Jul 29, 2026 PDF Available

Topic Overview

MedMentor EDU

Medicine — High-Yield Exam Notes

CLINICAL EXAMINATION

& Presenting Problems in

INFECTIOUS DISEASES

For MBBS • NEET-PG • INI-CET • FMGE • Viva & Bedside

Reference: Harrison • Davidson • Kumar & Clark • API

MedMentor EDU | medmentoredu.com

Contents at a Glance

SECTION I — Clinical Examination of Patients with Infectious Disease

1. Introduction

2. Basic Terminology & Concepts

3. Approach to the Patient with Suspected Infection

4. Detailed History Taking

5. General Physical Examination

6. Temperature Assessment

7. Skin, Nail & Soft-Tissue Examination

8. Head, Eye, Ear, Nose & Oral Examination

9. Lymph-Node Examination

10. Systemic Examination

11. Syndromic Clinical Approach

12. Microbiological Specimen Collection

13. Diagnostic Reasoning

14. Important Non-Infectious Mimics

15. Infection Prevention During Examination

16. Red-Flag Findings

Master Comparison Tables

Important Figures / Diagrams

Important Clinical Photographs

High-Yield Exam Pearls

SECTION I | CLINICAL EXAMINATION OF PATIENTS WITH INFECTIOUS DISEASE

1 | Introduction

1.1 Definition of Infectious Disease

Infectious disease — a clinical illness resulting from the invasion, multiplication or toxin production of microorganisms or parasites within a host.

Represents the outcome of interaction between three factors — the pathogen, the host and the environment (epidemiological triad).
Clinical (symptomatic) infection — organism produces recognisable disease. [IMPORTANT]
Subclinical (inapparent) infection — host is infected and may transmit, but has no overt symptoms; detectable only serologically or on screening.

1.2 Importance of Clinical Evaluation

A structured bedside evaluation in a febrile / infected patient aims to:

Identify the infection syndrome (e.g. pneumonia, meningitis, UTI, sepsis).
Localize the anatomical source of infection.
Assess illness severity and physiological reserve.
Recognize epidemiological clues (travel, exposure, contact).
Identify the likely causative pathogen.
Recognize host-related risk factors (immunosuppression, devices, comorbidity).
Detect complications early.
Determine urgency and timing of treatment.
Select appropriate microbiological and radiological investigations.
Decide on isolation and public-health / notification action.

1.3 Principles of Clinical Diagnosis

Syndromic diagnosis: grouping symptoms/signs into a recognisable clinical syndrome.
Anatomical diagnosis: identifying the organ/system involved.
Etiological diagnosis: establishing the causative organism.
Epidemiological diagnosis: using exposure, travel and contact to predict pathogen.
Microbiological diagnosis: confirmation by stain, culture, antigen, serology or molecular test.
Assessment of host immune status: defining the nature of any immune defect.
Infection vs non-infectious mimic: distinguishing sepsis from malignancy, autoimmune disease, drug fever, etc.
Evaluate and obtain cultures BEFORE antimicrobial therapy whenever feasible — but never delay life-saving treatment for sampling. [VERY HIGH-YIELD]

2 | Basic Terminology & Concepts

2.1 Infection-Related Definitions

Infection — invasion & multiplication of organisms in host tissue producing injury/immune response.

Colonization — organism present & multiplying on a surface without tissue invasion or host response.

Contamination — mere presence of organism on a specimen/surface without multiplication.

Carrier state — host harbours & sheds organism without clinical disease (e.g. Typhoid — chronic gallbladder carrier).

Reservoir — natural habitat where the pathogen lives & multiplies (human, animal, environment).

Source of infection — person/object from which infection is immediately acquired.

Vector — living carrier (usually arthropod) transmitting the pathogen.

Host — organism that harbours the pathogen.

Susceptible host — individual lacking effective immunity / with impaired defence.

Communicable infection: transmissible from host to host.
Non-communicable infection: not transmitted person-to-person (e.g. tetanus, botulism).
Community-acquired infection: acquired outside a healthcare setting.
Healthcare-associated / Hospital-acquired (nosocomial) infection: develops >48 h after admission or related to healthcare contact.
Opportunistic infection: caused by low-virulence organisms in an immunocompromised host (e.g. PCP, CMV, invasive candidiasis).
Endogenous infection: from the patient’s own flora.
Exogenous infection: acquired from an external source.
Localized / Focal / Multifocal / Disseminated: confined to one site / single distant focus / several foci / widespread bloodstream/organ spread.
Primary infection: first infection by an organism.
Secondary infection: new infection superimposed on a pre-existing one.
Latent infection: organism dormant, non-replicating, reactivates later (e.g. TB, HSV, VZV).
Recurrent infection: repeated episodes.
Reinfection: fresh infection by the same organism from an external source.
Relapse: return of the same illness before full recovery / after apparent cure by the original strain.
Recrudescence: reappearance of symptoms after a symptom-free interval without re-exposure (e.g. malaria).
Superinfection: new infection during treatment of another, often resistant (e.g. C. difficile after antibiotics).
Coinfection / Mixed / Polymicrobial: two or more organisms simultaneously; polymicrobial common in intra-abdominal & diabetic-foot sepsis.
Subclinical / Persistent / Chronic infection: asymptomatic / long-standing / prolonged infection (e.g. chronic HBV, HCV).

