Advanced Techniques in Diagnostic Microbiology

26. Molecular Strain Typing 455
patterns presumably provide increased levels of discrimination and allow detection
of substrains or strain variants that may evolve from an original strain (Boerlin
et al., 1996; Pujol et al., 1997; Olive and Bean, 1999). Several authors have compared
different genotyping methods for C. albicans. In general, there is a lack of
consensus on the method(s) of choice as well as the interpretation of results. The
use of a single method may not be optimal, and a combination of typing techniques
is often required to provide a comprehensive assessment of the epidemiology of
candidiasis (Vazquez et al., 1991; Bostock et al., 1993; Diaz-Guerra et al., 1997;
Pujol et al., 1997). For example, a combination of methods with high and low discriminatory
power may be useful for nosocomial source tracking because higher
discrimination allows detection of strain variants, whereas lower discrimination is
more helpful for determining isogeneity of organisms (Lopez-Ribot et al., 2000).
By using the Candida-specific DiversiLab Kit for strain discrimination and the
general DiversiLab Yeast Kit for lower discrimination, two purposes could be
served with this one technology.
Filamentous fungi such as Fusarium and Zygomycetes have also been shown
to contribute to hospital-acquired infections. Fusariosis, an emerging and severe
opportunistic mold infection, is typically a community-acquired mycosis (Raad
et al., 2002) however, the potential for nosocomial transmission has recently been
raised (O’Donnell et al., 2004). Godoy et al. recently showed the clinical utility
of manual rep-PCR for genotyping Fusarium (Godoy et al., 2004). Automated
rep-PCR was recently used to demonstrate discrimination of Fusarium species
and strains (Healy et al., 2005). Strain typing of Fusarium isolates using MLST
and AFLP established a single clonal lineage as a large part of the clinical isolates
examined from a study of three U.S. hospitals (O’Donnell et al., 2004). Additionally,
Zygomycetes are increasingly reported as causing lethal infections (Walsh
and Groll, 1999). Methods such as DNA sequencing and RFLP have shown subspecies
discrimination of different Zygomycetes species (Chakrabarti et al., 2003;
Kobayashi et al., 2004). Automated rep-PCR also successfully grouped multiple
Zygomycetes species (Kontoyiannis et al., 2005). There is a growing need for
strain typing to track the source of outbreaks for a wide variety of organisms.
Infections Caused by Community-Acquired Organisms,
Colonization, Recurrence, or Reinfection
There has been awareness of community-acquired pathogens, but that phenomenon
is now being more carefully studied as it appears that the level of community acquisition
is somewhat organism dependent. The prevalence of community-acquired
MRSA has increased, as confirmed by the use of microbial strain typing (Herold
et al., 1998; Fey et al., 2003), and the increase of community-acquired infections
makes the determination of HAI increasingly difficult. In order to understand
the transmission and source of MRSA outbreaks, strain typing must be used to
compare community-acquired and nosocomial pathogens at the genomic level