Infectious Diseases - Comprehensive Overview

Infectious diseases are caused by pathogenic microorganisms including bacteria, viruses, fungi, and parasites. They remain a leading cause of morbidity and mortality worldwide, particularly in low-resource settings. This article provides comprehensive coverage of major infectious diseases, their causative agents, transmission dynamics, clinical features, and management.

Overview of Pathogens

Pathogen Type	Characteristics	Size	Examples
Bacteria	Single-celled prokaryotes, cell wall, reproduce by binary fission	0.5-5 micrometers	Streptococcus, E. coli, Mycobacterium tuberculosis
Viruses	Obligate intracellular parasites, DNA or RNA genome, protein capsid	20-300 nanometers	SARS-CoV-2, influenza, HIV
Fungi	Eukaryotic, cell wall (chitin), can be unicellular or multicellular	2-100+ micrometers	Candida, Aspergillus, Dermatophytes
Parasites	Eukaryotic organisms living on/in host; protozoa or helminths	1 micrometer - meters	Plasmodium, Giardia, Taenia

COVID-19 (SARS-CoV-2)

Parameter	Detail
Pathogen	SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), single-stranded positive-sense RNA virus, family Coronaviridae
Reservoir	Bats (likely intermediate host unknown)
Transmission	Respiratory droplets, aerosols, fomites; airborne in certain settings
Incubation period	2-14 days (median 4-5 days)
Reproductive number (R0)	Initial wild-type: 2.5-3.5; variants: higher
Period of contagiousness	2 days before symptom onset to 10 days after (mild); up to 20 days (severe/immunocompromised)

COVID-19 Severity Classification

Severity	Features	Management
Asymptomatic	No symptoms, positive test	Isolation, monitoring
Mild	Fever, cough, sore throat, myalgia, headache, anosmia, ageusia; no dyspnea, normal imaging	Supportive care, symptomatic management
Moderate	Lower respiratory disease with dyspnea, SpO2 >=94% on room air, pulmonary infiltrates	Monitoring, supplemental oxygen as needed
Severe	SpO2 <94%, respiratory rate >30/min, PaO2/FiO2 <300, lung infiltrates >50%	Hospitalization, supplemental oxygen, dexamethasone, remdesivir
Critical	ARDS, septic shock, multi-organ dysfunction	ICU care, mechanical ventilation, proning, vasopressors

COVID-19 Treatments

Drug/Intervention	Mechanism	Indication
Remdesivir	RNA polymerase inhibitor	Hospitalized patients requiring supplemental oxygen
Dexamethasone	Corticosteroid, reduces inflammatory response	Severe/critical COVID (oxygen or ventilator requirement)
Nirmatrelvir/ritonavir (Paxlovid)	Protease inhibitor	High-risk outpatients (within 5 days of symptom onset)
Molnupiravir	Nucleoside analog (mutagenesis)	High-risk outpatients (alternative when Paxlovid contraindicated)
Baricitinib	JAK inhibitor	Hospitalized patients on oxygen
Tocilizumab	IL-6 receptor antagonist	Hospitalized patients with rapid respiratory decompensation
Convalescent plasma	Neutralizing antibodies	Limited role; immunocompromised patients

COVID-19 Vaccines

Vaccine Type	Examples	Dosing	Efficacy (initial series)
mRNA	BNT162b2 (Pfizer-BioNTech), mRNA-1273 (Moderna)	2 doses (primary) + boosters	90-95% against symptomatic infection (original strain)
Adenoviral vector	Ad26.COV2.S (J&J/Janssen), ChAdOx1 (AstraZeneca)	1-2 doses + boosters	66-72% (J&J); 70% (AZ)
Protein subunit	NVX-CoV2373 (Novavax)	2 doses	90% (original strain)
Inactivated	CoronaVac (Sinovac), BBIBP-CorV (Sinopharm)	2-3 doses	50-84%

SARS-CoV-2 Variants of Concern

WHO Label	Lineage	Key Features
Alpha	B.1.1.7	Increased transmissibility (50-80%)
Beta	B.1.351	Immune evasion, reduced vaccine efficacy
Gamma	P.1	Immune evasion, reinfection risk
Delta	B.1.617.2	Highly transmissible (60-80% more than Alpha), increased severity
Omicron	B.1.1.529	Highly transmissible, significant immune evasion, reduced severity (BA.1-BA.5, XBB, JN.1)

