Infectious Diseases

01

CNS Infections

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Meningitis · Clinical & Workup

Features: headache · neck stiffness · fever · photophobia · altered LOC · jolt accentuation · Kernig sign · Brudzinski sign.

Workup: CSF Gram stain · CSF culture · CSF PCR.

CT before LP: ↑ICP (papilledema · focal neuro deficits · altered MS) · immunocompromised · CVA · CNS mass · seizures.

CSF Profiles by Etiology

Type	Opening pressure	WBC	Glucose	Protein
Bacterial	200–500	1000–5000 (PMN)	<2.2	1–5
Viral	≤250	50–1000 (lymph)	2.5–3.5	<2
TB	↑	lymphocytes	<2.2	>1
Fungal	↑	lymphocytes	<2.2	>1
Lyme	↑	lymphocytes	2.5–3.5	<2

Empiric Antibiotics by Age

Age 18–50y (S pneumoniae, N meningitidis serogroup B, H influenzae) › vancomycin + ceftriaxone/cefotaxime/moxifloxacin + dexamethasone
Age >50y / immunocompromised (add L monocytogenes) › vancomycin + ceftriaxone/cefotaxime + ampicillin/cotrimoxazole + dexamethasone

Gram +ive diplococci

S pneumoniae

Penicillin G or ceftriaxone ×10–14d + dexamethasone ×4d.

Gram −ive diplococci

N meningitidis

CTX ×4–7d. Purpura fulminans is the classic sign.

Prophylaxis › ciprofloxacin 500mg PO ×1 or ceftriaxone 250mg IM ×1 or rifampicin 600mg PO BD ×2d.

Gram −ive coccobacilli

H influenzae

CTX ×4–7d.

Gram +ive bacilli

L monocytogenes

Ampicillin ×21d. Older adults & pregnancy.

Basal Skull Meningitis Differential

CN palsies + UMN signs. Consider: TB · Listeria · Cryptococcus · syphilis · Lyme.

TB: cranial neuropathies · mental status changes · SIADH · chronic meningitis › rifampin + isoniazid + pyrazinamide + ethambutol + dexamethasone
Lyme (Borrelia burgdorferi): tick bite · headache · photophobia · nausea · erythema migrans · unilateral or bilateral facial palsy
Leptospirosis: freshwater + rodent urine · uveitis · rash · red conjunctivae · LAD · hepatosplenomegaly

Viral meningitis: enteroviruses (May–Nov) · HSV1/HSV2 (recurrent) · VZV · CMV · EBV › nausea · vomiting · myalgia · pharyngitis · maculopapular rash · cough › CSF PCR › supportive Rx
Aseptic meningitis: NSAIDs · antimicrobials · IVIG

Healthcare-Associated Meningitis / Ventriculitis

Head trauma · neurosurgery · ventricular drains › headache · nausea · lethargy · altered LOC.

Rx: remove CSF shunt/hardware & external drain · vancomycin + ceftazidime/cefepime/meropenem ×10–14d (Gram +) / 21d (Gram −). Staph › add rifampicin. No response › intraventricular antibiotics.

Acyclovir-responsive

HSV Encephalitis

HSV-1. Altered LOC · fever · seizures · headache · focal deficits.

CSF PCR · LP › ↑RBC · ↑lymph · normal glucose. EEG › PLEDs. MRI › temporal lobe.

Rx: IV acyclovir ×14–21d.

Autoimmune mimic

Anti-NMDAR Encephalitis

Psychiatric changes · dyskinesias · autonomic instability.

Mosquito-borne

West Nile Neuroinvasive

Meningitis · encephalitis · myelitis · acute asymmetric flaccid paralysis. June–Oct. RF: older adults · immunocompromised.

Serum/CSF WNV IgM Ab › supportive.

JC virus

PML

Behavioral/cognitive changes · motor weakness · gait abn · visual field deficits · speech disturbances · seizures.

RF: AIDS · immunotherapy. MRI › T2 hyperintense white matter. CSF JCV PCR. Treat underlying cause.

Brain Abscess

Severe headache ± fever ± neck stiffness. Hematogenous · ENT source · penetrating trauma · neurosurgery.

Streptococci · Enterobacterales · anaerobes · S aureus. MRI › ring enhancement.

Rx: IV vancomycin + metronidazole + 3rd gen cephalosporin ×6–8 weeks. >2.5cm › LP CI · stereotactic excision + drainage.

Parasitic

Neurocysticercosis

Taenia solium. Mexico, Central/South America, Asia. Seizures.

CT › multiple cysts · calcified lesions · hydrocephalus. Rx: glucocorticoids + praziquantel.

Localized

Spinal Epidural Abscess

Localized pain radiating down spine. S aureus · E coli · TB (Pott) · brucellosis.

RF: endocarditis · IVDU · IV catheters · UTI · neurosurgery.

MRI with contrast › antibiotics ×6 weeks. Neuro signs › surgical drainage.

02

Community-Acquired Bacteremia & Endocarditis

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Infective Endocarditis · Clinical & Workup

Features: fever · malaise · fatigue · new murmur · ECG conduction abnormalities · petechiae · splinter hemorrhages · Osler nodes · Janeway lesions · Roth spots.

Workup: TTE + BCS ×2 › IV antibiotics ×4–6 weeks.

TEE indications: TTE nondiagnostic · complications · intracardiac leads/devices.

RF: immunosuppression · IVDU · indwelling catheters · implanted cardiac devices · older age.

Modified Duke Criteria

Definite: 2 major · OR 1 major + 3 minor · OR 5 minor · OR pathologic.

Possible: 1 major + 2 minor · OR 3 minor.

Major: microbiologic (BCS ×2 typical orgs; BCS ×3 rare; PCR Coxiella/Bartonella/T whipplei; Coxiella IgG >1:800) · imaging (echo, cardiac CT, FDG-PET) · surgical criteria
Minor: predisposition (prior IE, prosthetic valve, repair, CHD, regurg/stenosis, CIED, HOCM, IVDU) · T >38 · vascular phenomena (arterial emboli, septic pulmonary infarcts, cerebral/splenic abscess, mycotic aneurysm, ICH, conjunctival hemorrhage, Janeway, purulent purpura) · immunologic (RF, Osler nodes, Roth spots, immune-complex GN) · microbiologic not fulfilling major · imaging (PET)

Pathogen-Directed Therapy

Organism	Native valve	Prosthetic valve
MSSA	cloxacillin or cefazolin	cloxacillin/cefazolin + rifampicin + gentamicin
MRSA	vancomycin	vancomycin + rifampicin + gentamicin
S viridans, S gallolyticus/bovis	penicillin G or ceftriaxone or vancomycin	penicillin/ceftriaxone + gentamicin
E faecalis	ampicillin + gentamicin/ceftriaxone
E faecium	vancomycin + gentamicin
HACEK	ceftriaxone or ampicillin or ciprofloxacin
Candida	echinocandin / liposomal amphotericin + flucytosine › lifetime fluconazole

Surgical Indications

Valve dysfunction + acute HF
Large left-sided vegetations
Fungal / highly resistant organisms
Heart block · annular / aortic root abscess
Recurrent systemic embolization
Prosthetic valve dehiscence / relapse
S aureus prosthetic valve
Destructive penetrating lesions

Implantable cardiac device › surgical removal.

Associated Workup

S gallolyticus / Clostridium septicum › colonoscopy (colon cancer).

Culture-Negative Endocarditis

Pre-culture antibiotics · Bartonella (cats) · Coxiella burnetii (farm animals, milk) · Tropheryma whipplei · Brucella (farm animals, milk, Middle East) · Chlamydia psittaci (birds) · Legionella · Aspergillus · Histoplasma · M chimaera · marantic endocarditis (malignancy) · Libman-Sacks (SLE).

