The Use of DNA Methods to Characterize Biofilm Infection - Antibiofilm Agents: From Diagnosis to Treatment and Prevention - page 20

3 Advantages of DNA Diagnosis: The One Eye
An Oslerian (Sir William Osler) model of medicine mandates that the clinician
diagnose a malady as fully as possible to formulate the most appropriate treatment
available. Evidence-based medicine often requires not only diagnosis before the
treatment regimen but also frequent intervals of reevaluation during the treatment to
show efficacy. So, no matter the generation of the clinician or which model of
medicine to which the clinician ascribes, diagnosis of the condition is fundamental.
Diagnosis prior to treatment is especially important in the management of chronic
infections.
However, most clinicians treating chronic infections have abandoned the fun-
damental principle of initial diagnosis. The problem seems to lie not in the
clinicians but in the diagnostic tools available. Many different culturing methods
have been tried, yet they do not improve outcomes in the treatment of chronic
infections. The inadequacy of cultivation methods has led to a de facto management
of chronic infections by an educated guess, trial and error method.
The transition toward adopting molecular methods for medical microbiology
need not be difficult. For virology there are no other reliable methods other than
nucleic acid-based analysis. Almost a decade ago it was established that not only
was DNA-based testing more accurate and reliable than clinical culture, but it also
had the advantage of reduced time to diagnosis and high throughput (Mothershed
and Whitney 2006 ). New methods have also been developed to identify various
different antibiotic resistance determinants while at the same time providing
genetic surveillance for new and existing pathogens (Weile and Knabbe 2009 ).
Indeed from 2001 to 2007, 215 novel bacterial species were identified in human
infections by sequencing methods with 100 of these new species identified in four
or more individual patients (Woo et al. 2008 ). Molecular methods offer faster and
higher throughputs while staying true to the original purpose of identifying and
quantifying microbes. Recent studies demonstrate that close to 100 % sensitivity
and specificity can be achieved for evaluating clinical infections (Hansen
et al. 2010 ). One issue is that molecular methods may be identifying too many
microorganisms, leading the clinician to over treat a specific infection.
DGGE and imaging methods showed that there was much more diversity present
in wounds than clinical cultures were reporting (Davies et al. 2004 ; James
et al. 2008 ). Clinicians managing other chronic infections such as chronic
rhinosinusitis (Stephenson et al. 2010 ), cystic fibrosis (Goddard et al. 2012 ), middle
ear infections (Laufer et al. 2011 ), and burns utilized molecular methods to show
similar findings. It has been generally agreed that these and other chronic infections
are associated with bacteria propagating in biofilm phenotype (Del Pozo and Patel
2007 ). Although molecular methods can identify microbes regardless of their mode
of growth, the same is not true for clinical cultures. Molecular technology provides
the clinician a more robust understanding of the infection, but also forces the
clinician to consider multiple microbial species. At the same time, molecular