Gram-Negative Rods — Enterics and Non-Fermenters

• Lactose fermenters (pink on MacConkey) — the mnemonic CEEKS: Citrobacter, Enterobacter, Escherichia coli, Klebsiella, Serratia.
• E. coli: the leading cause of urinary tract infection and gram-negative sepsis; ETEC (traveller's diarrhoea), EHEC O157:H7 (Shiga-like toxin, bloody diarrhoea, haemolytic uraemic syndrome — and antibiotics are avoided), neonatal meningitis via the K1 capsule.
• Klebsiella: thick capsule, currant-jelly sputum, aspiration pneumonia in alcohol use and diabetes, and a common source of carbapenemase.
• Non-fermenters, oxidase-positive — Pseudomonas aeruginosa: blue-green pigment, grape-like odour, thrives in water. Causes burn wound infection, hot tub folliculitis, malignant otitis externa in diabetes, ventilator-associated pneumonia, and the chronic airway colonisation of cystic fibrosis. Exotoxin A blocks elongation factor 2. Ecthyma gangrenosum is its cutaneous hallmark.
• Non-fermenters, oxidase-negative include Shigella (no motility, invasive, Shiga toxin), Salmonella (motile, produces hydrogen sulphide, typhoid with rose spots, and osteomyelitis in sickle cell disease), and Proteus (swarming motility, urease producing struvite stones).

Two families, split by metabolism

• Enterobacterales (E. coli, Klebsiella, Enterobacter, Citrobacter, Serratia, Proteus, Salmonella, Shigella): facultative anaerobes that ferment glucose and are oxidase-negative. Within this group the MacConkey split is by lactose specifically — Salmonella, Shigella, and Proteus ferment glucose but not lactose, so they appear colourless on MacConkey.
• True non-fermenters (Pseudomonas aeruginosa, Acinetobacter, Stenotrophomonas, Burkholderia): obligate aerobes that oxidise rather than ferment sugars; Pseudomonas is the oxidase-positive exception used to separate it at the bench.

Stain and culture

• Gram stain: pink rods — thin peptidoglycan, outer membrane bearing lipopolysaccharide. Lipid A is the toxic moiety, the O-polysaccharide the serotype (O157), flagellin the H antigen, capsule the K antigen (O157:H7, E. coli K1).
• MacConkey agar: bile salts and crystal violet suppress gram-positives; lactose plus neutral red turns fermenters pink.
• EMB agar: E. coli gives a green metallic sheen.
• Sorbitol-MacConkey: E. coli O157:H7 fails to ferment sorbitol → colourless colonies.
• Pseudomonas: pyocyanin (blue) and pyoverdine (yellow-green) pigments, grape-like/corn-tortilla odour, growth at 42 °C. Serratia makes red prodigiosin; Proteus shows swarming motility over the whole plate.

Biochemical identification (classic panels)

• Indole: positive in E. coli; urease: Proteus (strong) and Klebsiella; citrate: Klebsiella/Enterobacter; H₂S on TSI: Salmonella and Proteus; motility: Salmonella yes, Shigella and Klebsiella no.

Endotoxin — the shared final pathway

• Lipid A released during growth and bacterial lysis binds LBP/CD14 and signals through TLR4-MD2 on macrophages, activating NF-κB and a torrent of TNF-α, IL-1, and IL-6. IL-1/TNF act on the hypothalamus (fever) and on endothelium (adhesion molecules, capillary leak).
• Inducible nitric oxide synthase drives vasodilation → low systemic vascular resistance with a compensatory high cardiac output: warm shock with bounding pulses and wide pulse pressure before decompensation.
• Endothelial and monocyte tissue factor expression plus complement (C3a, C5a) activation produce DIC — thrombocytopenia, prolonged PT/aPTT, elevated D-dimer, microvascular ischaemia. This is why any of these organisms, regardless of exotoxin repertoire, can present identically as septic shock.

Organism-specific chains

• **Uropathogenic *E. coli*: type 1 pili (FimH) bind uroplakin on bladder urothelium → cystitis; P fimbriae** bind Gal-Gal on renal epithelium → ascending pyelonephritis with flank pain and WBC casts.
• **Shiga toxin (EHEC, Shigella): B subunit binds Gb3, dense on colonic and glomerular endothelium; the A subunit cleaves an adenine from 28S rRNA of the 60S ribosome, halting protein synthesis → endothelial death, bloody diarrhoea, and microangiopathy producing the HUS** triad of schistocytic anaemia, thrombocytopenia, and acute kidney injury.
• ETEC: heat-labile toxin activates adenylate cyclase (↑cAMP), heat-stable toxin activates guanylate cyclase (↑cGMP) → secretory, non-inflammatory watery diarrhoea with no fecal leukocytes.
• ***Pseudomonas* exotoxin A: ADP-ribosylates elongation factor 2**, the same target as diphtheria toxin, causing host cell death; ExoU/ExoS delivered by type III secretion destroy tissue, and vascular invasion produces the necrotic ecthyma gangrenosum lesion.
• ***Proteus* urease splits urea to ammonia → alkaline urine → precipitation of magnesium ammonium phosphate (struvite**) staghorn calculi that harbour bacteria.
• Salmonella invades M cells over Peyer patches and survives inside macrophages, explaining bacteraemic typhoid rather than a purely luminal illness.

