A 42-year-old woman with a history of multiple sclerosis and recurrent urinary tract infections comes to the emergency department because of flank pain and fever. Her temperature is 38.8°C (101.8°F). Examination shows left-sided costovertebral angle tenderness. She is admitted to the hospital and started on intravenous vancomycin. Three days later, her symptoms have not improved. Urine culture shows growth of Enterococcus faecalis. Which of the following best describes the most likely mechanism of antibiotic resistance in this patient?

Alteration of peptidoglycan synthesis

Increased efflux across bacterial cell membranes

Alteration of penicillin-binding proteins

Alteration of ribosomal targets

A 52-year-old man presents with 2 months of diarrhea, abdominal pain, and fatigue. He reports a weight loss of 4 kg (8 lb). He also says his joints have been hurting recently, as well. Past medical history is unremarkable. Review of systems is significant for problems with concentration and memory. Physical examination is unremarkable. A GI endoscopy is performed with a biopsy of the small bowel. Which of the following histologic finding would most likely be seen in this patient?

Non-caseating granulomas in the small intestine

Absence of nerves in the myenteric plexus

Crypt hyperplasia with increased intraepithelial lymphocytes

A 42-year-old woman presents because of a painful mass she first noticed on her neck 1 week ago (see image). The mass has grown over the last few days. She has no history of serious illness and takes no medications. On physical exam, her temperature is 38.0°C (100.4°F), pulse is 86/min, respirations are 12/min, blood pressure is 135/80 mm Hg. The mass is tender and relatively soft and mobile. The overlying skin is warm. On her right ear, there is a series of small and healing skin punctures left by the bite of her neighbor's kitten 3 weeks ago. No other mass is detected in the neck, supraclavicular, axillary, or inguinal regions. Oral examination reveals several discolored teeth. Her lungs are clear to auscultation and heart sounds are normal. A biopsy of the neck mass is performed. Which of the following would be most useful in establishing the diagnosis?

Warthin-Starry silver stain for Bartonella henselae

Histologic evaluation for Reed-Sternburg cells

The Monospot test for Epstein-Barr virus

Toxoplasma IgG using enzyme-linked immunosorbent assay

Culture for facultative anaerobes

A 57-year-old HIV-positive male with a history of intravenous drug abuse presents to the emergency room complaining of arm swelling. He reports that he developed progressively worsening swelling and tenderness over the right antecubital fossa three days prior. He recently returned from a trip to Nicaragua. His past medical history is notable for an anaphylactoid reaction to vancomycin. His temperature is 101.4°F (38.6°C), blood pressure is 140/70 mmHg, pulse is 110/min, and respirations are 20/min. Physical examination reveals an erythematous, fluctuant, and tender mass overlying the right antecubital fossa. Multiple injection marks are noted across both upper extremities. He undergoes incision and drainage and is started on an antibiotic that targets the 50S ribosome. He is discharged with plans to follow up in one week. However, five days later he presents to the same emergency room complaining of abdominal cramps and watery diarrhea. Which of the following classes of pathogens is most likely responsible for this patient’s current symptoms?

Anaerobic flagellated protozoan

A group of scientists studied the effects of cytokines on effector cells, including leukocytes. They observed that interleukin-12 (IL-12) is secreted by antigen-presenting cells (APCs) in response to bacterial lipopolysaccharide. When a CD4+ T cell is exposed to this interleukin, which of the following responses will it have?

Responds to extracellular pathogens

An 8-year-old child is brought to the emergency department because of profuse diarrhea and vomiting that have lasted for 2 days. The boy was born at 39 weeks gestation via spontaneous vaginal delivery. He is up to date on all vaccines and is meeting all developmental milestones. Past medical history is noncontributory. The family recently made a trip to India to visit relatives. Today, his heart rate is 100/min, respiratory rate is 22/min, blood pressure is 105/65 mm Hg, and temperature is 37.2ºC (99.0°F). On physical examination, he appears unwell with poor skin turgor and dry oral mucosa. His heart has a regular rate and rhythm and his lungs are clear to auscultation bilaterally. His abdomen is sensitive to shallow and deep palpation. A gross examination of the stool reveals a 'rice water' appearance. Diagnostic microbiology results are pending. Which of the following is the best diagnostic test to aid in the identification of this patient's condition?

