Bacterial Syndromes and Clinical Integration

This section organises by clinical syndrome, pulling together the causative organisms from across bacteriology by the site of infection a patient actually presents with. This covers only the organism list, key specimen, and diagnostic approach for each syndrome, not specific drug choices, dosing, or duration.

Common bacterial groups. Neisseria meningitidis and Streptococcus pneumoniae are the two dominant causes in previously healthy older children and adults. Listeria monocytogenes affects neonates, the elderly, and the immunocompromised. Group B Streptococcus and E. coli affect neonates. Haemophilus influenzae type b was historically dominant in unvaccinated young children. Mycobacterium tuberculosis produces a subacute presentation.

Important specimen. CSF via lumbar puncture; blood cultures should also be taken, since bacteraemia frequently accompanies bacterial meningitis and may be positive even when CSF culture is not.

Major diagnostic approach. CSF Gram stain and culture, CSF cell count, protein, and glucose profile, bacterial meningitis classically shows neutrophilic pleocytosis, elevated protein, low glucose, distinct from the lymphocytic, normal-glucose profile of most viral meningitis and the lymphocytic, low-glucose profile of tuberculous meningitis, and PCR, increasingly used for rapid pathogen identification.

Common bacterial groups. Streptococcus pneumoniae is the leading overall cause of community-acquired pneumonia. Haemophilus influenzae and Moraxella catarrhalis occur particularly in patients with underlying chronic lung disease. Klebsiella pneumoniae is classically associated with alcohol use disorder or diabetes. Legionella pneumophila, Mycoplasma pneumoniae, and Chlamydia pneumoniae form the atypical pneumonia group.

Pseudomonas aeruginosa and Staphylococcus aureus cause healthcare-associated and ventilator-associated pneumonia. Mycobacterium tuberculosis produces a chronic, subacute presentation.

Important specimen. Sputum, quality-dependent, ideally with few squamous epithelial cells and abundant neutrophils to confirm a genuine lower respiratory sample rather than oral contamination, blood cultures, and urinary antigen testing, pneumococcal and Legionella.

Major diagnostic approach. Sputum Gram stain and culture, blood culture, urinary antigen testing, and PCR for atypical organisms and M. tuberculosis where clinically indicated. Chest imaging supports but does not itself provide microbiological diagnosis.

Common bacterial groups. Streptococcus pyogenes is the dominant bacterial cause requiring specific identification given the risk of rheumatic fever. Corynebacterium diphtheriae is rare in vaccinated populations, but critical not to miss given pseudomembrane formation and airway risk. Neisseria gonorrhoeae occurs in the context of oropharyngeal sexual exposure. Fusobacterium necrophorum is associated specifically with Lemierre's syndrome.

Important specimen. Throat swab.

Major diagnostic approach. Rapid streptococcal antigen testing, high specificity, variable sensitivity, a negative result in a high-suspicion case is often followed by culture, or throat culture for S. pyogenes, specific culture media, tellurite agar, if diphtheria is suspected. The great majority of pharyngitis overall is viral, and bacterial testing is specifically targeted at identifying the subset requiring antibiotic treatment or urgent recognition.

Common bacterial groups. Staphylococcus aureus causes the acute presentation, a leading overall cause. Viridans group streptococci cause the subacute presentation, classically following dental procedures on an abnormal valve. Enterococcus species occur particularly in older patients, sometimes following a urological or GI procedure. Staphylococcus epidermidis causes prosthetic valve endocarditis. The culture-negative endocarditis group includes Coxiella burnetii and Bartonella species.

Important specimen. Blood cultures, ideally multiple sets collected before starting antibiotics given the diagnostic reliance on demonstrating persistent, typical-organism bacteraemia.

Major diagnostic approach. Blood culture, with the modified Duke criteria, combining microbiological, clinical, and echocardiographic findings, as the standard diagnostic framework, and serology or PCR specifically when culture-negative endocarditis from a fastidious organism is suspected.

Common bacterial groups. Salmonella, Shigella, Campylobacter jejuni, diarrhoeagenic E. coli pathotypes, and Yersinia enterocolitica, Vibrio cholerae and V. parahaemolyticus, and Clostridioides difficile specifically in the context of recent antibiotic exposure.

Important specimen. Stool.

Major diagnostic approach. Stool culture on selective and differential media, stool PCR panels, increasingly standard given superior sensitivity and turnaround time for multiple pathogens simultaneously, C. difficile-specific toxin and PCR testing, only on unformed stool, since testing formed stool risks detecting asymptomatic colonisation rather than active disease, and stool microscopy for faecal leukocytes, which helps distinguish invasive, Shigella, Campylobacter, EIEC, from noninvasive, V. cholerae, ETEC, causes at the bedside.

Common bacterial groups. E. coli is the dominant overall cause. Staphylococcus saprophyticus occurs in young sexually active women. Klebsiella pneumoniae and Proteus species are associated with struvite stones. Enterococcus species, and, in healthcare-associated and catheter-related infection, a broader range including Pseudomonas aeruginosa.

Important specimen. Midstream urine, clean-catch, minimising skin and periurethral contamination, or catheter specimen where indicated.

