Bacteria

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Streptococcus pyogenes (Group A strep)

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Upper respiratory tract commensal in 3-5% of adults and up to 10% of children. Responsible for a variety of conditions, ranging from sore throat to necrotising fasciitis. There are a number of post-infectious ‘immunological’ conditions such as post-streptococcal glomerulonephritis and rheumatic fever. Gram-positive cocci that grow in pairs and chains. Facultative anaerobic. Catalase-negative, non-sporing, non-motile. β-haemolytic (complete haemolysis / clear zone on blood agar). Penicillin.

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Streptococcus pneumoniae

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Colonises the nasopharynx of 5 – 10% of healthy adults and 20 – 40% of healthy children. The rate of colonisation is seasonal, with an increase in winter. Causes meningitis, sinusitis, otitis media, endocarditis, septic arthritis, peritonitis, and a number of other infections. Gram-positive cocci that grow in pairs or chains. Catalase negative, optochin sensitive, lysed by bile salts. α-haemolytic (green discoloration due to breakdown of haemoglobin of blood agar). Penicillin.

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Staphylococcus aureus

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Found in the anterior nares (external portion of nostrils) of 10 – 40% of people. Can cause a wide range of conditions from superficial skin infections to severe life-threatening conditions e.g. toxic shock syndrome. Can cause skin and soft-tissue infections, pneumonia, bone and joint infections, systemic infections, prosthetic device-related infections. Gram-positive coccus in clusters. Non-motile, non-spore forming, catalase positive, coagulase positive, DNase positive. Flucloxacillin.

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Escherichia coli

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E. coli is the type species of the genus Enterobacteriaceae, and contains a variety of strains ranging from commensal organisms to highly pathogenic variants. Infections tend to infect the gut and urinary tract but almost any extra-intestinal site may be involved. Gram-negative, rod-shaped. Usually motile, usually ferment lactose. Ampicillin.

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Corynebacterium diphtheriae

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Diphtheria is rare in the UK but remains a common problem in developing countries and the former Russian states. The organism spreads via nasopharyngeal secretions, and can survive for months in dust and contaminated dry fomites. Incidence is highest in young children (>3–6 months old), when protective maternal antibodies wane. Anterior nasal infection presents with a serosanguinous or seropurulent nasal discharge often associated with a whitish membrane. Faucial infection is the most common site for clinical diphtheria. Clinical features include fever, malaise, sore throat, pharyngeal injection, development of a pseudomembrane which is initially white, then grey with patches or green or black necrosis. Cervical lymphadenopathy may result in a characteristic ‘bull neck’ and inspiratory stridor. Myocarditis occurs after 1–2 weeks, usually as the oropharngeal disease is improving. C. diphtheriae is a non-motile, non-sporing and non-capsulate Gram-positive rod. It is catalase-positive, urease-negative, nitrate-positive, pyrazinamidase-negative and cystinase-negative. It can reliably be identified with the API Coryne. Penicillin, antitoxin.

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Salmonella spp.

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Salmonellae are commensals and pathogens of a wide range of domesticated and wild animals. Some species, e.g. S. Typhi and S. Paratyphi are well adapted to humans and have no other host. In humans, salmonellae can be divided into those that cause enteric fever (S. Typhi and S. Paratyphi) and the non-typhoidal Salmonella spp. (NTS). Salmonellae are usually transmitted by the faeco-oral route. Can cause: Gastroenteritis; Enteric fever; Bacteraemia and endovascular infection; Salmonellosis in HIV – 20 to 100-fold increased risk - more likely to have severe invasive disease (enterocolitis, bacteraemia, meningitis); Localized infections; Chronic carrier state. which grow readily on routine media. They are motile, oxidase-negative, urease-negative, non-lactose fermenters (NLF). Enteric Fever. First-line treatment for imported cases of typhoid fever in the UK is now ceftriaxone. Non-typhoidal salmonella. Gastroenteritis does not usually require treatment, except in the immunosuppressed, neonates, the elderly and those at risk of bacteraemia. Suitable antibiotics include ampicillin.

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Shigella spp.

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Most cases of shigellosis in the UK occur in young children, although infection occurs in any age after travel to areas where hygiene is poor. S. sonnei is endemic in the UK, while S. boydii and S. dysenteriae, and most S. flexneri infections, originate outside the UK. . The organisms cause bacillary dysentery by an invasive mechanism identical to Enteroinvasive E. coli (EIEC). S. dysenteriae usually causes a more-severe illness, possibly with marked prostration and paediatric febrile convulsions. S. dysenteriae may also be associated with toxic megacolon and the haemolytic uraemic syndrome. S. flexneri and S. boydii may also cause severe disease, while S. sonnei usually causes mild symptoms. Shigella rarely invades other tissues, hence septicaemia and metastatic infection is unusual. Shigella organisms are non-motile, non-capsulated Gram-negative rods. Most appear as non-lactose fermenters after 18–24 h incubation on MacConkey or DCA (desoxycholate citrate) agar, but S. sonnei is the only late lactose fermenter. Shigella is urease, citrate and H2S-negative. Oral rehydration. For severe infections: ciprofloxacin, ampicillin.