Prophylaxis

Procedures: dental · respiratory with mucosal transection · piercing of infected skin.

Indications: prosthetic heart valve · previous IE · CHD · cardiac transplant.

Agents: amoxicillin or cephalexin or azithromycin or doxycycline.

A patient with S gallolyticus bacteremia owes the gut a colonoscopy.

S aureus Bacteremia

Source: skin · soft tissue · sinopulmonary. Echo · BCS every 2–3d until −ive · IV antibiotics ×14d.

MSSA › oxacillin/cefazolin. MRSA › vancomycin. Complicated › ×4–6 weeks.

Complications: endocarditis · vertebral diskitis · osteomyelitis.

Enterococci › ampicillin
Gram −ive Enterobacteriaceae (E coli) › antibiotics ×7d
S pneumoniae + pneumonia › antibiotics ×5–7d
VRE › daptomycin or linezolid
Fever / +ive BCS >3d antibiotics › suspect endocarditis · seek source control · seek abscess
S agalactiae · S viridans · S gallolyticus · Enterococcus › echo (IE)
S milleri › lung / brain / abdominal abscess
Pseudobacteremia: coagulase −ive Staph · Bacillus spp · Corynebacterium · Cutibacterium acnes · Micrococcus

03

Community-Acquired Pneumonia

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Clinical & Workup

Fever · productive cough · SOB · signs of consolidation › PA + lateral CXR · influenza NAAT.

Severity / hospitalization: PSI · IDSA/ATS · CURB-65.

Typical

Common Bacterial

S pneumoniae · H influenzae · influenza · RSV · parainfluenza · rhinovirus · adenovirus · coronaviruses.

Atypical · Severe CAP

Legionella pneumophila

Contaminated water supplies. Hyponatremia · GI symptoms.

PCR · urinary antigen › azithromycin or respiratory FQ.

Atypical · Walking

Mycoplasma pneumoniae

Headache · erythema multiforme · SJS · hemolysis.

Macrolide or respiratory FQ or doxycycline.

Atypical

Chlamydia pneumoniae

Headache · dry cough · photophobia · diarrhea.

Doxycycline.

Pathogen Patterns by Host

High risk (comorbidities, antibiotics, hospital): Klebsiella pneumoniae · Pseudomonas · S aureus (post influenza)
Alcoholism: S pneumoniae · H influenzae · Enterobacterales · Klebsiella
COPD: H influenzae · S pneumoniae · Moraxella · Legionella · Pseudomonas
Structural lung disease (bronchiectasis, CF): P aeruginosa · Burkholderia cepacia · Stenotrophomonas · S aureus · atypical mycobacteria
Aspiration: S pneumoniae · H influenzae · Enterobacterales
Age ≥65y: influenza · S pneumoniae · RSV · SARS-CoV-2
Post-viral: S aureus · Strep pyogenes · S pneumoniae

Animal Exposure → Pathogen

Exposure	Organism
Birds	Chlamydia psittaci · Histoplasma · Cryptococcus
Dogs	Bordetella bronchiseptica
Cats	Pasteurella multocida
Farm / pregnant animals	Coxiella burnetii · Brucella
Horses	Rhodococcus equi
Rodent droppings	Hantavirus
Rabbits	Francisella tularensis

CXR Pattern → Differential

Lobar: S pneumoniae · Legionella (multilobar)
Abscess / cavitary: oral anaerobes · S aureus · Klebsiella · Nocardia · Actinomyces · Rhodococcus · mycobacteria · endemic fungi
Interstitial: Legionella · Mycoplasma · Chlamydia · viruses
Pleural effusion / empyema: oral anaerobes · SAG · S aureus · S pneumoniae

Amoxicillin or doxycycline or macrolide (regional pneumococcal resistance <25%) ×5d
Comorbidities › respiratory FQ or co-amoxiclav/cefuroxime/cefpodoxime + macrolide/doxycycline ×5d
Penicillin allergy › respiratory FQ (levofloxacin/moxifloxacin)

Standard › IV β-lactam (CTX, ampicillin-sulbactam, ceftaroline) + macrolide or respiratory FQ ×5d
Severe / ICU › IV β-lactam + macrolide/respiratory FQ ± glucocorticoids
Sputum CS: ICU · S aureus RF · Pseudomonas RF · not responding · cavitary · underlying lung disease
BCS: ICU · MRSA RF · Pseudomonas RF
Urine pneumococcal/Legionella Ag: ICU · known exposure · immunocompromised

Standard + vancomycin or linezolid ×5d
RF: prior MRSA · recent hospitalization (≤90d) · recent IV antibiotics (≤90d) · post-influenza · Gram +ive cocci in clusters · not responding · IVDU · pleural lung nodules (septic pulmonary emboli) · cavitary lung lesions

Antipseudomonal β-lactam (piperacillin-tazobactam, cefepime, ceftaz, aztreonam, meropenem) + macrolide/levofloxacin ×5d
RF: prior Pseudomonas ≤1y · immunocompromised · structural lung disease · repeated antibiotics · recent hospitalization · recent IV antibiotics · recent MV
Pseudomonas & MRSA −ive on cultures › de-escalate

Chronic symptoms · weight loss · foul-smelling/tasting sputum · lung abscess/empyema (right lower lobe)
RF: poor dentition · dental caries · dysphagia · alcohol intoxication
Ampicillin-sulbactam or clindamycin or levofloxacin + metronidazole

Influenza › oseltamivir
PO transition: hemodynamically stable · clinically improving · tolerated PO
Prolonged antibiotics: cavitary · lung abscess · empyema · bacteremia · extrapulmonary infection · instability (persistent fever, abnormal vitals, hypoxia)
Caution: macrolides / FQ › QT prolongation

04

Health Care–Associated Infections

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Hand hygiene is the first and best antibiotic.

Isolation Precautions

Route	Pathogens	PPE
Airborne	measles	negative-pressure room · N95 mask
Contact	RSV · norovirus · C diff	single room · gloves & gown
Droplet	influenza · mumps · rubella · rhinovirus · parvovirus · pertussis · N meningitidis · GAS pneumonia	single room · face mask

HAP / VAP

≥48h hospitalization / intubation. S pneumoniae · MSSA · H influenzae · Pseudomonas · Stenotrophomonas.

MDR RF: recent IV antibiotics · septic shock · ARDS · ≥5d hospitalization · dialysis.

Rx: cefepime or piperacillin-tazobactam or levofloxacin or imipenem-cilastatin or meropenem ×7d.

MRSA RF › antipseudomonal β-lactam + vancomycin or linezolid.

Pseudomonas resistance › 2 antipseudomonal agents (β-lactam, ciprofloxacin/levofloxacin, aminoglycoside, colistin).

CAUTI

Remove catheter · URM · UCS ≥10³ CFU.

Symptomatic › antibiotics ×5–7d: PO ciprofloxacin/cotrimoxazole/co-amoxiclav · IV 3rd/4th gen cephalosporin · piperacillin-tazobactam · FQ · carbapenem.

Sepsis › IV 3rd/4th gen cephalosporin · piperacillin-tazobactam · carbapenem · FQ.

CLABSI

Fever · purulence · cellulitis › BCS (peripheral + central) · remove CVC + repeat BCS · IV antibiotics ×7–14d.