Influenza

Parameter	Detail
Pathogen	Influenza A, B, C, D viruses; orthomyxoviridae family; negative-sense RNA, segmented genome
Subtypes (Influenza A)	Based on hemagglutinin (H1-H18) and neuraminidase (N1-N11); currently circulating: H1N1, H3N2
Transmission	Respiratory droplets, aerosols, fomites
Incubation period	1-4 days (average 2 days)
Period of contagiousness	1 day before to 5-7 days after symptom onset
Antigenic drift	Gradual mutation (seasonal epidemics)
Antigenic shift	Abrupt change (pandemic potential; reassortment of animal/human strains)

Influenza Clinical Features

Symptom	Uncomplicated Influenza	Complicated Influenza
Onset	Abrupt (within hours)	Abrupt
Fever	High (38-40C), lasts 3-4 days	Persistent or recurrent
Cough	Dry, can persist 2+ weeks	May develop into pneumonia
Myalgia	Prominent, severe	Prominent
Headache	Severe, frontal	Severe
Fatigue	Profound	Profound
Sore throat	Common	Common
Rhinorrhea	Common	Common
GI symptoms	Less common (children)	May occur in severe cases

Influenza Complications

Complication	Risk Groups
Primary viral pneumonia	All ages, especially chronic lung disease
Secondary bacterial pneumonia (S. pneumoniae, S. aureus, H. influenzae)	Elderly, immunocompromised
Acute respiratory distress syndrome (ARDS)	Severe cases
Myocarditis, pericarditis	Rare
Encephalitis, transverse myelitis	Rare
Myositis, rhabdomyolysis	Children (especially influenza B)
Reye syndrome	Children with aspirin use

Influenza Antiviral Treatment

Drug	Class	Route	Duration	Indication
Oseltamivir	Neuraminidase inhibitor	Oral	5 days (treatment), 10-75 days (prophylaxis)	First-line; within 48 hours of symptoms for maximum benefit
Zanamivir	Neuraminidase inhibitor	Inhaled	5 days	Alternative; contraindicated in asthma/COPD
Peramivir	Neuraminidase inhibitor	IV	Single dose	Hospitalized patients
Baloxavir marboxil	Polymerase acidic endonuclease inhibitor	Oral	Single dose	Alternative; rapid viral RNA polymerase inhibition

Influenza Vaccines

Vaccine Type	Examples	Target Population
Inactivated influenza vaccine (IIV)	Multiple (Fluzone, Flulaval, Flucelvax)	>=6 months of age
Recombinant influenza vaccine (RIV)	Flublok	>=18 years (especially egg-allergic)
Live attenuated influenza vaccine (LAIV)	FluMist	2-49 years (non-pregnant, healthy)
High-dose IIV	Fluzone High-Dose	>=65 years
Adjuvanted IIV	Fluad	>=65 years

HIV/AIDS

Parameter	Detail
Pathogen	Human Immunodeficiency Virus (HIV-1, HIV-2); retrovirus, single-stranded RNA, reverse transcriptase
Reservoir	Humans (primates for SIV/HIV-2)
Transmission	Sexual contact (blood, semen, vaginal/rectal fluids), blood/blood products, perinatal (intrapartum, breastfeeding), needle sharing
Incubation period (acute infection)	2-4 weeks to seroconversion
Window period (4th generation test)	18-45 days
Window period (NAT)	10-33 days

HIV Disease Progression

Stage	CD4 Count	Clinical Features	Duration
Acute HIV infection	Normal to transient decrease	Flu-like illness (fever, lymphadenopathy, pharyngitis, rash, myalgia); high viral load	2-6 weeks
Clinical latency (asymptomatic)	>500 cells/microliter	Asymptomatic or persistent generalized lymphadenopathy (PGL)	Average 8-10 years (untreated)
Symptomatic HIV	200-500 cells/microliter	Oral thrush, oral hairy leukoplakia, herpes zoster, constitutional symptoms (weight loss, fever, night sweats), diarrhea	Variable
AIDS	<200 cells/microliter	AIDS-defining illnesses (see below)	Variable (without treatment)

AIDS-Defining Conditions (CDC)

Category	Conditions
Opportunistic infections	PCP pneumonia, esophageal candidiasis, cryptococcal meningitis, toxoplasmosis, CMV retinitis, MAI/MAC, recurrent bacterial pneumonia, progressive multifocal leukoencephalopathy (PML)
Malignancies	Kaposi sarcoma (HHV-8), non-Hodgkin lymphoma, invasive cervical cancer
Wasting syndrome	Involuntary weight loss >10% with diarrhea or weakness
Neurologic	HIV-associated dementia (HAD)

