The following content is based on NICE guidelines, NICE CKS, BNF treatment summaries, and BASHH guidelines wherever possible. In situations where UK-specific guidance is not available, well-established international guidelines or widely accepted standard practice have been used, as these do not differ meaningfully in management.
Management By Organ System
Cardiovascular
Main cardiovascular system infection is infective endocarditis, see this article for more information.
Respiratory
| Condition | Causative organism | 1st line | 2nd line | Article link |
|---|---|---|---|---|
| Community-acquired pneumonia | Streptococcus pneumoniae | Amoxicillin | Doxycycline / clarithromycin / erythromycin | Pneumonia |
| Atypical pneumonia | Mycoplasma pneumoniae, Legionella species, Chlamydia species, Coxiella burnetii | Clarithromycin (+ amoxicillin) | Doxycycline | Pneumonia |
| Hospital-acquired pneumonia | Gram -ve bacilli (esp. Pseudomonas aeruginosa, Klebsiella species, E. coli, Acinetobacter species), Staphylococcus aureus | Non-severe: co-amoxiclav
Severe: IV Tazocin (piperacillin with tazobactam) |
Pneumonia | |
| Acute bronchitis | Viral is more common, if bacterial: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis | Doxycycline (see full article for indications) | Amoxicillin / clarithromycin / erythromycin | Acute Bronchitis |
| Infective COPD exacerbation | Viral is more common, if bacterial: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis | Amoxicillin / doxycycline / clarithromycin | Chronic Obstructive Pulmonary Disease (COPD) | |
| Infective bronchiectasis exacerbation | Haemophilus influenzae, Pseudomonas aeruginosa | Amoxicillin | Clarithromycin / doxycycline | Bronchiectasis |
Ear, Nose, and Throat
| Condition | Causative organism | 1st line | 2nd line | Article link |
|---|---|---|---|---|
| Bacterial tonsillitis / pharyngitis | Group A β-haemolytic Streptococcus (Streptococcus pyogenes) | Phenoxymethylpenicillin (penicillin V) | Clarithromycin, erythromycin | Sore Throat |
| Acute rhinosinusitis | Viral is more common, if bacterial (Streptococcus pneumoniae, Haemophilus influenzae) | Phenoxymethylpenicillin (penicillin V) (see full article for indications) | Clarithromycin, erythromycin | Acute Rhinosinusitis |
| Acute otitis media | Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis | Amoxicillin | Clarithromycin, erythromycin | Acute Otitis Media (AOM) |
| Acute otitis externa | Staphylococcus aureus, Pseudomonas aeruginosa | Gentamicin / ciprofloxacin ear drops | Oral antibiotics | Acute Otitis Externa |
| Influenza | Influenza A & B viruses | Supportive management | Oseltamivir / zanamivir | Influenza |
| COVID-19 | SARS-CoV-2 | Supportive management | Antivirals (e.g. nirmatrelvir, ritonavir, remdesivir) and corticosteroids | |
| Acute epiglottitis | Haemophilus influenzae type B | IV ceftriaxone / cefotaxime | Chloramphenicol | |
| Croup | Parainfluenza virus | Oral dexamethasone | Nebulised adrenaline | Croup |
| Infectious mononucleosis | Epstein-Barr virus | Supportive care | ||
| Diphtheria | Corynebacterium diphtheriae | Diphtheria antitoxin + macrolide (clarithromycin / azithromycin / erythromycin) | ||
| Whooping cough | Bordetella pertussis | Macrolide (clarithromycin / azithromycin / erythromycin) | Co-trimoxazole | |
| Scarlet fever | Group A β-haemolytic Streptococcus (Streptococcus pyogenes) | Phenoxymethylpenicillin (penicillin V) | Macrolide (clarithromycin / azithromycin / erythromycin) | |
| Oral Candidiasis | Candida albicans (most common) | Miconazole oral gel (localised/mild disease)
*Extensive/Severe disease: oral fluconazole |
Nystatin suspension (localised/mild disease) |
Less commonly examined, but oral infections (pericoronitis and gingivitis) are typically managed with metronidazole (if indicated)
Urinary Tract
Most of the following conditions are caused by gram-negative enteric bacteria, particularly E. coli
- An exception is epididymo-orchitis in <35 y/o, which is most commonly caused by chlamydia and gonorrhoea
| Condition | 1st line | 2nd line | Link to article |
|---|---|---|---|
