that are often designed in response to unmet clinical needs – has revolutionized our approach to patient care and provides an essential foundation for future medical breakthroughs.”

The complexity of the healthcare landscape is reflected in the escalation of the importance of CML services and the need for flawless analysis, observe Miller, et al. (2018) who explain, “Unlike other areas of the diagnostic laboratory, clinical microbiology is a science of interpretive judgment that is becoming more complex, not less. Even with the advent of laboratory automation and the integration of genomics and proteomics in microbiology, interpretation of results still depends on the quality of the specimens received for analysis … Microbes tend to be uniquely suited to adapt to environments where antibiotics and host responses apply pressures that encourage their survival. A laboratory instrument may or may not detect those mutations, which can present a challenge to clinical interpretation. Clearly, microbes grow, multiply, and die very quickly. If any of those events occur during the preanalytical specimen management processes, the results of analysis will be compromised, and interpretation could be misleading.”

The journey begins when the infectious disease physician or healthcare epidemiologist needs some basic data from the CML, including answers to three critical questions, “Is my patient’s illness caused by a microbe? If so, what is it? What is the susceptibility profile of the organism so therapy can be targeted?” according to Miller, et al. (2018) who add, “To meet those needs, the laboratory requires a specimen that has been appropriately selected, collected, and transported to the laboratory for analysis. Caught in the middle, between the physician and laboratory requirements, are the medical personnel who select and collect the specimen and who may not know or understand what the physician or the laboratory needs to do their work. Enhancing the quality of the specimen is everyone’s job, so communication between the physicians, nurses, and laboratory staff should be encouraged and open with no punitive motive or consequences. The diagnosis of infectious disease is best achieved by applying in-depth knowledge of both medical and laboratory science along with principles of epidemiology and pharmacokinetics of antibiotics and by integrating a strategic view of host–parasite interactions. Clearly, the best outcomes for patients are the result of strong partnerships between the clinician and the microbiology specialist.”

However, outside of the healthcare trifecta of the infection preventionist (IP), healthcare epidemiologist and microbiologist, knowledge of the CML by the average healthcare worker may be scant. And mahy healthcare personnel may have never met their institution’s CML staff. As Benbachir (2018) observes, “The microbiologist is a daily privileged interlocutor of the infection control team (infection control doctor and infection control nurse) and the antimicrobial stewardship working group.”
“In my own experience of more than 30 years of public health and medical laboratory service, I believe that the level of understanding around general microbiology to be somewhere in the middle of the road,” says Rodney Rohde, PhD, MS, SM(ASCP)CM SV CM,MBCM, FACSc, chair and professor for the CLS Program at Texas State University College of Health Professions. “Since there is a ton of ongoing continuing education about hand hygiene, HAI prevention and antimicrobial resistance, I believe the understanding in those specific areas to be higher. However, generally, I don’t think understanding is high with important areas like mutation, virulence, immune responses to microbes, and medical laboratory testing at all. In fact, I would place those topics in the lower understanding not only among healthcare workers but also the public. Has the pandemic with COVID-19 raised awareness about microbiology, infectious agents, testing and the immune system? Certainly, but I still think all areas of society (outside the realm of clinical microbiology researchers and professionals) are in the lower range of understanding the critical impact microbiology plays in health, infection control and prevention, and global public health.”

Paul J. Pearce, PhD, principal of The Pearce Foundation for Scientific Endeavor, concurs. “Generally, healthcare personnel are unaware and lack understanding of the complex nature of microbial outbreaks,” Pearce says. “This is primarily due to lack of training in microbiology, epidemiology and the factors associated with outbreaks/pandemics. Healthcare personnel operate in a reactionary environment and seek to solve the immediate problems they encounter. Specific training in recognizing the underlying potential dangers and risks associated with outbreaks is necessary to properly prepare for future outbreaks.”

However, both Rohde and Pearce indicate that the pandemic is an opportunity to raise the profile of the CML.

“I absolutely believe the pandemic helped place a strong light of visibility on the medical laboratory and our services,” Rohde says. “Leaders must leverage this visibility now and going forward by clearly taking a seat at the table of healthcare and public health. Our profession provides more than 13 billion medical laboratory tests each year, including the more than 1 million COVID-19 tests we have conducted since the pandemic began. I and many others have offered our voice and appearances via explainer articles, research publications, podcasts, social media, legislative initiatives, national workforce committees, and subject matter experts during the pandemic. We must continue to raise awareness and visibility for recruitment and retention of college majors, as well as how our work in laboratory medicine provides more than 70 percent of all clinical decision-making for patient care.”

“COVID outbreaks did raise the profile of clinical laboratory services,” Pearce confirms. “Laboratories that promoted fast, accurate, and convenient testing for consumers benefited from making such testing available. Direct consumer access to routine laboratory testing could be of value in the future.”

