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Pandemic Preparedness Capabilities

Identification of molds and yeasts using Nanopore sequencing and MALDI-TOF.

PI(s)/Head responsible for the resource:

Johan Lindh

Host organisation(s):

Uppsala University

Resource description:

The department of Clinical microbiology and hygiene (KMB) at Uppsala university hospital adopted to the pandemic situation very fast, we were up and running with in-house established methods for RT-PCR analyses of SARS-CoV2 already in February, 2020. We have since then developed several different methods including sequencing protocols using Nanopore technology and mutantRTPCR.

We have today a large capacity in the area of SARS-CoV-2 analyses, both whole genome sequencing and in RTPCR and are also ready to detect new viruses. We have developed qualified methods and the use of 96 hole plates in all steps of above. Since all methods and instruments are validated and quality assured they are also used in other routine diagnosis. Our future perspectives in this area are to develop 18S sequencing methods in order to identifye molds and yeasts together with protocols to detect the same using MALDI-TOF.

Another method which can detect different microbes at a high output is the MALDI-TOF system. Today we have the system running at a capacity of 96 samples per hour and per instrument. A big advantage with this system, if compared with RTPCR, is that the detection is at the level of expressed proteins instead of genetic material. This is especially true if resistance to drugs will be measured.

Contact information:

Johan Lindh
Department of Medical Sciences, Clinical Microbiology, Uppsala University