The Use of DNA Methods to Characterize Biofilm Infection - Antibiofilm Agents: From Diagnosis to Treatment and Prevention - page 19

was complete and all the sub-plates identified by phenotypic methods (biochemis-
tries) the sub-plates were submitted for sequencing. The results showed that
5 wounds (10 %) were culture negative and 9 of the 46 remaining wounds (19 %)
had discrepant results between the bacterial isolate identified by culture versus
sequencing. For example, culturing methods identified P. aeruginosa , whereas
sequencing evaluating the same sub-plate identified Salmonella enterica . Once
again, culture failed to demonstrate the most abundant species over 50 % of the
time (Rhoads et al. 2012a ). It may be that one main reason clinicians struggle to
manage chronic infections is because traditional culturing methods consistently
report minor constituents of the infections rather than the dominant culprits.
Over 68 % of patients receive at least one course of antibiotics for the manage-
ment of their chronic wounds (Howell-Jones et al. 2005 ). Unfortunately, multiple
studies have demonstrated that treating wounds based on culture results does not
improve the outcomes of the healing of the wound (Lipsky et al. 2004 , 2011 ; Siami
et al. 2001 ). This information has led some investigators to conclude that even
though pathogens such as P. aeruginosa may be present in the wound, the pathogen
is not doing any harm. That conclusion is made because when chronic infections are
treated with anti-pseudomonal antibiotics specifically for P. aeruginosa identified
by culture, there is no improvement in wound healing outcomes (Joseph 2013 ). The
confusing results from clinical culture, which leads clinicians and scientists alike to
conclude that pathogens may not behave pathogenically or that bacteria don't
matter in certain chronic infections (O'Meara et al. 2010 ), may be due to the
inadequacies of the cultivation methods.
Although routine clinical cultures are inadequate for evaluating chronic infec-
tions, we must first determine if the proposed replacement (i.e., molecular methods)
is any better. That is, will adopting molecular methods improve clinical outcomes
for chronic infections produced by biofilm phenotype microorganisms? After all, by
growing bacteria, medical microbiologists can apply antibiotic discs and determine
the “real-world” sensitivity of the isolated bacteria. Also, even though it has been
demonstrated that DNA degrades quite quickly (2-3 days) once the bacteria dies
within the host infection (Post et al. 1996 ), there is no clear determination that the
microbial DNA identified by molecular methods is associated with a living bacte-
rial cell. However, in a chronic wound infection model, when wound biofilm was
comprehensibly diagnosed utilizing molecular methods and the microorganisms
identified specifically treated, healing outcomes did improve (Dowd et al. 2011 ).
Regardless, the primary tenant of medicine is for the clinician to fully diagnose the
disease, and as demonstrated above, clinical cultures are mostly blind to the
microbial reality of polymicrobial biofilm infection.