CMLs had to adapt their structure to respond to an unprecedented massive diagnostic demand of COVID-19, placing tremendous strain on personnel and resources. When examining the CML workload during the pandemic, for example, Catalán, et al. (2021) noted a 96.7 percent increase in the total number of samples processed, with the highest demands placed on the virology and serology areas. The average turnaround times during the study period were 6.7 hours for PCR (ranging from 1.3 hours to 8.1 hours) and 1.4 hours for antibody testing (range, 57 minutes to 1.9 hours). Overall, the CML costs increased 114.8 percent, with personnel hiring and extended shifts and laboratory materials accounting for most of the additional expenditures. The most expensive items were PCR reagents, reagents for SARS-CoV-2 IgG detection, SARS-CoV-2 extraction and purification, and nasopharyngeal sampling swabs and transport media.

Not only were CMLs impacted significantly, but COVID-19 reverberated through all hospital departments. “One must remember that SARS-CoV-2 was a novel virus,” Rohde emphasizes. “Our healthcare system had not faced this type of ongoing, novel virus in recent history and that means the impact for clinical lab services was felt from multiple angles. The healthcare system was in war on multiple fronts. For example, an immediate lack of adequate capacity to handle the surging patient volume, compounded by the lack of PPE, which led to an ongoing and devasting reduction of healthcare professionals in both patient facing areas (nursing, physicians, respiratory care) as well as those behind the scenes (laboratory, front-office, support areas).”

“Many clinical laboratories added methods, means and equipment to test for COVID,” Pearce says. “Prior to the pandemic there was a minimum amount of COVID testing, and the advent of COVID created many new testing opportunities for hospitals, clinics, businesses and industry.”

Rohde adds that due to the highly contagious nature and severity of the infection, “Physicians, nurses, and other healthcare professionals had to rethink, re-engineer, and remodel how the patient room and their care would be designed. They had to do this in real-time without historical data. This virus was so unknown that we were using influenza as an example and that turned out to be a poor surrogate because of so many asymptomatic carriers. Typically, we know when someone is sick due to signs and symptoms. Not always true with COVID-19.”

Rohde continues, “We must also address the overall mental and emotional health of healthcare workers, especially frontline workers. There was a real fear among healthcare personnel, including the clinical laboratory workforce, regarding the lack of PPE and how dangerous this microbe was to their own health.”

He adds, “This leads me to the impact on clinical lab services. Hospitals and other medical facilities were dealing with massive financial loss due to the cancellation of elective procedures and the disruption of routine care. While we know the clinical/medical laboratory was working non-stop to get COVID-19 testing volume, efficiency and accuracy up, on the other side of the coin, the laboratory was experiencing a dramatic reduction in other testing in some facilities due to all of these cancellations of elective procedures or routine care (such as annual physical examination, cancer screening, etc.). Ultimately, and in many ways ironic, due to these losses in finances, healthcare organizations often had to cut costs by the release or reduction of their workforce or to pivot to remote work, including clinicians working with telehealth technologies. I had reports from my own medical laboratory alumni and colleagues around the country who told me that people in the medical laboratory were losing hours or jobs. On the other hand, there were also reports of the medical laboratory workforce being worked to exhaustion and burnout once COVID-19 testing was FDA emergency approved. ‘Doing more with less’ seemed to become the common workplace policy in the laboratory. This is an ongoing issue today.”
Going forward it is also essential that clinical lab services and infection preventionists and hospital epidemiologists improve their communication and collaboration going forward, post-COVID.

“The global issue of antimicrobial resistance is of urgent importance and one that can no longer be viewed as not a U.S. issue,” Rohde emphasizes. “From ongoing HAIs to antifungal and other viral and parasitic resistance, the need for real-time communication between the medical laboratory and IP/epi is a necessity for healthcare and public health. In my experience, one of the best paths to put this communication in motion is to work with not only IP/epi but also pharmacy, nursing, and physicians. There is quite a bit of research and effort being shown to improve this communication via antibiotic/antimicrobial stewardship efforts like nudging. Efforts such as being a ‘stewie’ champion, alongside nudging and implementing appropriate antibiotic breakpoints in medical laboratories are practical tools that have shown positive outcomes. Likewise, the development of cross-functional teams and end users input for communication and team building is critical especially in technology / information sharing as well as standard IP/epi regular meetings and communication in-person and virtually.

As Benbachir (2018) acknowledges, “The CML is tasked with accurate, consistent and rapid identification of infectious agents at the species level and to identify any potential antibiotic/antimicrobial resistance patterns.”