Antiretroviral Therapy (ART) Drug Classes

Drug Class	Mechanism	Examples
Nucleoside reverse transcriptase inhibitors (NRTIs)	Chain terminators of viral DNA synthesis	Tenofovir (TAF/TDF), emtricitabine (FTC), abacavir (ABC), lamivudine (3TC)
Non-nucleoside reverse transcriptase inhibitors (NNRTIs)	Non-competitive inhibition of reverse transcriptase	Dolutegravir (DTG), bictegravir (BIC), raltegravir (RAL)
Protease inhibitors (PIs)	Inhibit viral protease (prevents maturation)	Darunavir (DRV), atazanavir (ATV), boosted with ritonavir/cobicistat
Integrase strand transfer inhibitors (INSTIs)	Block viral DNA integration into host genome	Dolutegravir, bictegravir, raltegravir, cabotegravir
Entry inhibitors	Block viral entry into CD4 cells	Maraviroc (CCR5 antagonist), enfuvirtide (fusion inhibitor)
Pharmacokinetic enhancers	Boost levels of other ARVs	Ritonavir, cobicistat

Current First-Line ART Regimens

Regimen	Components	Notes
Bictegravir/TAF/FTC	INSTI + 2 NRTIs	Single-tablet regimen (Biktarvy)
Dolutegravir/TAF/FTC	INSTI + 2 NRTIs	Single-tablet regimen
Dolutegravir + TDF/3TC	INSTI + 2 NRTIs	Most common resource-limited setting
Darunavir/cobicistat + TAF/FTC	Boosted PI + 2 NRTIs	Alternative (high barrier to resistance)

HIV Prevention

Method	Efficacy	Notes
Condoms	>99% with perfect use	Consistent use recommended
PrEP (TDF/FTC or TAF/FTC)	>90% reduction when adherent	Daily oral or event-driven (2-1-1 regimen for men)
PrEP (cabotegravir LA)	>90% reduction	Injectable every 2 months
PEP	>80% reduction if started within 72 hours	28-day course of 3-drug regimen
Treatment as prevention (U=U)	Zero transmission when viral load <200 copies/mL	Undetectable = Untransmittable
Needle exchange programs	Reduces transmission by 50-80%	Harm reduction

Viral Hepatitis

Hepatitis A, B, C Comparison

Feature	Hepatitis A (HAV)	Hepatitis B (HBV)	Hepatitis C (HCV)
Virus type	ssRNA (picornavirus)	dsDNA (hepadnavirus)	ssRNA (flavivirus)
Transmission	Fecal-oral	Blood, sexual, perinatal	Blood (primarily)
Incubation period	15-50 days (avg 28)	45-160 days (avg 90)	14-180 days (avg 50)
Chronic infection	No	Yes (90% of neonates, 5% of adults)	Yes (55-85%)
Vaccine	Yes (inactivated)	Yes (recombinant)	No
Treatment	Supportive	Nucleoside analogs (entecavir, tenofovir), pegylated interferon	Direct-acting antivirals (DAAs)
Cure	Self-limited	Suppression (functional cure)	>95% cure rate (DAAs)
Liver cancer risk	No	Yes (if chronic)	Yes (if chronic)

Hepatitis B Serology

Serologic Marker	Interpretation
HBsAg positive	Current infection (acute or chronic)
anti-HBs positive	Immunity (from vaccine or resolved infection)
anti-HBc (total) positive	Past or current infection
anti-HBc IgM positive	Recent (<6 months) infection
HBeAg positive	High viral replication (high infectivity)
anti-HBe positive	Low viral replication
HBV DNA detectable	Active viral replication

Hepatitis C Treatment (DAAs)

Regimen	Genotypes	Duration	SVR Rate
Glecaprevir/pibrentasvir	1-6	8 weeks (treatment-naive, no cirrhosis)	>95%
Sofosbuvir/velpatasvir	1-6	12 weeks	>95%
Ledipasvir/sofosbuvir	1, 4, 5, 6	8-12 weeks	>95%
Sofosbuvir/velpatasvir/voxilaprevir	1-6 (retreatment)	12 weeks	>95%

Tuberculosis (TB)

