Clinical Microbiology, Infection Prevention & Epidemiology: The Trifecta Fighting HAIs


By Kelly M. Pyrek

Diekema and Saubolle (2011) remind us that "Preventing infections requires the ability to detect them when they occur, which is why the clinical microbiology laboratory (CML) plays a key role in healthcare-associated infection (HAI) prevention."

To review, the CML contributes to infection prevention efforts in several critical ways, including surveillance, outbreak detection and management, antimicrobial stewardship, deliberations of the infection control committee, and education.  

For example, Diekema and Saubolle (2011) observe that, "Review of CML data remains the most common method for case finding in HAI surveillance; therefore, the most important role of the CML is to promptly and accurately detect nosocomial pathogens and their antimicrobial resistance patterns. The CML must also work with the infection prevention program and the information technology department to determine how microbiology data are delivered and linked to other surveillance data to streamline this process." 

The researchers acknowledge the increasing degrees of time pressure applied to the CML for it to produce increasingly rapid test results: "As hospital lengths of stay decrease, the window of clinical relevance becomes smaller and smaller."

Technology is revolutionizing the CML, and healthcare epidemiologists and infection preventionists (IPs) are scrambling to keep up with the myriad developments. 

"Rapid diagnostics, particularly using molecular methods, is able to provide information to providers in incredibly efficient timeframes," says Duane W. Newton, PhD, D(ABMM), FIDSA, director of the Clinical Microbiology Laboratory at the University of Michigan as well as 
associate director of the Division of Clinical Pathology for Michigan Medicine. "It allows healthcare providers -- including physicians, pharmacists and IPs -- to make management decisions sooner."

Newton points to multiplex panels for positive blood cultures, which provide rapid identification and offers limited resistance gene information. "This information can help IPs with instituting precautions more quickly," Newton says. Other advancements include multiplex panels for respiratory pathogen detection and can help inform bed placement, co-horting and isolation precautions; as well as multiplex panels for GI pathogen detection.

Another advancement making a significant impact on patient care, according to Newton, is integration of rapid diagnostic testing via matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). According to Huang and Newton (2013), "MALDI-TOF with antimicrobial stewardship team (AST) intervention has the potential for early organism identification, customization of antibiotic therapy, and improvement in patient outcomes." In their study, the researchers assessed the impact of this combined approach on clinical and antimicrobial therapy-related outcomes in patients with bloodstream infections. The AST provided evidence-based antibiotic recommendations after receiving real-time notification following blood culture Gram stain, organism identification, and antimicrobial susceptibilities. Outcomes were compared to a historic control group.

Huang and Newton (2013) included in their final analysis a total of 501 patients with bacteremia or candidemia: 245 patients in the intervention group and 256 patients in the preintervention group. They found that MALDI-TOF with AST intervention decreased time to organism identification (84.0 vs. 55.9 hours), and improved time to effective antibiotic therapy (30.1 vs 20.4 hours, P = .021) and optimal antibiotic therapy (90.3 vs. 47.3 hours). Mortality (20.3 percent vs. 14.5 percent), length of intensive care unit stay (14.9 vs. 8.3 days) and recurrent bacteremia (5.9 percent vs. 2.0 percent) were lower in the intervention group on univariate analysis, and acceptance of an AST intervention was associated with a trend toward reduced mortality on multivariable analysis.

It has been more than a decade since automation systems were introduced to the laboratory environment; since then, "it has rapidly proved its value by increasing productivity, allowing a continuous increase in sample volumes despite limited budgets and personnel shortages," according to Croxatto, et al. (2016), who add, "The laboratory automation systems are rapidly evolving to provide improved hardware and software solutions to optimize laboratory efficiency."

"Total lab automation in microbiology has the potential to shorten time to detection of positive cultures," Newton affirms. "Laboratories can then shift staffing to read cultures when ready, so there is increased 24/7 availability of culture results."

Finally, advancements key to the CML include molecular coming to the point-of-care (POC) environment for respiratory viruses and Group A strep. "This could impact IPs in different ways," Newton says, "such as fewer patients coming to the emergency department for testing, or more positive patients identified in an ambulatory setting."

Newton emphasizes that "technology is improving interpretation and reporting of results in the healthcare setting by making more information available sooner, thus offering clinicians a greater basis to make decisions. It's also improving the detection of pathogens that were not able to be easily detected before, and more specific diagnoses can be made."

Swift, dependable results are beneficial for the healthcare institution's antimicrobial stewardship program. As Diekema and Saubolle (2011) observe, "Antimicrobial stewardship efforts are directly dependent on reports from the CML, so good communication between the laboratory, pharmacy, infection prevention program, and a stewardship team is essential." 

To that end, Diekema and Saubolle (2011) add, "It is paramount that the clinical microbiologist participates on the infection prevention/control committee and acts as a consultant to infection preventionists. He or she is the best person to provide expertise in the interpretation of culture results, advice about the utility of microbiological approaches to an infection control problem, and input regarding the CML resources needed to accomplish the goals of the committee. He or she should describe how changes in the methods used for detection, identification, and susceptibility testing of nosocomial pathogens will impact the infection prevention program. The benefits of close collaboration and interaction between the CML and the IPP are difficult to measure but are real. One large survey of CML directors found that those hospitals with CML directors on the infection prevention/control committee were more likely to have CML involvement in formulary decisions, to produce an annual antibiogram, and to provide molecular typing support."

It is essential, then, that IPs strive toward optimal communication and collaboration with their institution's CML. 

