Medical Microbiology and Infection at a Glance. Stephen H. Gillespie

Molecular techniques

      Southern blotting and nucleic acid hybridization

      A labelled DNA probe can bind to components of the pathogen and be detected by the activity of its attached label. This technique is specific and rapid, but less sensitive because there are no amplification steps.

      Nucleic acid amplification tests

      Nucleic acid amplification tests (NAATs) amplify specific regions of the pathogen genome (DNA or RNA) to make the diagnosis until there is sufficient for detection. Primers are designed to bind to target a specific pathogen sequence and a polymerase synthesizes new nucleic acid over multiple cycles. Automated systems and commercial kits can follow this process in real time and make these tests available in many laboratories. NAATs have the advantage that they can detect slow or difficult to grow organisms, or make a diagnosis in the patient who has taken antibiotics. PCR can also detect virulence determinants or resistance determinants creating a surrogate susceptibility result (e.g. rpoB gene mutation for rifampicin resistance in M. tuberculosis).

      Whole genome sequencing

      The reducing cost of sequencing the whole pathogen sequence means that this is increasingly widely available. It provides extremely detailed information on the pathogen. Using complex manipulations of the genomic data it is possible to determine the relationship between organisms and identify their transmission. It has become vital in tracking viruses like influenza, and resistant or virulent bacteria in community or hospital outbreaks. Rapid availability of data can rapidly rule in or rule out an outbreak.

6 Antimicrobial therapy – principals and concepts

      Antibiotics aim to kill organisms while causing no harm to the patient – this concept is known as selective toxicity. It is best achieved by inhibiting a pathogen function that human cells do not have. Bacteria have a rigid cell wall with peptidoglycan that human cells lack and can be inhibited by penicillin. Finding selective targets is more difficult for eukaryotic pathogens that can have similar pathways to humans. Similarly challenging are obligate intracellular pathogens such as viruses where detailed knowledge of viral reproduction is required to create effective treatments.

      The difference between the dose necessary for treatment and that which causes harm is usually large and is known as the therapeutic index. The aminoglycosides are exceptions to this because doses just above the therapeutic level can be toxic. While all antimicrobials have potential unwanted effects, fortunately serious unwanted effects are not frequent. We aim, therefore, to provide an effective antibiotic regimen that maximizes the chance of a successful outcome with the least risk of adverse events.

Adverse events

      Gastrointestinal tract

      Mild gastrointestinal upset is probably the most frequent side effect of antibiotic therapy. Antibiotic activity can upset the balance of the normal flora within the gut (β‐lactams are especially likely to do this) resulting in overgrowth of commensal organisms such as Candida spp. Alternatively, antibiotic therapy may provoke diarrhoea or, more seriously, pseudomembranous colitis (see Chapter 24).

      Skin

      Cutaneous manifestations range from mild urticaria or maculopapular, erythematous eruptions to erythema multiforme and the life‐threatening Stevens–Johnson syndrome. Most cutaneous reactions are mild and resolve after discontinuation of therapy.

      Haemopoietic system

      Patients receiving chloramphenicol or antifolate antibiotics may exhibit dose‐dependent bone marrow suppression. More seriously, aplastic anaemia may rarely complicate chloramphenicol therapy. High doses of β‐lactam antibiotics may induce granulocytopenia. Antibiotics are a rare cause of haemolytic anaemia. Many antibiotics cause a mild reversible thrombocytopenia or bone marrow depression.

      Renal system

      Aminoglycosides may cause renal toxicity by damaging the cells of the proximal convoluted tubule. Patients who are elderly, have pre‐existing renal disease or are also receiving other drugs with renal toxicity are at higher risk. Tetracyclines may also be toxic to the kidneys.

      Liver

      Isoniazid and rifampicin may cause hepatitis; this is more common in patients with pre‐existing liver disease. Other agents associated with hepatitis are tetracycline, erythromycin, pyrazinamide, ethionamide and, very rarely, ampicillin or fluoroquinolones. Cholestatic jaundice may follow tetracycline or high‐dose fusidic acid therapy.

Acute allergy and intolerance

      Allergy to antibiotics is relatively common with a wide spectrum of impacts. Anaphylaxis from beta‐lactam antibiotics is potentially life‐threatening, but rare. A history of penicillin anaphylaxis must be captured on a patient’s medical record. Severe skin and systemic reactions such as Stevens–Johnson syndrome associated, for example, with co‐trimoxazole, can also be life‐threatening. Other allergic reactions can include skin reactions such as fixed drug eruptions.

Targeting treatment

      It is important to ensure that sufficient antibiotic reaches the site of infection. This means it is important to understand where the organisms are and how the antibiotic is absorbed and distributed in the body. For example, for effective treatment of meningitis it is essential that the antibiotic crosses the blood–brain barrier well. This factor, called pharmacokinetics, allows treatment plans based on knowing antibiotic absorption, distribution and protein binding of drugs. Some agents such as aminoglycosides are polar and largely located in the extracellular fluid. They do not penetrate so well into lung or bone and this may limit their application in some infections.

      In the development of new antibiotics the way in which the new agent is absorbed and distributed throughout the body is studied by careful sampling.

Monitoring therapy

      This is achieved by serial measurement of the concentration of an antibiotic in the serum or at the site of infection (e.g. in the CSF for meningitis).

      This may be necessary in the following.

       To assist in the management of an infection with intermediate susceptibility (if inhibition of an organism occurs only at high antibiotic concentrations, it is important to ensure sufficient concentrations are found at the site of infection, e.g. in Pseudomonas meningitis, antibiotic concentrations should be measured in the CSF).

       To reduce the risk of toxicity, which is important where the therapeutic index is low. Serum levels of e. g. aminoglycosides should be measured in serum taken at key times in relation to intravenous or intramuscular dosage, which allows the dose to be adjusted according to normograms. Also there should be careful adherence to guidelines, e.g. for a high peak the dosage may be reduced, or for a high trough level the medication is given less frequently).

7 Antibacterial agents – pharmacology and modes of action