The Centers for Disease Control and Prevention (CDC) has outlined the ways in which microbiology laboratory staff can impact antibiotic stewardship programs. In its Core Elements of Hospital Antibiotic Stewardship Programs (2019) it outlines several areas where the activities of CML personnel, as part of the antibiotic stewardship program team, have been expanded. As the CDC (2019) acknowledges, “It is important for the members of the antibiotic stewardship program to regularly communicate and collaborate. This can be challenging in instances where laboratory services are provided offsite from clinical care settings and there is not daily interaction between clinical infectious diseases, stewardship program, and microbiology personnel.”

The CDC (2020) recommends that CML personnel should be integrated into the functions of the antibiotic stewardship program, explaining that, “Their expertise is important in the areas of diagnostic stewardship, development of antibiograms to support optimal antibiotic use, the introduction of new diagnostic tests into the laboratory, the implementation of new antibiotic susceptibility testing interpretative criteria, and education of clinicians on laboratory testing practices.”
It also advises the support and promotion of education and communication between the laboratory and clinicians about test characteristics (e.g., test performance, expected turn-around-time, etc.). Specifically, it says that clinicians should be educated about how specific tests should be used in clinical situations, including whether a particular test is better for ‘ruling in’ or ‘ruling out’ a condition. The CDC adds that whenever possible, test characteristics should be communicated in the electronic health record at the point of ordering. Clinicians should also be educated when new tests or order sets are introduced within the healthcare facility.
For the future, Pearce advocates for an increase in “routine training, such as seminars, articles and continuing education, that includes forward-thinking topics that may or may not be related to current issues could encourage all concerned to expand their knowledge base and understanding of potential outbreaks.”

To that end, clinical microbiologists have a unique and privileged viewpoint of the next pandemic and the importance of preparedness now.

“I have more urgent view of this issue, since I spent the first decade of my career in public health in a hybrid role as a molecular epidemiologist working between the microbiology/molecular bench and in the Zoonosis Control Division in the field doing surveillance and human case work-ups,” Rohde explains. “I believe the medical laboratory must look at the local level now with global eyes. A One Health perspective is the new framework where animal/plant health + environmental health + human health = One Health.”

Rohde continues, “From a practical standpoint, medical laboratory leaders must change in fundamental ways. For example, we can no longer sign long-term vendor contracts with laboratory suppliers for our raw materials. That practice must end. If COVID-19 taught us nothing else, we must understand that the medical and public health laboratory must now utilize multiple vendors across a diverse array of assays, equipment and supplies to protect us more broadly against the supply chain issue for raw materials. Medical and public health laboratories must also work to integrate communication across multiple external and internal agencies/people from a single point of data entry (for example, a laboratory information system that can talk to local, county, state, national and perhaps global systems to deliver patient results in real-time). Laboratories must prepare for Big Data analysis and the onboarding of high throughput capability utilizing state-of-the-art molecular/genomic/proteonomic tools like whole genome sequencing, CRISPR, next-generation sequencing, and wastewater surveillance of microbial detection. The medical/clinical laboratory must plan now for cross-training of personnel due to dangerous and ongoing staffing shortages, including how to assist medical laboratory educational programs for clinical site/affiliation support to increase recruitment of future professionals. Likewise, there is a need for salary increases, flexible staffing to meet the new professionals view on work/life balance, tuition assistance with both debt and new degrees, and other attractive benefits for the multi-generational workforce. The medical laboratory must also work with the CDC’s Laboratory Response Network and other entities regarding desktop simulations for all these issues (staffing, supply chain, funding, automation, pivoting to onboarding of new testing platforms, etc.) now, not later.”

Pearce emphasizes that “Clinical laboratories must establish policies and procedures, beyond addressing regulatory compliance issues, that are based on collaboration, research, history, Koch's Postulates and avoid reliance on social media and undocumented, unscientific and inaccurate hype.”

American Clinical Laboratory Association (ACLA). The Value of Clinical Laboratories: Supporting Patient Health & Medical Innovation. Undated.
Catalán P, Alonso R, et al. The challenge of COVID-19 for a Clinical Microbiology Department. Diagn Microbiol Infect Dis. 2021 Oct; 101(2): 115426. doi: 10.1016/j.diagmicrobio.2021.115426
Centers for Disease Control and Prevention (CDC). Key Activities and Roles for Microbiology Laboratory Staff in Antibiotic Stewardship Programs. Updated August 2020. Available from:
Centers for Disease Control and Prevention (CDC). Core Elements of Hospital Antibiotic Stewardship Programs. 2019. Available at:
Miller JM, Binnicker MJ, et al. A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. Vol. 67, No. 6. Pages e1-e94. August 31, 2018.
Pence MA and Liesman R. Clinical microbiology. Published online 2020 Jun 19. doi: 10.1016/B978-0-12-815499-1.00055-7. PMCID: PMC7303905