Clinical Microbiology and Infection Prevention are Essential Partners


One crucial yet potentially underused partnership in the battle against healthcare-acquired infections (HAIs) is that between the infection preventionist and the clinical microbiology laboratory (CML) professional.

Pfaller and Herwaldt (1997) point to the symbiotic relationship and describe the roles of each party: “The work required of the clinical microbiology laboratory and of the infection control program has become increasingly demanding, and intertwined as the decade of the 1990s has progressed. To do their jobs effectively and efficiently, these two groups must work as a team, using the expertise from each discipline to improve patient care. As in the past, the microbiology laboratory must be able to detect and identify microorganisms so that the clinicians can diagnose and treat established infections and the infection control team can monitor, prevent, and control infections in the hospital environment. Given the rapid changes in nosocomial pathogens, in medical care, and in healthcare delivery, staff members from the laboratory and from infection control must collaborate continuously and must communicate openly. The relationship between the microbiology laboratory and the infection control program is critical to the success of both groups.”

That relationship has been threatened in recent years when, in a cost-containment effort, managed care attempted to “restructure, centralize or consolidate laboratory services, including clinical microbiology laboratories, into larger working groups that serve multiple hospitals and retain fewer staff with dedicated microbiology expertise,” according to Peterson, et al. (2001). Peterson noted that this restructuring was occurring at a time when infectious diseases rose from the fifth leading cause of death in the U.S. to the third leading cause (a 58 percent increase), and while multidrug-resistant organisms were now seen routinely in community and hospital settings. Peterson, et al. (2001) observe, “In addition to detecting infectious microbes and determining useful therapy, laboratories of the 21st century must now recognize new pathogens and support the national infrastructure needed for surveillance to ensure food safety and counter bioterrorism. Meeting these challenges may not be compatible with the current administrative strategies for laboratory restructuring and/or consolidation.”

Constriction of CMLs parallels the ongoing struggles infection prevention and control departments have with securing increased staff, resources and funding in order to perform basic functions. One such function both parties have in common is surveillance. Recent focus on emerging infectious diseases, pandemic outbreaks and even bioterrorism calls for stepped-up surveillance efforts. Canton (2005) notes, “Clinical microbiology laboratories play a pivotal role in these programs. They have the first opportunity to detect these problems and should participate in the design of reporting strategies and dissemination of this information ... early implementation of response strategies should be designed and performed with the cooperation of microbiology laboratories, and intervention and response protocols should be defined with the participation of clinical microbiologists.”

Thus acknowledging its critical role, what is the average CML’s capacity? Diekema, et al. (2001) state that although CMLs play an important role in supporting infection control efforts, there is a paucity of data to describe the extent to which CMLs provide these supportive functions. The researchers surveyed 109 CML directors in a national study to assess measures recommended to support resistance-control efforts. Among 75 surveys returned 70 CMLs use automated susceptibility testing, but only 36 CMLs reported using confirmatory tests for ESBL detection. The study also revealed that CMLs usually participate (82 percent) on the infection control committee, but only 59 percent are involved in antibiotic formulary decisions. The CML compiles antibiograms for physicians and infection control staff at most hospitals (82 percent). CML representation on the IC committee is associated with CML involvement in formulary decisions, compilation and frequent updating of the antibiogram. Most (87 percent) CMLs immediately notify the infection preventionist when an important pathogen is detected.

Dialogue between CML professionals and clinicians, it would seem, is imperative. Peterson, et al. (2001) note, “Effective communication is one of the most important characteristics of a microbiology laboratory ... Provision must be adequate for bidirectional interaction, because the information provided is nearly always qualitative and interpretive. Face-to-face meetings ... as dictated by the patient’s needs, best accomplish this goal.”

Peterson, et al. (2001) point to a survey of CML directors revealing their concerns that lab consolidation/restructuring would foster poor communication between physicians and laboratory personnel, as well as compromised infection control surveillance resulting from a lack of personal interaction with staff at the hospital. An article in a College of American Pathologists newsletter acknowledged a concern about remote-site labs contributing to the loss of subtle communication between the laboratory and the infectious diseases physician and adversely impacting patient-care outcomes. Virk, et al. (2000) note, “Effective surveillance (for resistance identification and control) depends on a fully equipped, efficient, and accurate microbiology laboratory that maintains close contact with clinicians.”

