Microbiology Foundations

Bacteria are prokaryotes, they lack a membrane-bound nucleus and organelles. They have a cell wall (peptidoglycan in most), a plasma membrane, ribosomes, and circular DNA. They reproduce by binary fission (simple division). Classified as Gram-positive (thick peptidoglycan wall, stains purple) or Gram-negative (thin peptidoglycan with outer membrane, stains pink). This distinction affects antibiotic susceptibility.

Viruses are not cells, they consist of genetic material (DNA or RNA) surrounded by a protein coat (capsid), sometimes with a lipid envelope. They cannot reproduce independently; they hijack host cell machinery. Enveloped viruses (like influenza) are easier to kill with disinfectants because the lipid envelope is fragile. Non-enveloped viruses (like norovirus) are more resistant.

Fungi include yeasts (unicellular, reproduce by budding, e.g., Candida) and molds (multicellular, grow as hyphae). Fungi have cell walls made of chitin (not peptidoglycan), which is why antibacterial drugs don't work against them. Fungal infections (mycoses) are treated with antifungals that target ergosterol in fungal cell membranes.

Protozoa are single-celled eukaryotes (e.g., Plasmodium causing malaria, Giardia). Helminths are multicellular worms (roundworms, tapeworms, flukes). Parasites have complex life cycles often involving intermediate hosts. Transmission is often fecal-oral, vector-borne, or through contaminated water/food.

Prions are infectious misfolded proteins that cause other normal proteins to misfold. They contain no DNA or RNA. They are extremely resistant to standard sterilization methods (heat, chemicals, radiation). Examples include Creutzfeldt-Jakob disease. Prions cannot be treated with antibiotics, antivirals, or antifungals.

The infectious agent's properties determine how dangerous it is: virulence (ability to cause severe disease), toxin production (exotoxins secreted, endotoxins structural), infectious dose (how many organisms needed to cause infection — TB requires very few; Vibrio cholerae requires millions), and survival outside the host (spores last years; enveloped viruses die in minutes). MRSA example: S. aureus is a highly virulent pathogen that produces toxins, can survive on surfaces for weeks, and has a low infectious dose for vulnerable hosts.

The reservoir is the natural habitat where the pathogen sustains itself. Reservoirs include: humans (colonized carriers, infected patients), animals (zoonotic diseases — Salmonella in poultry, rabies in bats), and the environment (soil for Clostridium tetani spores, contaminated water for Legionella, IV bags, ventilator circuits). MRSA example: The primary reservoir is colonized humans — approximately 30% of the population carries S. aureus in the anterior nares (nose), and 1–3% carry MRSA specifically. Healthcare workers can be asymptomatic MRSA carriers.

Common portals of exit: respiratory tract (coughing, sneezing, talking — TB, influenza, COVID-19), gastrointestinal tract (fecal material — C. diff, Salmonella, Hepatitis A), skin and wounds (drainage, exudate — MRSA, VRE), blood (needlestick injuries, blood transfusions — HIV, Hepatitis B/C), urinary tract (catheter drainage). MRSA example: MRSA exits its human reservoir through nasal secretions (when a colonized person touches their nose then touches a surface) and through wound drainage in infected patients.

Five modes: (1) Direct contact — physical touch between infected and susceptible person (MRSA, VRE, C. diff). (2) Indirect contact — via fomites like stethoscopes, doorknobs, bed rails. (3) Droplet — large particles >5 μm, travel ≤3 feet (influenza, meningococcal, pertussis) — surgical mask required. (4) Airborne — droplet nuclei <5 μm, float for hours (TB, measles, varicella) — N95 + negative pressure required. (5) Vehicle — contaminated food/water/blood (Salmonella, Hepatitis A, HIV transfusion). (6) Vector — arthropods (Lyme via tick, malaria via Anopheles mosquito, dengue via Aedes mosquito). MRSA example: Primarily indirect contact — healthcare worker touches a contaminated surface or patient, then touches the next patient without hand hygiene.

Portals of entry mirror the portals of exit: respiratory tract (inhalation of airborne/droplet organisms), GI tract (ingestion of contaminated food/water), skin (most organisms require a break in intact skin — cuts, wounds, IV insertion sites, catheter insertion points), mucous membranes (eyes, nose, mouth — direct inoculation), blood (needlesticks). MRSA example: MRSA most commonly enters through breaks in skin integrity — surgical incisions, IV catheter sites, pressure ulcers, lacerations — because intact skin is an effective barrier even against MRSA.