2.2 Presence of Organisms in Blood

Bacteraemia: bacteria in blood.
Fungaemia: fungi in blood.
Viraemia: virus in blood.
Parasitaemia: parasites in blood (e.g. malaria).
Toxaemia: circulating microbial toxins (e.g. diphtheria, tetanus, toxic shock).
Transient bacteraemia: short-lived, e.g. after dental work / catheterization.
Intermittent bacteraemia: periodic release from a focus (abscess).
Continuous bacteraemia: sustained release — hallmark of intravascular infection (infective endocarditis, infected line).

2.3 Natural History of Infection

Timeline of an Infectious Illness

Exposure

↓

Incubation period

↓

Prodromal period

↓

Illness (clinical) phase

↓

Convalescence

↓

Recovery / Carrier state / Sequelae

Incubation period: interval from exposure to first symptom.
Prodrome: early non-specific symptoms preceding the characteristic illness.
Period of communicability: time during which the host can transmit infection.
Convalescence: recovery phase; may still shed organism.
Complications & Sequelae: acute complications and lasting damage after resolution.

2.4 Chain of Infection

Chain of Infection

Infectious agent

↓

Reservoir

↓

Portal of exit

↓

Mode of transmission

↓

Portal of entry

↓

Susceptible host

Infection control works by breaking any single link in this chain (e.g. hand hygiene interrupts transmission). [IMPORTANT]

2.5 Host–Pathogen Interaction

Pathogen factors

Virulence, infectious dose, toxin production, tissue tropism.

Host factors

Immune response, genetic susceptibility, age, nutrition, comorbidity.
Microbiome balance and mucosal/skin barrier integrity.

Environmental factors

Crowding, sanitation, climate, vector density, healthcare exposure.

3 | Approach to the Patient with Suspected Infection

3.1 Initial Clinical Priorities

Resuscitate first; diagnose in parallel. Follow the ABCDE approach:

A – Airway: patency; risk in epiglottitis, deep-neck / retropharyngeal infection.
B – Breathing: rate, SpO₂, work of breathing; recognise respiratory failure.
C – Circulation: BP, pulse, perfusion, capillary refill; recognise shock.
D – Disability: GCS, focal deficit, meningism; recognise altered mental status.
E – Exposure: full skin survey — rash, eschar, wounds, devices; check temperature.

Simultaneously screen for time-critical infections:

Meningitis / encephalitis.
Necrotizing soft-tissue infection.
Severe / cerebral malaria.
Fulminant hepatic failure.
Immediate isolation and urgent empirical antimicrobials may be required before results return. [IMPORTANT]

3.2 Goals of the Initial Assessment

Confirm or refute infection.
Determine severity (sepsis / septic shock).
Identify the likely source and probable pathogen.
Identify predisposing/host factors.
Obtain appropriate specimens before therapy.
Start urgent treatment and plan source control.
Prevent onward transmission.

Clinical Approach to Suspected Infection

Resuscitate (ABCDE)

↓

Confirm infection & assess severity

↓

Localize source + estimate pathogen

↓

Obtain cultures / specimens

↓

Empirical antimicrobials + source control

↓

Reassess & de-escalate on results

4 | Detailed History Taking

4.1 Presenting Complaints

Common infective presenting symptoms — record onset, duration, progression & severity:

Constitutional: fever, chills, rigors, sweating, fatigue, malaise, myalgia, arthralgia, headache, weight loss, night sweats.
Respiratory: cough, dyspnoea, chest pain, sore throat, dysphagia.
Gastrointestinal: vomiting, diarrhoea, abdominal pain, jaundice.
Genitourinary: dysuria, urinary frequency, flank pain, genital discharge, genital ulcers.
Neurological: altered sensorium, seizures, neck stiffness, focal neurological deficit.
Musculoskeletal: joint pain, bone pain, back pain.
Cutaneous / other: rash, soft-tissue swelling, lymph-node enlargement.