Rapid diagnostic test for cholera toxin

Emerging bacterial pathogens for USMLE Step 2 CK: High-Yield Microbiology Lessons

Emerging Pathogens - The New Threats

Carbapenem-Resistant Enterobacteriaceae (CRE)
- Nosocomial threat (Klebsiella, E. coli); high mortality.
- Carry resistance genes (KPC, NDM-1) on mobile plasmids.
- Requires newer agents like ceftazidime-avibactam.

Carbapenem and Colistin Resistance Mechanisms in Bacteria

Elizabethkingia anophelis
- Healthcare-associated outbreaks, targeting the immunocompromised.
- Causes bacteremia and respiratory infections.
- Intrinsically multidrug-resistant.
Borrelia mayonii
- A newer agent of Lyme disease in the Upper Midwest USA.
- Associated with unusually high spirochetemia, nausea, and diffuse rashes.

⭐ CREs like Klebsiella pneumoniae can transfer carbapenemase genes (e.g., KPC) horizontally via plasmids, rapidly spreading resistance among different bacterial species.

Superbugs - The Resistance Crew

ESKAPE Pathogens: Major sources of nosocomial, multidrug-resistant infections (MDROs).
- 📌 Enterococcus faecium (VRE)
- Staphylococcus aureus (MRSA)
- Klebsiella pneumoniae (ESBL, CRE)
- Acinetobacter baumannii
- Pseudomonas aeruginosa
- Enterobacter spp.
Key Resistance Mechanisms & Treatments:
- MRSA: Altered PBP2a from mecA gene → Use Vancomycin, Linezolid, Daptomycin.
- VRE: Altered peptidoglycan precursor (D-Ala-D-Lac) → Use Linezolid, Daptomycin.
- ESBL Producers: Hydrolyze most penicillins/cephalosporins → Use Carbapenems.
- CRE: Carbapenemase production → Use Ceftazidime-avibactam, Colistin, Tigecycline.

⭐ VRE Resistance: The classic mechanism involves the terminal D-Ala of the peptidoglycan side chain being replaced by D-Lactate, preventing vancomycin binding.

Bacterial antibiotic resistance mechanisms

Atypical Threats - Oddballs & Outsiders

Tropheryma whipplei (Whipple Disease)
- Gram-positive; PAS-positive foamy macrophages found in lamina propria.
- Presents with chronic malabsorptive diarrhea, weight loss, and migratory arthralgia.
- 📌 Mnemonic: Foamy WHIPPed cream in a CAN (Cardiac, Arthralgias, Neurologic).
Bartonella henselae
- Gram-negative rod causing Cat Scratch Disease; painful, swollen lymph nodes.
- In immunocompromised patients, causes bacillary angiomatosis (vascular lesions).
- Diagnosis: Warthin-Starry silver stain.
Coxiella burnetii
- Obligate intracellular organism causing Q Fever.
- Transmitted via aerosols from infected farm animals (cattle, sheep).
- Presents as atypical pneumonia with high fever and severe headache. Can lead to culture-negative endocarditis.

⭐ Whipple's Disease Classic Tetrad: migratory large-joint arthralgias, abdominal pain/diarrhea, weight loss, and fever. Neurologic signs like oculomasticatory myorhythmia are highly specific.

High‑Yield Points - ⚡ Biggest Takeaways

Carbapenem-resistant Enterobacteriaceae (CRE) are a top nosocomial threat; resistance genes (KPC, NDM-1) are often on plasmids.

Community-acquired MRSA (CA-MRSA), especially the USA300 strain, commonly causes purulent skin and soft tissue infections.

Vancomycin-resistant Enterococci (VRE) are a key cause of UTIs and bacteremia in hospitalized patients.

Hypervirulent C. difficile (NAP1/BI/027) produces excess toxins, causing severe, recurrent colitis.

Multidrug-resistant Acinetobacter baumannii is a critical cause of ventilator-associated pneumonia in the ICU.

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