First Principles of Clinical Microbiology: Collection, Handling, and Diagnostics

Michael A Bachman and William D LeBar, University of Michigan, Ann Arbor, MI, United States
© 2018 Elsevier Inc. All rights reserved.

Introduction to Clinical Microbiology 1

Colonization and Infection 1
Detection, Quantification and Characterization 2
Pre-Analytic, Analytic, and Post-Analytic Phases of Testing 2
Specimen Collection 3
Specimen Transport 4
Specimen Processing 5
Specimen Testing 5
Antimicrobial Susceptibility Testing 6
Concluding Remarks 6
References 6
Further Reading 7

Introduction to Clinical Microbiology

Clinical microbiology focuses on the isolation and characterization of infectious organisms so they can be managed and treated in
patients. Infections can be caused by bacteria, fungi, viruses, and parasites. To diagnose an infection, a sample must be collected
from a patient at a body site where the detection of a pathogen or its associated biomarkers is likely to signify disease. The specimen
must be transported to the laboratory in a manner that preserves the specimen for the intended testing. Then the specimen must be
tested in a way that is sensitive and specific for the suspected organism causing the disease. Finally, these results must be
communicated back to a clinician in a way that he or she can interpret and act on appropriately.
Clinical microbiology is arguably the first discipline of personalized medicine. As an example, a patient has the signs and
symptoms of a urinary tract infection, including increased urgency, frequency, and pain with urination. A urine sample is collected
and cultured quantitatively. Within 24 h, the clinical microbiology laboratory reports the species and quantity of bacteria found in
the urine. 1–2 days later, the laboratory reports the susceptibility of that patient’s bacterial isolate to a panel of antibiotics approved
to treat urinary tract infections. The patient’s clinician can then choose an antibiotic that is predicted to be effective against that
patient’s infection.
A pioneering microbiologist, Robert Koch, established the paradigm of clinical microbiology that is still in practice today. In
proving that the bacterium Bacillus anthracis caused the disease anthrax, he developed what have become known as Koch’s postulates
which are: (1) the microorganism must be observed in all cases of the disease, (2) the microorganism must be isolated and grown in
pure culture, (3) microorganisms from the pure culture, when inoculated into a susceptible animal, must reproduce the disease, (4)
the microorganism must be observed in and recovered from the experimentally diseased animal. Many pathogens have been linked
to disease by fulfilling these postulates. For these pathogens, clinical microbiology labs can diagnose infections in patients with
compatible signs and symptoms by isolating the microorganism in pure culture, or detecting it by an alternative method. When
Koch’s postulates have not been met, interpretation of detection of the microorganism in a patient can be challenging or impossible.

Colonization and Infection

The primary goal of the clinical microbiology laboratory is to aid in the diagnosis of infections. However, many pathogens can live
on or in a body site without causing signs and symptoms of disease. For bacteria, fungi, and parasites this is termed colonization,
and establishes a normal flora of microbes in certain body sites. For viruses, an analogous process is latent infection, where the virus
or viral genes persist within cells for long periods of time. Detecting colonization or latent viral infection can mislead a physician by
incorrectly implicating the wrong microbe to explain a patient’s medical condition. To accurately diagnose infections, the clinical
microbiologist must have knowledge of the normal flora of various body sites. For example, Streptococcus pneumoniae is a frequent
colonizer of the nasopharynx, particularly in young children. However, it can also cause meningitis and bloodstream infections.
Isolation of S. pneumoniae from either the CSF or blood is compelling evidence that it is causing an infection whereas isolation from
the throat is not. S. pneumoniae also causes pneumonia, but diagnosis can be challenging since the site of colonization is near the site
of infection and may be sampled inadvertently. Therefore, diagnosis of pneumonia requires careful processes to ensure that the
lungs, and not the upper respiratory tract, have been cultured.
Viral infections require integration of time and body location into diagnosis. Cytomegalovirus infects 40%–50% of people in the
United States and approaches 100% in some countries (Specter, 2009). When it first infects someone, it may produce signs and
symptoms of an infection. Once it establishes a latent infection within cells, it can persist for years or a lifetime without causing