S aureus › echo · IV antibiotics ≥2–4 weeks
Coagulase-negative staph (S epidermidis) › IV antibiotics ×5–7d
Enterococcus › IV antibiotics ×7–14d
Gram −ive bacilli › IV antibiotics ×7–14d
Candida › fundoscopy (endophthalmitis) · antifungal ×14d after −ive BCS
Metastatic / deep-seated infection › IV antibiotics ×4–6 weeks
Repeat BCS until −ive

Needlestick Injury · Post-Exposure

Source & status	Action
HBV vaccine responder	No action
HBV non-responder + source HBsAg +ive	HBIG ×2 separated by 1 month
Anti-HBs <10 + HBsAg +ive	HBIG ×1 + revaccination + post-vacc testing
Unvaccinated + HBsAg +ive	HBIG ×1 + vaccination + post-vacc testing
HCV +ive / unknown	HCV RNA at 3–6 weeks & 4–6 months
HIV +ive / unknown	PEP ×4 weeks · testing at 6 weeks, 3 mo, 6 mo

1–2 weeks pre-op › MSSA/MRSA nasal swab +ive › intranasal mupirocin ×5d

05

Viral Infections

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Influenza

High fever · headache · fatigue · dry cough · sore throat · nasal congestion · rhinorrhea · myalgia.

Rx: oseltamivir 75mg PO BD ×5d (SE: N/V) · zanamivir inhaled · peramivir IV.

Testing indications: hospitalization + acute respiratory infection / acute worsening of chronic cardiopulmonary disease.

Treatment indications: hospitalization · severe · progressive · RF (age ≥65y, pregnant, 2wk postpartum, immunocompromised, comorbidities).

Outbreak › chemoprophylaxis (zanamivir/oseltamivir ×7d or baloxavir ×1) + vaccinate patients & HCPs.

Complications: influenza pneumonia · secondary bacterial pneumonia (S pneumoniae, S aureus).

Severe disease RF: immunosuppression · chronic pulmonary disease · age ≥65y · pregnancy · postpartum · DM · significant CVD/kidney/liver/heme disease · BMI ≥40 · NMD · LTCF resident.

Coronaviruses · SARS-CoV-2

Fever · fatigue · dry cough · GI symptoms · loss of taste/smell · multisystem inflammatory syndrome.

Testing: RAT · NAAT (symptomatic, close contact ≥5d). Re-infection ≤3 months › RAT.

MERS-CoV: pneumonia · diarrhea · AKI.

Severe disease RF: age ≥65y · pregnancy · immunocompromised · obesity · smoking · DM · heart disease · HTN · chronic lung disease · CP · intellectual disability · SCD · CKD · liver disease · mental health disorders.

Complications: ARDS · myocarditis · CM · cytokine storm · shock · AKI · thrombosis · multisystem inflammatory syndrome.

High risk (immunocompromised, unvaccinated pregnant, LTC, comorbidities) › nirmatrelvir-ritonavir 300/100mg BD ×5d or remdesivir 200mg IV ×1d then 100mg IV ×2d
Moderate (low-flow O₂) › dexamethasone 6mg PO OD ×10d + remdesivir › immunomodulators (tocilizumab, sarilumab, baricitinib, tofacitinib)
Severe (MV, ECMO) › dexamethasone + immunomodulators

mRNA vaccine › myocarditis · pericarditis · anaphylaxis · Bell’s palsy.

Primary VZV

Chickenpox

Fever · erythema + vesicles · pruritus.

Complications: impetigo · pneumonia · encephalitis · hepatitis.

HZV · Reactivation

Shingles

Dermatomal pain + vesicular rash. Age ≥50y › vaccine. Severe/recurrent/young › HIV testing.

≤72h › valacyclovir or famciclovir or acyclovir. Disseminated › IV + contact & airborne precautions.

Sight-threatening

Zoster Ophthalmicus

1st division trigeminal nerve › ophthalmology referral.

Cranial neuritis

Ramsay Hunt Syndrome

Herpes zoster oticus: vesicles in ears · diminished taste anterior 2/3 tongue · ipsilateral facial paralysis › ENT referral.

Postherpetic neuralgia

PHN

Gabapentin · pregabalin · TCAs · topical lidocaine · topical capsaicin.

EBV (Mononucleosis)

Severe fatigue · headache · sore throat · fever · posterior cervical LAD · splenomegaly · lymphocytosis.

Anti-VCA IgM · heterophile Ab (monospot).

Complications: aseptic meningitis · encephalitis · hepatitis · hemolytic anemia · thrombocytopenia · B-cell lymphoma · T-cell lymphoma · Hodgkin lymphoma · nasopharyngeal carcinoma.

Oral hairy leukoplakia › HIV testing. Ampicillin › morbilliform rash.

CMV in the Immunocompromised

CMV syndrome: fever · fatigue · malaise · neutropenia · atypical lymphocytosis · thrombocytopenia · elevated AST/ALT.

CMV end-organ disease: encephalitis · ventriculitis · myocarditis · pneumonitis · colitis · hepatitis · nephritis · pancreatitis · cystitis.

PCR · CMV IgM.

Pre-transplant › CMV IgG +ive or PCR › valganciclovir PO prophylaxis.

Immunocompromised / severe › ganciclovir IV or valganciclovir PO.

Mpox

Monkeypox

MSM · painful vesicular lesions · fever · painful LAD · respiratory symptoms.

PCR orthopoxvirus DNA. Severe/IC › tecovirimat · vaccinia immune globulin · cidofovir · brincidofovir.

HSV

Herpes Simplex

Grouped vesicles · erythematous base · painful.

Measles

Rubeola

High fever · rhinorrhea · cough · Koplik spots · conjunctivitis · diffuse macular rash.

PCR RNA · measles IgM.

Complications: otitis media · pneumonia · encephalitis · SSPE.

06

Infectious GI Syndromes

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Stool Workup Indications

Dysentery (mucoid/bloody diarrhea, fever, abdominal cramping, tenesmus) · sepsis · immunocompromised · hospitalization · T ≥38.3 ≥3d › empiric azithromycin. Severe › BCS.

Bacterial · Bloody

Campylobacter

Undercooked poultry. Fever · chills · watery diarrhea (occasionally bloody) · crampy abdominal pain.

Complications: GBS · IBS · intestinal perforation · GN · erythema nodosum · hemolytic anemia · reactive arthritis.

Severe › azithromycin or ciprofloxacin.

Bacterial · Dysentery

Shigella

Fecal-oral. Fever · abdominal cramps · tenesmus · bloody/mucus stools · vomiting.

Complications: HUS · reactive arthritis · erythema nodosum · GN · IBS.

Severe/IC › ciprofloxacin or azithromycin or ceftriaxone.

Bacterial

Salmonella

Poultry · eggs · milk · reptiles · amphibians. Fever · chills · watery diarrhea · cramps · myalgia.

Enteric (typhoid) fever: fever · abdominal pain · rash · hepatosplenomegaly · bradycardia › bone marrow / duodenal fluid CS.

Severe › ciprofloxacin · ceftriaxone · azithromycin · TMP-SMX · amoxicillin · ampicillin. SCD › osteomyelitis.

Severe RF: infants · age ≥50y + significant joint/valvular/endovascular/cardiac disease · IC · age ≥65y.

Bacterial · Watery

ETEC (Travelers')

Watery diarrhea · abdominal cramping. Supportive. Activity restriction › ciprofloxacin or azithromycin or rifaximin.

Bacterial · Bloody

EHEC / STEC

Beef · zoonotic. Bloody diarrhea · crampy abdominal pain › stool CS Shiga toxin.

Supportive. Complications: HUS.

Bacterial

Yersinia

Undercooked pork. Fever · diarrhea · RLQ pain · pharyngitis.