Host susceptibility is increased by: age extremes (neonates lack mature immune systems; elderly have immunosenescence), immunosuppression (HIV, chemotherapy, high-dose steroids, organ transplant medications), chronic diseases (diabetes impairs neutrophil function, renal failure impairs lymphocyte function), malnutrition (protein deficiency impairs antibody production), invasive devices (IV lines, catheters, ventilators bypass physical barriers), and certain medications (proton pump inhibitors reduce stomach acid protection). MRSA example: A post-operative diabetic patient with a central line who received broad-spectrum antibiotics represents the highest-risk host — multiple susceptibility factors converge.

Mechanism: The mecA gene encodes an altered penicillin-binding protein (PBP2a) that beta-lactam antibiotics (penicillins, cephalosporins, carbapenems) cannot bind. Since beta-lactams work by inhibiting PBP enzymes that build the cell wall, organisms with PBP2a are resistant to ALL beta-lactams. Treatment: Vancomycin (IV, first-line for serious infections), linezolid, daptomycin (for bacteremia), or trimethoprim-sulfamethoxazole (for skin/soft tissue). Precautions: Contact isolation. Screening: nasal swab cultures. Decolonization: mupirocin nasal ointment + chlorhexidine bathing.

Mechanism: The vanA/vanB genes encode enzymes that substitute D-Ala-D-Lac for the normal D-Ala-D-Ala terminus of peptidoglycan precursors. Vancomycin binds D-Ala-D-Ala, so the substitution eliminates the binding target — vancomycin can no longer inhibit cell wall synthesis. Treatment: Linezolid or daptomycin. Precautions: Contact isolation (gloves + gown on room entry). VRE can survive on environmental surfaces for weeks, making environmental cleaning critical.

Mechanism: Enterobacteriaceae (E. coli, Klebsiella) produce extended-spectrum beta-lactamase enzymes (encoded on plasmids, easily transferred between species) that hydrolyze the beta-lactam ring of most penicillins and cephalosporins, including third-generation cephalosporins. These enzymes are inhibited by beta-lactamase inhibitors but standard combinations may not be sufficient. Treatment: Carbapenems (meropenem, ertapenem) are the drugs of choice for serious ESBL infections. Precautions: Contact isolation. Risk factors: prior antibiotic use, healthcare exposure, travel to endemic regions.

Mechanism: CRE produce carbapenemase enzymes (most commonly Klebsiella pneumoniae carbapenemase, KPC) that hydrolyze carbapenems — the last-resort beta-lactams. Some CRE also have additional mechanisms (porin loss, efflux pumps). This creates pan-resistant organisms with extremely limited treatment options. Treatment: Colistin (polymyxin B, nephrotoxic), ceftazidime-avibactam, meropenem-vaborbactam, cefiderocol. Mortality in CRE bacteremia approaches 50%. Precautions: Contact isolation, cohorting, enhanced environmental cleaning.

Mechanism: C. difficile itself is not a multi-drug-resistant organism, but is CAUSED by antibiotic use. Antibiotics (especially clindamycin, fluoroquinolones, broad-spectrum cephalosporins) kill normal gut flora. Without competitive exclusion, C. diff spores germinate, the organism overgrows, and produces toxins A and B that destroy colonocytes → pseudomembranous colitis → profuse watery diarrhea, fever, leukocytosis. Treatment: Stop the offending antibiotic if possible. Oral vancomycin or fidaxomicin (preferred over metronidazole). Recurrent C. diff: fecal microbiota transplant (FMT) achieves 90%+ cure rate. Precautions: Contact isolation. Spores are NOT killed by alcohol — SOAP AND WATER mandatory. Bleach-based cleaning of the environment.

Broad-spectrum antibiotics kill not only the target pathogen but also collateral normal flora. Consequences: (1) C. difficile overgrowth → pseudomembranous colitis (profuse watery diarrhea, fever, leukocytosis). (2) Vaginal Candida overgrowth → vulvovaginal candidiasis (itching, cottage-cheese discharge, burning). (3) Oral Candida (thrush) — especially in patients also on inhaled corticosteroids. Prevention: Targeted antibiotic selection, shortest effective duration, probiotics (moderate evidence for C. diff prevention).