Escherichia coli

• Cystitis/pyelonephritis: dysuria and frequency; fever, flank pain, and WBC casts signal upper tract disease. Risk: female anatomy, sexual activity, catheters, obstruction.
• Gram-negative sepsis: the commonest cause; source is usually urinary or biliary. Hypotension with warm extremities early.
• Neonatal meningitis (K1 capsule): fever or hypothermia, poor feeding, bulging fontanelle in the first month.
• Diarrhoea: ETEC watery traveller's diarrhoea; EHEC O157:H7 afebrile bloody diarrhoea from undercooked beef, unpasteurised products, or petting zoos, with HUS appearing about a week in, typically in a child.

Klebsiella pneumoniae

• Aspiration pneumonia with currant-jelly sputum, upper-lobe cavitation and bulging fissure, in alcohol use disorder and diabetes.
• Hypervirulent (hypermucoviscous) strains: pyogenic liver abscess with metastatic endophthalmitis or meningitis, classically in patients of East/Southeast Asian origin.
• Healthcare-associated UTI, bacteraemia, and carbapenem-resistant infection.

Pseudomonas aeruginosa

• Ventilator-associated pneumonia; burn wound sepsis; hot-tub folliculitis (pruritic pustules in a bathing-suit distribution); malignant (necrotising) otitis externa with granulation tissue at the bony-cartilaginous junction and possible cranial nerve VII palsy in elderly diabetics; osteomyelitis after a puncture wound through a sneaker; corneal keratitis in contact lens wearers; endocarditis in injection drug use; chronic mucoid airway colonisation in cystic fibrosis and bronchiectasis; ecthyma gangrenosum — a painless necrotic ulcer with black eschar — in neutropenic patients with bacteraemia.

Others

• Proteus mirabilis: recurrent UTI with alkaline urine and staghorn struvite stones.
• Salmonella: non-typhoidal gastroenteritis from poultry, eggs, or reptiles; osteomyelitis in sickle cell disease; typhoid fever with stepwise fever, relative bradycardia, rose spots, and later intestinal perforation.
• Shigella: very low infectious dose, day-care and person-to-person spread, febrile dysentery with tenesmus and occasional seizures in young children.
• Serratia/Enterobacter/Citrobacter: nosocomial device- and line-associated infection with inducible AmpC resistance.

Start with the syndrome, then culture before antibiotics

• The Surviving Sepsis Campaign advises blood cultures (two sets) and a serum lactate before antimicrobials in suspected sepsis, with antibiotics within one hour of recognised septic shock. Organ dysfunction is scored by SOFA under the Sepsis-3 definitions; qSOFA (altered mentation, respiratory rate ≥22, systolic BP ≤100 mmHg) is a bedside prompt, not a diagnostic test.

Urinary tract

• Urinalysis first: pyuria, positive leukocyte esterase, and nitrite — Enterobacterales reduce nitrate to nitrite, so a negative nitrite does not exclude infection (and Pseudomonas is often nitrite-negative).
• Urine culture is confirmatory; the classic significant threshold is ≥10⁵ CFU/mL, though lower counts are accepted in symptomatic women. Culture is not required for uncomplicated cystitis per the IDSA/ESCMID uncomplicated cystitis guidance but is required for pyelonephritis, recurrence, or treatment failure.
• Alkaline urine with pH above 7 plus coffin-lid struvite crystals points to **urease-positive *Proteus***; image for staghorn calculus.

Diarrhoeal illness

• CDC and the IDSA infectious diarrhoea guideline recommend simultaneous stool culture and a Shiga toxin immunoassay (or toxin gene NAAT) for bloody diarrhoea, because non-O157 STEC are missed by sorbitol screening alone. Sorbitol-MacConkey shows colourless (non-sorbitol-fermenting) O157:H7 colonies.
• HUS is a clinical-laboratory diagnosis: schistocytes on smear, thrombocytopenia, rising creatinine, elevated LDH, low haptoglobin, and a negative direct Coombs test.

Respiratory and other sites

• Sputum or lower-respiratory sampling with semiquantitative culture is preferred by the IDSA/ATS HAP/VAP guideline; mucoid Pseudomonas on cystic fibrosis surveillance culture is diagnostic of chronic infection.
• Malignant otitis externa: markedly elevated ESR/CRP with CT or MRI showing skull-base osteomyelitis; culture guides therapy.
• Typhoid: blood cultures early, stool and urine later; bone marrow culture is the most sensitive. The Widal serology is unreliable and is no longer recommended.
• Final identification is by MALDI-TOF with susceptibility interpreted against CLSI breakpoints; report carbapenemase testing when carbapenem-resistant.

