Case Studies in Clinical Microbiology
Continuing Education Credits
This recently revised and updated course (2023) provides interactive case studies which cover pertinent current topics in clinical microbiology. Numerous images enhance the text and interactive questions help the student master the material.
Objectives
- Correlate presenting clinical signs and symptoms with the organism identifications for the cases being presented.
- Outline the presumptive and definitive characteristics for the laboratory identification of the bacterial species being presented.
- Discuss the diagnostic and therapeutic implications of making a correct organism identification.
Course Outline
- Introduction
- Course Organization
- Acute Urethral Discharge
- Case Study: Acute Urethral DischargeA 25-year-old female presents to the emergency room with an acute urethral discharge of two days duration.The image shows the Gram-stained smear that was obtained. Many polymorphonuclear (PMN) leukocytes and intracellular and extracellular gram-negative diplococci were observed. Based on the clinical history and the Gram stain observation, a diagnosis of gonorrh
- Neisseria gonorrhoeae
- True or False: Neisseria gonorrhoeae is the most common cause of septic arthritis among sexually active adults in the United States.
- Presumptive Laboratory Identification: Neisseria gonorrhoeae
- Additional Testing Information
- The positive oxidase reaction as shown in the image (yellow arrow) rules out which of the following two look-alike organisms of N. gonorrhoeae?
- Definitive Laboratory Identification: Neisseria gonorrhoeae
- True or False: The carbohydrate utilization reaction seen in the image will alone provide the necessary testing for definitive identification of N. gonorrhoeae.
- Acute Onset Pneumonia
- Case Study: Acute Onset PneumoniaA 70-year-old transient with a productive cough, pleuritic chest pain radiating to the mid back, fever, and chills was seen in the emergency department. Expectorated sputum was sent to the laboratory for Gram stain and culture. The Gram stain report to be issued based on the microscopic characteristics seen in the image would most correctly be, "Many WBCs with ____
- Case Study, Part Two: Acute Onset PneumoniaA 70-year-old transient with a productive cough, pleuritic chest pain radiating to the mid back, fever, and chills was seen in the emergency department. Expectorated sputum was sent to the laboratory for Gram stain and culture.The Gram stain is reported as "Many WBCs with gram-positive cocci (GPC) in pairs." The possible presumptive identifications might
- Streptococcus pneumoniae
- True or False: Streptococcus pneumoniae is the most common bacterial cause of community-acquired pneumonia.
- True or False: The pneumococcal vaccine is particularly effective in children less than two years of age.
- Laboratory Identification of Streptococcus pneumoniae
- Case Study, Part Three: Acute Onset PneumoniaA 70-year-old transient with a productive cough, pleuritic chest pain radiating to the mid back, fever, and chills was seen in the emergency department. Expectorated sputum was sent to the laboratory for Gram stain and culture.The Gram stain is reported as "Many WBCs with gram-positive cocci (GPC) in pairs." The possible presumptive identifications migh
- A drop of 10% deoxycholate was placed on an area of growth as shown in the image. This test is often used to differentiate S. pneumoniae from viridans streptococci. What is the name of this test?
- Susceptibility Testing of Streptococcus pneumoniae
- The zone of inhibition around the disk shown in the image has been measured at 23 mm. Based on this result, you should:
- True or False: For S. pneumoniae isolates recovered from cerebrospinal fluid (CSF), the oxacillin screen test alone is not sufficient for determining susceptibility to penicillin.
- True or False: When a MIC for penicillin is performed, minimum inhibitory concentration (MIC) susceptibility tests should be performed against other beta-lactam antibiotics on important S. pneumoniae isolates from blood cultures and other sterile body fluids.
- Pneumococcal Resistance
- Gram-Negative Sepsis
- Case Study: Gram-Negative Sepsis A 67-year-old man is admitted to the hospital with a cough, right lower chest pain accentuated by deep breathing, and fever. He has a history of chronic obstructive pulmonary disease (COPD), secondary to a long history of smoking. His temperature on admission is 102.5°F, and auscultation (listening to chest sounds) reveals rales in the right lower lung field.
- True or False: The reactions seen in the portion of the biochemical strip shown in the image effectively rule out Escherichia coli.
- Review of Extended-Spectrum Beta-Lactamases (ESBLs)
- True or False: Isolates of Escherichia coli, Klebsiella pneumoniae, K. oxytoca, and clinically significant isolates of Proteus mirabilis may possess extended-spectrum beta-lactamase (ESBL) activity.
- Extended-Spectrum Beta-Lactamases (ESBLs) Guidelines
- Extended-Spectrum Beta-Lactamase (ESBL) Screening by Disk Diffusion and Broth Microdilution
- Extended-Spectrum Beta-Lactamase (ESBL) Phenotypic Confirmation by Disk Diffusion and Broth Microdilution
- Extended-Spectrum Beta-Lactamase (ESBL) Activity
- Carbapenemases in Enterobacterales
- Which of the following antibiotics is preferred as the most sensitive indicator when detecting carbapenem resistance?