HIV destroys CD4+ helper T cells. As CD4 count falls, specific opportunistic infections emerge: CD4 >500: relatively normal immune function; CD4 200–500: bacterial pneumonias, herpes zoster reactivation, oral candida; CD4 <200: Pneumocystis jirovecii pneumonia (PCP) — most common AIDS-defining illness, presents with progressive dyspnea, dry cough, low-grade fever; CD4 <100: Toxoplasma gondii encephalitis, Cryptococcal meningitis; CD4 <50: CMV retinitis (can cause blindness), Mycobacterium avium complex (MAC) — disseminated infection with fever, night sweats, weight loss. ART (antiretroviral therapy) prevents these by maintaining CD4 counts.

Chemotherapy ablates bone marrow → neutropenia (ANC <500) → bacteria and fungi that normal neutrophils would immediately kill can cause life-threatening infections. High-risk organisms: Pseudomonas aeruginosa (febrile neutropenia emergency — treat empirically within 1 hour), Candida species (candidemia), Aspergillus fumigatus (invasive pulmonary aspergillosis — mold from environmental sources). Transplant patients on calcineurin inhibitors (tacrolimus, cyclosporine) are at risk for: CMV (cytomegalovirus) reactivation, EBV → post-transplant lymphoproliferative disorder, Pneumocystis jirovecii (PCP prophylaxis with TMP-SMX given to all transplant patients).

Catheters and invasive devices bypass the body's most effective infection barrier — intact skin. CAUTI (catheter-associated UTI): E. coli from own periurethral flora tracks along catheter surface → bladder colonization → infection. Most common HAI type. Prevention: Only insert when necessary, maintain closed drainage system, daily perineal care, remove ASAP. CLABSI (central line-associated bloodstream infection): Skin flora (S. epidermidis, S. aureus) migrate along catheter track or via hub contamination → bloodstream → sepsis. Prevention: Maximal sterile barriers, chlorhexidine site prep, daily necessity assessment.

Insertion bundle: Hand hygiene before procedure. Maximal sterile barrier precautions (cap, mask, sterile gown, sterile gloves, full-body sterile drape). Chlorhexidine skin antisepsis (allow to dry completely). Optimal site selection (subclavian preferred over femoral). Daily reassessment of line necessity — remove as soon as clinically appropriate. Maintenance bundle: Daily inspection of site. Chlorhexidine-impregnated dressing. Scrub the hub (15 seconds friction before each access). Change tubing per protocol. Aseptic technique for all access. CLABSI rate is a reportable quality metric and affects hospital reimbursement.

Appropriate indications for urinary catheter: urinary retention, hourly output monitoring in critically ill patients, perioperative in select procedures, stage 3–4 pressure injuries in incontinent patients, end-of-life comfort. NOT appropriate for: incontinence, immobility convenience, routine post-op in non-urological surgery. Insertion: Sterile technique, correct catheter size. Maintenance: Maintain closed drainage system (never disconnect), keep drainage bag below bladder level, secure catheter to prevent urethral trauma, daily meatal care with soap/water, patient hygiene. Nurse-driven removal protocol: prompt removal when indication resolves.

Mechanism: Microaspiration of oropharyngeal secretions past the cuff of the endotracheal tube → lower respiratory tract colonization → pneumonia. Bundle: (1) Head of bed elevation 30–45° (reduces gastric reflux and passive aspiration). (2) Daily oral care with chlorhexidine 0.12% (reduces oral bacterial burden). (3) Subglottic secretion suctioning (specialized ETTs with suction port above cuff). (4) Daily sedation interruption and spontaneous breathing trials (reduces ventilator days, the primary risk factor). (5) Cuff pressure monitoring (maintain 20–30 cmH₂O). (6) Daily reassessment of extubation readiness.

Pre-operative: Appropriate prophylactic antibiotic within 60 minutes of incision (within 120 minutes for vancomycin/fluoroquinolones). Re-dose for prolonged procedures. Hair removal with clippers (not razors — razors create microabrasions). Chlorhexidine-alcohol skin prep (superior to povidone-iodine). Pre-op bathing with chlorhexidine night before and morning of surgery. Intra-operative: Maintain normothermia (hypothermia impairs neutrophil function and wound perfusion). Maintain glucose <180 mg/dL in diabetic patients. Minimize OR traffic. Post-operative: Sterile dressing for 24–48 hours. Hand hygiene before wound assessment. Monitor for signs of SSI: redness, warmth, swelling, purulent drainage, fever &gt;38.5°C after post-operative day 3.