Urinary tract

• Uncomplicated cystitis (IDSA/ESCMID): nitrofurantoin, trimethoprim-sulfamethoxazole where local resistance is low, or fosfomycin. Fluoroquinolones are reserved because of FDA-labelled tendinopathy, neuropathy, and aortic risks.
• Pyelonephritis: a third-generation cephalosporin (ceftriaxone) or fluoroquinolone, narrowed by culture; obstruction requires drainage, not just antibiotics.

Sepsis and pneumonia

• Empiric coverage follows local antibiogram and risk factors. The IDSA/ATS HAP/VAP guideline recommends an antipseudomonal beta-lactam (piperacillin-tazobactam, cefepime, ceftazidime, or meropenem), adding a second antipseudomonal agent of a different class when there is septic shock, structural lung disease, or high local resistance — then de-escalating to monotherapy once susceptibilities return. Aminoglycosides should not be used alone for pneumonia (poor lung penetration).
• Febrile neutropenia (IDSA): antipseudomonal monotherapy such as cefepime, given the risk of Pseudomonas bacteraemia and ecthyma gangrenosum.

Resistance patterns that change the drug

• ESBL (common in E. coli and Klebsiella): IDSA antimicrobial-resistance guidance favours a carbapenem (meropenem) for bloodstream and serious infections rather than piperacillin-tazobactam; nitrofurantoin or TMP-SMX remain options for cystitis.
• Inducible AmpC (Enterobacter, Citrobacter, Serratia): avoid third-generation cephalosporins — use cefepime or a carbapenem.
• Carbapenem-resistant Enterobacterales: ceftazidime-avibactam, meropenem-vaborbactam, or imipenem-relebactam; for metallo-beta-lactamase producers, ceftazidime-avibactam plus aztreonam, or cefiderocol.
• **Difficult-to-treat *Pseudomonas*: ceftolozane-tazobactam** or ceftazidime-avibactam.

Syndrome-specific points

• EHEC/STEC: antibiotics and antimotility agents are avoided — they increase the risk of HUS (CDC/IDSA). Management is volume support and dialysis as needed.
• Traveller's diarrhoea: azithromycin (or rifaximin for non-invasive disease) plus oral rehydration.
• Typhoid: ceftriaxone or azithromycin given widespread fluoroquinolone resistance from South Asia.
• Cystic fibrosis: inhaled tobramycin for eradication and chronic suppression per Cystic Fibrosis Foundation guidance.
• Vaccination: typhoid vaccines (Vi polysaccharide, oral Ty21a) for travellers per ACIP; no vaccine exists for E. coli, Klebsiella, or Pseudomonas.

• Two-step algorithm: lactose on MacConkey first, then oxidase. Pink colony → CEEKS. Colourless and oxidase-positive → Pseudomonas. Colourless and oxidase-negative → Salmonella, Shigella, Proteus. Memorise this before memorising any syndrome.
• Endotoxin has no exotoxin equivalent in vaccinology: lipid A signals through TLR4, is not secreted, is heat-stable, and cannot be toxoided — a favourite distractor against Shiga toxin and exotoxin A, which are secreted, heat-labile A-B toxins.
• Two toxins, two ribosomal targets: Shiga toxin cleaves an adenine from 28S rRNA (60S subunit); Pseudomonas exotoxin A ADP-ribosylates EF-2, exactly like diphtheria toxin. Do not conflate them.
• The single best next step in suspected EHEC: stool culture plus Shiga toxin assay and supportive care — withhold antibiotics and antimotility drugs, because they raise HUS risk. A stem describing a child with bloody diarrhoea after a barbecue is testing this restraint.
• HUS versus TTP: HUS is Shiga-toxin, kidney-dominant, in a child; TTP is ADAMTS13 deficiency with prominent neurologic findings. Both show schistocytes with a negative Coombs test — the negative Coombs distinguishes microangiopathy from autoimmune haemolysis.
• **Alkaline urine + staghorn calculus = urease-positive *Proteus***; the coffin-lid struvite crystal is the buzzword, and stone removal is required for cure.
• The organism-host pairings examiners love: Salmonella osteomyelitis in sickle cell disease; Pseudomonas osteomyelitis after a nail through a sneaker; Pseudomonas malignant otitis externa in the elderly diabetic; Klebsiella currant-jelly pneumonia in alcohol use disorder; E. coli K1 neonatal meningitis; ecthyma gangrenosum in neutropenia.
• Common distractor: Klebsiella and Proteus are both urease-positive, but only Proteus swarms and only Klebsiella is a lactose fermenter with a thick capsule.