One area of concern of CML directors revealed by the survey is the lack of medical technologists, pathologists and/or medical microbiologists dedicated to the performance of microbiology testing. CMLs untouched by restructuring and which maintained testing conducted by experienced, dedicated personnel continued to show proficiency and that errors in bacterial identification and susceptibility testing were made less than 5 percent of the time. Conversely, restructured CMLs staffed with generalists continued to make many serious errors in identification and susceptibility testing in greater than 30 percent of samples. Baron, et al. (1996) report on a survey of 500-plus infectious disease physicians; 78 percent of these members of the Infectious Diseases Society of America (IDSA) thought that consultative services by a doctoral-level CML director was extremely important to quality outcomes, and enhanced the level of trust established between the lab. Baron, et al. (1996) found higher quality scores for labs whose director was certified in the practice of medical microbiology, as opposed to those labs whose director had not obtained specialty training.

Better lab direction leads to better data which contributes to improved use of the results of susceptibility testing for antibiotic resistance. Peterson, et al. (2001) confirm, “Development of rational therapeutic guidelines needed for prudent use of antimicrobial agents in the battle against emerging drug resistance cannot be accomplished without ongoing review of results of susceptibility testing by the professionals in the microbiology laboratory and the practicing physician. Distrust of results of testing in microbiology laboratories makes formulary control of antibiotics difficult to enforce and invariably leads to increasing therapeutic empiricism, which is something that should be abandoned as part of the historical practice of medicine.”

Another concern related to capacity issues is CMLs’ ability to accurately detect emerging resistance to antimicrobial agents. In 1998 the CDC surveyed its 447 laboratories in its Active Bacterial Core Surveillance and Emerging Infections Program networks to assess their ability to detect Staphylococcus aureus intermediately resistant to vancomycin and Enterobacteriaceae that produce extended-spectrum beta lactamases (ESBLs). Peterson, et al. (2002) report that of the 416 laboratories that responded (93 percent), 369 (89 percent) actually performed microbiology testing. Additionally, 66 (33 percent) laboratories did not use an acceptable method to confirm the detection of S. aureus that is intermediately resistant to vancomycin, and more than 73 percent failed to use recommended methodology to detect ESBLs (98 used adequate screening methods for ESBLs).

Investigators Lance Peterson and Gary Noskin reported their findings at Northwestern Memorial Hospital after several years of experience with a CML fully staffed and equipped to both handle infection control needs as well as report their data to the CDC. Peterson and Noskin (2001) say that after making the CML an integral component of a hospital-wide infection control effort, the 700-bed medical center saved more than $2 million related to preventing HAIs, and that each year they avoided approximately 285 of these infections that likely would have resulted in at least 10 deaths. Peterson and Noskin reported the cost of the enhancement of the CML was about $400,000 annually, but that it resulted in a five-fold return on the investment that improved patient care.

Peterson and Noskin (2001) admit that while building and maintaining a highly functional CML can be costly especially at a time when reimbursement for laboratory testing is declining, but they advocate for government incentives to hospitals to do so. They suggest that grants ranging from $300,000 to $500,000 annually from the CDC or from the Agency for Health-Care Research and Quality could help “start a program of enhanced, comprehensive healthcare infection control and prevention.” As Peterson and Noskin (2001) explain, “While such a grant program would cost up to $2 billion each year if all U.S. hospitals participated, the projected reduction in cost of treating nosocomial infections could reach over five times that amount. Monitoring compliance and outcome should be part of the annual grant renewal process. Such an approach is consistent with a recently released report delineating the federal response to reducing medical errors. Our data strongly suggest such an investment will not only reduce illness and death but also avert the high costs of treating avoidable infections.”

