Hunting for Pathogens

Our Diagnostic laboratories offers a wide range of targeted analytical tests to detect the presence of bacteria, viruses, fungi and parasites. An interview with Prof. Gilbert Greub, Director of our Institute of Microbiology.

What diseases can you diagnose in your laboratory?

Historically speaking, microbiology has enabled us to identify the pathogens that cause infectious diseases, which can sometimes be very serious, such as pneumonia, endocarditis or pyelonephritis. (Editor's note: infections affecting respectively the lungs, the heart and the kidneys). But we have recently come to the conclusion that microbes could also be the cause of other types of diseases. Here in Lausanne, we suspect, for example, that Chlamydia pneumoniae bacteria might be the cause of a certain kind of asthma. However, we should be aware that we all carry about half a kilo of bacteria which, contrary to popular belief, play an important role in the proper functioning of our bodies. An imbalance of this bacterial population can have many consequences. Thus, a change in the bacterial composition of the intestine may be associated with obesity.

What is the volume of your workload?

Our laboratory receives from 300 to 500 samples every day, on which we conduct one or more tests, which is equivalent to about 800 analyses every day. We mainly identify the pathogens responsible for respiratory infections, such as pneumonia or bronchitis, or urinary infections, such as cystitis. But, as we are a hospital laboratory, we also handle samples taken from severe or very unusual cases. For example, we recently discovered an infection never seen before here at the CHUV. The infection is called sparganosis and was caused by the larvae of a parasitic worm which, instead of completing its natural cycle in the body of a dog, accidentally contaminated a human host, our patient.

That takes a lot of hard work! What kinds of tests do you conduct?

Taking as an example pneumonia, which can be caused by numerous bacteria or viruses, we examine the patient's sputum, typically using three methods. Firstly, a microscopic examination, which provides a preliminary indication of the presence or absence of bacteria and their quantity. It allows us to magnify the germs one thousand times, so we see them with a size of one millimetre. The diagnosis can then be refined by cultivating the sputum. This is done in dishes containing agar medium, which is inoculated and incubated for 24 to 48 hours, so we can detect most bacteria potentially involved in the patient's pneumonia. Lastly, once we have isolated the suspected microorganism, we analyse its resistance to antibiotics and send our findings to the treating physician.

But why do you need to identify precisely the pathogen causing the pneumonia?

If we know the precise identity of the pathogen, we can choose the most appropriate antibiotic treatment, with less side effects than a combination of multiple antibiotics. Moreover, this gives us an indication of its mode of transmission, which helps us to guide public health measures during an epidemic. In 2012, for example, a dozen cases of pneumonia were caused by Coxiella burnetii, and the original source was identified as a farm in the canton of Vaud with a flock of 1,200 infected sheep.

And do you also practise molecular biology?

Of course! What we analyse is the DNA or RNA of the pathogen. For this purpose, we increasingly use PCR techniques, which consist of extracting, amplifying and detecting a gene that is specific to a particular bacterium or virus, or a gene that is common to several different organisms. Continuing with our example of pneumonia, these techniques allow us to identify bacteria that cause atypical pneumonia, such as Chlamydia pneumoniae, mycoplasma or several respiratory viruses, particularly in the case of immunosuppressed patients. Thus, the real challenge for the treating physician is not simply to diagnose a case of pneumonia, but to identify its cause, as dozens of different pathogens may be responsible for the infection.

That's like finding a needle in a haystack!

Yes, it can sometimes be quite complicated! Since 2012, we also have a Clinical Genomics and Metagenomics laboratory, which is an area in which we were forerunners. In that laboratory, we analyse the genome, that is to say the entire set of genes of these micro-organisms, keeping in mind that each bacterium has between 1000 and 5000 genes... This approach greatly facilitates the identification of patients infected with the same strain of bacteria, which helps us to detect certain epidemics. As for metagenomics, which involves the sequencing of the entire DNA of a microbial community present in a given location, for example in the gastrointestinal flora, we are currently using this technique mostly in research projects. But it will soon be included in our diagnostic arsenal, especially for obesity, which is a very promising field!

• Microscopy and cultures

  Direct examination by microscopy and culturing

• Molecular diagnostic and mycobacteriology unit

  PCR and other molecular amplification techniques
  Mycobacteriology

• Serology laboratory

  Indirect diagnosis of microbial infections through the detection of antibodies in the serum of the patients

• Genomics and metagenomics laboratory

  DNA sequencing of the genome(s) of a microbe or of a complex microbial community

• Rapid tests laboratory

  Immuno-chromatographic tests, rapid and automated PCRs