4.2 History of Fever

The single most important symptom — characterise it fully:

Onset & duration: date, mode (abrupt/gradual); acute (<1 wk), subacute, or chronic/prolonged.
Height & measurement: maximum documented temperature; site & method of recording.
Pattern: continuous, intermittent, remittent, or relapsing; note diurnal variation. [COMMON MCQ]
Associated features: chills, rigors, sweating; response to antipyretics/antibiotics; associated rash & organ-specific symptoms.
Relative bradycardia (Faget sign): pulse-temperature dissociation — typhoid, brucellosis, leptospirosis, drug fever, factitious fever. [FAVORITE EXAM QUESTION]
Relative tachycardia: pulse rises more than expected — toxic states, myocarditis, PE, dehydration.
Previous & contextual episodes: past similar episodes; fever after transfusion, surgery, medication/infusion, vaccination, or travel; fever with neutropenia/immunosuppression.

4.3 Symptom-Based Source Localization

Respiratory

Cough, sputum, haemoptysis, dyspnoea, pleuritic pain; assess aspiration risk.

Cardiovascular

New murmur symptoms, heart failure, embolic symptoms; prosthetic valve or cardiac-device history (endocarditis risk).

Gastrointestinal & Hepatobiliary

Vomiting, diarrhoea, abdominal pain, dysentery, jaundice, right-upper-quadrant pain; recent food exposure.

Genitourinary

Dysuria, frequency, urgency, flank pain; vaginal / urethral discharge; pelvic pain; pregnancy-related symptoms.

Neurological

Headache, photophobia, neck stiffness, confusion, seizure, focal deficit, weakness, sensory symptoms.

Musculoskeletal

Mono- / poly-arthritis, back pain, bone pain, muscle pain; prosthetic-joint symptoms.

Skin & Soft Tissue

Rash, painful swelling, wound discharge, ulcer, abscess.
Rapid progression, pain out of proportion, or crepitus → suspect necrotizing infection. [VERY HIGH-YIELD]
Note recent trauma or animal bite.

4.4 Epidemiological History

Why it matters

Exposure history often predicts the pathogen before any test — it is the highest-yield part of ID history-taking.

A. Travel History

Countries/regions & exact place of stay; dates & duration; rural vs urban; season.
Accommodation; trekking, camping, cave exposure; contact with local healthcare facilities.
Illness during travel; ill travel companions.
Prophylaxis: pre-travel vaccination; malaria chemoprophylaxis and adherence.

B. Food & Water Exposure

Untreated water, ice, street food, raw vegetables, unwashed fruits.
Unpasteurized milk / soft cheese (Brucella, Listeria); undercooked eggs (Salmonella); raw/undercooked meat, pork, poultry.
Seafood & shellfish (Vibrio, hepatitis A); reheated rice (B. cereus); canned/fermented food (botulism).
Community feast or recognised outbreak.

C. Environmental Exposure

Freshwater swimming (leptospirosis, schistosomiasis); sea-water; floodwater; sewage; soil / barefoot walking (hookworm, melioidosis).
Construction / dust exposure (fungi); farming; gardening; caves (histoplasmosis); AC / water-system exposure (Legionella).

D. Animal & Vector Exposure

Domestic, farm & wild animals; rodents; birds; bats; slaughterhouse / veterinary exposure.
Animal bites & scratches (rabies, Pasteurella, Bartonella).
Vectors: mosquitoes, ticks, mites, fleas, lice, sandflies, blackflies.

E. Occupational Exposure

Healthcare & laboratory work; agriculture, veterinary work, mining, sewage work; food handling; military service; animal handling; hospital cleaning; waste disposal.

F. Contact & Outbreak History

Contact with TB, meningitis, respiratory viral or exanthematous disease.
Household clustering; school / hostel / prison / shelter / institutional / healthcare-associated outbreaks.

G. Sexual History

Number & gender of partners; sexual practices; condom use.
Genital ulcers/discharge; previous STI; HIV testing; partner illness; pregnancy possibility; sexual-assault history where relevant.

H. Blood & Needle Exposure

Blood transfusion, organ transplantation, tattooing, piercing, needlestick injury.
Injection drug use / needle sharing; unsterile procedures; traditional scarification; dental procedures.

4.5 Past Medical History

Previous infections — TB, HIV, viral hepatitis; recurrent infections.
Recent hospital / ICU admission; recent surgery.
Comorbidity — diabetes, CKD, chronic liver disease, chronic lung disease, heart disease, malignancy, autoimmune disease, malnutrition.
Splenectomy or functional asplenia → risk of overwhelming encapsulated-organism sepsis (OPSI). [VERY HIGH-YIELD]
Prosthetic material — heart valve, joint, vascular graft, pacemaker/ICD, CSF shunt, long-term catheter.
Dialysis; previous multidrug-resistant organism carriage.

4.6 Drug History

Recent antibiotics (duration, adherence); previous antimicrobial resistance.
Immunosuppressants — corticosteroid dose & duration, chemotherapy, biologicals, immunomodulators, post-transplant regimens.
Proton-pump inhibitors; anticoagulants; drugs known to cause fever.
Allergies: drug allergies & previous adverse reactions (essential before prescribing).
Prophylactic antimicrobials; antiretroviral therapy; anti-tuberculosis therapy.

