Infection Control Today: Microbiology 101 for the ICP

Microbiology 101 for the ICP

By John Roark

A symbiotic connection between infection control and microbiology is essential. Understanding the basics of this vast area of study is the first step in establishing this connection.

“It is important for the infection control practitioner (ICP) to establish a good working relationship with the director of microbiology or the chief of the department so that they can feel comfortable enough to pursue any future matter,” says Philip M. Tierno, Jr., PhD, director of clinical microbiology and immunology, associate professor, departments of microbiology and pathology at New York University Medical Center, and author of The Secret Life of Germs. “It would also be wise for any new ICP personnel to spend a week or more in the department, learning its dynamic in order to better understand the workflow and the capacity of the lab.”

ICPs should consult with microbiology on a daily basis in order to red-flag any matter that may be brewing within the institution, Tierno continues. “The ICP should work with microbiology to develop working algorithms for detecting specific organisms, or for following outbreaks. The microbiology lab would be the first entity within the hospital to identify a unique bug, an antibiotic-resistant strain or other notable organism, and, as such, it is important for the two-way channel between the departments to be open and well-used. Microbiology should accompany infection control (IC) to areas of the hospital that may need investigating, culturing, air sampling, etc. The concept of inter-departmental teamwork is the hallmark of a good institution, and is recommended by all accrediting agencies such as the Joint Commission on the Accreditation of Healthcare Organizations (JCAHO).”

“Microbes have been around a long time, and I think we have a good capability of identifying which bacteria we’re finding,” says Janice Fuls, a research fellow for Dial Corporation. “There are new emerging pathogens like SARS. Probably the hardest challenges for hospitals are new organisms or viruses. Methicillinresistant Staphylococcus aureus (MRSA) was originally hospital-acquired. Now there’s this new community-acquired MRSA. Those are probably some of the biggest challenges for a microbiologist — when you have an organism that is either resistant or different. Those are new challenges that present themselves.”

Microorganisms are everywhere, which is both a debit and an asset. “Microbes are good, and a necessary part of our survival,” says Joan M. Wideman, MS, MS, MT(ASCP) SLS, CIC, an independent infection control consultant. “For example, if we didn’t have microbes in our gut, we wouldn’t be able to digest food. They help protect against other microbes.” However, important to note is that what is normal flora for one person can be harmful and potentially disease-causing for another — especially those with chronic diseases, the immune-suppressed or the immunocompromised.

Knowing the Basics

Having a working knowledge of microbiology can aid in correctly interpreting laboratory reports. A few useful terms include: normal flora (customary microbes for that site), transient organisms (temporary flora, such as on the hands for hours or days), contamination (not normally found or artifact due to handling, collection or processing), colonization (a not normally found potential pathogen that isn’t causing a problem), or potential pathogen (can cause disease).

Bacteria may be grouped by Gram stain reaction, the most commonly available rapid test. Usually bacteria are divided into Grampositive or Gram-negative; some may also be Gram-variable, and most bacteria and many fungi will stain with this method. Often, cellular matter is present in specimens, and the types of cells can give a clue to the body’s response; the presence of certain cell types, such as white blood cells (neutrouphils or PMNs), can indicate an infectious process. Other microbes may require special stains for detection, such as mycobacteria (M. tuberculosis or TB).

Beside the Gram stain, microbes can be grouped by their shape and arrangement. For example, cocci are little spheres, and their arrangement might be in pairs (diplococci), chains or clusters. Bacteria may be bacilli or rod-shaped, varying in length from short or long, and may even appear in chains or other formations. Spirochetes can appear like little springs or curvy bacilli.

In addition to Gram staining, other rapid detection methods are available. A variety of immunological or serological testing methods are often used with results available in a few hours (e.g., DNA probe for common Chlamydia detection or RPR test for syphilis). Other rapid tests can detect the antigen (i.e., the microbe or a component), a toxin or serology based on the body’s response (i.e., antibody produced).

Bacteria may also be categorized by growth conditions or tolerance to air. They can be aerobic (needing air or oxygen to grow) or anaerobic (unable to tolerate the presence of oxygen) or facultative anaerobes (able to tolerate lack of oxygen for a period of time).


Put simply, fungi are microorganism that lack chlorophyll. Unlike bacteria, fungi have genetic material arranged on chromosomes, and a membrane surrounding the nucleus. Often fungi are grouped as those in the yeast form (e.g., Candida albicans or Torulopsis glabrata) vs. the mold or fuzzy forms (e.g., Aspergillus or Penicillium). Some, based on incubation factors, can show both yeast and mold forms.


Mycobacterium can be defined as a group of bacteria with many disease-causing members. Most often implicated in infection are Mycobacterium tuberculosis and Mycobacterium avium-complex (MAC). The ICP should be aware of other non-tuberculosis mycobacteria (NTM), which can cause opportunistic infections in patients, easily grow in water lines, ice chests, and in clinical equipment exposed to contaminated sources.


A virus is an infectious agent that replicates itself only within cells of living hosts. Viruses are often detected by serological testing, either by detection of the antigen (virus or a component) or antibody (the body’s response). These may be available as rapid tests, send-outs to specialty laboratories or testing of paired sera (acute and convalescent phases). Most hospital laboratories do not have the ability or resources to detect viruses from clinical specimens by culture.

Based on what is anticipated to be causing an infection, the physician must determine what type of specimen(s) to submit for laboratory testing, says Wideman. “Depending upon the site of specimen collection, the microbiology laboratory selects the appropriate culture procedure. Each grouping of specimen sources has different incubation conditions, requirements or other factors to optimally recover the potential pathogens for that site. For instance, sputum, urine, wound and blood specimens are all handled differently.”