Physical barriers: Intact skin (mechanical barrier; low surface pH ~5.5 inhibits most bacteria; sebum contains bactericidal fatty acids). Mucous membranes (trap pathogens; cilia beat contaminated mucus toward the pharynx — mucociliary escalator). Cough and sneeze reflexes expel organisms from the airway. Stomach acid (pH 1.5–3.5) kills most ingested pathogens (reduced efficacy with PPIs — increased susceptibility to Salmonella, Listeria, C. diff). Lacrimation, saliva, urine flow (mechanical flushing), vaginal acidity. Clinical implication: Disruption of ANY barrier increases infection risk — endotracheal intubation bypasses the mucociliary escalator; antacids raise gastric pH; urinary catheters interrupt urine flow.

Inflammatory response: Pattern recognition receptors (Toll-like receptors) on innate cells detect PAMPs (pathogen-associated molecular patterns — e.g., LPS on Gram-negative bacteria). Triggers release of cytokines (IL-1, IL-6, TNF-α) → vasodilation + increased vascular permeability → redness (rubor), heat (calor), swelling (tumor), pain (dolor), loss of function. Clinically: local infection = local inflammation; systemic infection = fever (pyrogens act on hypothalamus), leukocytosis (WBC >11,000), elevated CRP and ESR. Phagocytes: Neutrophils (PMNs) — most abundant, arrive first at infection site within 30–60 min, engulf and destroy bacteria via oxidative burst (reactive oxygen species). Low neutrophil count (neutropenia) → profound infection susceptibility. Macrophages — tissue residents, arrive after neutrophils, engulf organisms and present antigens to T cells to initiate adaptive response.

Natural Killer (NK) cells: Lymphocytes of the innate immune system that kill virus-infected cells and tumor cells WITHOUT needing prior sensitization or antibody. They recognize the ABSENCE of MHC I on cell surfaces — virus-infected cells and cancer cells often downregulate MHC I to hide from cytotoxic T cells, but this makes them visible to NK cells. Kill mechanism: perforin pores + granzyme injection → target cell apoptosis. Complement system: ~30 plasma proteins that activate in a cascade (classical pathway triggered by antibody-antigen complexes; alternative pathway triggered directly by pathogens; lectin pathway triggered by mannose on bacterial surfaces). Functions: Opsonization (C3b tags bacteria for phagocytosis — makes them 'delicious' to phagocytes), Membrane Attack Complex (MAC, C5b-9) — punches holes in bacterial outer membranes → lysis, Chemotaxis (C5a attracts neutrophils to infection site), Inflammation (C3a, C5a trigger mast cell degranulation → histamine release).

Antigen presentation: After phagocytosis, macrophages and dendritic cells process pathogen antigens and present fragments on MHC Class II molecules. Helper T cells (CD4+) recognize MHC II + antigen complex → activated → release cytokines that orchestrate the entire adaptive immune response. Cytotoxic T cells (CD8+) recognize virus-infected cells or cancer cells presenting antigen on MHC Class I → release perforin and granzymes → kill infected cell. Clinical relevance: HIV destroys CD4+ T cells — removing the conductor of adaptive immunity. Organ transplant rejection: recipient's CD8+ T cells attack donor cells as foreign. Immunosuppressants (tacrolimus, cyclosporine) block T cell activation to prevent rejection.

B cell activation: Helper T cells (CD4+) provide co-stimulation → B cells differentiate into plasma cells → secrete immunoglobulins (antibodies). Antibody classes: IgM — first antibody produced after initial exposure (acute infection marker, pentameric structure, effective at complement activation). IgG — most abundant (75%), long-term protection, crosses placenta (passive immunity in newborns for first 3–6 months), long half-life. IgA — secretory antibody in mucosal surfaces (saliva, tears, breast milk, GI/respiratory tract secretions) — frontline mucosal defense. IgE — binds mast cells and basophils → immediate hypersensitivity (allergy, anaphylaxis); also parasitic defense. IgD — B cell surface receptor, signaling function. Memory cells: After primary infection, long-lived memory B and T cells persist. On re-exposure (or vaccination), memory cells mount a faster, stronger secondary response → clinical immunity. Vaccination principle: Expose immune system to antigen (attenuated organism, killed organism, subunit, or mRNA encoding antigen) without disease → memory formed → protection.