4.7 Immunization History

Childhood vaccination status.
Influenza, COVID-19, pneumococcal, meningococcal, Hib, hepatitis A & B, tetanus, diphtheria, pertussis, rabies, varicella, MMR, HPV.
Travel vaccines.
Vaccination after splenectomy and before planned immunosuppression / transplantation is a key exam & clinical point. [IMPORTANT]

4.8 Host Risk Assessment

Identify factors that increase susceptibility or predict specific organisms:

Extremes of age, frailty, malnutrition, pregnancy, puerperium.
Diabetes, renal failure, liver failure, chronic lung disease, alcohol dependence.
Immune defects: HIV, neutropenia, lymphopenia, primary immunodeficiency, hypogammaglobulinaemia, complement deficiency, asplenia.
Malignancy, transplantation, chemotherapy, biological therapy, prolonged corticosteroids.
Breaches of barriers — burns, wounds, pressure injuries, indwelling devices.

5 | General Physical Examination

5.1 General Survey

Consciousness & orientation; toxic appearance; distress; respiratory effort.
Hydration & nutrition; cachexia.
Pallor, icterus, cyanosis, clubbing.
Lymphadenopathy; oedema; skin rash.
Body habitus, mobility, frailty.

5.2 Vital Signs

Temperature; pulse rate & character; respiratory rate; blood pressure.
Oxygen saturation; urine output; capillary refill time; peripheral temperature; mental status.
Tachypnoea is often the earliest and most sensitive sign of deterioration in sepsis. [VERY HIGH-YIELD]

5.3 Assessment of Severity

Look for features indicating sepsis / septic shock and organ dysfunction:

Hypotension, tachypnoea, hypoxia, altered sensorium, oliguria.
Poor peripheral perfusion, prolonged capillary refill, elevated lactate.
Features of shock; signs of DIC; multi-organ dysfunction.

Early-warning / severity scores

Score	Basis	Key use
qSOFA	RR ≥22, SBP ≤100, altered mentation (≥2 = high risk)	Rapid bedside sepsis screen
SOFA	6 organ systems scored 0–4	Defines organ dysfunction in Sepsis-3
NEWS2	RR, SpO₂, O₂, temp, BP, HR, consciousness	Track-and-trigger deterioration

Sepsis-3 definition

Sepsis = life-threatening organ dysfunction caused by a dysregulated host response to infection (SOFA rise ≥2).

Septic shock = sepsis + vasopressor requirement to keep MAP ≥65 mmHg + lactate >2 mmol/L despite fluids.

6 | Temperature Assessment

6.1 Normal Body Temperature

Normal range: approx. 36.5–37.5 °C (oral ~37 °C).
Circadian variation: lowest in early morning, peak in late afternoon/evening (~0.5–1 °C swing). [COMMON MCQ]
Influenced by age (lower/blunted in elderly), menstrual cycle (rises after ovulation), exercise, environment and measurement technique.

6.2 Measurement Sites

Site	Note
Oral	Convenient; affected by drinks / mouth-breathing
Axillary	Reads ~0.5 °C lower; least reliable
Tympanic	Quick; reflects core; technique-dependent
Temporal	Non-invasive skin scan; screening use
Rectal / Core	Most accurate estimate of core temperature

Know the advantages & limitations of each; core (rectal/bladder/oesophageal) is the reference standard.

6.3 Abnormal Temperature States

Fever (pyrexia) — regulated rise in temperature due to an elevated hypothalamic set-point (pyrogen-mediated).

Hyperpyrexia: temperature >41.5 °C.

Hyperthermia — unregulated rise with a NORMAL set-point; heat production/absorption exceeds loss (heat stroke, NMS, malignant hyperthermia) — does NOT respond to antipyretics.

Hypothermia — core temperature <35 °C; may accompany overwhelming sepsis in the elderly (poor prognostic sign).

Factitious fever & measurement error: suspect if fever pattern is atypical, no tachycardia, and normal inflammatory markers.

Fever vs Hyperthermia

Fever responds to antipyretics; hyperthermia does NOT.

Hyperthermia is a medical emergency requiring active cooling.

7 | Skin, Nail & Soft-Tissue Examination

7.1 Primary Lesions

Macule: flat, <1 cm colour change.
Papule: raised, <1 cm.
Plaque: raised, flat-topped, >1 cm.
Nodule: raised, deep, >1 cm.
Vesicle / Bulla: fluid-filled <0.5 cm / >0.5 cm.
Pustule: pus-filled.
Wheal: transient oedematous plaque.
Ulcer: full-thickness epidermal + dermal loss.
Eschar: black necrotic crust (e.g. scrub typhus).