RF: iron overload states. Complications: reactive arthritis · hemolytic anemia · perforation · erythema nodosum.

Severe/IC › ciprofloxacin. Bacteremia/sepsis › ceftriaxone + gentamicin.

Bacterial

Vibrio

Undercooked shellfish. Bloody diarrhea · fever · vomiting · cramping.

Severe › doxycycline or ciprofloxacin or azithromycin. Septicemia › doxycycline + ceftriaxone.

Viral

Norovirus

Watery diarrhea · fever · vomiting › NAAT.

Parasite

Giardia

Watery diarrhea · cramping · nausea · steatorrhea · flatulence · weight loss.

EIA · NAAT · stool O&P. Rx: tinidazole or nitazoxanide or metronidazole.

Parasite

Cryptosporidium

Swimming pools. Watery diarrhea · cramping · malaise · weight loss.

Modified acid-fast stain · DFA · EIA · NAAT. Rx: nitazoxanide. HIV › effective ART.

Parasite

Amebiasis

Asymptomatic · dysentery · abdominal pain · fever · weight loss.

Rx: tinidazole or metronidazole then paromomycin or diloxanide. Complication: perforation.

Parasite

Cyclospora

Tropical/subtropical produce. Watery diarrhea · bloating · flatulence · weight loss · nausea · anorexia · crampy pain.

Rx: TMP-SMX.

Clostridioides difficile

Watery diarrhea · crampy abdominal pain · malaise · nausea · fever › stool toxin NAAT.

Rx: DC non-essential antibiotics & PPI + fidaxomicin 200mg PO BD ×10d or vancomycin 125mg PO QDS ×10d or metronidazole 500mg PO TDS ×10d.

RF: antibiotics · chemotherapy · older age · severe comorbidities · IBD · solid organ transplant · GI surgery · PPIs.

Contact isolation + handwashing (soap + water).

CT abdomen › colonic wall thickening · mucosal edema · fat stranding. Colonoscopy › pseudomembranes.

C diff Severity & Recurrence

Stage	Definition	Treatment
Severe	WBC ≥15 or Cr ≥133	fidaxomicin or vancomycin
Fulminant	sepsis · shock · ileus · perforation · toxic megacolon	vancomycin 500mg PO QDS + metronidazole 500mg IV TDS
Ileus	—	vancomycin 500mg PR QDS
1st relapse (≤3 mo)	—	fidaxomicin or vancomycin taper-pulse
≥2nd relapse	—	vancomycin taper-pulse · vanc + rifaximin · FMT

Severe RF: age ≥65y · immunosuppression · T >38 · albumin <30
Recurrence RF: recurrent CDI ≤6 months · age ≥65y · immunocompromised · severe CDI

07

Urinary Tract Infections

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Lower UTI

Cystitis

Dysuria · suprapubic pain · frequency · hematuria. URM (leukocytes, nitrites) · ≥10 leukocytes/μL + bacteriuria.

Rx: nitrofurantoin 200mg PO BD ×5d or TMP-SMX PO BD ×3d CI if received ≤3 months or fosfomycin 3g PO ×1.

Upper UTI

Pyelonephritis

Fever · chills · flank pain · N/V. UCS · BCS.

Outpt: ciprofloxacin ×7d or levofloxacin ×5d.

Inpt: ceftriaxone or cefepime or tazocin or carbapenem.

US/CT indications: persistent fever ≥72h · persistent bacteremia.

Perinephric abscess › percutaneous drainage.

Complicated

Complicated UTI

Male · pregnant · CAUTI · kidney disease · IC · obstruction · recent antibiotics.

UCS › ciprofloxacin 500mg PO OD ×7–10d or TMP-SMX PO BD ×7–14d or 3rd/4th gen cephalosporin or tazocin or FQ.

Sepsis

Urosepsis

3rd/4th gen cephalosporin · carbapenem · tazocin · FQ.

Pregnancy

UTI in Pregnancy

Nitrofurantoin (2nd/3rd trimester) · co-amoxiclav · cefpodoxime · cefixime · fosfomycin › UCS.

Recurrent

Recurrent UTI

≥3 UTIs ≤12 mo or ≥2 UTIs ≤6 mo. Options: postcoital prophylaxis · continuous prophylaxis · self-initiated therapy.

Asymptomatic Bacteriuria · Treat When

Pregnancy · invasive urologic procedure. Otherwise: do not treat.

08

Sexually Transmitted Infections

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STI PEP

MSM or transgender woman with bacterial STI ≤12 months › doxycycline 200mg ×1 within 72h.

Gonorrhea

Urine/swab NAAT › ceftriaxone 500mg IM ×1 + azithromycin 1g PO ×1 or doxycycline 100mg PO BD ×7d › TOC.

Male: urethral discharge · dysuria · urethral itch · testicular pain · rectal pain/proctitis. Complications: strictures · fistulas · epididymitis.
Female: vaginal/cervical discharge · low abdominal pain · dysuria · dyspareunia · rectal pain. Complications: PID · ectopic pregnancy · Fitz-Hugh-Curtis.
DGI: oligo/monoarthritis · dermatitis (peripheral necrotic pustules) · tendon sheath inflammation · endocarditis · meningitis. Synovial fluid CS · BCS · pustule swab NAAT.
Recurrent DGI › terminal complement deficiency (CH50).
Complicated › ceftriaxone 2g IM/IV OD + azithromycin 1g PO ×1.

Chlamydia

Urine/swab NAAT › azithromycin 1g PO ×1 or doxycycline 100mg PO BD ×7d CI: pregnancy.

LGV: painless genital ulcer · painful inguinal LAD › doxycycline 100mg PO BD ×21d.

TOC indications (4 weeks): LGV · unclear compliance · persistent symptoms · pregnancy · prepubertal.

Scrotal pain

Epididymitis

Chlamydia · gonorrhea › ceftriaxone + doxycycline.

Insertive anal › ceftriaxone + levofloxacin. Older male + r/o gonorrhea › levofloxacin.

Pelvic

PID

Uterine/adnexal tenderness · CMT · fever · mucopurulent cervical discharge.

Cervical swab NAAT · pregnancy test (ectopic).

Outpt: ceftriaxone + doxycycline + metronidazole ×14d or cefoxitin + probenecid + doxycycline + metronidazole ×14d.

Hospitalize: no improvement >48–72h · inability to tolerate PO · severe · pelvic abscess · pregnancy › IV ceftriaxone + doxycycline + metronidazole or cefotetan + doxycycline or cefoxitin + doxycycline. No improvement › US (TOA).

Syphilis

NTT (VDRL, RPR) + TT (immunoassays, TPPA, FTA-ABS) · HIV testing.

Primary: chancre › IM benzathine penicillin ×1
Secondary (2–8 wk): fever · rash · non-tender generalized LAD · mucous patches · condylomata lata › IM benzathine PCN ×1
Latent: +ive serology, no clinical signs. Early ≤1y › IM benzathine PCN ×1. Late >1y › weekly ×3
Tertiary: gummatous lesions · syphilitic aortic aneurysm · neurosyphilis (tabes dorsalis, syphilitic dementia)
Neurosyphilis: lymphocytic meningitis · ocular · otosyphilis › CSF lymph >5/μL · ↑CSF protein · +CSF VDRL › IV penicillin G ×10–14d
PCN allergy › doxycycline or ceftriaxone

NTT −ive: previously treated · primary · late latent · tertiary. TT +ive indefinitely.

LP indications: neuro symptoms · inadequate serologic response · tertiary.

Argyll Robertson pupils: small, no reaction to light, intact accommodation.