Parameter	Detail
Pathogen	Mycobacterium tuberculosis complex (M. tuberculosis, M. bovis, M. africanum)
Transmission	Airborne droplet nuclei (1-5 micrometers)
Incubation period (latent to active)	Weeks to years; highest risk within 2 years
Infectiousness	Untreated pulmonary/laryngeal TB; ceases after 2 weeks of effective therapy
Global burden	~10.6 million cases/year, ~1.6 million deaths/year

Latent vs Active TB

Feature	Latent TB Infection (LTBI)	Active TB Disease
Symptoms	None	Cough (>3 weeks), fever, night sweats, weight loss, hemoptysis
Chest X-ray	Normal	Abnormal (upper lobe infiltrates, cavitary lesions)
Sputum smear/culture	Negative	Positive
Infectious	No	Yes (pulmonary/laryngeal)
Treatment	3-9 months (isoniazid, rifampin, or combination)	6-9 months (4-drug regimen)

First-Line TB Treatment Regimen

Phase	Duration	Drugs	Notes
Intensive phase	2 months	Isoniazid (H), Rifampin (R), Pyrazinamide (Z), Ethambutol (E)	Daily dosing (or 5 days/week DOT)
Continuation phase	4 months	Isoniazid (H), Rifampin (R)	Daily or 3x/week DOT
Extension (cavitary/culture-positive at 2 months)	7 months total	Isoniazid (H), Rifampin (R)	Continue continuation phase to 7 months

Drug-Resistant TB

Type	Definition	Treatment
MDR-TB	Resistant to isoniazid AND rifampin	Longer regimen (9-20 months) with fluoroquinolones, injectable agents, and second-line drugs
XDR-TB	MDR-TB plus resistance to fluoroquinolones and injectable agents	Highly individualized, novel agents (bedaquiline, linezolid, pretomanid)
Pre-XDR	MDR-TB resistant to either fluoroquinolones or injectables	Individualized based on DST

Pneumonia

Community-Acquired vs Hospital-Acquired Pneumonia

Feature	Community-Acquired Pneumonia (CAP)	Hospital-Acquired Pneumonia (HAP)	Ventilator-Associated Pneumonia (VAP)
Onset	In community or <48h after admission	>=48h after admission	>=48h after intubation
Common pathogens	S. pneumoniae, H. influenzae, M. pneumoniae, C. pneumoniae, L. pneumophila, respiratory viruses	P. aeruginosa, S. aureus (including MRSA), E. coli, K. pneumoniae, Acinetobacter	Same as HAP (more resistant)
Empiric treatment (low severity)	Amoxicillin or macrolide (azithromycin) monotherapy	Antipseudomonal beta-lactam + antipseudomonal fluoroquinolone or aminoglycoside	Same as HAP
Empiric treatment (moderate-severe)	Beta-lactam + macrolide or respiratory fluoroquinolone	MRSA coverage (vancomycin/linezolid) if risk factors	MRSA coverage
Duration	5-7 days (minimum)	7-8 days (may extend if slow response)	7-8 days

CURB-65 Severity Score for CAP

Criteria	Points
C - Confusion (new disorientation)	1
U - Urea >7 mmol/L (BUN >20 mg/dL)	1
R - Respiratory rate >=30/min	1
B - Blood pressure (SBP <90 or DBP <=60 mmHg)	1
65 - Age >=65 years	1

Interpretation: 0-1: outpatient (30-day mortality 0.7-3.2%); 2: short hospitalization/observation (9.2%); 3-5: severe, consider ICU (15-50%).

Urinary Tract Infection (UTI)

Type	Location	Typical Pathogens	Symptoms	Treatment
Cystitis (uncomplicated)	Bladder	E. coli (75-95%), S. saprophyticus, Klebsiella, Enterococcus	Dysuria, frequency, urgency, suprapubic pain	Nitrofurantoin (5 days), TMP-SMX (3 days), fosfomycin (single dose)
Pyelonephritis	Kidney	E. coli, Proteus, Klebsiella, Enterobacter	Fever, flank pain, CVA tenderness, nausea/vomiting	Fluoroquinolone (ciprofloxacin, levofloxacin), or ceftriaxone then oral
Complicated UTI	Any + complicating factors	Broader: Pseudomonas, Enterococcus, Candida	Variable; may be asymptomatic	Culture-directed; broader antibiotics (antipseudomonal if risk factors)
Catheter-associated UTI (CAUTI)	Bladder/kidney	P. aeruginosa, Enterococcus, Proteus, E. coli	Fever, leukocytosis, catheter obstruction	Remove/change catheter, culture-directed therapy

