For education and revision only. Not individual medical advice; check current NICE/BNF and local guidance before clinical use. Clinical safety and terms.
Microbiology: Bacteriology - structure, classification and important pathogens
🦠 Bacteriology - structure, classification and important pathogens. Bacteria cause most of the serious infections seen in UK hospitals and general practice: pneumonia, urinary tract infection, cellulitis, sepsis, meningitis and healthcare-associated infection. Knowing how bacteria are built, how they are classified by Gram stain and shape, and how they cause disease (virulence factors and toxins) lets you predict which organism is likely, which antibiotic will work, and which public health action is needed. Your four questions for any infection: Where is it (site predicts organism)? Who is the host (age, immunity, devices, travel, exposures)? What does the Gram stain or culture show? Which toxin or virulence factor explains the clinical picture?
Bacterial Structure
Prokaryotes - no nucleus (circular chromosome in the nucleoid), 70S ribosomes, no membrane-bound organelles; divide by binary fission (some every 20 minutes).
Cell wall - peptidoglycan - target of β-lactams (block transpeptidases - penicillin-binding proteins) and glycopeptides (vancomycin binds D-Ala-D-Ala).
Gram-positive - thick peptidoglycan with teichoic acids; no outer membrane.
Gram-negative - thin peptidoglycan plus an outer membrane containing lipopolysaccharide (LPS, endotoxin) - a barrier to many antibiotics (vancomycin cannot cross it) and the trigger of septic shock.
Capsule - polysaccharide; resists phagocytosis (Streptococcus pneumoniae, Haemophilus influenzae type b, Neisseria meningitidis, Klebsiella). Basis of conjugate vaccines; asplenic patients are at risk of overwhelming infection with encapsulated organisms.
Flagella (motility), pili/fimbriae (adhesion - E. coli to uroepithelium; sex pili for conjugation), biofilm (on prosthetic joints, lines, catheters, valves - resists antibiotics; usually needs device removal).
Spores (Clostridium, Bacillus) - resist heat, drying and alcohol; alcohol hand gel does not kill C. difficile spores - use soap and water and chlorine-based cleaning.
Plasmids - extrachromosomal DNA carrying resistance and toxin genes; transferred by conjugation.
Mycoplasma has no cell wall (β-lactams useless); Chlamydia and Rickettsia are obligate intracellular.
Enterotoxins - cholera, ETEC (travellers' diarrhoea), S. aureus and Bacillus cereus (preformed - vomiting within 1–6 hours).
Shiga toxin - Shigella and E. coli O157 (STEC) → bloody diarrhoea and haemolytic uraemic syndrome; avoid antibiotics and antimotility agents in suspected STEC.
Gram-positive cocci in clusters; catalase-positive.
Staphylococcus aureus (coagulase-positive) - carried in the nose by about 30% of people. Causes boils, cellulitis, impetigo, wound infection, septic arthritis, osteomyelitis (commonest cause), infective endocarditis (people who inject drugs - tricuspid valve), pneumonia (after influenza), line infections, bacteraemia (always investigate source and treat for at least 14 days, echo; S. aureus in blood is never a contaminant), food poisoning, toxic shock, scalded skin syndrome (exfoliative toxin, children).
MRSA - mecA gene → altered PBP2a; treat with vancomycin, teicoplanin, linezolid, daptomycin; doxycycline, co-trimoxazole or clindamycin for some community infections per sensitivities. Screening and decolonisation (nasal mupirocin, chlorhexidine wash) per local policy.
Coagulase-negative staphylococci (S. epidermidis) - skin commensal; common blood culture contaminant but a real pathogen on prosthetic devices (lines, joints, valves, shunts - biofilm).