Tabes dorsalis: dorsal column (vibration, proprioception) · dorsal roots (hyporeflexia)
Jarisch-Herxheimer reaction: acute febrile illness ≤24h treatment

HSV (Genital)

Multiple vesicular lesions · erythematous base › NAAT.

Primary: regional LAD · fever · malaise › acyclovir or famciclovir or valacyclovir ×7–10d
Oral: gingivostomatitis · pharyngitis › herpes labialis
Genital: HSV-2 most common
Complications: keratitis · encephalitis
HIV + HSV: extensive oral/perianal ulcers · esophagitis · colitis · chorioretinitis · acute retinal necrosis · tracheobronchitis · pneumonia
Recurrent: episodic self-start vs long-term suppressive

HPV

Genital Warts

Condyloma acuminata. Podophyllotoxin · imiquimod · trichloroacetic acid · cryotherapy · surgical removal.

HPV vaccine.

Recurrent NGU

Mycoplasma genitalium

Recurrent nongonococcal urethritis / cervicitis › NAAT › doxycycline 100mg BD ×7d then moxifloxacin/azithromycin.

Painful ulcer

Chancroid

Deep · exudative · painful genital ulcers · tender inguinal LN.

09

Skin & Soft Tissue Infections

▾

BCS Indications in SSTI

Systemic toxicity · immunocompromised · malignancy · animal bites · immersion injuries.

Surface Infections

Type	Features
Erysipelas	Brightly erythematous · distinct elevated borders · fever · lymphangitis · regional LAD
Cellulitis	Deeper dermis + SC fat · less distinct borders. RF: lymphedema · tinea pedis · chronic venous insufficiency
Impetigo	β-hemolytic Strep · Staph › honey-colored crusted pustules
Folliculitis	Erythematous papules/pustules · trunk · axillae · buttocks › topical mupirocin/clindamycin/retapamulin. S aureus, Pseudomonas (hot tub)

Saltwater · Cirrhotic

Vibrio vulnificus

Sepsis · cellulitis · hemorrhagic bullae. Saltwater exposure · seafood consumption · cirrhosis.

Rx: 3rd gen cephalosporin (ceftazidime, ceftriaxone, cefotaxime) + doxycycline.

Cat scratch

Bartonella henselae

Cat scratch/lick/bite. Vesicular/papular lesions · LAD · nodular lymphangitis.

Rat bite

Streptobacillus moniliformis

Rat bite/scratch. Fever · vomiting · headache · myalgia · maculopapular/hemorrhagic/purpuric rash · polyarticular arthritis.

Fish tank

Mycobacterium marinum

Chronic · nodular · distal extremities. Fish tanks · marine environments.

Gardening

Sporotrichosis

Chronic · nodular · distal extremities. Plants/soil.

Dog bite · Asplenia

Capnocytophaga canimorsus

Sepsis · dog bite · asplenia.

Neutropenic

Pseudomonas

Ecthyma gangrenosum: ≥1 necrotic ulcer with erythematous border/halo.

Bites

Human/animal bite › co-amoxiclav
Human › tetanus vaccine. Hand › surgical evaluation
Animal › tetanus + rabies vaccine
Severe › β-lactam/ampicillin-sulbactam/tazocin · carbapenem · ceftriaxone · FQ + clindamycin/metronidazole

Furuncle · carbuncle · abscess › I&D + CS
Mild/moderate › TMP/SMX or doxycycline; MRSA › TMP/SMX; MSSA › cephalexin
Severe › IV vancomycin · linezolid · daptomycin · telavancin · ceftaroline. MRSA › vancomycin; MSSA › cefazolin
Recurrent MRSA › decolonization (topical intranasal mupirocin + chlorhexidine washes + bleach baths) + decontamination of personal items

Mild › PO penicillin · cephalexin · dicloxacillin · clindamycin ×5d
Moderate/severe › IV penicillin · ceftriaxone · cefazolin · clindamycin ×5d
Limited impetigo › topical mupirocin

IV vancomycin

Necrotizing Fasciitis

Erythema · systemic toxicity · gangrene/anesthesia · hard induration · hemorrhagic bullae · pain out of proportion.

Emergent surgical debridement + carbapenem/tazocin + vancomycin/daptomycin + clindamycin.

Type 2 (GAS): younger · minor trauma/bruise › penicillin + clindamycin
Type 1 (polymicrobial): older · DM · pelvic wounds › tazocin + vancomycin or carbapenem
Aeromonas hydrophila: freshwater › ciprofloxacin/ceftriaxone + doxycycline
XR › SC gas

Clostridial Myonecrosis (Gas Gangrene)

Trauma-associated wounds · colonic neoplasms. Abrupt-onset severe pain · violaceous discoloration · rapid progression · bullae · crepitus · shock · MOF.

Toxic Shock Syndrome

Type	Setting	Features	Treatment
Staph TSS	Tampons · nasal packings · surgical wounds · skin ulcers · burns · catheters · IVDU	T ≥39 · SBP <90 · diffuse macular rash + desquamation · dysfunction ≥3 organ systems	MSSA: nafcillin/cefazolin + clindamycin; MRSA: vancomycin + clindamycin
Strep TSS	Necrotizing fasciitis · GAS sterile site	SBP ≤90 · ≥2 findings (AKI, ↑LFTs, macular rash/soft tissue necrosis, coagulopathy/thrombocytopenia/DIC, ARDS)	Penicillin + clindamycin

Invasive GAS chemoprophylaxis: cephalexin/clindamycin ×10d
TSS general: IVF + clindamycin/linezolid

Diabetic Foot Infections

Purulent discharge · warmth · tenderness · swelling › XR (soft tissue gas, foreign body, bony involvement) · CS (deep tissue curettage, biopsy) · ABI › foot care · glycemic control.

Mild (erythema <2cm beyond ulcer) › PO cephalexin/dicloxacillin/coamoxiclav/clindamycin
Purulent / MRSA RF › PO doxycycline/cotrimoxazole + β-lactam
Moderate (erythema ≥2cm, deeper than skin + SC) › IV β-lactam / carbapenem / metronidazole + FQ / 3rd gen cephalosporin + anti-MRSA (vancomycin, daptomycin, linezolid)
Severe: fever · tachycardia · tachypnea · leukocytosis · hypotension
Surgical consult: debridement · resection · amputation · revascularization
Macerated wounds / previous antibiotics › antipseudomonal therapy
Osteomyelitis RF: exposed bone · large (>2cm) · chronic (>6 wk) › XR

10

Osteomyelitis

▾

Clinical & Workup

Pain over affected bone. RF: DM · chronic illness · IVDU.

Monomicrobial: hematogenous. Polymicrobial: SSTI · trauma · surgery.

BCS · CRP · bone biopsy · XR · MRI/CT.

Necrosis › debridement.

Empiric: ceftriaxone ± vancomycin (MRSA RF) ± metronidazole (sacral) ×4–6 weeks.

Stable + chronic › bone biopsy CS › antibiotics. Prosthetic › surgical removal + anti-staph + rifampin.

Site-Specific Organisms

Site / Setting	Organisms
Pott disease (vertebral)	TB
Foot	Pseudomonas
Sternal	S aureus
Sternoclavicular	S aureus · Pseudomonas · IVDU
SCD	Salmonella · S aureus
Foreign body / prosthetic	S aureus · coagulase-neg Staph · Cutibacterium acnes
DM	Strep · Gram −ive bacilli · anaerobes
Immunocompromised	Candida · Aspergillus · Mycobacterium

Vertebral Osteomyelitis

New/worsening back pain · fever › MRI › vancomycin/daptomycin + ceftriaxone/ceftazidime/cefepime/FQ. Usually S aureus.