Cellulitis

Parameter	Detail
Definition	Acute bacterial infection of the dermis and subcutaneous tissue
Common pathogens	Streptococcus pyogenes (group A strep), Staphylococcus aureus (including MRSA)
Risk factors	Skin breaks (trauma, ulcers, tinea pedis), lymphedema, venous insufficiency, obesity, diabetes, immunosuppression
Presentation	Erythema, warmth, edema, tenderness; may have fever, chills, leukocytosis
Distinguishing from necrotizing fasciitis	Cellulitis: well-demarcated erythema, less pain; NF: severe pain out of proportion, bullae, crepitus, systemic toxicity
Treatment (mild)	Oral antibiotics: cephalexin, clindamycin, TMP-SMX + cephalexin (if MRSA concern)
Treatment (moderate-severe)	IV antibiotics: cefazolin, ceftriaxone, clindamycin, vancomycin (if MRSA)
Duration	5-14 days depending on severity and response

Sepsis

Parameter	Detail
Definition	Life-threatening organ dysfunction caused by a dysregulated host response to infection
Septic shock	Sepsis with persistent hypotension requiring vasopressors and lactate >2 mmol/L despite adequate fluid resuscitation
qSOFA criteria (quick SOFA)	1. Respiratory rate >=22/min, 2. Altered mental status, 3. SBP <=100 mmHg (>=2 points: high risk of poor outcome)
Common sources	Pneumonia (most common), UTI, intra-abdominal infections, skin/soft tissue, bloodstream

Sepsis Management (Hour-1 Bundle)

Intervention	Detail
Measure lactate	Lactate >=2 mmol/L indicates tissue hypoperfusion
Obtain blood cultures	At least 2 sets before antibiotics
Administer broad-spectrum antibiotics	Within 1 hour of recognition
Begin fluid resuscitation	30 mL/kg crystalloid (balanced solution preferred)
Apply vasopressors	Norepinephrine (first-line) if MAP <65 mmHg despite fluids

Sepsis Definitions (Sepsis-3)

Condition	Description
Infection	Suspected or documented infection
Sepsis	Infection + SOFA score >=2 (acute increase)
Septic shock	Sepsis + vasopressor requirement to maintain MAP >=65 mmHg + lactate >2 mmol/L
SOFA score components	PaO2/FiO2, GCS, MAP, vasopressors, bilirubin, platelets, creatinine, urine output

Vaccine-Preventable Diseases

Disease	Vaccine Type	Dosing Schedule	Efficacy
Measles, Mumps, Rubella	MMR (live attenuated)	2 doses (12-15 months, 4-6 years)	97% (measles, 2 doses)
Diphtheria, Tetanus, Pertussis	DTaP/Tdap (toxoid/acellular)	5 doses (2, 4, 6, 15-18 months, 4-6 years); Tdap booster at 11-12	>95% (diphtheria, tetanus); 85% (pertussis)
Polio	IPV (inactivated)	4 doses (2, 4, 6-18 months, 4-6 years)	>99%
Varicella (chickenpox)	VAR (live attenuated)	2 doses (12-15 months, 4-6 years)	90% (any disease); 98% (severe)
Herpes zoster (shingles)	RZV (recombinant adjuvanted)	2 doses (>=50 years)	>90%
HPV	9vHPV (recombinant)	2-3 doses (starting at 11-12 years)	>99% (prevents HPV-related cancers)
Pneumococcal (PCV20, PPSV23)	Conjugate/polysaccharide	1-2 doses based on age/risk	45-85% (depending on serotype)
Meningococcal (MenACWY, MenB)	Conjugate/recombinant	1-2 doses (11-12 years, 16 years); MenB per shared decision	>85%
Rotavirus	RV1/RV5 (live attenuated)	2-3 doses (2, 4, 6 months)	70-90% (severe disease)
Hepatitis A	HepA (inactivated)	2 doses (12-23 months, 6-18 months later)	>95%
Hepatitis B	HepB (recombinant)	3 doses (birth, 1-2 months, 6-18 months)	>90%
Influenza	IIV, RIV, LAIV (see above)	Annual	40-70% (season-dependent)
COVID-19	mRNA, adenoviral, protein subunit	Primary series + boosters	90%+ (severe disease)
RSV (older adults)	RSVPreF (recombinant)	Single dose (>=60 years)	83% (lower respiratory tract)
RSV (infants)	nirsevimab (monoclonal)	Single dose (season)	>70% (severe disease)