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MI6.1-3 | CNS Infections — Meningitis & Encephalitis — SDL Guide (Part 2)

Reading and Interpreting CSF Gram Stain (MI6.3)

The CSF Gram stain is the most immediately actionable bedside diagnostic tool in meningitis. Systematic reading:

Procedure for CSF Gram stain:
1. Centrifuge CSF at 3000 rpm × 10 min to concentrate organisms.
2. Use the sediment for smear preparation; air dry, heat fix.
3. Perform Gram stain as standard (see staining practical module).
4. Examine under oil immersion (×1000) — scan at least 30 fields.

CSF Gram stain interpretation — organism-specific patterns:

Gram stain finding	Likely organism	Empiric treatment
Gram-negative diplococci (intracellular, kidney-shaped)	Neisseria meningitidis	Benzyl penicillin OR ceftriaxone
Gram-positive diplococci (lancet-shaped, encapsulated)	Streptococcus pneumoniae	Ceftriaxone + dexamethasone
Gram-positive rods	Listeria monocytogenes	Ampicillin
Gram-positive cocci in clusters	Staphylococcus aureus (post-neurosurgery)	Vancomycin
Gram-negative rods (neonates, elderly, immunocompromised)	E. coli, Klebsiella	Ceftriaxone + gentamicin
Gram-negative coccobacilli	Haemophilus influenzae	Ceftriaxone
No organisms seen; lymphocytic, low glucose	TBM suspected	ZN stain, GeneXpert, ADA

Educational diagram showing intracellular Gram-negative diplococci of Neisseria meningitidis in a neutrophil, CSF Gram-stain sensitivity ranges, and urgent meningitis treatment workflow. — **Panel A:** CSF Gram-stain field showing neutrophil, multilobed nucleus, intracellular Gram-negative kidney-bean diplococci, paired cocci arrangement, and clear capsule haloes of Neisseria meningitidis.. **Panel B:** Bar chart of CSF Gram-stain sensitivity: S. pneumoniae 90-95%, N. meningitidis 75-90%, Gram-negative rods 50-80%, Listeria 33-50%, with antibiotic pretreatment warning.. **Panel C:** Clinical workflow for suspected bacterial meningitis: raised ICP assessment, blood cultures, immediate ceftriaxone, CT before LP, CSF Gram stain/culture, organism identification, and MIC-guided therapy..

Sensitivity of CSF Gram stain by organism:
• S. pneumoniae: 90-95% in untreated cases
• N. meningitidis: 75-90%
• Gram-negative rods: 50-80%
• Listeria: 33-50%
• After antibiotic pretreatment: sensitivity drops significantly — cultures may become negative within hours

Reporting a CSF culture result:
• Positive culture: organism name, colony morphology, biochemical profile, antibiotic sensitivity profile (MIC)
• Negative culture with positive Gram stain: may indicate antibiotic pretreatment, fastidious or slow-growing organisms (Mycobacterium, viruses)
• For TBM: report AFB count per NTEP grading; note colony growth time on culture

CLINICAL PEARL

In suspected bacterial meningitis, do not delay antibiotics to wait for LP results if the patient shows signs of raised ICP (papilloedema, focal neurological signs, GCS <10). In such cases, take blood cultures, start empiric ceftriaxone immediately, then arrange CT head before LP. Every 30-minute delay in antibiotic therapy in bacterial meningitis increases mortality by approximately 5%. The Gram stain sensitivity drops significantly once antibiotics are given — but antibiotic sterilises CSF cultures within 2-4 hours; the biochemical profile (cells, protein, glucose) persists and guides diagnosis.

Encephalitis — Causes, Pathogenesis, and Diagnosis

Encephalitis = inflammation of the brain parenchyma (not just meninges). Often combined with meningeal involvement (meningoencephalitis).

Key distinction from meningitis:
• Meningitis — meningeal signs dominant (neck stiffness, Kernig's, Brudzinski's)
• Encephalitis — altered consciousness, seizures, focal deficits, behavioural changes

Major viral causes of encephalitis:

Virus	Transmission	Key feature	India context
Herpes simplex virus 1 (HSV-1)	Reactivation via trigeminal nerve	Temporal lobe involvement (limbic encephalitis); haemorrhagic necrosis; treat with aciclovir	Sporadic; commonest treatable cause worldwide
Japanese encephalitis virus (JEV)	Culex mosquito bite	Acute encephalitis; thalamic lesions on MRI; CSF — lymphocytic, mildly elevated protein, normal glucose	Endemic India (UP, Bihar, Assam, Odisha); seasonal (monsoon/post-monsoon); JE vaccine national program
Nipah virus	Bats → infected pigs/humans; human-to-human spread	Acute encephalitis with respiratory involvement; high mortality (40-70%); BSL-4 pathogen	Kerala outbreaks 2018, 2019, 2023
Rabies virus	Dog/bat bite	Furious or paralytic form; Negri bodies in Purkinje cells; universally fatal once symptomatic	India: 36% of global rabies deaths
Enteroviruses	Faecal-oral	Enterovirus 71 — hand, foot, mouth disease + brainstem encephalitis	Epidemic in India
West Nile Virus	Culex mosquito	Meningoencephalitis; flaccid paralysis	Cases in Kerala, Karnataka