| Lower UTI (i.e. cystitis) | Trimethoprim / nitrofurantoin | Amoxicillin / cefalexin | Urinary Tract Infection (UTI) in Adults |
| Upper UTI (i.e. pyelonephritis) | Cefalexin | Ciprofloxacin | Acute Pyelonephritis |
| Prostatitis | Ciprofloxacin / ofloxacin | Trimethoprim | Prostatitis (Acute) |
| Epididymo-orchitis | <35 y/o: ceftriaxone + doxycycline
>35 y/o: levofloxacin / ofloxacin |
Epididymo-Orchitis |
Sexual Health
| Condition | Causative organism | 1st line | 2nd line | Link to article |
|---|---|---|---|---|
| Chlamydia | Chlamydia trachomatis | Doxycycline | Azithromycin | Chlamydia |
| Gonorrhoea | Neisseria gonorrhoea | Ceftriaxone (IM) | Cefixime + azithromycin (oral) | Gonorrhoea |
| Syphilis | Treponema pallidum | Benzathine penicillin G (IM) | Syphilis | |
| Pelvic inflammatory disease | Chlamydia trachomatis (most common), Neisseria gonorrhoea | Ceftriaxone (IM) + doxycycline + metronidazole | Pelvic Inflammatory Disease (PID) | |
| Genital herpes | Herpes simplex virus | Aciclovir / valaciclovir | Genital Herpes | |
| Trichomonas vaginalis | Trichomonas vaginalis | Metronidazole | ||
| Bacterial vaginosis | Gardnerella vaginalis | Metronidazole (oral)
AlternativeIf prefer topical treatment / cannot tolerate oral treatment : intravaginal metronidazole gel / clindamycin cream |
Clindamycin / tinidazole (oral) | Bacterial Vaginosis (BV) |
| Vulvovaginal candidiasis | Candida albicans | Fluconazole (oral) | Clotrimazole (topical) | Candidiasis (Vulvovaginal) |
Gastrointestinal
Note that most infectious diarrhoea does not require antibiotics. They are only considered in proven secondary to bacteria, severe or high-risk cases.
| Condition | 1st line | 2nd line | Link to article |
|---|---|---|---|
| Helicobacter pylori | PPI + amoxicillin + clarithromycin or metronidazole | PPI + clarithromycin + metronidazole | Helicobacter Pylori Infection |
| Clostridioides difficile | Vancomycin (oral)
If severe: vancomycin (oral) + metronidazole (IV) |
Fidaxomicin (oral) | Clostridioides Difficile Infection |
| Campylobacter jejuni | Clarithromycin | ||
| Salmonella (non-typhoid) | Ciprofloxacin / cefotaxime | ||
| Shigella | Ciprofloxacin / azithromycin | ||
| Chorea | Doxycycline | ||
| E. coli | Avoid antibiotics | ||
| Giardia lamblia | Metronidazole | ||
| Entamoeba histolytica | Metronidazole | ||
| Whipple’s disease | IV ceftriaxone followed by co-trimoxazole |
Dermatology
| Condition | Causative organism | 1st line | 2nd line | Article link |
|---|---|---|---|---|
| Impetigo | Staphylococcus aureus | Topical hydrogen peroxide | Topical / oral antibiotics | Impetigo |
| Cellulitis and erysipelas | Staphylococcus aureus, Streptococcus pyogenes | Flucloxacillin
If near the eye: co-amoxiclav |
Clarithromycin / erythromycin / doxycycline | Cellulitis and Erysipelas |
| Mastitis | Staphylococcus aureus | Flucloxacillin (see full article for indications) | Erythromycin / clarithromycin | Mastitis and Breast Abscess |
| Human and animal bites | Human: Eikenella corrodens, Animal: Pasteurella species | Co-amoxiclav | Doxycycline + metronidazole | Human and Animal Bites |
| Shingles (herpes zoster) | Varicella zoster virus (reactivation) | Aciclovir / valaciclovir / famciclovir (see full article for indications) | Shingles | |
| Molluscum contagiosum | Molluscum contagiosum virus | Conservative management | Molluscum Contagiosum | |
| Tinea capitis / corporis / pedis / cruris | Dermatophytes | Scalp (tinea capitis): oral terbinafine / griseofulvin
Other body areas: topical terbinafine / imidazole |
Fungal Skin Infection | |
| Fungal nail infection (onychomycosis) | Dermatophytes (Trichophyton rubrum most common) | Oral terbinafine | Oral itraconazole | Fungal Nail Infection (Onychomycosis) |
| Pityriasis versicolor | Malassezia furfur (yeast) | Topical ketoconazole | ||
| Scabies |
Sarcoptes scabiei (mite infestation) |
Permethrin cream / oral ivermectin | Scabies | |
| Roundworm | Ascaris lumbricoides | Oral mebendazole |
Note that all viral exanthems (e.g. measles, mumps, rubella, chickenpox, parvovirus B19, roseola, hand foot and mouth disease) require supportive care only. Except for high-risk chickenpox, which may need aciclovir.