Encyclopedia of Microbiology, 4th Edition https://doi.org/10.1016/B978-0-12-801238-3.66116-0 1

2 First Principles of Clinical Microbiology: Collection, Handling, and Diagnostics

further symptoms. CMV can also reactivate from a latent infection to cause disease. Finally, some viruses cause an acute infection but
are eventually cleared by the immune system. But the infection may trigger an immune response that can be measured as antibodies
against the virus. If detection of antibodies (serology) is used as part of the diagnosis, then past infection must be distinguished from
current infection, and latent infection must be distinguished from primary infection or reactivation.
For many infections, colonization of one body site is a prerequisite for infection of another. This is particularly important for
antibiotic-resistant bacteria, for which infections are difficult to treat. For example, colonization of the intestinal tract with
vancomycin-resistant enterococci (VRE) is concerning because that patient may subsequently become infected or could spread
that bacteria to another patient in the hospital. Therefore, clinical microbiology laboratories now also seek to identify patients
colonized with microbes that could later cause significant infections.

Detection, Quantification and Characterization

At a minimum, diagnosis of infection requires detection of the pathogen or a pathogen-specific host response. Detection can be
through targeted or non-targeted approaches. The enduring non-targeted approach, as pioneered by Koch, is culture. A specimen is
introduced onto nutrient-containing media in either agar or a broth. The breadth of organisms that can grow on the media is limited
only by the nutrients supplied and the time, temperature and atmospheric conditions of incubation.
Different combinations of media can be used to aid in detection and identification of suspected pathogens from a particular
body site. Sheep blood agar supports growth of many, but not all, types of bacteria. Sheep blood agar can also differentiate bacteria
for preliminary identification, as groups including Staplylococci and Streptococci hemolyze the blood creating clearings around
their colonies. Media additives, such as antibiotics or other chemicals, can be used to select for certain organisms and aid in their
rapid identification. MacConkey agar is selective for enteric bacteria such as Escherichia coli and Salmonella because it contains crystal
violet and bile salts that are inhibitory to many other bacteria and differential because it contains lactose (Atlas, 2015). Most E. coli
ferment lactose, reducing the pH of the media and causing the neutral red indicator to turn pink. Salmonella can grow in bile salts but
doesn’t ferment lactose and has clear colonies. The combination of sheep blood agar and MacConkey allows growth of many
bacteria and can also aid in rapid diagnosis once a colony grows.
Targeted approaches to diagnosis include detection of molecules produced by the pathogen (antigens), pathogen-specific
immune responses (antibodies or cell-mediated immunity), and RNA or DNA specific to the pathogen (molecular diagnostics).
With these approaches, the timing of infection must be accounted for because they do not necessarily distinguish between viable
and nonviable organisms. Antigens and nucleic acid may persist in the body for surprisingly long periods after clearance of viable
pathogen. Pathogen-specific antibodies may last for the lifetime of the patient. In combination with direct detection of the
organisms, these approaches can distinguish current from past infection, and primary, latent, and reactivation infections.
In addition to detection, diagnosis may also require quantification. Most diagnostic approaches in clinical microbiology focus
on the detection of a pathogen that, when found in that body site indicates infection. But as mentioned above, colonization and
latent infections can confound interpretation of simply detecting a bacteria or virus. Quantification is one method to improve the
specificity of testing. For bacteria, quantification can aid in diagnosis of infections near sites of colonization, such as urinary tract
infections. For viral infections, quantification is valuable in distinguishing latent infection from primary infection or reactivation.
Latent infection by CMV can cause shedding of virus from mucosal surfaces and into the blood. Detection of a low level of CMV in
the blood, along with the presence of CMV-specific antibodies would be consistent with latent infection. But higher levels in the
blood, and an increase over time, indicate reactivation of the infection.
Characterization of a detected microbe is needed to determine its significance. Typically, identification to the species level is
required to assess the likelihood of causing the infection and the prognosis. However, not all strains within a species may be
pathogenic. Some strains have genes that enable virulence, the ability to cause disease, whereas other strains are avirulent. This
variation is striking for E. coli, where some isolates colonize our intestines harmlessly, while others cause urinary tract infections,
diarrhea, meningitis, and bloodstream infections. In recognition of these differences, Stanley Falkow created Molecular Koch’s
postulates to identify the genes that enabled virulence of certain isolates within a species (Falkow, 1988). This concept has begun to
enter the clinical microbiology laboratory in the form of directed molecular tests. For example, diarrhea-causing strains of E. coli can
be detected based on their gene content among the billions of bacteria and potential bystander E. coli in a stool sample from a
patient. In other cases, antibiotic resistance is a primary concern in diagnosing both infection and colonization. From the intestinal
tract, detection of VRE can be used to implement precautions to prevent spread to other patients, whereas detection of susceptible
Enterococcus has little medical significance. Detection of VRE in the blood typically requires a rapid change in treatment to make sure
an effective antibiotic is used.