Microbes in some clinical specimens may only need a few hours to demonstrate detectible growth (such as those found in the blood), or may take several days or even weeks to grow.

Microorganism Survival

Microorganisms may use protective mechanisms to survive. For example, Bacillus spp. and Clostridium difficile form spores. But there’s a plus-side to these bad bugs. Spore-forming organisms, which are the most difficult to kill, are used to test the effectiveness of sterilizers.

A few organisms form capsules that can also help with detection. In a number of organisms, the cell wall design offers protection in the environment but requires a special staining like acid-fast bacilli (Mycobacteria) or certain fungi.

“As part of their survival, organisms may produce toxins that adversely affect humans,” says Wideman. A few examples include toxic shock syndrome (with Staphylococcus aureus as the most common cause) necrotizing fasciitis — also known as flesh-eating disease — which can be caused by Streptococcus pyogenes; and botulism — foodborne illness caused by a toxin produced by Clostridium botulinum.

What Happens in the Microbiology Lab

Most laboratories generate an antibiogram — a report that contains a summary of common organisms recovered and their resistance patterns to commonly prescribed antibiotics. “Each setting is often unique for the patient population served in that geographic area,” says Wideman. “Some reports may include differentiation between isolates recovered from inpatient and outpatient specimens. This periodic report assists the physician in ordering prompt and appropriate antibiotics (emperic therapy) based on the most likely bacteria for the site while awaiting final culture and susceptibility results.

The ICP may be asked about performing cultures from environmental sources. “There are certain areas where it is appropriate to have regular environmental cultures, such as water used for hemodialysis, sterilizer spore testing, and occasionally for select pharmaceutical preparations that are batched and stored,” says Wideman. “However, other environmental culturing should not be done without purpose or direction, for example, as part of an outbreak investigation.”

Working Together

Microbiologists may assist the ICP by reporting on trends of different organisms recovered. “The ICP should include a member from the laboratory on the infection control committee,” says Wideman. “Sometimes the representative is a pathologist, while other IC committees may include a microbiologist, depending on the size and culture — no pun intended — of the organization. If you’ve never done so, schedule a few meetings with the microbiologists and other laboratory technologists. They are happy to show you things; how bacteria or fungi look on a media plate, what analysis and antimicrobial testing is performed; what the microbes look like under the microscope.”

The ICP may partner with the physician and/ or the laboratory in reporting of communicable diseases. “Depending on applicable laws within each locality, states often determine who is responsible for reporting what testing results,” Wideman explains. “For example, the physician may be ultimately responsible for reporting certain diseases, while laboratories are required to report recovery of select organisms. ICPs and laboratories may also be involved with identifying and reporting certain emerging infectious diseases. Many states or regions have set up a system based on syndromic surveillance to help identify potential outbreaks or emerging diseases. Most areas have established a health alert network (HAN) that’s a part of the funding to enhance the public health infrastructure since 9/11 to help detect outbreaks, bioterrorism events or pandemics. Funding may come from different grants; money is now available to assist labs in enhancing their ability to identify microbes.” Laboratories are also participating with updating protocols and procedures to coordinate sending specimens to regional or state-designated laboratories for further testing.”

ICPs and microbiologists working together can help meet challenges head-on. “If you’re noting organisms in blood cultures that may not be obvious pathogens, a good performance improvement (PI) activity may focus on how blood cultures are collected and the methods used to interpret and report results,” says Wideman. “This PI can be beneficial in several ways: not only due to unnecessary expense of ‘working something up,’ but will the patient be given treatment for something that is not there (e.g., skin flora)? Thus a task force looking at blood culture contamination rates and what can be done to lower such rates is a win-win collaboration.”

Wideman offers another example: “If you’re noting a pattern of urine specimens that are contaminated with the patient’s normal genital and fecal flora, how does one interpret if that patient truly has a urinary tract infection (UTI) vs. organisms recovered from the genital area? What can the team do to address and improve appropriate urine specimen collection, processing, and reporting? The laboratory can help the ICP when investigating potential clusters or outbreaks by saving specimens and/or doing further testing. There are many different methods that may be used to determine if recovered microbes are related or appear to originate from the same source.”

Once armed with a working knowledge of the important role microbiology plays in infection control, ICPs can facilitate a synergy between the departments.

“Talk to them,” says Wideman. “Create a partnership, establish a good working relationship and recognition of their profession. We are all aware that there are shortages in many professions including infection control. Historically, in the 1970s, when infection control first was recognized as a valuable specialty and through today, individuals with nursing backgrounds are probably the largest professional cohort that become ICPs. Medical technologists, especially those from microbiology, are the second largest group. Those with epidemiology backgrounds or a master’s degree in public health are probably the third-largest group. The ICP may be able to recruit laboratory personnel to become future ICPs. Invite them to your infection control organization meetings. Include them in various task forces that promote methods to reduce the risk of infectious diseases at your facility and in the community. Promote patient and worker safety related to emerging pathogens and healthcare associated infections.”

“I think that because the ICP has access to the patient’s medical records, they can investigate leads provided by the microbiologist in order to better define questionable culture results or a current epidemiological investigation,” says Tierno, again stressing the importance of synchronicity between the departments. “Additionally, it is imperative for ICPs to notify the microbiology lab about which strains of bacteria they would like to be saved for future send- out or typing needs or other investigatory processes while investigating an outbreak. Also, because the ICP is the intermediary between the medical and nursing staff of the hospital and the lab, the ICP can also be a critical link for pursuing very sensitive aspects of a particular investigation or for spreading recommendations made by microbiology concerning the infectious process or sanitizing processes, or, in general, to educate the staff based upon the findings of a particular completed investigation. A cooperative effort opens doors ordinarily closed and allows for a more efficient investigatory process. Simply put, it is a win-win situation for all.”