Peterson, et al. (2001) emphasize, “With national attention focused on an increase in infectious diseases and the goal of improving the quality of healthcare outcomes, a consensus must be reached as to what threat infectious diseases problems pose and what resources are needed to improve microbiology laboratory infrastructure so that the laboratory can deal with them ...On the basis of our current knowledge, it appears that the management of infectious diseases will be best accomplished by the maintenance of clinical microbiology laboratories on the same campus as the healthcare institution(s) they serve, to provide the American public and the physicians who care for them with the necessary diagnostic testing, means of epidemiological detection, and future innovation required in an era of emerging and reemerging infectious diseases. The microbiology laboratories of the United States, partnering with state health departments and the Centers for Disease Control and Prevention, are the first line of detection and defense in the event of new emerging microbial resistance, outbreaks of foodborne illness, or a bioterrorist attack. These laboratories directly serve the patient through accurate and timely detection of infectious microbes, and this information is critical to the quality treatment of infectious diseases. Successful detection and interpretation of results clearly require adequate staffing with specially trained medical technologists and supervision by laboratory directors who have received training in a clinical and/or medical microbiology program that qualifies them for certification by the American Board of Pathology or the American Board of Medical Microbiology. The microbiology laboratory also is a crucial component of the infection control team responsible for preventing healthcare-associated infections, thus promoting good patient care outcomes that save money.”



Pfaller MA and Herwaldt LA. The clinical microbiology laboratory and infection control: Emerging pathogens, antimicrobial resistance, and new technology. Clin Infect Dis. 1997 Oct;25(4):858-870.


Peterson LR, Hamilton JD, Baron EJ, Tompkins LS, J. Miller M, Wilfert CM, Tenover FC, and Thomson RB. Role of clinical microbiology laboratories in the management and control of infectious diseases and the delivery of healthcare. Clin Infect Dis. 32:4, 605-611. 2001.


Canton R. Role of the microbiology laboratory in infectious disease surveillance, alert and response. Clin Micro Infect. 11:s1, 3-8. May 2005.


Diekema D, et al. Clinical microbiology laboratory support for infection control and antimicrobial resistance control. Abstract K-1213. Intersci Conf Antimicrob Agents Chemother. 2001 Dec 16-19; 41.


Peterson LR and Noskin GA. New technology for detecting multidrug-resistant pathogens in the clinical microbiology laboratory. Emerg Infect Dis. March 2001.


Baron EJ, Francis D, Peddecord KM. Infectious disease physicians rate microbiology services and practices; guest commentary. J Clin Microbiol 1996;34:496-500.

Microbiology 101: Antibiograms

Most laboratories generate an antibiogram, a report that contains a summary of common organisms recovered and their resistance patterns to commonly prescribed antibiotics. This report assists the physician in ordering prompt and appropriate antibiotics based on the most likely bacteria for the site while awaiting final culture and susceptibility results.

This susceptibility statistical data, consisting of the cumulative and ongoing summary of the patterns of antimicrobial susceptibility of clinically important microorganisms, are critical to public health. To help CMLs with the preparation of cumulative antimicrobial susceptibility test data reports, the Clinical and Laboratory Standards Institute (CLSI) has issued an updated “Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data; Approved Guideline—Third Edition” (M39-A3).

Rebecca T. Horvat, PhD, director of clinical microbiology at the University of Kansas Hospital, says, “Antimicrobial resistance continues to increase in clinical pathogens. Monitoring these changes and making a determination of significant developments can be challenging. A rationale approach to monitoring new resistance patterns allows healthcare institutions to develop reasonable protocols to identify changes that affect treatment option. The M39-A3 continues to give some clear advice and ideas on calculating and presenting antimicrobial susceptibility data.”

This document includes the following updates:

• Added various options for presenting data when the incidence of a specific multidrug-resistant organism is significant in a facility.

• Expanded recommendations for calculating percent susceptible for subsets of isolates (e.g., specific wards, patient types, and body sites).

• Added recommendations for calculating the percentage of isolates susceptible to either or both of two antimicrobial agents that might be considered for combination therapy.

Q&A with Janet Hindler

Janet A. Hindler, MCLS, MT(ASCP), is a senior specialist in the Clinical Microbiology Laboratory at UCLA Medical Center in Los Angeles

ICT: In the number of years you have been at UCLA Medical Center, have you witnessed any upswing in the utilization of the clinical microbiology lab by infectious disease physicians and/or infection preventionist that might be anecdotally related to the increase in antibiotic resistance and the rise of the so-called superbugs?