Surgery indications: neurologic deficits · spinal cord compression · spinal instability · progression/recurrence.

RF: elderly · IC · IVDU · PICC/Ports · HD · previous spinal surgery · degenerative disease.

Empiric antibiotics indications: severe sepsis · progressive neuro deficit · spinal instability · epidural abscess.

11

HIV/AIDS

▾

Screening & Diagnosis

Annual screening for high-risk: rapid test › EIA HIV Ab, HIV p24 Ag › HIV-1 Ab, HIV-2 Ab / NAAT.

Acute HIV: HIV Ab/Ag +ive · HIV-1/2 −ive · NAAT +ive.

Acute symptoms: fever · night sweats · LAD · headache · malaise · weight loss · pharyngitis · rash.

Initial Workup

CD4 count · viral load (RNA) · genotype viral resistance.

Co-infections: TB (TST/IGRA, CXR) · CMV IgG · toxoplasma IgG · HBV/HCV · measles · varicella.

STIs: syphilis · chlamydia · gonorrhea · HPV (cervical/anal cancer).

Immunizations: HAV · HBV · annual influenza · COVID · HPV · pneumococcal · Hib · meningococcal · RSV · HZV. Avoid live vaccines if CD4 <200.

ART Regimens

2 NRTIs + INSTI / NNRTI / PI.

PrEP naive › bictegravir + tenofovir + emtricitabine · dolutegravir + tenofovir + emtricitabine/lamivudine
PrEP history › darunavir + tenofovir + emtricitabine/lamivudine
TDF CI: CKD · osteopenia
Abacavir CI: CVD · HLA-B*57:01 (hypersensitivity)

IRIS is a paradoxical worsening of preexisting infection after ART start — treat the underlying infection, with glucocorticoids and/or NSAIDs if needed.

Opportunistic Infections by CD4

CD4	Conditions
200–500	Candidiasis · recurrent HSV / VZV · oral hairy leukoplakia (EBV) · Kaposi’s sarcoma (HHV-8) · sinusitis · bacterial pneumonia · cervical dysplasia · CVD · CVA · CKD · psoriasis · seborrheic dermatitis · molluscum · bacillary angiomatosis (Bartonella) · ITP
<200	HIV myelopathy · visceral KS · endemic fungi · aspergillosis · cryptococcus · PJP · malignancy (NHL, HL, anal/liver/cervical/vulvar)
<100	Toxoplasmosis · PML · cryptococcal meningoencephalitis
<50	CMV (retinitis, colitis) · MAC · CNS lymphoma · HAND

CD4 <200

PJP Pneumonia

Gradual onset · dry cough · progressive dyspnea · desaturation with ambulation · pneumothorax.

CXR: diffuse bilateral interstitial infiltrates.

Rx: TMP-SMX 15–20mg/kg IV ×21d.

Severe (PaO₂ <70 or A-a gradient ≥35) › prednisone 40mg PO BD ×5d then 20mg BD ×5d then 20mg OD ×11d.

CD4 <200 › TMP-SMX or dapsone prophylaxis until CD4 ≥200 ≥3 mo.

CD4 <100

Toxoplasmosis

Encephalitis · chorioretinitis · pneumonitis · focal neurologic syndrome · mono-like syndrome.

MRI › multiple ring-enhancing lesions.

Rx: sulfadiazine + pyrimethamine + folic acid. Ongoing clinical/radiographic disease › chronic maintenance.

CD4 <100 + toxo IgG +ive › prophylaxis (TMP-SMX · dapsone + pyrimethamine).

CD4 <100

Cryptococcal Meningoencephalitis

Subacute · fever · malaise · headache · nuchal rigidity · photophobia · vomiting · confusion · lethargy.

CSF leukocytes <50 (mononuclear) · mildly elevated protein · normal/low glucose.

CD4 <50

MAC

Lymphadenitis › clarithromycin + azithromycin or clarithromycin ×12 months.

Esophagitis

Esophageal Candidiasis

Retrosternal burning · odynophagia › PO fluconazole.

JC virus

PML

Confusion · neurologic · visual symptoms.

CSF JC virus › brain biopsy. MRI › nonenhancing hypodense white matter lesions.

CD4 <50

CNS Lymphoma

Brain biopsy. MRI › solitary lesion in periventricular/periependymal area or corpus callosum.

Latent TB in HIV

TST ≥5 mm or +ive IGRA › isoniazid + rifampin ×3 months.

HIV in Pregnancy

Use TMP-SMX for PJP prophylaxis as indicated.

Suppressed VL › infant IV zidovudine ×4 wk
VL >1000 near delivery › IV zidovudine · infant 3-drug ART
Avoid breastfeeding

PrEP & PEP

PrEP: emtricitabine + TDF OD or cabotegravir. Testing: HIV Ag/Ab · HBV · HCV · STIs · RFT
PEP: tenofovir + emtricitabine/lamivudine + bictegravir/dolutegravir ≤72h ×28d. Testing: HIV at 4–6 wk + 3 mo

10-yr ASCVD risk >20% › high-intensity statin
10-yr ASCVD risk 5–20% › moderate-intensity statin

12

Infectious Arthritis

▾

Clinical & Workup

Pain · limited joint movement · swelling · warmth · erythema · fever · constitutional symptoms · monoarthritis · hip · knee.

Pathogens: S aureus · Salmonella (SCD) · zika · dengue · chikungunya.

Arthrocentesis: synovial fluid Gram stain & CS · cell count (WBC >50) · crystal exam (polarized light microscopy).

MRI › synovial enhancement · joint effusion.

RF: alcohol use · DM · CKD · cancer · prosthetic joints · age >80y or <5y · SCD (encapsulated orgs) · hypogammaglobulinemia (Mycoplasma) · complement deficiencies (Neisseria).

Empiric Antibiotics

Vancomycin or vancomycin + 3rd gen cephalosporin or vancomycin + antipseudomonal
MRSA › vancomycin; MSSA › nafcillin or cefazolin
Enteric Gram −ive bacilli › 3rd gen cephalosporin (ceftriaxone, cefotaxime)
Pseudomonas › ceftazidime, cefepime, tazocin

Joint drainage · ortho consult (washout). Prosthetic › device removal › antibiotics › new device.

DGI

Gonococcal Arthritis

Tenosynovitis · vesiculopustular skin lesions · migratory polyarthralgias › IV ceftriaxone.

Arthritis-dermatitis syndrome: cutaneous lesions (papules/macules › pustules) · tenosynovitis · polyarthralgia · fever · chills › NAAT genital/rectal/pharyngeal.

Purulent gonococcal: no systemic features/dermatitis › synovial fluid CS.

Spirochete

Lyme Arthritis

>6 months post infection · oligoarthritis · synovitis · swelling · erythema · knee.

Synovial fluid PCR › PO doxycycline/amoxicillin ×28d › IV ceftriaxone ×2–4 weeks.

Gram −

Gram-Negative Arthritis

Prosthetic joints · older · IC · postop · IV catheters · IVDU.

Fungal

Fungal Arthritis

Subacute monoarthritis · systemic fungal infection › synovial biopsy.

Rx: amphotericin B or echinocandin or azoles.

Mycobacterial

TB Arthritis

Synovial biopsy is diagnostic.

13

Tuberculosis

▾

Latent TB

TST ≥15mm (affected by BCG) · IGRA. May be −ive in immunocompromised.

Rx: rifampin + isoniazid ×3 months · rifampin ×4 months · isoniazid ×9 months.