Bacterial encephalitis:
• Listeria monocytogenes — brainstem encephalitis (rhombencephalitis)
• Mycobacterium tuberculosis — tuberculous encephalitis
• Rickettsia — scrub typhus (leading cause of febrile encephalitis in South India)

Parasitic:
• Plasmodium falciparum — cerebral malaria (sequestration of parasitised RBCs in cerebral capillaries)
• Trypanosoma brucei — sleeping sickness (not endemic in India but global context)
• Toxoplasma gondii — ring-enhancing lesions in HIV/AIDS

Three-panel brain MRI schematic comparing HSV encephalitis temporal lobe hyperintensity, Japanese encephalitis bilateral thalamic lesions, and toxoplasmosis ring-enhancing brain lesion. — **Panel A:** HSV encephalitis with medial temporal lobe hyperintensity, inferior frontal involvement, hemorrhagic foci, CSF lymphocytic pleocytosis with RBCs, and HSV PCR as gold standard.. **Panel B:** Japanese encephalitis with bilateral thalamic lesions, possible basal ganglia involvement, mosquito exposure cue, and JEV IgM MAC-ELISA in CSF or serum as first-line diagnosis.. **Panel C:** Toxoplasma encephalitis with basal ganglia or corticomedullary ring-enhancing lesion, central necrosis, surrounding edema, and immunocompromised host association..

Laboratory diagnosis of encephalitis:
• CSF: usually lymphocytic pleocytosis, normal glucose; RBCs in HSV (haemorrhagic)
• PCR on CSF: gold standard for HSV (sensitivity >95%), JEV, Enterovirus, Nipah
• Serology: JEV IgM in CSF or serum (MAC-ELISA) — first-line for JE; Nipah ELISA
• Brain biopsy: reserved for atypical/diagnostic uncertainty — shows Negri bodies (rabies), Cowdry A inclusions (HSV), perivascular cuffing
• EEG: temporal lobe periodicity in HSV; diffuse slowing in others

SELF-CHECK

A 35-year-old farmer from Bihar presents in August with fever, headache, altered sensorium, and seizures following a course of mosquito bites. CSF shows 120 lymphocytes/mm³, protein 90 mg/dL, glucose 55 mg/dL (blood glucose 90 mg/dL). Gram stain is negative. What is the most appropriate next diagnostic test?

A. CSF culture on Löwenstein-Jensen medium for Mycobacterium

B. CSF GeneXpert (CBNAAT) for tuberculosis

C. CSF and serum Japanese encephalitis virus IgM (MAC-ELISA)

D. India ink preparation for Cryptococcus

Reveal Answer

Answer: C. CSF and serum Japanese encephalitis virus IgM (MAC-ELISA)

The clinical picture — Bihar, August (post-monsoon), mosquito exposure, lymphocytic CSF with normal glucose and negative Gram stain — is classic for Japanese encephalitis virus (JEV) infection. MAC-ELISA for JEV IgM in CSF or serum is the gold standard diagnostic test. TBM would show lower glucose and more protein; Cryptococcus would be suspected in immunocompromised patients with very low glucose and a positive India ink or CrAg test.

SELF-CHECK

On CSF Gram stain from a 22-year-old with purulent meningitis, you see lancet-shaped Gram-positive diplococci. What is the most likely organism and the drug of choice?

A. Neisseria meningitidis — benzyl penicillin

B. Streptococcus pneumoniae — ceftriaxone plus dexamethasone

C. Listeria monocytogenes — ampicillin

D. Haemophilus influenzae — chloramphenicol

Reveal Answer

Answer: B. Streptococcus pneumoniae — ceftriaxone plus dexamethasone

Lancet-shaped (flame/candle-shaped) Gram-positive diplococci in CSF are pathognomonic of Streptococcus pneumoniae (pneumococcal meningitis). Treatment of choice is ceftriaxone (or benzyl penicillin if sensitive) plus dexamethasone to reduce inflammation and prevent neurological complications (deafness). Neisseria meningitidis appears as Gram-negative kidney-shaped diplococci. Listeria produces Gram-positive rods, not diplococci.