Pre-Analytic, Analytic, and Post-Analytic Phases of Testing

Clinical microbiology testing, like all clinical laboratory testing, has three phases: pre-analytic, analytic, and post-analytic (Table 1).
All phases are critical to making the correct diagnosis, and errors in any of them can lead to incorrect results and poor outcomes for
the patient. The pre-analytic phase is all steps that take place before the samples are analyzed (Lifshitz, 2017). This includes assessing
the need for the test, placing an order, determining the site for collection and collecting the sample, identifying the sample properly,
 First Principles of Clinical Microbiology: Collection, Handling, and Diagnostics 3

Table 1 Laboratory considerations for patients with suspected infection

Pre-analytic considerations Analytic considerations Post-analytic considerations

Differential diagnosis Processing triage Result interpretation

Test ordering Assessment of specimen quality Action taken
Specimen collection Rejection criteria
Specimen transport Media selection
Selection of transport device Appropriate incubation
Examination/enumeration
Result reporting

transporting the specimen to the lab, and preparing the sample for analysis (Table 2). The analytic phase of testing includes
inoculation and incubation of the specimen, detection, quantification, and characterization of pathogens, and recording test results
(Table 3). The post-analytic phase includes the reporting of the test result, the clinician accessing the report and then interpreting the
result, integrating it with other clinical data and acting on the result in the care of the patient (Table 4).
Although errors can occur at any stage of testing, the majority of testing errors occur in the pre-analytic phase. In this phase, the
microbiology laboratory consults on which tests to order to diagnose a suspected infection, what type of specimen to collect, and
how to transport the specimen. The clinical microbiology lab assumes direct responsibility for the testing towards the end of the pre-
analytical phase when the specimen is received in the lab and is responsible throughout the analytic phase until the result is reported
in the patient’s medical record. In the post-analytic phase, the laboratory can educate the clinicians on how to interpret the result.