S. saprophyticus - UTI in young sexually active women.
Neonatal sepsis, pneumonia and meningitis; intrapartum antibiotic prophylaxis for carriers and risk factors (RCOG)
β-haemolytic, Groups C and G
S. dysgalactiae
Cellulitis, pharyngitis, bacteraemia
α-haemolytic
Streptococcus pneumoniae
Commonest cause of community-acquired pneumonia, otitis media, sinusitis, meningitis, bacteraemia; capsule; urinary antigen test; vaccines (PCV and PPV23)
α-haemolytic
Viridans streptococci (S. mitis, S. sanguinis, S. mutans)
Mouth flora; dental caries; subacute infective endocarditis on abnormal valves
Group D / other
S. gallolyticus (bovis)
Endocarditis - colonoscopy for colorectal cancer
Anginosus group
S. anginosus, S. intermedius
Abscesses (brain, liver, empyema)
Enterococci
E. faecalis, E. faecium
UTI, intra-abdominal and biliary infection, endocarditis; intrinsically resistant to cephalosporins; VRE (vancomycin-resistant, mostly E. faecium) in hospitals
Penicillin remains the drug of choice for Group A streptococcus (no resistance); amoxicillin for most pneumococci and E. faecalis.
Gram-positive Rods - Clostridia, Listeria and Others
Clostridioides difficile - spore-forming anaerobe; antibiotic-associated diarrhoea and colitis (cephalosporins, co-amoxiclav, clindamycin, quinolones; PPIs increase risk); diagnosis by GDH antigen plus toxin testing; treat with oral vancomycin first line (fidaxomicin for recurrence or high risk; NICE NG199); isolate, soap and water; faecal microbiota transplant for recurrent disease. Severe disease - WCC >15, rising creatinine, temperature >38.5°C, colitis on imaging.
Clostridium tetani - tetanus (spores in wounds; trismus, risus sardonicus, spasms, autonomic instability); human tetanus immunoglobulin, metronidazole, wound debridement, vaccination.
Clostridium botulinum - botulism (food-borne, wound - people who inject drugs, infant - honey); descending symmetrical flaccid paralysis with cranial nerve palsies and preserved consciousness; antitoxin urgently (via UKHSA).
Listeria monocytogenes - grows at fridge temperatures (soft cheeses, pâté, deli meats); meningitis in neonates, older people (>50), pregnancy and immunosuppression; in pregnancy - fever, miscarriage, stillbirth, neonatal sepsis. Intrinsically resistant to cephalosporins - add amoxicillin to ceftriaxone for meningitis in those over 60 or immunocompromised.
Bacillus anthracis (anthrax - cutaneous black eschar, inhalational, injection anthrax in heroin users); Bacillus cereus (reheated rice - vomiting).
Corynebacterium diphtheriae - grey pseudomembrane, bull neck, myocarditis; rare in the UK (vaccination) but imported cases occur; antitoxin plus antibiotics; notifiable.
Actinomyces israelii - chronic abscesses with sinuses and "sulphur granules" (cervicofacial, IUD-associated pelvic); long-course penicillin. Nocardia - pulmonary and brain abscesses in the immunocompromised; co-trimoxazole.
Neisseria meningitidis - Gram-negative diplococcus carried in the nasopharynx by about 10% (teenagers and young adults more); meningococcal septicaemia (non-blanching purpuric rash, shock, DIC, Waterhouse–Friderichsen adrenal haemorrhage) and meningitis. Give IM/IV benzylpenicillin before transfer in suspected meningococcal disease in the community; ceftriaxone in hospital. Notify urgently - close contacts receive ciprofloxacin (or rifampicin) prophylaxis via UKHSA. Serogroup B now commonest in the UK (MenB vaccine in infants; MenACWY in teenagers). Complement deficiency (C5–C9) and eculizumab increase risk.
Neisseria gonorrhoeae - urethritis with purulent discharge, cervicitis, PID, proctitis, pharyngitis, disseminated gonococcal infection (pustular rash, tenosynovitis, septic arthritis), ophthalmia neonatorum; NAAT diagnosis with culture for sensitivities before treatment; ceftriaxone 1 g IM single dose (BASHH); rising resistance; test of cure; partner notification.
Escherichia coli - commonest cause of UTI and Gram-negative bacteraemia; neonatal meningitis (K1 capsule), intra-abdominal infection, travellers' diarrhoea (ETEC), STEC O157 (HUS). ESBL-producing E. coli and Klebsiella are resistant to cephalosporins - carbapenems, or nitrofurantoin/fosfomycin/pivmecillinam for lower UTI per sensitivities.