Screening indications: high TB prevalence · congregate settings · immunocompromised · TNF-α inhibitors.

TST Cutoffs

Threshold	Population
≥5mm	HIV · contact active TB ≤2y · CXR fibronodular disease · immunosuppressive drugs · CKD stage 4/5
≥10mm	Arrival high-prevalence countries <5y · substance use disorder · high-risk congregate settings · age <5y · high risk for active TB
≥15mm	General population (no specific RF)

Active TB

CXR · sputum AFB ×3 · TB sputum/tissue culture.

Rx: rifampin + isoniazid + pyrazinamide + ethambutol ×2 months then rifampin + isoniazid ×4 months. Alternative: moxifloxacin + rifapentine + isoniazid + pyrazinamide ×8 weeks then moxifloxacin + rifapentine + isoniazid ×9 weeks.

AFB +ive › NAAT to exclude nontuberculous mycobacteria. Airborne isolation.

Pulmonary: cough · chest pain · hemoptysis · fever · chills · night sweats · weight loss
Pleural TB › thoracentesis −ive › pleural biopsy −ive › pleural fluid adenosine deaminase
TB meningitis: CSF lymphocytic pleocytosis · ↑protein · ↓glucose · NAAT
Meningitis / pericarditis › steroids
Pregnancy › rifampin + isoniazid + ethambutol
Non-infectious: TB treatment >2 weeks · symptom improvement · AFB ×3 −ive

TB Drug Side Effects

Drug	Side effects
Isoniazid	Hepatotoxicity · peripheral neuropathy · rash. Add pyridoxine to prevent neuropathy.
Rifampin	Drug interactions · rash · hepatotoxicity
Pyrazinamide	Hepatitis · rash · arthralgia
Ethambutol	Optic neuritis · rash › visual acuity + color vision testing

14

Nontuberculous Mycobacterial Infections

▾

Species: M avium complex (MAC) · M kansasii · M xenopi · M abscessus

AIDS · CD4 <50

MAC

Fever · night sweats · weight loss · GI symptoms · lymphadenitis.

Rx: azithromycin + ethambutol + rifampin/rifabutin.

Endocarditis · Outbreak

M chimaera

Hospital-acquired prosthetic valve endocarditis.

SSTI

Rapid Growers

M chelonae · M fortuitum · M abscessus.

Nodular cutaneous lesions › ulcerate · recurrent abscesses · chronic discharging sinuses · nodular lymphangitis.

Pulmonary NTM Diagnosis

Clinical (cough · dyspnea · weight loss · fatigue) + radiologic (CXR nodular/cavitary · CT bronchiectasis) + ≥2 sputum culture / BAL culture / biopsy.

Rx: 3 drugs › macrolide + ethambutol ± rifampicin ± aminoglycoside.

NTM can cause false +ive TST.

15

Travel Medicine

▾

Fever in the Returning Traveller

Differential: malaria · typhoid/enteric fever · dengue · chikungunya · Zika · viral hepatitides · rickettsioses · brucellosis · leptospirosis · Q-fever · Ebola · STIs · acute HIV.

Initial workup: malaria thick + thin smears ×3 (over 24h) · stool C&S · stool O&P · C diff · dengue PCR/serology · chikungunya PCR/serology · Zika PCR/serology · hepatitis serology · HIV · STI screen · viral PCR swab (SARS-CoV-2, influenza).

Malaria

Cyclical rigors · fever · drenching sweats · headache · myalgia · GI symptoms · anemia · thrombocytopenia · splenomegaly · ↑ALT/AST.

Geography: Sub-Saharan Africa · Asia · Central/South America · Caribbean.

Species: P falciparum (severe) · P ovale · P vivax · P malariae · P knowlesi (severe) · P simium.

Dx: thick + thin blood smear ×3 (over 24h).

P falciparum › atovaquone-proguanil or artemether-lumefantrine or quinine + doxycycline/clindamycin/tetracycline
Non-falciparum › chloroquine/hydroxychloroquine or atovaquone-proguanil or quinine + doxycycline
P ovale / P vivax › add primaquine (CI: G6PD) for hypnozoite eradication

§ Severe Malaria

Criteria: hyperparasitemia >10% · altered mental status · prostration · seizures · Hb <7 · pulmonary edema · jaundice · significant bleeding · metabolic acidosis (HCO₃ <15, lactate ≥5) · AKI (Cr >265, urea >20) · glucose <2.2.

Rx: ICU › IV artesunate ×48h then PO follow-on therapy.

Blackwater fever: DIC · jaundice · hemoglobinuria.

§ Malaria Chemoprophylaxis

Atovaquone-proguanil (CI: CrCl <30)
Doxycycline
Mefloquine — preferred in pregnancy
Primaquine
Chloroquine / hydroxychloroquine — safe in pregnancy
Tafenoquine (CI: G6PD)

Arbovirus · Avoid NSAIDs

Dengue

Biphasic fever · chills · frontal headache · retro-orbital pain · severe myalgia/arthralgia · lumbosacral pain · extensor surface petechiae · thrombocytopenia · leukopenia · ↑ALT/AST.

Dx: RT-PCR · viral antigen · serology. Rx: supportive · avoid NSAIDs.

Severe: hemorrhagic fever · shock · encephalopathy · liver failure · myocarditis.

Arbovirus · Chronic arthralgia

Chikungunya

Fever · rigors · maculopapular rash · small joint polyarthralgia · relapsing/chronic arthralgia for months–years · leukopenia · ↑ALT/AST.

Dx: RT-PCR · serology. Rx: supportive.

Arbovirus · Teratogenic

Zika Virus

Fever · rash · arthralgia · conjunctivitis · GBS · meningoencephalitis · myelitis · fetal malformation.

Dx: RT-PCR (serum, urine) · NAAT · IgM. Rx: supportive.

Enteric Fever (Typhoid — S typhi / paratyphi)

Prolonged fever · headache · arthralgia · myalgia · pharyngitis · anorexia · rose spots · diarrhea/constipation · abdominal pain · relative bradycardia · hepatosplenomegaly · leukopenia · anemia · thrombocytopenia · ↑ALT/AST.

Dx: blood/stool/urine/skin/bone marrow culture. Rx: IV ceftriaxone or ciprofloxacin or azithromycin.

Complications: bacteremia (empyema, muscle abscess, endovascular) · intestinal hemorrhage/perforation · encephalopathy.

Rickettsial Infections

Fever · headache · malaise · conjunctivitis · pharyngitis · maculopapular/vesicular/petechial rash · eschar + regional lymphadenopathy.

Syndromes: African tick-bite fever · Mediterranean spotted fever · scrub typhus.

Dx: serology · PCR. Rx: doxycycline ×5–7d.

Complications: shock · meningoencephalitis · organ damage.

Brucellosis

Fever · myalgia · arthralgia · fatigue · headache · night sweats · hepatosplenomegaly · peripheral arthritis · sacroiliitis · spondylitis · ↑ALT/AST · anemia · leukopenia/leukocytosis.

Exposure: unpasteurized dairy · undercooked meat · infected animals. Endemic in Mediterranean, Balkans, Persian Gulf, Middle East, Central/South America.

Dx: blood/bone marrow/body fluids/tissue culture · Brucella Ab doubling. Rx: doxycycline + rifampin/gentamicin.

Neurobrucellosis › ceftriaxone + doxycycline + rifampin.

Yellow Fever & Travelers' Diarrhea

Yellow fever: fever · malaise · headache · acute hepatitis (nausea, vomiting, epigastric pain, jaundice) · kidney injury · coagulopathy · shock. Dx: RT-PCR · IgM. Endemic in sub-Saharan Africa and tropical South America. Vaccination required for travelers.