Specimen Collection

Proper specimen collection in the pre-analytic phase is essential to diagnose infections. This responsibility rests with the ordering
clinician, who makes the choice of specimen site and collection technique. Based on the patient presentation, the clinician must
make a list of pathogens that may be causing the patient’s disease. Next, the clinician needs to decide on the best specimen to make
the diagnosis. In general, there are four types of specimens for microbiology: tissue, body fluids, swabs, and foreign objects. Often
the decision of specimen type is straightforward. If suspecting a bloodstream infection, the clinician should collect a sample of the
patient’s blood. However, sometimes the choice of specimen is more complex. If suspecting pneumonia caused by Legionella
pneumophila or S. pneumoniae, the first specimen collected may be urine to detect a pathogen-specific antigen since this approach is
rapid, relatively inexpensive, and usually non-invasive for the patient. Collecting multiple specimens consecutively or concurrently
can increase the chances of making the diagnosis. For either of these organisms, the clinician may also collect a lower respiratory
specimen for detection by culture or molecular methods, and a blood culture may detect S. pneumoniae in a patient with
pneumonia.
In addition to collecting from the most informative site, the amount of specimen collected determines the chances of detecting
the pathogen. With few exceptions, more specimen is better. In the case of diagnosing a bloodstream infection, the standard of care
is to collect multiple specimens over time and with relatively large volumes (16–20 mL for an adult). This is because, despite the
dramatic symptoms and deadly outcomes of bacteremia, the numbers of circulating bacteria (colony forming units, or cfu) can be
less than 5 per mL. For other body fluids, again more is better and the laboratory can concentrate the specimen if needed. If the
pathogen is suspected to be infecting body tissue, then as large a specimen as is safe and feasible should be collected. A saying in
clinical microbiology is “Give me a liter or a lobe” (Paxton, 2004).
The method of specimen collection significantly impacts both the likelihood of detecting the pathogen. Swabs are a common
method of collecting specimens for microbiology testing, but are only useful to diagnose certain infections. They are ideal for
diagnosis of upper respiratory and urogenital infections, where vigorous sampling can collect infected epithelial cells and exudate.
Swabs are less useful for diagnosing infections of tissue since they are only sampling the surface of the infected site. A biopsy of the
specimen is almost always superior (Baron et al., 2013).
Collection technique is critical to avoid contamination with members of the body’s colonizing bacteria, or microbiota. For
bloodstream infections, the skin overlying the sampled must be cleaned rigorously, and the rates of contamination by skin bacteria
are a standard measure of quality of care in a hospital. Similarly, urine must be collected in a way that minimizes contamination by
bacteria colonizing the urethra and surrounding skin. Sampling the lung either requires protecting the sampling instrument on its
way through the throat, or demonstrating that the sample is from the lower respiratory tract based on the type of human cells
present in the specimen.
Timing of specimen collection is also important for both correct interpretation of results and maximizing chances of recovering
the pathogen. The Plasmodium parasites that cause malaria periodically lyse out of red blood cells causing the symptom of fever.
Therefore, collecting a specimen before a fever increases the chance that they will be detected within red blood cells by microscopy.
Culture-based methods rely on a specimen with viable organisms, so at least one specimen should be collected prior to giving
4 First Principles of Clinical Microbiology: Collection, Handling, and Diagnostics

Table 2 Variables in pre-analytical phase of microbiology testing

Differential diagnosis Test ordering Specimen type Specimen collection Specimen transport

Bacteria Culture Body fluid Timing relative to infection Selection of transport device
Fungi Molecular Tissue Cleaning of site Temperature
Virus Antigen Swab Method and equipment Preserved vs. unpreserved
Parasite Antibody Foreign object

Clinical microbiology laboratory acts as a consultant.

Table 3 Variables in analytic phase of microbiology testing

Assessment
Processing of specimen Rejection Media Appropriate
triage quality criteria selection incubation Examination/enumeration Result reporting

Centrifugation Microscopy Inadequate Adequate Temperature Detection Detected/not detected

volume nutrients
Decontamination Visual Improper Selective for Percent carbon Quantification (culture, Quantification
inspection temperature suspected dioxide molecular)
pathogen
Homogenization Measurement Contamination Differentiates Oxygen/ Characterization (species Characterization of pathogen,
of volume or incorrect pathogens reducing identification, antibiotic including interpretation of
body site capacity resistance, virulence antimicrobial susceptibility
(anaerobic genes) testing (if applicable)
organisms)
Separation Indicators of Flora, contamination, or Comments on flora or
oxygen pathogen contamination
exposure

Clinical laboratory assumes responsibility for testing.

Table 4 Variables in post-analytic phase of microbiology testing

Result interpretation Action taken

Is this result consistent with the signs, symptoms, and other clinical data from the patient? Is there an alternative Supportive care
explanation?
Does this represent colonization, active infection, latent infection, past infection, or contamination? Addition or alteration of prescribed
antimicrobials
Does the infection need to be treated? Additional diagnostic testing

Clinical laboratory provides education on result interpretation and acts as a consultant.

antibiotics. The timing of specimen collection relative to the suspected onset of infection is also important. If collected early, the
pathogen may not have replicated sufficiently to be detectable in the specimen. If collected late, its density may be waning.
Pathogen-specific host responses develop over time and the timing of specimen collection can determine if a response is detected,
and if that response indicates past or current infection.