Musculoskeletal
Both are most commonly caused by Staphylococcus aureus
| Condition | 1st line | 2nd line | Link to article |
|---|---|---|---|
| Septic arthritis | Flucloxacillin | Clindamycin | Septic Arthritis |
| Osteomyelitis | Flucloxacillin | Clindamycin | Osteomyelitis |
Central Nervous System
| Condition | Causative organism | 1st line | 2nd line | Link to article |
|---|---|---|---|---|
| Bacterial meningitis | Neisseria meningitidis, Streptococcus pneumoniae | IV ceftriaxone | Chloramphenicol | Meningitis |
| Viral meningitis | Enteroviruses | Supportive management | ||
| Tuberculosis meningitis | Mycobacterium tuberculosis | Rifampicin + isoniazid + pyrazinamide + ethambutol | ||
| Fungal meningitis | Cryptococcus neoformans | IV amphotericin B + flucytosine | ||
| Encephalitis | Herpes simplex virus | IV aciclovir |
Multi-System Infections
Overview Table
Key management principles:
- Viral infections → supportive care (no routine antivirals)
- Bacterial infections → antibiotics
- Protozoal and helminthic parasitic infections → specific anti-parasitic agents
| Condition | Causative organism | Organism type | 1st line management |
|---|---|---|---|
| Dengue fever | Dengue virus (Flavivirus) | Virus | Supportive management |
| Yellow fever | Yellow fever virus (Flavivirus) | ||
| Chikungunya fever | Chikungunya virus (Togavirus) | ||
| Malaria | Plasmodium spp. (esp. Plasmodium falciparum) | Protozoan parasite | Artemether–lumefantrine |
| Schistosomiasis | Schistosoma spp. | Parasitic helminth (a worm / fluke) | Praziquantel |
| Leptospirosis | Leptospira interrogans | Bacteria | Doxycycline |
| Toxoplasmosis | Toxoplasma gondii | Protozoan parasite | Pyrimethamine (+ folinic acidreduces myelotoxic risks of pyrimethamine) PLUS sulfadiazine
Click to view treatment indications Treatment is indicated in: |
| Rickettsial infectionsIncluding Rocky Mountain spotted fever, ehrlichiosis, anaplasmosis and typhus group rickettsioses | Bacteria of the order RickettsialesIncludes Rickettsia, Orientia, Anaplasma, Ehrlichia, Neoehrlichia, and Neorickettsia | Bacteria | Doxycycline |
Management By Organism
Overview Table
This section highlights high-yield, organism-specific antimicrobial prescribing principles. Always prioritise culture and sensitivity results over standard “1st line” recommendations, in both exams and clinical practice.
| Organism | 1st Line Antibiotic |
|---|---|
| MSSA (Methicillin-Sensitive Staphylococcus aureus) | Flucloxacillin* |
| MRSA (Methicillin-Resistant Staphylococcus aureus) | Vancomycin / teicoplanin / linezolid |
| Pseudomonas aeruginosa | Ciprofloxacin / piperacillin–tazobactam (Tazocin) |
| ESBLExtended-spectrum beta-lactamase-producing Enterobacterales (e.g., E. coli, Klebsiella) | Meropenem |
| VRE (Vancomycin-Resistant Enterococcus) | Linezolid / daptomycin |
*Although the term MSSA means “methicillin-sensitive Staphylococcus aureus”, methicillin is no longer used in clinical practice. The name is retained historically to indicate sensitivity to standard β-lactam antibiotics such as flucloxacillin and co-amoxiclav.
Management By Patient Population
This is a practical summary rather than a list of exhaustion. The principles here cover common exam scenarios and day-to-day prescribing decisions.
For specific drug queries, check the BNF/BNF-C and local trust policy.
Children
Main ones to avoid in children:
- Tetracyclines (risk of teeth discolouration and bone growth suppression)
- Fluoroquinolones (e.g. ciprofloxacin) (risk of cartilage toxicity)
Pregnancy
Main safe ones in pregnancy:
- Beta-lactams (penicillins and cephalosporins)
- Erythromycin (1st line alternative in those with penicillin allergic)
- Nitrofurantoin (but only 1st and 2nd trimester)