"Infection prevention is built on an understanding of infectious disease transmission," says Hilary M. Babcock, MD, MPH, FSHEA, FIDSA, medical director of the BJC Infection Prevention and Epidemiology Consortium, emphasizing the importance of the novice IP grasping the principles of epidemiology and microbiology and applying them to their work in HAI prevention. " Understanding transmission requires an understanding of microbiology as well as principles of epidemiology," adds Babcock, who is also medical director of occupational health at Barnes-Jewish and St. Louis Children's Hospitals; and professor of medicine in the Infectious Disease Division at Washington University School of Medicine. "Basic microbiology concepts of importance for Infection Prevention include what kinds of organisms are found where (reservoirs), what kinds of clinical syndromes they cause in patients (e.g., pneumonia vs skin infections), how well they survive in the natural and the healthcare environment, how they are transmitted to and among people, and how the microbiology lab identifies them. Epidemiology is summarized as the who, what, where, when and how of disease.  Understanding these principles allows IPs to investigate clusters of infections and to promote practices that interrupt disease transmission."   

For the intermediate to advanced IP, staying abreast of the aforementioned advances in molecular diagnostics, can significantly affect their performance.

"Advances in microbiology lab practices can have a profound impact on infection prevention programs," Babcock says. "More rapid identification of organisms from clinical cultures can allow earlier isolation of contagious patients, as well as earlier recognition of clusters of infections. In addition, advanced molecular techniques can provide rapid identification of respiratory and gastrointestinal viral infections, facilitating earlier adoption of appropriate isolation and environmental cleaning interventions. Also, detailed molecular characterization of organisms can determine whether clusters of infections are due to a single source or not, which has significant implications for control."

Babcock continues, "Updates in the available technology will impact the capabilities of the infection prevention program in many ways.  Working together, these advances can be leveraged to provide safer care for patients. Microbiology lab representation should be included in infection prevention committee meetings and new staff in each department should be introduced to each other to keep close and collegial ties between the groups." She adds, "Infection preventionists and healthcare epidemiologists are critical partners in leading healthcare facilities to provide safe care to all their patients. Healthcare epidemiologists bring a deep knowledge of infectious disease epidemiology, transmission, clinical impact and treatment. They are experienced in outbreak investigation and response and can engage physicians in discussions about safe practices. A strong collaboration between Infection Prevention Specialists and healthcare epidemiologists leads to a better program and better outcomes. SHEA and APIC have an annual leadership course specifically designed for the preventionist/epidemiologist team that is an excellent opportunity to strengthen that relationship." 

Newton acknowledges that the communication flow between infection prevention, hospital epidemiology and clinical microbiology must include managing expectations of and for each department. 

"Just because a test is available, doesn’t mean it should be used in every situation," says Newton, providing an example of assumptions that can serve as barriers to collaboration. "Lab can and should be consulted with to understand appropriate utilization. In addition, molecular tests can’t differentiate infection from colonization, live from dead, so interpretation is imperative to be taken in the right clinical context. Work with the lab to understand benefits and limitations of tests, both in-house and send-outs."

Newton adds, "From a very practical perspective, culturing of environmental samples (water, surfaces, tubing, etc.) is fraught with problems. There are specific reference labs that use validated procedures for processing and testing these types of specimens, and most hospital-based labs are not skilled in these processes. As a result, the interpretation of results (positive or negative) is challenging and often does not justify the resources expended. I feel like a significant amount of conversation should occur between the IP and the lab if this type of testing is being considered, so that a clinically appropriate and resource efficient approach can be identified jointly."
Newton says the relationship between the IP and the CML can be enhanced by improved understanding, "Largely because we view each other as partners on the clinical team, working together to improve patient care. I think both sides know what the others’ respective roles are, but it is critical to view each other as working together, not one 'serving' the other."

He adds, "I think it can be enhanced by continuing to engage in communication, understanding each other’s needs and capabilities, through regular meetings and updates. We have gained a lot from the lab visits from our IPs when they share their stories about how the information the lab provided has been used, such as specific surveillance initiatives, outbreak investigations where we did special cultures or collected isolates or data, so the technologists could understand how their extra effort was advancing our mutual clinical mission. Also, not every hospital lab has a doctoral level microbiologist that can be identified/used as a clinical point person for the IP, so extra work may need to happen to identify the lab-based resources to function as clinical/medical liaisons with the IP."

Newton says it is critical for IPs to have a good grounding in clinical microbiology. "I teach clinical microbiology to MPH students in our School of Public Health, many of whom end up doing infection prevention-related work.  I think it is so important for users of lab data to understand how that information is generated, what it means, and importantly, what it is not telling you."

Regarding clinical microbiology-related knowledge gaps among IPs, Newton says, "I think there are more opportunities to engage with each other in educational activities at a professional level (local, regional and national meetings). Maybe propose joint meetings or cross-pollenate more at national meetings.  I find those opportunities to be very valuable, personally. Continue to maintain the dialogue, as technologies change, organism names change, priorities change -- regular communication ensures that everyone is on the same page."

Croxatto A, Prodhom G, Faverjon F, RochaisY and Greub G. Review: Laboratory automation in clinical bacteriology: what system to choose? Clinical Microbiology and Infection. Vol. 22, No. 3. Pages 217-235. March 2016.

Diekema DJ and Saubolle MA. Clinical Microbiology and Infection Prevention. Proceedings of Camp Clin Micro 2011.

Huang AM, Newton D, Kunapuli A, Gandhi TN, Washer LL, Isip J, Collins CD, Nagel JL. Impact of rapid organism identification via matrix-assisted laser desorption/ionization time-of-flight combined with antimicrobial stewardship team intervention in adult patients with bacteremia and candidemia. Clin Infect Dis. 2013 Nov;57(9):1237-45. 

Newton DW and Novak-Weekley S. Enhancing the Function of Clinical Microbiology Laboratories: Can We Navigate the Road Less Traveled? Proceedings of Camp Clin Micro. 2011.


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