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Results show that VLU infections are polymicrobial with no single bacterium
colonizing the wounds. The most ubiquitous and predominant organisms include
various anaerobes, Staphylococcus, Corynebacterium, and Serratia. Topological
analysis of VLU shows some notable differences in bacterial populations across the
surface of the wounds highlighting the importance of sampling techniques during
diagnosis. Metagenomics provide a preliminary indication that there may be proto-
zoa, fungi and possibly an undescribed virus associated with these wounds.
The polymicrobial nature of VLU and previous research on diabetic foot ulcers
and surgical site infections suggest that the future of therapy for such wounds lies in
the core of the logical and proven multiple concurrent strategy approach, which has
been termed “biofi lm-based wound care” and the use of individualized therapeutics
rather than a single treatment modality.
Sequencing for Study of Antibiotic Resistance in Bacteria
Antibiotic resistance can gradually evolve through the sequential accumulation of
multiple mutations. To study this evolution, scientists at Harvard Medical School
have developed a selection device, the ‘morbidostat’, which continuously monitors
bacterial growth and dynamically regulates drug concentrations to constantly chal-
lenge the evolving population. They analyzed the evolution of resistance in E. coli
under selection with single drugs, including chloramphenicol, doxycycline and tri-
methoprim. Over a period of ∼20 days, resistance levels increased dramatically,
with parallel populations showing similar phenotypic trajectories. WGS of the
evolved strains identifi ed mutations both specifi c to resistance to a particular drug
and shared in resistance to multiple drugs (Toprak et al. 2011 ). Chloramphenicol
and doxycycline resistance evolved smoothly through diverse combinations of
mutations in genes involved in translation, transcription and transport. In contrast,
trimethoprim resistance evolved in a stepwise manner, through mutations restricted
to the gene encoding the enzyme dihydrofolate reductase (DHFR). Sequencing of
DHFR over the time course of the experiment showed that parallel populations
evolved similar mutations and acquired them in a similar order.
Sequencing for Predicting the Virulence of MRSA
Microbial virulence is a complex and often multifactorial phenotype, intricately
linked to a pathogen’s evolutionary trajectory. Toxicity, the ability to destroy host cell
membranes, and adhesion, the ability to adhere to human tissues, are the major viru-
lence factors of many bacterial pathogens, including S. aureus. A study assayed the
toxicity and adhesiveness of 90 MRSA isolates and found that while there was
remarkably little variation in adhesion, toxicity varied by over an order of magnitude
between isolates, suggesting different evolutionary selection pressures acting on these
two traits (Laabei et al. 2014 ). The authors performed a GWAS and identifi ed a large
number of loci, as well as a putative network of interacting loci that are signifi cantly
associated with toxicity. Despite this apparent complexity in regulation of toxicity, a
11 Personalized Management of Infectious Diseases