Major diagnostic approach. Urinalysis, leukocyte esterase, nitrites, the latter reflecting nitrate-reducing organisms such as most Enterobacterales, notably not produced by Enterococcus or S. saprophyticus, a useful negative predictive clue, and urine culture with colony count interpretation, a specific quantitative threshold used to distinguish true infection from contamination or low-level colonisation, context-dependent on specimen type and clinical presentation.

Common bacterial groups. Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, and Mycoplasma genitalium.

Important specimen. Genital, rectal, or oropharyngeal swab depending on exposure site; blood for syphilis serology.

Major diagnostic approach. Nucleic acid amplification testing, PCR, is now standard for gonorrhoea, chlamydia, and M. genitalium given superior sensitivity to culture. Culture is retained specifically where susceptibility testing is needed, particularly relevant for N. gonorrhoeae given its evolving resistance. The paired nontreponemal and treponemal serology algorithm is used for syphilis.

Common bacterial groups. Staphylococcus aureus and Streptococcus pyogenes are the two dominant causes across the spectrum from simple cellulitis to necrotising fasciitis. Clostridium perfringens causes gas gangrene. Pasteurella multocida is associated with animal bite wounds. Polymicrobial anaerobic and facultative flora cause diabetic foot infection and deep or contaminated wounds.

Important specimen. Deep tissue or aspirated pus where possible, a superficial swab of an open wound is frequently contaminated by colonising skin flora and is a comparatively poor specimen, and blood cultures if systemic signs are present.

Major diagnostic approach. Gram stain and culture of deep tissue or pus. Clinical assessment, rapidity of progression, presence of crepitus, disproportionate pain, systemic toxicity, is critical for recognising the surgical emergencies within this syndrome group, necrotising fasciitis, gas gangrene, that require urgent surgical intervention alongside, not instead of, microbiological workup.

Common bacterial groups. Staphylococcus aureus is the dominant overall cause across essentially all patient groups. Salmonella species show a specific association in sickle cell disease patients. Pseudomonas aeruginosa occurs particularly following nail puncture wounds through footwear, and in patients who inject drugs. Polymicrobial flora occurs in contiguous-spread osteomyelitis from an adjacent diabetic foot ulcer.

Important specimen. Bone biopsy is the diagnostic gold standard, since a superficial wound or sinus tract swab overlying osteomyelitis frequently reflects colonising surface flora rather than the true deep bone pathogen, a common and clinically important source of diagnostic error.

Major diagnostic approach. Bone culture and histology, biopsy, ideally obtained before or independent of antibiotic therapy where feasible, and blood cultures, positive in a meaningful proportion of cases, particularly in haematogenous osteomyelitis, and a useful noninvasive alternative when bone biopsy is not immediately available or appropriate.

Common bacterial groups. Staphylococcus aureus is the dominant overall cause. Neisseria gonorrhoeae is a specific and important cause in sexually active young adults, often as part of disseminated gonococcal infection with its associated triad of migratory polyarthralgia, tenosynovitis, and pustular skin lesions. Streptococcus species and Kingella kingae, particularly relevant in young children, a HACEK-group-related organism, also cause septic arthritis.

Important specimen. Synovial, joint, fluid aspirate, obtained before starting antibiotics wherever clinically feasible given the time-sensitive, joint-destructive nature of untreated septic arthritis.

Major diagnostic approach. Synovial fluid Gram stain, culture, and cell count, a markedly elevated, neutrophil-predominant white cell count supports a septic rather than purely inflammatory or crystal-induced process, though clinical correlation remains essential, and blood cultures in parallel.

Common bacterial groups. Essentially any organism can cause bacteraemia given an appropriate portal of entry and sufficient host vulnerability. The specific likely organism is best inferred from the suspected primary source: a urinary source favours E. coli, an intra-abdominal source favours a polymicrobial Enterobacterales and anaerobe mix, a catheter-related source favours S. aureus, coagulase-negative staphylococci, or Gram negative nonfermenters, and endocarditis-associated bacteraemia favours the organisms that typically cause endocarditis.

Important specimen. Blood cultures, ideally multiple sets from separate sites before antibiotic therapy.

Major diagnostic approach. Blood culture remains the single most important test. Identifying and, where possible, sampling the suspected primary source in parallel, urine, wound, intra-abdominal fluid, is essential for both diagnosis and source control, since bloodstream infection is, in the great majority of cases, secondary to a primary focus elsewhere rather than a truly primary event.

Common bacterial groups. Polymicrobial by default, reflecting the mixed colonic flora from which most intra-abdominal infection arises: E. coli and other Enterobacterales together with Bacteroides fragilis and other anaerobes, the classic combination underlying peritonitis, diverticulitis, and intra-abdominal abscess following bowel perforation or surgery.

Important specimen. Peritoneal fluid or abscess aspirate, obtained via image-guided drainage or at surgery; blood cultures in parallel if systemic signs are present.

Major diagnostic approach. Gram stain and both aerobic and anaerobic culture of the aspirated fluid. Empirical antibiotic coverage in this syndrome specifically must address both the facultative Gram negative and the anaerobic components of the expected polymicrobial flora.