This week I am spending most of my time learning about clinical microbiology practices down at the Hospital in Truro, which is super interesting. The labs receive more than 300.000 samples a year: blood, urine, sputum, faeces, pus and skin swabs (as well as rarer samples such as corneal scrapings or tips of intravenal lines). It is the job of microbiologists to work out which organism(s) are causing disease and what antibiotics they are susceptible to. This is then entered in a centralized computer database accessed by consultants who are responsible to come up with a plan of action.
To identify bacterial types, microbial ecologists such as myself are used to sequencing a marker gene (ususally 16S) and using the BLAST algorithm to query a giant sequence database to find a match. For reasons of history, cost and speed this is not the case in clinical labs, instead, a combination of selective media, antibiotics and metabolic tests are used (not forgetting a healthy dose of experience). On Monday, I looked at bugs growing from sputum samples (either coughed up or, if that is not possible, retrieved by washing lungs with a saline solution).
Chris, pictured above, showed me the array of plates used to screen sputum samples: blood agar, CAP agar (another type of blood agar), bacitracin chocolate agar, CLED agar, manitol salt agar (for Staphylococcus aureus), SABC agar (for yeasts), Burkholderia cepacia agar, Pseudomonas agar, and in some cases Legionella or Listeria agar as well.
A blood agar plate and a chocolate agar plate. Chocolate agar is made using boiled blood; the nutrients released by the damaged red blood cells allow some species to grow that cannot feed on actual blood, in this case Haemophilus influenza. By the way, H. influenza does not cause influenza (a virus does), however, it was frequently encountered in lungs of patients weakened by that disease, hence the misnomer.
On Tuesday, I had a look at plates inoculated with urine. Urine samples (preserved in boric acid) first go through one of the two flow cytometers (named Alex and Belinda) that count bacteria, blood cells and other particles. Based on the ratio of bacteria and blood cells, the computer decides which samples will be cultured (less than half). Here chromogenic ‘orientation’ agar is used, where different bacterial types grow into differently coloured colonies. Most (not all) Escherichia coli turn pink, whereas other ‘coliforms’ turn blue. To save cost, two samples go on one plate. In the photo above, the top sample contains colourless Staphylococcus aureus and the bottom sample E. coli. Besides those, I saw Staphylococcus saprophyticus, Streptoccus pneumoniae, Pseudomonads, Proteus, enterococci, coliforms and lactobacilli. At the end of the day I could pick out most!
Colony growth, colour and morphology can only tell you so much, that is why there are a battery of other tests to differentiate between species. For example, an antiserum test kit depicted above is used to tell different types of Streptococcus apart. This is important, as these different types are associated with different complications. Sterile babys scraping Group B streptococci from the reproductive tract during birth can be off to a bad start and so pregnant women are always screened for them.