7.2 Rash Assessment

Blanching vs non-blanching is the single most important bedside distinction. [VERY HIGH-YIELD]
Non-blanching petechiae / purpura: suggest bleeding into skin — meningococcaemia, vasculitis, DIC, severe dengue.
Describe: petechiae, purpura, ecchymosis, palpable purpura, retiform purpura, target lesions.
Distribution: central vs peripheral; centripetal (trunk-outward) vs centrifugal (extremities-inward).
Palms & soles involvement: secondary syphilis, Rocky Mountain spotted fever, hand-foot-mouth disease, infective endocarditis. [FAVORITE EXAM QUESTION]
Note mucosal involvement and dermatomal distribution (herpes zoster).

7.3 Important Infective Cutaneous Signs

Sign	Association
Cellulitis / Erysipelas	Strep. pyogenes, Staph. aureus (erysipelas = sharply demarcated)
Abscess	Localised pus collection, often S. aureus
Necrotizing fasciitis	Pain out of proportion, crepitus, rapid spread — surgical emergency
Ecthyma gangrenosum	Pseudomonas bacteraemia (neutropenia)
Eschar	Scrub typhus, anthrax, rickettsial spotted fevers
Erythema migrans	Lyme disease (Borrelia)
Janeway lesions / Osler nodes	Infective endocarditis (painless / painful)
Splinter haemorrhages	Infective endocarditis, vasculitis
Rose spots	Typhoid fever
Herpes zoster / Varicella	VZV — dermatomal / centripetal vesicles
Mpox lesions	Deep-seated, umbilicated, same-stage lesions
Scabies burrows	Sarcoptes scabiei; web spaces
Cutaneous larva migrans	Serpiginous track — hookworm larvae
Tungiasis / Myiasis	Flea / fly-larvae infestation
Leprosy patch	Hypopigmented anaesthetic patch (sensory loss)
Kaposi sarcoma	HHV-8 in advanced HIV
Disseminated molluscum	Advanced HIV / immunosuppression
Injection track marks	IV drug use — endocarditis / bloodstream infection risk

7.4 Wound & Device Examination

Inspect surgical wounds, drains, central-line site, peripheral cannula site, urinary catheter.
Examine diabetic foot, pressure sores, prosthetic-device pocket, dialysis access, injection sites.
Any indwelling device is a potential nidus — always examine and consider removal in unexplained sepsis. [IMPORTANT]

8 | Head, Eye, Ear, Nose & Oral Examination

8.1 Eye

Conjunctivitis; conjunctival suffusion (leptospirosis); uveitis.
Chorioretinitis: CMV, toxoplasma, candida.
Roth spots: retinal haemorrhages with pale centres — infective endocarditis. [COMMON MCQ]
CMV retinitis (advanced HIV); endophthalmitis; papilloedema (raised ICP).

8.2 Ear, Nose & Sinuses

Otitis externa & media; mastoid tenderness; sinus tenderness; nasal discharge.
Facial swelling / black nasal eschar in a diabetic → suspect rhino-orbital mucormycosis. [VERY HIGH-YIELD]

8.3 Oral & Pharyngeal Examination

Oral ulcers; oral thrush (candidiasis); oral hairy leukoplakia (EBV, HIV marker).
Herpetic lesions; poor dentition, gingivitis, periodontitis (endocarditis / anaerobic source).
Tonsillar exudate; pharyngeal erythema; pseudomembrane (diphtheria).
Koplik spots: bluish-white buccal spots — pathognomonic early sign of measles. [FAVORITE EXAM QUESTION]
Peritonsillar swelling (quinsy); parotid swelling (mumps, suppurative parotitis).

9 | Lymph-Node Examination

Palpate all groups systematically:

Cervical, supraclavicular, axillary, epitrochlear, inguinal, popliteal.

Assess for each node

Size, number, tenderness, consistency, mobility, matting, fluctuation.
Overlying skin changes; sinus formation.
Distribution: localized vs generalized lymphadenopathy; note the drainage territory.

Feature	Suggests
Tender, mobile, soft	Acute infective (reactive) node
Firm, matted, sinus	Tuberculous lymphadenitis
Hard, fixed, painless	Malignancy / metastasis
Generalized	HIV, EBV, CMV, syphilis, toxoplasma, lymphoma
Epitrochlear	Secondary syphilis, cat-scratch, HIV
Left supraclavicular (Virchow)	Intra-abdominal malignancy — non-infective

Distinguish infectious from non-infectious causes (lymphoma, metastasis, sarcoidosis). [IMPORTANT]

10 | Systemic Examination

10.1 Respiratory System

Upper-airway obstruction; pneumonia with consolidation; pleural effusion; empyema; lung abscess; cavitation; bronchiectasis.
Tuberculosis; aspiration pneumonia; Pneumocystis pneumonia; septic pulmonary emboli.
Respiratory failure & ARDS are the feared endpoints — monitor SpO₂ and work of breathing. [IMPORTANT]

