In the Institute of Microbiology, thanks to a strong research and development process, all the molecular tests are mainly based on in house tests and run in a fully automated unique platform to efficiently detect viral, bacterial, fungal and parasitic nucleic acids (Greub et al. 2016). After 10 years of continuous developments, our laboratory currently proposes 91 different real-time TaqMan PCRs (42 bacterial, 32 viral, 9 fungal and 8 for parasites). The tests are proposed four times a day, in a (semi-)quantitative format. Several flexible syndromic tests panels are available for etiological diagnosis of meningitis, encephalitis, sexually-transmitted infections, as well as respiratory tract infections, to name a few. In addition, our institute propose a large variety of specific PCRs allowing the molecular detection of intracellular bacteria and fastidious micro-organisms including Bartonella henselae and B. quintana, Chlamydia pneumoniae, C. psitacci and C. trachomatis, Coxiella burnetii, Mycobacterium tuberculosis, Legionella pneumophila, Mycoplasma pneumoniae and M. hominis, as well as Rickettsia spp. Using real-time PCR routinely on various samples with excellent accuracy let us shift to a molecular syndromic approach. Thus, a panel of PCR targeting different micro-organisms frequently involved in a given clinical situation can be tested on a single specimen during the same day.
On the other hand, when cultures are remaining dramatically negative especially if intracellular or difficult to grow bacteria (or fungi) are responsible of the disease or when antibiotics were administrated before sampling, broad-range conventional PCRs may be used to identify some additional or unexpected pathogens.