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Vibrio cholerae

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There are ~20 cases of cholera imported into the UK every year. Cholera is prevalent in Central and South America, Africa, and Asia. V. cholerae usually causes the typical profuse watery diarrhoea of cholera, which may rapidly lead to hypovolaemic shock and death from dehydration. Milder cases are similar to other causes of secretory diarrhoea, and asymptomatic infections also occur. Non-O1 V. cholerae usually causes mild, sometimes bloody diarrhoea, but may occasionally be severe and resemble cholera. Patients exposed to aquatic environments may suffer from wound infections, and bacteraemia and meningitis have been reported. Vibrios are short, curved or ‘comma-shaped’, aerobic Gram-negative rods, which are motile by a single polar flagellum. They ferment both sucrose and glucose but not lactose, and reduce nitrate to nitrite. Most are oxidase-positive and produce indole.

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Mycobacterium tuberculosis

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M. tuberculosis infects one-third of the world’s population and is the most-frequent infectious cause of death worldwide. Infection is usually acquired by inhalation of infectious droplet nuclei. Ninety per cent of primary infections are asymptomatic. Pulmonary tuberculosis is the most common presentation. Tuberculosis may also disseminate (military TB) or affect almost any other organ (extra-pulmonary TB): pleural cavity, pericardium, lymph nodes, GI tract, and peritoneum, GU (genitourinary) tract, skin, bones and joints, and CNS. M. tuberculosis is an aerobic, non-sporing, non-motile, weakly Gram-positive bacillus with a thick cell wall containing mycolic acid, which renders it acid-fast (Ziehl–Neelsen (ZN) stain). Treatment is with combination chemotherapy for several months. For most types of tuberculosis, the usual regimen is a 2-month intensive phase with three or four drugs, followed by a 4-month continuation phase. The two most commonly used antibiotics are isoniazid and rifampicin.

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Clostridium tetani

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C. tetani causes ~10 cases of tetanus/year in the UK. Tetanus is a notifiable disease. Localized tetanus involves muscle rigidity and painful spasms near the wound site. Usually a prodrome of generalized tetanus, with symptoms summarised by ROAST (rigidity, opisthotonus, autonomic dysfuction, spasms, and trismus). C. tetani is a motile, obligate anaerobe which classically produces ‘drumstick’ terminal spores. It often stains Gram-negative. C. tetani produces a thin spreading film on enriched blood agar, due to the motility by peritrichous flagella. Involve ICU early. Give tetanus immunoglobulin (TIG); wound debridement, and antimicrobials including metronidazole or penicillin. Vaccination with tetanus toxoid following recovery is important to prevent future episodes.

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Haemophilus influenzae

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Haemophilus influenzae capsular type 3 (Hib) used to be a common cause of meningitis in childcare. The annual incidence of invasive Hib disease dropped dramatically after introduction of the Hib conjugate vaccine in 1993. H. influenzae inhabits the upper respiratory tract of humans; 25–80% of healthy people carry non-capsulate organisms, while 5–10% carry capsulate strains (~50% of which are capsular type b). Invasive infections – e.g. meningitis, epiglottitis, bacteraemia with no clear focus, septic arthritis, pneumonia, cellulitis. Non- invasive infections – e.g. otitis media, sinusitis, purulent exacerbations of COPD. Haemophilus influenzae is a small, fastidious Gram-negative coccobacillus. These organisms only grow in the presence of X and V factors. Less-serious H. influenzae infections can be treated with oral ampicillin. First-choice antibiotics for life-threatening H. influenzae infections are 3rd-generation cephalosporins, e.g. ceftriaxone.

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Neisseria gonorrhoeae

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N. gonorrhoeae only infects humans and causes the sexually transmitted infection gonorrhoea. Increasing rates of antimicrobial resistance, together with its persistence and association with poor reproductive health outcomes have made it a major public health concern. Gonorrhoea commonly presents as a purulent disease of the urethral mucous membrane and also the cervix in females. Secondary local complications (e.g. epididymitis, salpingitis, pelvic inflammatory disease) and metastatic complications (e.g. arthritis) may occur if the primary infection is inadequately treated. Other manifestations of disease include disseminated gonococcal infection (skin lesions, painful joints, and fever), ophthalmia neonatorum (purulent conjuncitivitis of the newborn), peri-hepatic inflammation (Fitz-Hugh–Curtis); and rarely endocarditis or meningitis. Rectal or pharyngeal infection is often asymptomatic, and identified through contact tracing. Gram-negative diplococci (in association with neutrophils from urethral swabs). Oxidase-positive. Ceftriaxone.