Klebsiella pneumoniae - hospital-acquired pneumonia, UTI, liver abscess (hypervirulent strains), lobar pneumonia with "red currant jelly" sputum in alcohol dependence; carbapenemase-producing Enterobacterales (CPE) - a major threat (KPC, NDM, OXA-48).
Salmonella - non-typhoidal (S. enteritidis, S. typhimurium - poultry, eggs; gastroenteritis; invasive in sickle cell disease - osteomyelitis); enteric (typhoid/paratyphoid) fever - S. Typhi and Paratyphi after travel to South Asia (fever, relative bradycardia, rose spots, splenomegaly, constipation then diarrhoea); blood culture; increasing resistance (XDR typhoid from Pakistan) - azithromycin or carbapenem per sensitivities; notifiable.
Shigella - bloody diarrhoea with small infective dose; outbreaks among men who have sex with men (MSM) with high resistance.
Campylobacter jejuni - commonest bacterial cause of gastroenteritis in the UK (undercooked poultry); bloody diarrhoea, abdominal pain (can mimic appendicitis); Guillain–Barré syndrome and reactive arthritis follow; clarithromycin if severe.
Helicobacter pylori - urease-positive curved rod; peptic ulcer, gastric cancer, MALT lymphoma; urea breath test or stool antigen (stop PPI 2 weeks before testing); triple therapy (PPI + amoxicillin + clarithromycin or metronidazole) for 7 days.
Pseudomonas aeruginosa - aerobic non-fermenter, green pigment, grape-like smell; cystic fibrosis and bronchiectasis, ventilator-associated pneumonia, burns, otitis externa (malignant otitis externa in diabetes), hot tub folliculitis, neutropenic sepsis, keratitis with contact lenses. Antipseudomonal agents: piperacillin–tazobactam, ceftazidime, meropenem, ciprofloxacin (the only oral option), aminoglycosides, colistin.
Haemophilus influenzae - non-typeable strains cause COPD exacerbations, otitis media, sinusitis; type b (now rare after Hib vaccine) caused epiglottitis and meningitis.
Bordetella pertussis - whooping cough (catarrhal phase, paroxysmal cough with whoop and post-tussive vomiting, apnoea in infants; lymphocytosis); macrolides; maternal vaccination in pregnancy (from 16 weeks); notifiable. Resurgence in England in 2024.
Legionella pneumophila - from contaminated water systems (air conditioning, showers, hotels); pneumonia with confusion, diarrhoea, hyponatraemia, deranged LFTs; urinary antigen test (serogroup 1); macrolide or quinolone; notifiable.
Mycoplasma pneumoniae - young adults, epidemics every few years; gradual onset, dry cough, headache; extrapulmonary features - cold agglutinin haemolysis, erythema multiforme/SJS, myocarditis, encephalitis, Guillain–Barré; macrolides or doxycycline (no cell wall - β-lactams ineffective).
Mycoplasma genitalium - non-gonococcal urethritis, cervicitis and PID; high macrolide resistance; test resistance markers.
Chlamydia trachomatis - commonest bacterial STI in the UK; often asymptomatic; urethritis, cervicitis, PID (tubal infertility, ectopic pregnancy), epididymo-orchitis, reactive arthritis, neonatal conjunctivitis and pneumonia; lymphogranuloma venereum (serovars L1–L3 - proctitis in MSM); trachoma (serovars A–C - leading infectious cause of blindness worldwide). Doxycycline 100 mg twice daily for 7 days first line (BASHH).
Chlamydia psittaci (now Chlamydophila) - psittacosis from birds (parrots, pigeons) - pneumonia with headache, splenomegaly.
Acid-fast bacilli (waxy mycolic acid wall) - stain with Ziehl–Neelsen or auramine; slow growing (culture takes 2–6 weeks); NAAT/GeneXpert detects M. tuberculosis and rifampicin resistance within hours.
