17.1 — Bacteria

Around 38 trillion bacteria live in and on you, and fewer than a hundred species cause most human disease (Chapter 1.1). The overwhelming majority are harmless or actively useful.

And the story of bacterial infection over the last century is the most positive in medicine. In 1900, infectious disease was the leading cause of death everywhere. Today, in most of the world, a bacterial infection is something you take tablets for.

How they are described

Gram stain and shape (Chapter 3.7), and between them they narrow the possibilities within an hour of a sample arriving.

Gram-positive cocci in clusters — Staphylococcus. In chains — Streptococcus. Gram-negative rods — the gut organisms: E. coli, Klebsiella, Salmonella. Gram-negative diplococci — Neisseria: meningitis and gonorrhoea. Acid-fast bacilli — mycobacteria, needing a different stain entirely (Chapter 17.8).

Aerobic or anaerobic — anaerobes dominate the gut, the mouth and deep abscesses, and they are why abscess pus smells the way it does.

The ones worth knowing

Staphylococcus aureus — carried harmlessly in the nose by around 30 percent of people, and the commonest cause of skin and wound infection. Also causes bone and joint infection, endocarditis (Chapter 7.2) and toxic shock syndrome.

MRSA is the same organism with resistance to the standard penicillin-type antibiotics. Not more virulent — just harder to treat.

Streptococcus pyogenes (Group A strep) — sore throat, impetigo, cellulitis, scarlet fever. And, uncommonly, necrotising fasciitis (Chapter 14.5).

Its most consequential complication is rheumatic fever — antibodies against the bacterium cross-reacting with heart valves (Chapter 13.6). Entirely preventable by treating the sore throat, which is why this unglamorous intervention still matters enormously where the disease persists.

Streptococcus pneumoniae — pneumonia, meningitis, ear infection. Vaccination has substantially reduced invasive disease in both children and older adults.

Escherichia coli — the commonest cause of urinary infection (Chapter 10.5), and some strains cause severe gut infection.

Clostridioides difficile — the antibiotic-associated colitis of Chapter 9.6.

Clostridium tetani and botulinum — toxin producers (Chapters 6.2, 14.4).

Neisseria meningitidis — meningococcal disease (Chapter 11.10), and vaccination has changed its epidemiology dramatically.

Helicobacter pylori — peptic ulcer and gastric cancer (Chapter 9.2).

Borrelia burgdorferi — Lyme disease, from tick bites. The characteristic expanding circular rash appears in most cases and is diagnostic enough to treat on sight, without waiting for serology, which is often negative early.

How bacteria cause harm

Three ways, and the distinction matters for treatment.

Direct invasion and tissue destruction.

Toxins. Exotoxins are secreted proteins, often extremely potent — tetanus, botulinum, diphtheria, cholera. Endotoxin is the lipopolysaccharide in the Gram-negative outer membrane, released when the bacterium dies, and it is the main driver of Gram-negative sepsis (Chapter 3.7).

Which produces a genuine clinical paradox: killing bacteria can transiently worsen the illness, as endotoxin and other contents are released — the Jarisch–Herxheimer reaction in syphilis being the clearest example (Chapter 15.13).

The immune response itself. Much of the damage in bacterial meningitis and in severe pneumonia comes from inflammation rather than from the organism — which is why steroids are given alongside antibiotics in some bacterial meningitis.

Biofilms

Bacteria growing as a community encased in a self-produced matrix, attached to a surface.

And they are far harder to treat than free-floating organisms — up to a thousand times more resistant to antibiotics, because penetration is poor and the deeper cells are metabolically dormant.

Which explains a set of otherwise puzzling clinical situations. Infected prosthetic joints, heart valves and catheters frequently cannot be cured without removing the device. Dental plaque is a biofilm. So is the chronic Pseudomonas colonisation in cystic fibrosis lungs (Chapter 2.8).

"Remove the foreign body" is not a failure of medical treatment — it is the treatment.

Diagnosis

Culture remains the reference standard, and it is slow — 24 to 48 hours for growth, plus another day for sensitivities.

Which is why treatment is started empirically — best guess based on the likely organism and local resistance patterns — and narrowed when results arrive (Chapter 17.12).

Molecular tests are faster, detecting bacterial DNA within hours, and increasingly identify resistance genes at the same time.

Blood cultures should be taken before antibiotics wherever possible, because a single dose substantially reduces the yield.

Where this stands now

The encouraging summary.

Most bacterial infections are curable with a short course of an oral antibiotic.

Vaccines have removed several from ordinary experience. Hib meningitis, once the commonest cause of bacterial meningitis in children, has essentially disappeared where the vaccine is given (Chapter 13.5). Diphtheria, tetanus and pertussis are all vaccine-preventable.

Basic hygiene remains extraordinarily effective. Handwashing prevents more infection than most antibiotics treat, and clean water has saved more lives than any drug.

And the genuine concern is resistance (Chapter 17.12), which is a problem of stewardship rather than of biology — and one that is at least partly within collective control.

What the next page fixes

Bacteria are living cells that can be killed. Chapter 17.2 covers organisms that are not alive in the ordinary sense, cannot be killed by antibiotics, and are handled by an entirely different set of tools.