Specimen Transport

Once a specimen is collected, it must be transported to the laboratory in a manner that preserves the viability of the pathogen or the
analyte that will be detected. For culture-based testing, preserving viability is paramount. Transport is usually at room temperature,
but can differ with the type of microbe suspected (Leber, 2016). Swabs are often inserted into a tube with liquid media for transport,
and separate transport devices are available for bacteria and viruses to preserve their viability. Bacteria with anaerobic metabolism
may be killed by exposure to oxygen. Large pieces of tissue and volumes of fluid preserve viability and anaerobic conditions for
short periods, reinforcing the hyperbole of “Give me a liter or a lobe.” Smaller samples should be placed in specialized transport
tubes that maintain anaerobic conditions and have color (Eh) indicators to determine if oxygen has contaminated the specimen.
Swabs are generally a poor choice for anaerobic cultures because they sample the surface of the infection and not the infection itself,
 First Principles of Clinical Microbiology: Collection, Handling, and Diagnostics 5

but swab transport media are effective at maintaining viability of any anaerobes recovered. Blood culture bottles serve as both the
transport and culture vessel. For molecular diagnostic tests, transport tubes may have additives that preserve DNA and RNA but not
the pathogen itself. For each test that can be ordered, clinical microbiology laboratories publish handbooks stating what body site of
specimen to sample, what volume is suggested, the minimum required volume, the type of tube or container to be used, the
temperature for transport, and how quickly the sample must reach the laboratory.

Specimen Processing

Once the specimen reaches the laboratory, usually it must be processed before it can be tested. Specimen processing involves
concentration, decontamination, homogenization, separation, or a combination of these processes. These choices are made based
on a combination of what the clinician ordered and established policies in the laboratory, shifting responsibility for the specimen
from the clinician to the laboratory.
Large volumes of fluid can be concentrated by centrifugation, pelleting the pathogen and human cells at the bottom of the tube.
Although receiving more specimen is better, there are limits on the volume that than be added to a culture plate or tested in an
instrument. The supernatant is removed and this pellet, potentially enriched in pathogens, can be tested further.
Decontamination is important to detect slow growing pathogens like Mycobacteria and Legionella, where small numbers of
contaminating bacteria can overgrow the pathogen of interest. This can obscure the detection of these organisms in broth and agar
cultures. Decontamination techniques use harsh chemical treatments, such as sodium hydroxide, that Mycobacteria can withstand
more readily than other types of bacteria and acid shock that enriches for Legionella. This is a balancing act, and laboratories aim for
low but detectable rates of contamination to indicate that the process was not so harsh as to also kill the suspected bacterium.
In a specimen with multiple anatomic parts or fluid phases, the choice is to combine through homogenization or separate.
Tissues can be homogenized by sterile, mechanical processes such as tissue grinders and Stomachers, combining specimen with
saline or culture media to release pathogens for detection. In contrast, blood can be tested whole, or separated into serum or plasma
components. The type of blood transport tube determines the blood compartment that is tested, so the clinician must again decide
where to look for the pathogen to maximize chances of detection.
To process a specimen properly, the technician must predict if the specimen contains one or multiple bacteria. This can
determine if testing should be done in a liquid form or on agar. In specimens such as blood and sterile body fluids, there is usually
only one pathogen, so the specimen can be tested as a homogeneous liquid by culture or other means. Other specimens will have
multiple microbes present, either because they are part of a polymicrobial infection, or the pathogen and some colonizing microbes
may be present. These specimens should be processed in a way that enables detection of each microbe separately. Through culture,
this means inoculating the sample on selective and differential agar so colonies of each bacterium can be visualized and analyzed
separately. For molecular methods, the test must detect multiple microbes as well as it detects single pathogens. Often if one
pathogen is predominant, it can consume reagents in a molecular test, analogous to contaminating bacteria overgrowing myco-
bacteria in culture. To interpret mixed cultures, quantification can be helpful, but this must be anticipated at the time of specimen
processing. Quantitative cultures on solid media, using a defined inoculum, can distinguish infection from colonization as
discussed above for urine cultures. Even if the volume of sample cultured was not precisely measured, relative quantitation can
be done to indicate that one pathogen is predominant in the sample.

