Application of next-generation sequencing in microbiology

Increasing numbers of infections with multidrug-resistant bacteria and emerging zoonotic pathogens are considered significant challenges for the global public health. The application of modern technologies to develop new diagnostic strategies for the benefit of patients and to identify novel infectious etiologies is of great importance. Nucleic acids are the building blocks of all known forms of life. Next-generation sequencing platforms can determine millions of nucleic acids in parallel and open up new fields in medical diagnostics.NGS can be applied to cultured bacteria to obtain information on the entire bacterial genome (whole-genome sequencing, WGS). We applied WGS to create genetic fingerprints of antibiotic-resistant Enterococcus bacteria, a common cause of hospital outbreaks, in order to unravel transmission routes and outbreak dynamics in a regional German university medical center. Furthermore, we evaluated WGS to accelerate antimicrobial resistance prediction of Mycobacterium tuberculosis (the cause of tuberculosis).

Nucleic acids can also be extracted without culture directly from sample material to detect bacteria, fungi, parasites and viruses using NGS. However, this novel and promising approach still faces many challenges prior to its incorporation into clinical diagnostics. We applied and optimized this approach to detect microbes and antimicrobial resistance genes in clinical patient samples, animal samples and samples from the hospital environment.

Dissertation: http://hdl.handle.net/11370/06c7a9d9-7e21-424d-9b34-e0079ff44071