4.3 Identifying Gram-negative organisms

Gram-negatives are found in a range of clinical samples. As they are common causes of UTI, urine culture media are designed to isolate them. They are also an important cause of bloodstream infection – either Gram-negative sepsis, for example from a urinary source, biliary sepsis or an IV line infection, or as enteric fever caused by Salmonella typhi or paratyphi so can be isolated from blood cultures. When found in superficial swabs they are often growing as contaminants or colonising an existing wound.

The approach taken to identify Gram-negative organisms depends on several factors.

  1. The site of the body where the sample was taken. In Activity 11, for example, you learned which type of sample would be most likely to yield which key pathogen.
  2. The likelihood of the sample from this site containing a mixture of organisms – commensals or contaminants
  3. Whether there is already a presumptive identification. For example, stool samples are usually cultured on media which selects for enteric pathogens. When S. typhi and S. paratyphi are suspected, blood cultures may also be taken to look for these organisms. The identification process of these organisms from blood cultures will be longer than from stool samples as you do not have the benefit of seeing the appearance on the selective medium.

In practice, identification of Gram-negative organisms often proceeds by a process of elimination; one positive test result dictates the choice of a secondary test and so on. This process requires laboratory technologists to have the appropriate knowledge and skills to perform this screening process.

The following sections outline how the six Gram-negative key GLASS surveillance pathogens are identified for laboratories without access to MALDI-TOF/automated systems.

4.2 Identifying Gram-positive cocci

4.3.1 Enterobacterales species