- Recurrent Urinary Tract Infection
- Case Study: Recurrent Urinary Tract Infection (UTI) A 72-year-old woman had a history of recurrent UTIs over the past several months, for which she had received different regimens of antibiotics, including ampicillin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Relapses often occur ten days to two weeks after cessation of therapy. The current flare-up, manifested by dysuria, lower abdominal
- Pyrrolidonyl Arylamidase (PYR) Differential
- The spot test that is helpful in separating Enterococcus species (positive as shown in the image) from the viridans streptococci and S. pneumoniae (both negative) is:
- Enterococcus Identification
- Enterococcus faecium Identification
- Vancomycin Resistance
- True or False: This image shows a quadrant plate containing brain heart infusion (BHI) agar supplemented with 6 μg/mL of vancomycin. The right upper quadrant was inoculated with the test strain of Enterococcus faecium. The presence of growth in the inoculated quadrant indicates resistance to vancomycin.
- What is the most important modifiable risk factor for enteric colonization with vancomycin-resistant Enterococcus faecium (VREF)?
- Acute Enteritis with Sepsis
- Case Study: Acute Enteritis with Sepsis A 63-year-old man was seen in the emergency department with complaints of sudden onset of fever, chills, and abdominal pain accompanied by mild diarrhea. A blood sample was drawn for a complete blood count (CBC) and a blood culture. A second blood culture was drawn from the opposite arm, with 10 mL of blood placed into an aerobic and anaerobic bottle. The CB
- The Gram stain shown in the image was prepared from a positive anaerobic blood culture bottle after 36 hours incubation. Based on the morphology of the bacterial cells (some with spores, noted by the blue arrows), what is the most likely identification?
- Need for Identification and Further Investigation
- Colony Morphology
- Use of Quad Plates for Identification
- Clostridium septicum Micromethod Panel Test
- True or False: It is important to establish a species identification of C. septicum in blood culture isolates because of its close association with carcinoma of the colon.
- Match the frequently associated conditions with their corresponding anaerobes.
- Each of the following statements is true concerning Clostridium septicum infections except:
- Post Traumatic Wound Infection
- Case Study: Post-Traumatic Wound InfectionAn 18-year-old female incurred a deep penetrating injury of the dorsum of her right foot when a kitchen knife fell from a platter she was carrying while going barefoot. The initial injury partially resolved; however, three days later, the foot began to swell and became red and painful. A deep subcutaneous abscess developed, with a central sinus tract from
- Colony Morphology
- The organisms in the image were observed in a smear prepared from the colony shown before this page. Which of the following tests will help confirm the identification of Staphylococcus aureus?
- True or False: The tube coagulase test, shown in the image (upper tube positive), should be performed on all S. aureus-suspicious isolates, giving an adverse slide coagulase reaction.
- Mannitol Salt Agar
- Methicillin (oxacillin)-resistant Staphylococcus aureus: Oxacillin Salt Agar
- Methicillin (oxacillin)-resistant Staphylococcus Disk Test
- Cefoxitin Surrogate Test
- Predisposing Factors for MRSA Infection and Decreasing the Risk of Colonization
- Factors predisposing infections with methicillin (oxacillin)-resistant Staphylococcus aureus (MRSA) include:
- Decreasing the risk of staphylococcal colonization of indwelling catheters in the future may involve:
- True or False: Patients with MRSA infections have uniformly poorer outcomes than those infected with sensitive strains.
- Exfoliative Toxins Causing Staphylococcal Scalded-Skin Syndrome
- The staphylococcal toxins causing scalded skin syndrome (SSSS) act specifically at the site which involves the following layers of skin:
- Tests that might help assess methicillin (oxacillin) resistance mechanisms in S. aureus include:
- Splenic Abscess
- Case Study: Spleen SpecimenA 23-year-old man had complained of right lower quadrant abdominal pain for approximately one week. Initially, the pain was sharp and localized to a small area just above the right iliac crest. The pain subsided for approximately two days but then recurred more diffusely over the lower abdomen, accompanied by cramping and mild diarrhea. The onset of fever and vomiting pr
- Most strains of S. anginosus group carry the F antigen (see image of Lancefield typing test). Rare strains that carry the group A antigen can be differentiated from S. pyogenes by which of the following laboratory tests?
- CO2 Incubation
- Biochemical Testing
- Overview of Streptococcus anginosus Group
- True or False: Most infections caused by the S. anginosus group (S. milleri group) can be effectively treated with penicillin or a first-generation cephalosporin.
- True or False: Epidural and subdural abscesses are clinical manifestations uncommon for the S. anginosus group.
- Which is a clinical condition often associated with the Streptococcus anginosus group?
