3 The pre-analytical stage

The clinical presentation of an infectious disease reflects the interaction between the host, the microorganism and the environment. When they are assessing a patient, the clinician – who could be a doctor, clinical officer, nurse, physician associate, community healthcare worker, etc. – needs to consider:

• the patient’s history and reported symptoms
• any physical findings
• any risk factors that might pre-dispose them to particular infections, such as whether they are immunosuppressed, what diseases are prevalent locally or any occupational exposures.

A clinician must also consider any local outbreaks of diseases such as cholera, or disease outbreaks in healthcare facilities related to antimicrobial-resistant organisms. For AMR, a history of recent healthcare exposure and whether or not the patient has recently taken antimicrobials is also important, because these are risk factors for resistant infections.

Signs and symptoms also vary according to the site and severity of infection; they may be localised or systemic, with fever, chills and hypotension. For example, patients with an uncomplicated UTI may have localised symptoms such as pain on passing urine; but if the infection is more severe and involves their kidneys, they may have back or loin pain, fever and chills, weakness and tenderness, and are likely to be unwell. Patients with bloodstream infections are likely to be very unwell, with systemic fever and low blood pressure.

The origin of the infection also needs to be considered. Exogenous infections are acquired from the environment or animal sources, or from another person; for example, non-surgical wounds may become contaminated, or infections such as meningococcal meningitis may spread person-to-person. Endogenous infections are caused by normal flora: for example, Enterococcus faecalis, which is a part of normal gastrointestinal tract flora, can be introduced into the blood during surgical intervention in the patient.

Figure 3 gives an overview of these interactions.

Figure 3 The epidemiological triad.

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An infection can depend on factors of the host (such as susceptibility to infection, immune status, genetic profile, age, race, gender), environment (temperature, humidity, crowding, food, water, pollution, healthcare facilities) or the microorganism (virulence factors, infectious dose tropism of the organism to the site of infection).

Figure 3 The epidemiological triad.

Although this courses focuses on bacterial infections, you should remember that patients presenting with fever may have other types of infection, and the history and examination should consider all the possible infection types. Again, the patient’s exposure history and information about local prevalence of infections is important: for example, whether the region has malaria or dengue, or whether the patient has travelled to an area with particular infections.

The GLASS Manual for Early Implementation (WHO, 2015) states that, as a minimum, the following core information must accompany each patient sample sent for AST:

• a unique identifier
• patient name
• patient date of birth
• patient gender
• specimen type
• date of specimen collection
• hospital or community origin (see sample request form; any date of hospital admission would be required from the source data).

Additional information (such as hospital name, ward or department, patient diagnosis, medical history, referral, antimicrobial therapy, etc.) may be requested according to local and national protocols.

Figure 4 Sample form to be sent with a sample from a patient as a request for AST, taken from the GLASS Manual for Early Implementation, Annex 2 (WHO, 2015)

This information can be read into SEDRI-LIMS or a comparable system via a barcode or QR code.