JH: There has been an increase in utilization of the microbiology laboratory for performing many tests including bacterial cultures which are linked to antimicrobial susceptibility tests. This may be due to an increase in the variety of antimicrobial resistance patterns now seen among commonly encountered bacteria. For example, we have noted an increase in the number of Staphylococcus aureus isolated from outpatients that cannot be attributed to any significant changes in patient populations served by our laboratory. We can assume that more physicians are culturing wounds to determine if their patients have MRSA. We have also noted increases in blood cultures submitted and here we can speculate that this might be a result of physicians being more cautious about the possibility that a febrile patient has a bloodstream infection that could be due to a multidrug-resistant organism (MDRO) where standard empiric antimicrobial regimens might fail. It is important to maintain an awareness that resistant rates in a facility are totally dependent on culturing practices and many facilities do not have specific guidelines for when to do cultures. If a facility only performs cultures on the sicker patients, they are likely to have higher rates of resistance.

ICT: Do you think in general that clinicians utilize the lab as much as they could/should in the fight against pathogenic organisms?

JH: Physicians may not use the microbiology laboratory as much as they could. For bacteriology, this is partly due to the slow turnaround time. Laboratories must strive to release preliminary results as soon as they become available and make sure physicians are aware of the availability of any new test results. We are seeing increased utilization of some molecular tests, such as those used to detect certain viruses where the turnaround time is much quicker than most tests for bacteria. We definitely need more rapid diagnostic methods for bacterial pathogens coupled with methods to detect resistance among them. Detecting resistance with current rapid technologies is a challenge because of the variety of resistance mechanisms that can occur among bacteria.

ICT: Has your facility seen a spike in HA-MRSA and CA-MRSA cases? Have timely antibiograms helped clinicians switch from empiric treatment to more tailored antibiotic prescribing and other treatment?

JH: We do not perform any tests that definitively differentiate HA-MRSA from CA-MRSA, however like many others, we have seen increases in our rates of MRSA that peaked in 2004 and have remained relatively stable over the past four years. This holds true for isolates from both inpatients and outpatients. With the percentages of Staphylococcus aureus that are MRSA hovering around 40 percent to 60 percent in most U.S. facilities, a physician would rely on laboratory tests to rule out MRSA in patients with suspected staphylococcal infections prior to prescribing agents that do not cover for MRSA. Analysis of susceptibility test results on a subset of S. aureus that only includes MRSA isolates could help guide use of anti-MRSA drugs. For example, if the percentage of MRSA susceptible to clindamycin among outpatients is high, clindamycin might be empirically prescribed for suspected staphylococcal infections.

ICT: How can clinicians best use cumulative antimicrobial susceptibility test data to make sound clinical decisions?

JH: Laboratories should have the ability to not only produce an annual cumulative antimicrobial susceptibility test data report (e.g., cumulative antibiogram) but also to extract additional data to answer specific questions as they arise in order to support empiric prescribing practices. For example, with increasing fluoroquinolone resistance among gram-negative bacilli, an emergency room may wish to know if fluoroquinolone resistance rates for E. coli isolates from urine are the same among all age groups. Having these data could assist a facility to develop a protocol for empiric therapy of cystitis in outpatients that might differ for various age groups. It is not uncommon to find higher rates of fluoroquinolone resistance among isolates from elderly patients. For another example, an ICU might wish to know the percentage of Pseudomonas aeruginosa isolates that are susceptible to either tobramycin or piperacillin-tazobactam or both agents to help guide empiric therapy decisions. If the percentages of susceptible isolates are low, they may wish to examine data for alternative combinations of drugs.

The annual cumulative antibiogram generated by most facilities includes isolates tested from all types of patient populations. Although this may help answer some questions to guide empiric therapy of initial infections, more refined analyses are generally more useful. To expand the use of cumulative antibiogram data we need to: 1) ensure all laboratories have the technology to easily analyze antimicrobial susceptibility data in a variety of ways and in a timely manner; 2) work with clinicians to identify those data that would be most useful in guiding empiric therapy decisions; and 3) educate those involved with antimicrobial therapy about the value of cumulative antibiogram data.

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