- Cellulitis
- Case Study: CellulitisA 40-year-old woman with a long history of diabetes mellitus developed swelling and erythema of the left lower leg following superficial abrasion of the skin after a fall. The patient developed a high fever and mild prostration. The cellulitis of the lower leg is shown in the upper image. Note that the acute inflammation is most evident as red areas of streaking at abrasion s
- Beta hemolytic colonies grew from the blood culture bottle after 18 hours of incubation as seen in the image. Which of the following tests would not be helpful in making a preliminary identification?
- Group A Strep Disk Testing
- True or False: The reaction shown in the image establishes the identification of a group A beta-hemolytic Streptococcus.
- Invasive Streptococcal Infection
- Major Factors Related to Strong Resistance
- What is a major complication of toxic shock syndrome related to group A streptococci, leading to 50% mortality?
- What factors are related to the strong resistance of certain strains of group A streptococci to phagocytosis?
- Neonatal Meningitis
- Case Study: Neonatal Meningitis
- Case Study: Neonatal Meningitis (continued) A Brown-Brenn-modified Gram stain was performed on one of the tissue biopsy specimens. Organisms were seen in the image. Based on the history and the appearance of the bacteria, what is the most likely identification?
- The top image shows the surface of blood agar after 24 hours of incubation at 35°C in 10% CO2. Tiny, translucent, gray colonies are growing on it, surrounded by a narrow zone of "soft" beta hemolysis. There was no growth on the MacConkey plate.The lower image shows a close-in view of the colony growth after 48 hours of incubation. Considering the possible presumptive identifications suggested
- What test(s) may be performed to establish a presumptive differential identification between group B streptococci and L. monocytogenes?
- Gram Stain
- True or False: The image shows three tubes: (1) motility agar (note subsurface flare shown by arrows); (2) esculin hydrolysis (+); and (3) VP (+). The reactions illustrated here are sufficient to rule out Erysipelothrix rhusiopathiae.
- Motility
- Listeria monocytogenes
- Virulence Factors
- Virulence Factors, continued
- Which of the following is not related to the virulence of Listeria monocytogenes?
- Which of the following factors has not led to the current increase in the incidence of listeriosis?
- True or False: A characteristic of L. monocytogenes' virulence is its unique ability to invade peripheral nerves and rapidly enter the brain.
- Cellulitis of the Arm
- Case Study: Cellulitis Lesion
- Colony Morphology
- HACEK
- Biochemical Testing of Eikenella
- A bacterial isolate that produces pitting of the agar and has a bleach-like odor is probably E. corrodens. What are the closely related species that must be ruled out?
- Which of the following results in most Eikenella cellulitis infections?
- In view of the feedback to the previous question, what is the most likely reason that the clinical correlation does not seem to fit in this case?
- Eikenella corrodens Correlation with Insulin-Dependent Diabetes Mellitus
- Bite Wounds
- True or False: Human bite wound infections often lead to complications and are more severe than infected bites from other animals.
- In patients with Insulin-Dependent Diabetes Mellitus (IDDM), all of the following situations can be causes of infection with E. corrodens, except:
- References
- References
Additional Information
Level of Instruction: Intermediate
Intended Audience: Medical
laboratory scientists, medical laboratory technicians, microbiology professionals, laboratory supervisors,
and laboratory managers. This course is also appropriate for MLS and MLT
students and pathology residents.
Author Information: Elmer W. Koneman, MD, was Professor Emeritus, Department of Pathology, University of Colorado School of Medicine for many years until his passing in 2020. Residing in Breckenridge, CO, Dr. Koneman was a Board Certified Pathologist and author of numerous journal articles and books, including Koneman’s Color Atlas and Textbook of Diagnostic Microbiology, 7th Edition, 2016 (Jones & Bartlett Learning). Koneman was affiliated with the Colorado Association for Clinical Laboratory Education (CACMLE) and Instructional Design Consultants, specializing in interactive training and distance learning in clinical microbiology.
The author has no conflict of interest to disclose.
Reviewer Information:
Dr. Julie Ann West is certified by the American Society for Clinical Pathology (ASCP) as a Medical Laboratory Scientist (MLS) and as a Specialist in Microbiology (SM). In addition, Dr. West has earned a PhD in Public Health - (Infectious Disease) Epidemiology - and is Certified in Public Health (CPH) by the National Board of Public Health Examiners. Dr. West is experienced as a Technical Specialist, Safety Officer, Educator, and Lead in the Veterans Administration Healthcare System and has prior experience as an Administrative Laboratory Director.
Laurie Bjerklie, MA, MLS(ASCP)CM, is
a Lead Education Developer. She earned a B.S. in Medical Laboratory Science
from the University of North Dakota and an M.A. in Curriculum and Instruction
from Saint Xavier University. She has over 15 years of experience in higher
education and has held program director and faculty positions in both MLT and
MLS programs.
Course Information: This course provides interactive case studies that cover pertinent current topics in clinical microbiology. Numerous images enhance the text, and interactive questions help students master the material.