95 Genetic determinants in MRSA carriage 5 acquired resistance genes related to resistance, of which the presence or absence corresponded to the phenotypic susceptibility in all isolates. However, alternative survival mechanisms to antibiotic exposure, such as tolerance and persistence, are not detectable by measuring MICs. Other potential factors influencing MRSA eradication outcome, e.g., therapy incompliance and host genetics [28], were not assessed in our study. There are some limitations of this study. It is a single-center study with a small sample size, a heterogeneous population, and a limited number of failed treatments. In addition, we did not always confirm that treatment failure was caused by the same clone, or acquisition of a different MRSA. However, given the very low prevalence of MRSA in the Netherlands, this would be highly unlikely. Furthermore, we did not correct for multiple testing. However, since it is an explorative study in a relatively undiscovered subject, we believe the results are still valid and useful in targeting future research. For this explorative purpose, we focused on pathogen factors and only added a limited number of host characteristics (i.e., sex, age, and complicated versus uncomplicated carriership). Other host factors—including host genetics—may influence the risk of treatment failure as well. Lastly, we investigated genes with a previously reported role in virulence. Future genome-wide association studies could perhaps identify signatures with novel genetic factors implicated in intracellular survival and biofilm formation that predict eradication failure. However, this requires a larger and preferably prospective data set. In conclusion, this explorative study showed a higher eradication failure rate in complicated MRSA carriers with ciprofloxacin-resistant MRSA lineages, which are predominantly healthcare-associated. In contrast, carriers of livestock-associated MRSA and the major community-associated ST8 and ST6 lineages were generally successfully decolonized. Further studies are warranted to confirm the higher eradication failure risk of ciprofloxacin-resistant lineages, and identify the underlying mechanisms. The identification of lineages that are prone to eradication failure is of clinical relevance, since it could influence the initiation and monitoring of MRSA eradication therapy.
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