**3.5.2 PCR strategies**

antibiotic susceptibility.

Universal bacterial detection by PCR-based amplification of the 16S rRNA gene allows the identification of bacteria or fungi which are not viable by conventional culture methods. The overall sensitivity may be higher compared with culture (Bergin et al., 2010; Dempsey et al., 2007; Ince et al., 2004; Levine et al., 1995; Panousis et al., 2005; Tunney et al., 1999). On the other hand, singular specific PCR assays (Kobayashi et al., 2009; Piper et al., 2009; Tarkin et al., 2003) or multiplex assays (Achermann et al., 2010) are sensitive but limited to the organisms included in the test panel.

Although important antibiotic resistance mechanisms like methicillin resistance can be identified genotypically with PCR (Kobayashi et al., 2009; Tarkin et al., 2003), for most substance classes phenotypic susceptibility testing will be necessary in the foreseeable future.

There is no straightforward method to determine whether microbial DNA as detected by PCR reflects living organisms. On the other hand, it cannot be ruled out that previous therapy with antibiotics hampers the sensitivity not only of culture, but also of PCR (Achermann et al., 2010).