10.2 Cardiovascular System

New or changing murmur; prosthetic-valve dysfunction; heart failure.
Peripheral signs of infective endocarditis; embolic phenomena; mycotic aneurysm; conduction abnormality; pacemaker-pocket infection.
Fever + new regurgitant murmur = infective endocarditis until proven otherwise — apply the Modified Duke criteria. [VERY HIGH-YIELD]

10.3 Abdominal Examination

Hepatomegaly; splenomegaly; splenic tenderness; RUQ tenderness; Murphy sign; ascites; peritonism; ileus; abdominal mass; psoas sign.
Focal collections: liver abscess, cholangitis, appendicitis, intra-abdominal abscess.
Tender hepatosplenomegaly in a febrile traveller — think malaria, enteric fever, visceral leishmaniasis. [COMMON MCQ]

10.4 Genitourinary Examination

Renal-angle (costovertebral) tenderness; suprapubic tenderness.
Genital ulcers; urethral / vaginal discharge; pelvic tenderness.
Epididymo-orchitis; prostatitis; perianal infection; perirectal abscess.

10.5 Nervous System

Conscious level & GCS; encephalopathy / encephalitis.
Meningeal signs: neck stiffness, Kernig sign, Brudzinski sign, photophobia. [FAVORITE EXAM QUESTION]
Raised intracranial pressure; cranial neuropathy; focal deficit; cerebellar signs; seizures.
Spinal tenderness / epidural abscess; peripheral neuropathy; acute flaccid paralysis.
Specific pattern signs: trismus & risus sardonicus (tetanus); hydrophobia & aerophobia (rabies).

10.6 Musculoskeletal System

Septic arthritis (usually monoarthritis); polyarthritis; prosthetic-joint infection.
Osteomyelitis; vertebral osteomyelitis; discitis; sacroiliitis.
Pyomyositis; myositis; tenosynovitis; reactive arthritis.
An acutely hot, swollen, restricted single joint is septic arthritis until aspirated & proven otherwise. [VERY HIGH-YIELD]

11 | Syndromic Clinical Approach

Grouping the presentation into a fever syndrome rapidly narrows the differential:

Syndrome	Think of
Fever without focus	Early bacteraemia, enteric fever, malaria, viral
Fever with rash	Meningococcaemia, dengue, measles, rickettsia, drug
Fever with jaundice	Leptospirosis, viral hepatitis, malaria, cholangitis
Fever with thrombocytopenia	Dengue, malaria, leptospirosis, sepsis, rickettsia
Fever with pancytopenia	Enteric fever, visceral leishmaniasis, HLH, sepsis
Fever with eosinophilia	Helminths, drug reaction, tropical eosinophilia
Fever with lymphadenopathy	EBV, CMV, HIV, TB, toxoplasma, lymphoma
Fever with hepatosplenomegaly	Malaria, enteric fever, kala-azar, brucellosis
Fever with respiratory symptoms	Pneumonia, influenza, COVID-19, TB
Fever with diarrhoea	Enteric fever, gastroenteritis, C. difficile
Fever with altered sensorium	Meningitis, encephalitis, cerebral malaria, sepsis
Fever with focal deficit	Brain abscess, TB meningitis, encephalitis
Fever with shock	Septic shock, TSS, meningococcaemia, dengue
Fever with eschar	Scrub typhus, rickettsial spotted fevers
Fever with arthritis	Septic arthritis, gonococcal, reactive, viral
Fever after travel	Malaria, enteric fever, dengue, rickettsia
Fever after animal bite	Rabies, Pasteurella, Capnocytophaga
Fever after surgery	Wound / deep infection, HAP, UTI, line, VTE
Fever in pregnancy	UTI/pyelonephritis, Listeria, chorioamnionitis
Fever in immunocompromised	Opportunistic + typical organisms
Fever with prosthetic material	Device-related infection / biofilm
Fever with intravascular catheter	Catheter-related bloodstream infection

Fever + eschar + regional lymphadenopathy in endemic India — classic for scrub typhus. [FAVORITE EXAM QUESTION]

12 | Microbiological Specimen Collection

12.1 General Principles

Collect appropriate cultures BEFORE starting antimicrobials — but never delay life-saving therapy. [VERY HIGH-YIELD]
Select the correct specimen; obtain sufficient volume; use aseptic technique & correct container.
Label correctly; record collection site & time; provide relevant clinical information.
Ensure timely transport in the correct transport medium; observe biosafety precautions.

12.2 Types of Specimens

Blood; urine; sputum; endotracheal aspirate; bronchoalveolar lavage.
CSF; stool; pus; tissue; bone; joint aspirate.
Pleural, ascitic & pericardial fluid; genital / nasopharyngeal / throat swabs.
Skin scraping; nail clipping; bone marrow.