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Pseudomonas spp.

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P. aeruginosa is widespread in soil, water, and other moist environments. Humans may be colonized with P. aeruginosa at moist sites such as the perineum, ear, and axilla. It is a highly successful opportunistic pathogen, especially in the hospital setting. This success is largely due to its resistance to many antibiotics, ability to adapt to a wide range of physical conditions, and minimal nutritional requirements. P. aeruginosa causes a wide spectrum of conditions: Community-acquired infections are rare, and tend to be mild and superficial. Examples include otitis externa, varicose ulcers, and folliculitis associated with jacuzzis. Nosocomial infections with P. aeruginosa tend to be more severe and more varied than community infections. P. aeruginosa may account for ~10% of all hospital-acquired infections. Examples include pneumonia, urinary tract infections, surgical wound infections, bloodstream infections, and respiratory infections. Cystic fibrosis patients, burns patients and mechanically ventilated patients are at particular risk. Other conditions associated with P. aeruginosa include endocarditis (IDUs and prosthetic valves), eye infections, bone and joint infections, postoperative neurosurgical infections, and eye and ear infections. This non-sporing, non-capsulate, motile Gram-negative rod is a strict aerobe. Antipseudomonal agents include the fluoroquinolones (these are the only oral option), ceftazidime, ticarcillin, piperacillin, carbapenems (imipenem, meropenem), aminoglycosides (gentamicin, tobramycin, amikacin), polymixins (colistin), and aztreonam.

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Campylobacter jejuni

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C. jejuni is the commonest cause of diarrhoea in most developed countries. Campylobacter gastroenteritis is variable in terms of symptoms and severity. In severe cases, GI haemorrhage, toxic megacolon, and Haemolytic Uraemic Syndrome (HUS) have been reported. Other complications include meningitis, deep abscesses, cholecystitis, and reactive arthritis. Approx. 25% cases of Guillain-Barré syndrome (GBS) have documented preceding Campylobacter gastroenteritis – the LOS cell surface structures act as critical factors in triggering GBS through ganglioside mimicry. Campylobacter organisms are spiral-shaped flagellate bacteria belonging to rRNA superfamily VI. This small, spiral GNR has a single unsheathed flagella at one or both poles and is extremely motile. Oxidase-positive. Rehydration and symptom relief is usually adequate, as Campylobacter infection is usually self-limiting in 5–7 days. However, in severe dysenteric disease, erythromycin or ciprofloxacin may be prescribed.

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Helicobacter pylori

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H. pylori is a spiral-shaped flagellate bacteria belonging to rRNA superfamily VI, which colonizes humans (it is found in approx 50% of the world population). H. pylori is associated with 95% of duodenal and 70% of gastric ulcers. Epidemiological studies have highlighted the association of H. pylori and gastric cancer, and WHO classifies H. pylori as a group 1 carcinogen. This GNR is shaped like a helix (hence its name) and has a tuft of sheathed unipolar flagella. It is strictly micro-aerophilic and requires CO2 for growth. It is relatively inactive biochemically, except for strong urease production. Triple therapy is given in specific circumstances and consists of a proton pump inhibitor (PPI) e.g. omeprazole and two antibiotics (e.g. amoxicillin, clarithromycin, or metranidende).

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Chlamydia

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Small, obligately intracellular (they are unable to produce ATP themselves), Gram-negative organisms. Three species produce human disease: Chlamydia trachomatis, C. psittaci, and C. pneumoniae. They differ antigenically, in host cell preference and in antibiotic susceptibility. Chlamydophila pneumoniae: The cause of 3–10% of community-acquired pneumonia cases among adults. Adolescents tend to experience a mild pneumonia/bronchitis, whereas older adults can experience more severe disease and repeated infections. Fifty per cent of young adults have serological evidence of previous infection. Unlike C. psittaci, human-to-human transmission by respiratory secretions is the norm. In most populations infection is more common in males and this may reflect cigarette use. Incubation is 3–4 weeks and symptoms of a URTI are followed by bronchitis or pneumonia 1–4 weeks later. Most infections are asymptomatic or cause only mild symptoms. Other features: hoarse voice, non-productive cough, headache. Fever is often absent. Symptoms can be very prolonged even with appropriate treatment. Small, obligately intracellular (they are unable to produce ATP themselves), Gram-negative organisms. Outside a host cell they are tiny (300 nm diameter), inactive ‘elementary’ bodies. They infect cells primarily by receptor-mediated endocytosis. Erythromicin, doxycyline or azithromycin or other depending on circumstances.