Specimen Testing

Testing methodologies each have their own benefits and drawbacks relative to the pathogen being sought. Direct microscopy of a
specimen provides a rapid and inexpensive way to detect pathogens. In addition to the Gram stain for bacteria, specific stains for
fungi, mycobacteria, and blood parasites are routinely performed. The Gram stain also allows evaluation of human somatic cell
types present in the specimen as a measure of specimen adequacy and risk of contamination from colonized body sites. The
sensitivity of direct microscopy depends on the volume of sample used and the ability of the stain to highlight the organism.
Fluorescent stains can increase the sensitivity of microscopy, and are used routinely to detect fungi and mycobacteria.
Antigen detection is of primary utility in non-invasive investigation of infections that infect deep tissues or fluids. The specimens
tested are typically blood or urine that can be readily obtained from a patient. These approaches are particularly useful for fungal
infections, where culture is slow and may require invasive procedures to sample the lungs or other sites of infection. Antigen
detection may also be helpful in stool to diagnose parasitic infections. The main challenge with these approaches is cross-reactivity
with other antigens found in these body fluids or other pathogens that cause a similar disease presentation.
The utility of antibody detection (serology) varies widely and is specific for each pathogen. In general, serology is used when
other direct approaches of detection do not perform well. For fastidious bacteria and fungi, serology may be the only reliable
method to determine if a patient has been infected. In other infections, the pathogen is present at very low concentrations or only
transiently, making direct detection difficult. Furthermore, the patient may present with symptoms as the pathogen burden wanes.
For example, encephalitis from arboviruses (e.g., west Nile virus) is most effectively diagnosed by serology from cerebrospinal fluid
as opposed to viral detection. Serology is one of the few diagnostic methods that can provide information about time of infection,
but the interpretation is specific to each pathogen. The clinician must have a basic understanding of the immune response to the
6 First Principles of Clinical Microbiology: Collection, Handling, and Diagnostics

suspected infection to know how long it takes to mount an initial IgM antibody response, when an IgG response may emerge, and
how long each of them persist.
The strengths and drawbacks of culture are implicit in the fact that it requires growth of the organism of interest. The strengths are
that it is a largely unbiased approach that may identify rare organisms causing a disease. It is also inexpensive. The main drawback is
that culture is only as fast as the organism’s growth rate and requires hours to days. It is also limited by which organisms the culture
media can support for growth. Culture is a largely manual method, but the development of automated systems for specimen
processing, incubation, and monitoring of growth is likely to speed up time to diagnosis and further reduce costs through decreased
personnel time.
Current molecular detection methods are targeted to one or a set of pathogens of interest. These can be performed directly from a
specimen or used for pathogen identification after culture. Molecular assays can either give a qualitative result of present or absent,
or quantify the pathogen relative to the volume of sample. The benefits of molecular methods are exquisite sensitivity and specificity
and precise quantification of pathogens. The main drawbacks are their directed nature and high cost. Unbiased sequencing
techniques, that identify nucleic acids directly from samples, are an intriguing approach to rapidly identify and perhaps quantify
specimens in patient samples. Although not currently in wide use, these approaches have the potential to disrupt and revolutionize
clinical microbiology.