Blood cultures

Take ≥2 sets from separate venepuncture sites before antibiotics.

Adequate volume is the single biggest determinant of yield.

Growth in multiple bottles / continuous bacteraemia suggests true intravascular infection.

12.3 Diagnostic Methods

Direct microscopy: Gram stain, acid-fast (Ziehl-Neelsen) stain, fungal (KOH/calcofluor) stain.
Culture & antimicrobial-susceptibility testing (gold standard for many bacteria).
Antigen detection; serology & paired (acute + convalescent) serology.
Molecular: nucleic-acid amplification (PCR), multiplex PCR, molecular resistance testing.
Histopathology; immunohistochemistry; point-of-care tests.

12.4 Interpretation Principles

Distinguish sterile vs non-sterile site; colonization vs invasive disease; contamination.
Weigh pre-test probability; sensitivity & specificity; false-positive / false-negative results.
Account for the effect of prior antibiotics and cross-reactive serology.
Always correlate microbiology with the clinical picture — a positive culture is not always the cause of disease. [IMPORTANT]

13 | Diagnostic Reasoning

Structured Diagnostic Reasoning

Identify the syndrome

↓

Localize the anatomical source

↓

Determine severity

↓

Assess host immune defect

↓

Estimate likely organisms (+ incubation, travel, exposure)

↓

Exclude non-infectious mimics

↓

Plan source control & reassess after treatment response

Recognize occult infection and multiple simultaneous infections.
Evaluate the need for source control (drainage, device removal, debridement).
Reassess the diagnosis if there is no response to appropriate therapy.
Seek microbiology / infectious-disease consultation when indicated.

14 | Important Non-Infectious Mimics

Not all fever is infection — always consider these mimics, especially in PUO:

Malignancy (lymphoma, leukaemia, renal cell carcinoma); autoimmune disease; vasculitis.
Drug fever & drug eruption; thromboembolism (DVT/PE).
Endocrine emergencies — adrenal crisis, thyroid storm.
Heat stroke; transfusion reaction.
Haemophagocytic lymphohistiocytosis (HLH): fever, cytopenias, high ferritin, hepatosplenomegaly — easily mistaken for sepsis. [VERY HIGH-YIELD]
Adult-onset Still disease; inflammatory bowel disease; crystal arthritis; factitious illness.
Withdrawal syndromes; pancreatitis; tissue necrosis; postoperative inflammation.

15 | Infection Prevention During Examination

Hand hygiene is the single most effective measure to prevent healthcare-associated infection. [VERY HIGH-YIELD]
Apply standard precautions to every patient.

Precaution	Example organisms
Contact	MRSA, C. difficile, resistant Gram-negatives, scabies
Droplet	Influenza, meningococcus, pertussis, mumps
Airborne	TB, measles, varicella (require N95 + negative-pressure room)

Eye & face protection; respiratory hygiene; appropriate personal protective equipment.
Safe injection practice; sharps disposal; source isolation; protective isolation.
Decontamination of equipment; environmental cleaning; management of occupational exposure.

16 | Red-Flag Findings

Time-critical infections — act immediately

Septic shock; meningitis; encephalitis; necrotizing fasciitis.

Severe malaria; fulminant hepatitis; toxic shock syndrome; purpura fulminans.

Acute epiglottitis / airway obstruction; DIC; severe hypoxia; acute kidney injury.

Altered sensorium; rapidly progressive rash.

Any febrile immunocompromised or asplenic patient — treat as emergency.

Fever in an asplenic patient may herald overwhelming post-splenectomy infection (OPSI) — give antibiotics within the hour. [FAVORITE EXAM QUESTION]

Master Comparison Tables

Infection vs Colonization vs Contamination

Feature	Infection	Colonization	Contamination
Multiplication	Yes	Yes	No
Tissue invasion	Yes	No	No
Host response	Present	Absent	Absent
Treatment	Usually required	Usually not	Not required

Relapse vs Recrudescence vs Reinfection

Term	Meaning
Relapse	Same strain returns before full cure
Recrudescence	Symptoms recur after a symptom-free interval, no re-exposure
Reinfection	New infection by same organism from external source
Superinfection	New (often resistant) infection during treatment

Epidemiological Clue → Likely Infection

Exposure / clue	Likely infection
Freshwater + jaundice	Leptospirosis
Unpasteurized milk	Brucellosis, Listeria
Reheated rice	Bacillus cereus
Cave / bird droppings	Histoplasmosis
Air-conditioning / water tower	Legionella
Tick bite + eschar	Rickettsial spotted fever
Mite bite + eschar (India)	Scrub typhus
Animal bite	Rabies, Pasteurella
Rodent + flood	Leptospirosis, hantavirus
Sick returning traveller	Malaria until excluded