Travelers' diarrhea (ETEC): fluid replacement. Prophylaxis (immunocompromised, IBD) › bismuth. Moderate/severe › azithromycin or rifaximin or ciprofloxacin.

16

Fever of Unknown Origin

▾

Definition

T >38.3°C ≥3 weeks, undiagnosed after 2 outpatient visits or 3 days inpatient.

Differential

IE · TB · abscess · neoplasm · complicated UTI · CTD · hyperthyroidism · subacute thyroiditis · drug fever · septic thrombophlebitis · PE · C diff · aspergillosis · candidiasis · allograft rejection · HIV-associated (CMV, cryptococcosis, MAC, toxoplasmosis, lymphoma, IRIS).

Standard Workup

BCS · CBC · RFT · LFT · ESR · URM · TB workup · HIV · TSH · ANA · hepatitis serology · RF · CXR · echo.

Leptospirosis

Fever · myalgia · conjunctivitis · cytopenias · hypokalemia · sterile pyuria.

Exposure: animal waste (soil, water).

Rx (mild): doxycycline · azithromycin.

Weil's disease (severe): jaundice · AKI · ARDS · pulmonary hemorrhage › IV ceftriaxone or penicillin or doxycycline.

17

Tick-Borne Diseases

▾

Lyme Disease (Borrelia burgdorferi)

Erythema migrans · flu-like illness · arthritis. Endemic in Northeast / mid-Atlantic / Midwest US.

Dx: serology · PCR. Testing not needed if EM + tick exposure.

Rx: doxycycline or amoxicillin or cefuroxime.

Carditis (heart block, myocarditis, pericarditis) › IV ceftriaxone
Neuroborreliosis (CN palsy, meningitis, radiculopathy, encephalopathy, peripheral neuropathy) › IV ceftriaxone
Prophylaxis: tick exposure in endemic area + blacklegged deer tick + attached ≥36h › doxycycline 200mg ×1 within ≤72h

Babesiosis

~1 month post tick bite · fever · fatigue · chills · headache · myalgia · cough · jaundice · hepatosplenomegaly · hemolytic anemia · thrombocytopenia · ↑ALT/AST · AKI. Endemic in Northeast + upper Midwest US.

Dx: PCR · serology · PBS › intra-erythrocytic tetrad (Maltese cross).

Rx: atovaquone + azithromycin ×7–10d. Severe › exchange transfusion.

Ehrlichiosis & Anaplasmosis

Ehrlichiosis (Lone Star tick) & Anaplasmosis (blacklegged deer tick).

Fever · headache · myalgia · AKI · ARDS · meningoencephalitis · ↑AST/ALT · leukopenia · thrombocytopenia.

Dx: PCR · serology · PBS › morulae. Rx: doxycycline.

Rocky Mountain Spotted Fever (Rickettsia rickettsii)

Fever · nausea · myalgia · dyspnea · cough · headache · macular › petechial rash (ankles, wrists, palms, soles › central) · thrombocytopenia · ↑ALT/AST.

Dx: PCR. Rx: doxycycline. Pregnancy › chloramphenicol.

Doxycycline is the empiric answer for almost every tick-borne illness — including children. The traditional concern about tooth staining does not apply to short courses.

18

Fungal Infections

▾

Candidemia

RF: broad-spectrum antibiotics · ICU admission · CVC · TPN · neutropenia · immunosuppressive drugs · intra-abdominal surgery · necrotizing pancreatitis · Candida colonization at ≥3 sites.

Workup: TTE (IE) · fundoscopy (endophthalmitis).

Rx: echinocandin + intravascular device removal.

Pregnancy › amphotericin B
CNS / eye › amphotericin B

Asthma · Hypersensitivity

ABPA

↑IgE · asthma · brown sputum · eosinophilia · bronchiectasis.

Rx: inhaled / PO steroids.

Fungal ball · Pre-existing cavity

Aspergilloma

Cough · hemoptysis · dyspnea · weight loss · fever · chest pain.

Rx: surgical resection ± antifungal. Multiple › antifungal ×6 months.

Immunocompromised

Invasive Aspergillosis

Neutropenia · organ transplant · hematologic malignancy. Cough · fever · hemoptysis · pleuritic chest pain.

Dx: serum/sputum galactomannan · BAL PCR · tissue biopsy. CT chest › halo sign.

Rx: voriconazole ± echinocandin ×≥6 weeks.

Cryptococcal Meningitis

AIDS with CD4 <100 · headache · fever · malaise · nuchal rigidity · photophobia · vomiting · confusion · lethargy (subacute course).

Dx: CSF cryptococcal antigen · CSF culture · serum cryptococcal Ag. LP › elevated opening pressure.

Rx: liposomal amphotericin B + flucytosine › fluconazole ≥1y.

Endemic Mycoses

Organism	Geography	Clinical	Rx
Blastomyces	Midwestern / SE / south central US	Skin lesion · pneumonia · skin/joint infections	Itraconazole ×6–12mo; severe › ampho B
Coccidioides	Southern Arizona · south central CA · SW New Mexico · west Texas	Erythema nodosum · erythema multiforme · pneumonia · meningitis	Fluconazole
Histoplasma	Midwestern US	Pneumonia	Itraconazole; severe › ampho B

Cutaneous · Lymphocutaneous

Sporotrichosis

Papules along lymphatic channels. Exposure: landscaping · gardening.

EMERGENCY · Surgical

Mucormycosis

RF: poorly controlled DM · hematologic malignancies · iron overload · HSCT.

Rhino-orbital-cerebral infection.

Rx: urgent surgical debridement + amphotericin B.

Endemic mycoses follow geography, and geography follows the patient. Always ask where someone has lived — not just where they have travelled.

A study guide to infectious diseases.

CSF Profiles by Etiology

S pneumoniae

N meningitidis

H influenzae

L monocytogenes

HSV Encephalitis

Anti-NMDAR Encephalitis

West Nile Neuroinvasive

PML

Neurocysticercosis

Spinal Epidural Abscess

Pathogen-Directed Therapy

Common Bacterial

Legionella pneumophila

Mycoplasma pneumoniae

Chlamydia pneumoniae

Animal Exposure → Pathogen

Isolation Precautions

Needlestick Injury · Post-Exposure

Chickenpox

Shingles

Zoster Ophthalmicus

Ramsay Hunt Syndrome

PHN

Monkeypox

Herpes Simplex

Rubeola

Campylobacter

Shigella

Salmonella

ETEC (Travelers')

EHEC / STEC

Yersinia

Vibrio

Norovirus

Giardia

Cryptosporidium

Amebiasis

Cyclospora

C diff Severity & Recurrence

Cystitis

Pyelonephritis

Complicated UTI

Urosepsis

UTI in Pregnancy

Recurrent UTI

Epididymitis

PID

Genital Warts

Mycoplasma genitalium

Chancroid

Surface Infections

Vibrio vulnificus

Bartonella henselae

Streptobacillus moniliformis

Mycobacterium marinum

Sporotrichosis

Capnocytophaga canimorsus

Pseudomonas

Toxic Shock Syndrome

Site-Specific Organisms

Opportunistic Infections by CD4

PJP Pneumonia

Toxoplasmosis

Cryptococcal Meningoencephalitis

MAC

Esophageal Candidiasis

PML

CNS Lymphoma

Gonococcal Arthritis

Lyme Arthritis

Gram-Negative Arthritis

Fungal Arthritis

TB Arthritis

TST Cutoffs

TB Drug Side Effects

MAC

M chimaera