Antimicrobial Susceptibility Testing

Once a pathogen has been detected, antimicrobial susceptibility testing is a key part of clinical microbiology testing. A few
pathogens have predictable susceptibility or resistance to certain antibiotics, so further testing is unnecessary. But for pathogens
where isolates vary in their ability to resist an antibiotic, antimicrobial susceptibility testing is critical to guide effective treatment of
the infection. Bacteria, yeast, and mycobacteria are routinely tested for susceptibility in clinical laboratories. Anaerobic bacteria,
molds, and viruses are more difficult to test, so susceptibility testing is usually performed in specialized reference laboratories or in
response to treatment failures.
The goal of antimicrobial susceptibility testing is to predict if an infection with the detected pathogen can be treated with
normally achievable antibiotic concentrations at the site of the infection. In most cases this is done through phenotypic testing.
Varying concentrations of an antibiotic are added to a culture of the pathogen isolated from the patient, and the minimum
concentration of antibiotic that inhibits growth is recorded (Minimum Inhibitory Concentration, MIC). This result is interpreted as
the isolate being susceptible or resistant to the antibiotic based on what is known about patterns of resistance within the microbial
species and pharmacokinetics and pharmacodynamics of the antibiotic in patients.
Genetics of the microbe often determines if it is susceptible or resistant to an antibiotic, so genotypic testing can also be useful.
When the mechanistic relationship between a gene and resistance to an antibiotic is robust and predictable, molecular tests with
their exquisite sensitivity and specificity can produce rapid and reliable results. However, the genetic diversity of microbes is such
that many mutations or genes could lead to resistance against the same antibiotic. In these cases, phenotypic testing is more useful
than genotypic testing. Again, as molecular techniques move towards unbiased approaches, rapid detection of multiple genotypes
that yield the same phenotype may be possible.

Concluding Remarks

Clinical microbiology is focused on the detection, characterization, and quantification of pathogens from patient samples to enable
the diagnosis, treatment, and management of infections. Clinical microbiologists must be experts in all aspects of pre-analytic,
analytic, and post-analytic phases of microbiology testing. We must educate clinicians on the critical aspects of test selection,
specimen collection and transport, and result interpretation that occurs outside the laboratory. We must also ensure excellent
quality of testing within the laboratory, from the time when the laboratory receives the sample until the result is posted. This
requires a combination of biological knowledge of how and where microbes colonize, remain latent, and cause symptomatic
disease as well as an understanding of the analytical principles, strengths and drawbacks of each testing modality. As new
technologies are introduced to the field, clinical microbiologists will be able to diagnose infections more rapidly and precisely
than ever before.

References
Atlas R (2015) Reagents, stains, and media. ProQuest, In: Jorgensen JH, Pfaller MA, and Carroll KC (eds.) Manual of clinical microbiology, 11th. edn, Washington, DC: ASM Press.
Baron EJ, Miller JM, Weinstein MP, Richter SS, Gilligan PH, Thomson RB Jr., Bourbeau P, Carroll KC, Kehl SC, Dunne WM, Robinson-Dunn B, Schwartzman JD, Chapin KC,
Snyder JW, Forbes BA, Patel R, Rosenblatt JE, and Pritt BS (2013) A guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2013 recommendations
by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)(a). Clinical Infectious Diseases 57: e22–e121.
Falkow S (1988) Molecular Koch’s postulates applied to microbial pathogenicity. Reviews of Infectious Diseases 10(Suppl 2): S274–6.
Leber AL (2016) Clinical microbiology procedures handbook. Washington, DC: ASM Press.
Lifshitz MS (2017) Optmizing laboratory workflow and performance. In: Mcpherson RA and Pincus MR (eds.) Henry’s clinical diagnosis and management by laboratory methods, 23rd
edn, St. Louis, Missouri: Elsevier.
 First Principles of Clinical Microbiology: Collection, Handling, and Diagnostics 7

Paxton A (2004) Swapping swabs for syringes and scalpels. CAP Today 1. http://wwwcaptodayonline.com/Archives/feature_stories/0804Swabs.html.
Specter S (2009) Clinical virology manual. Washington, DC: ASM Press.

Further Reading

Burd EM (2010) Validation of laboratory-developed molecular assays for infectious diseases. Clinical Microbiology Reviews 23(3): 550–576.
Turnidge JD (2015) Susceptibility test methods: General considerations. ProQuest, In: Jorgensen JH, Pfaller MA, and Carroll KC (eds.) Manual of clinical microbiology, 11th edn.
Washington, DC: ASM Press.
Wilson ML (2015) Laboratory detection of bacteremia and fungemia. ProQuest, In: Jorgensen JH, Pfaller MA, and Carroll KC (eds.) Manual of clinical microbiology, 11th edn.
Washington, DC: ASM Press.