Host Immune Defect → Likely Organism

Defect	Characteristic organisms
Neutropenia	Gram-negatives, Pseudomonas, Candida, Aspergillus
T-cell defect / HIV	PCP, CMV, TB, toxoplasma, cryptococcus
B-cell / hypogamma	Encapsulated bacteria (pneumococcus, Hib)
Complement deficiency	Neisseria (recurrent meningococcus)
Asplenia	Encapsulated organisms → OPSI
Prosthetic material	Coagulase-negative staph, biofilm formers

Peripheral Signs of Infective Endocarditis

Sign	Nature
Osler nodes	Painful pulp nodules (immune)
Janeway lesions	Painless palm/sole macules (embolic)
Roth spots	Retinal haemorrhage, pale centre
Splinter haemorrhages	Subungual linear streaks
Clubbing	Chronic / subacute IE

Rash Morphology → Differential

Rash	Consider
Non-blanching petechiae	Meningococcaemia, DIC, vasculitis
Maculopapular	Measles, rubella, drug, early rickettsia
Vesicular	Varicella, HSV, zoster, mpox
Eschar	Scrub typhus, anthrax, rickettsia
Palms & soles	Syphilis, RMSF, hand-foot-mouth, IE
Rose spots	Typhoid fever

Important Figures / Diagrams

Insert the following labelled figures for revision (compiled here for the chapter):

Chain of infection — six links diagram.
Host–pathogen–environment (epidemiological) triangle.
Clinical approach to suspected infection — flow algorithm.
Syndromic approach to fever — branching chart.
Complete infectious-disease examination sequence.
Lymph-node examination map (regional groups).
Meningeal signs — Kernig & Brudzinski illustration.
Rash morphology chart (primary lesions).
Infection source-localization algorithm.
Correct microbiological specimen pathway.
Standard and transmission-based precautions diagram.

Important Clinical Photographs

High-yield clinical images to recognise for exams & viva:

Cellulitis; erysipelas; necrotizing fasciitis.
Ecthyma gangrenosum; scrub-typhus eschar.
Dengue rash; meningococcaemia (purpura).
Varicella; herpes zoster; mpox lesions.
Janeway lesions; Osler nodes; splinter haemorrhages.
Oral candidiasis; oral hairy leukoplakia; Kaposi sarcoma.
Tuberculous lymphadenitis; erythema migrans.
CMV retinitis; diabetic foot infection.
Injection-site abscess; pressure-sore infection.
Disseminated molluscum contagiosum.
Secondary syphilis involving palms and soles.

High-Yield Exam Pearls

CLINICAL EXAMINATION — MUST-KNOW FACTS

Colonization = multiplication without invasion; infection = invasion + host response; contamination = neither.

Continuous bacteraemia = intravascular infection (endocarditis / infected line).

Relative bradycardia (Faget sign): typhoid, brucellosis, leptospirosis, drug & factitious fever.

Non-blanching rash → meningococcaemia / DIC / vasculitis until proven otherwise.

Palms & soles rash: secondary syphilis, RMSF, hand-foot-mouth, infective endocarditis.

Koplik spots = pathognomonic of measles (prodrome).

Rose spots = typhoid; eschar = scrub typhus / rickettsia / anthrax.

Roth spots, Osler nodes, Janeway lesions, splinter haemorrhages = infective endocarditis.

Fever + new regurgitant murmur = IE → apply Modified Duke criteria.

Conjunctival suffusion + jaundice + AKI = leptospirosis (Weil disease).

Hot swollen single joint = septic arthritis until aspirated.

Asplenic / immunocompromised + fever = emergency (OPSI risk).

SEPSIS & SEVERITY — MUST-KNOW FACTS

Sepsis-3: organ dysfunction (SOFA ≥2) from dysregulated host response to infection.

Septic shock: vasopressors to keep MAP ≥65 + lactate >2 despite fluids.

qSOFA ≥2 (RR ≥22, SBP ≤100, altered mentation) flags high risk at the bedside.

Tachypnoea is the earliest sign of deterioration; hypothermia in sepsis is a poor sign.

Take blood cultures (≥2 sets) before antibiotics — never delay therapy.

Hand hygiene is the most effective infection-control measure.

EPIDEMIOLOGY & MICROBIOLOGY — MUST-KNOW FACTS

Sick returning traveller with fever = exclude malaria first.

Neutropenia → Pseudomonas / Candida / Aspergillus; ecthyma gangrenosum = Pseudomonas.

Asplenia / B-cell defect → encapsulated organisms; complement defect → recurrent Neisseria.

Airborne precautions: TB, measles, varicella (N95 + negative-pressure room).

Paired serology (acute + convalescent) confirms many viral / atypical infections.

Positive culture from a non-sterile site may be colonization — correlate clinically.

CLINICAL EXAMINATION & Presenting Problems in INFECTIOUS DISEASES