Mycobacterium tuberculosis - airborne spread; primary infection (Ghon focus + hilar node = Ghon complex) → usually latent TB; reactivation in about 5–10% over a lifetime (higher with HIV, anti-TNF, steroids, diabetes, CKD, malnutrition, silicosis, transplant). Pulmonary (cough >3 weeks, haemoptysis, weight loss, night sweats, upper lobe cavitation), lymph node, miliary, TB meningitis, spinal (Pott's disease), genitourinary (sterile pyuria), pericardial, abdominal.
Treatment (NICE NG33):RIPE - rifampicin, isoniazid (+ pyridoxine), pyrazinamide and ethambutol for 2 months, then rifampicin and isoniazid for 4 months (longer for CNS disease - 12 months with steroids; also steroids for pericarditis). Directly observed therapy where adherence is a concern. Notify; contact tracing by the TB service.
Latent TB testing - interferon-gamma release assay (IGRA) or Mantoux; treat (3 months rifampicin + isoniazid, or 6 months isoniazid) in close contacts, new entrants from high-incidence countries, and before biologics or transplantation.
Multidrug-resistant TB (resistant to rifampicin and isoniazid) - specialist regimens (e.g. BPaLM: bedaquiline, pretomanid, linezolid ± moxifloxacin).
BCG vaccine - neonates at higher risk (living in high-incidence areas or parents/grandparents from high-incidence countries); protects against severe childhood TB.
Non-tuberculous mycobacteria (M. avium complex, M. abscessus, M. kansasii) - chronic lung disease in bronchiectasis, CF, COPD; disseminated MAC in advanced HIV; M. marinum (fish tank granuloma).
Mycobacterium leprae - leprosy (anaesthetic skin patches, thickened nerves) - imported cases only in the UK.
Tests - treponemal antibody (EIA/CLIA - stays positive for life) plus non-treponemal RPR/VDRL (activity marker - falls with treatment). Dark-ground microscopy or PCR of lesions.
Treatment - benzathine benzylpenicillin IM (single dose for early syphilis; three weekly doses for late latent); Jarisch–Herxheimer reaction (fever and flu-like illness within 24 hours of treatment). Screen in pregnancy.
Borrelia burgdorferi - Lyme disease (ticks - New Forest, Scottish Highlands, Lake District): erythema migrans (expanding target rash - diagnose clinically and treat without testing), then facial palsy (often bilateral), meningitis, radiculopathy, heart block, arthritis; doxycycline 21 days (NICE NG95).
Leptospira - leptospirosis (Weil's disease) - rat urine in fresh water (rowers, sewer workers, farmers, travellers); fever, myalgia, conjunctival suffusion, then jaundice, AKI, pulmonary haemorrhage; doxycycline or benzylpenicillin.
Scenario. Two blood cultures grow Staphylococcus aureus in a man with a recently inserted hip prosthesis. What is the management?
Answer: Treat as true S. aureus bacteraemia - remove or assess infected devices, echocardiography (TOE if high risk), IV anti-staphylococcal therapy (flucloxacillin, or vancomycin if MRSA) for at least 14 days from the first negative culture (longer if complicated), repeat cultures, orthopaedic review for prosthetic joint infection, infectious diseases input.
Scenario. A university student is admitted with meningococcal septicaemia. Who needs prophylaxis?
Answer: Household and close contacts in the previous 7 days (people who slept in the same household, intimate kissing contacts) - single-dose ciprofloxacin via the UKHSA health protection team. Healthcare workers only if directly exposed to respiratory droplets (e.g. intubation without a mask). Notify immediately on clinical suspicion.
Scenario. An 82-year-old develops profuse diarrhoea on day 5 of co-amoxiclav for pneumonia. WCC 18, creatinine rising.
Answer: Severe C. difficile infection - stop the precipitating antibiotic if possible, review PPIs, isolate with enteric precautions, send stool for GDH and toxin, start oral vancomycin 125 mg four times daily for 10 days, monitor for toxic megacolon (abdominal X-ray), surgical review if deteriorating.