Characterization of polymicrobial infections in macaques with chronic cranial implants and evaluation of alternative antimicrobial strategies

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2018.Cataloged from PDF version of thesis.Includes bibliographical references (pages 221-242).Macaques are the most commonly used non-human primate in cognitive neuroscience research due to similarities between the macaque and human brain. Cephalic recording chambers (CRCs) are often surgically implanted to obtain neuronal recordings. CRCs represent a persistent source of microbial contamination, which can occasionally progress to clinical sequelae of meningitis and brain abscesses. In this thesis, we first examined aerobic and anaerobic bacterial species colonizing CRCs using both traditional culture-dependent methods and 16S microbiota culture-independent methods. We evaluated the most prevalent species, and compared CRC bacterial communities to skin, oral and fecal bacterial communities. Our results indicated that CRC bacterial communities are predominantly composed of anaerobic flora and are relatively unique between individual macaques. Additionally CRC bacterial communities are more similar to skin and oral bacterial communities than fecal bacterial communities, indicating that fecal contamination of CRCs is a less likely source of contamination. Aerobic culture and sensitivity data from samples collected in 2011 identified Staphylococcus aureus, Enterococcus faecalis and Proteus spp. as the most prevalent species isolated, and that E.faecalis isolates displayed marked resistance to multiple antimicrobial classes. Routine CRC sanitization procedures were revised in September 2014 to prohibit antimicrobial use within CRCs, and we evaluated how E.faecalis lineages persisted and evolved between 2011 and 2017. We identified a shift in sequence type (ST) from ST4 and ST55, predominating in 2011, to ST48 predominating in macaques implanted after 2013. ST48 lineages were less resistant to antimicrobials and stronger biofilm producers as compared to ST4 and ST55 lineages. We concluded that loss of selective pressure from antimicrobial use within CRCs permitted ST48 to emerge as the predominant lineage due to its strong biofilm-forming abilities. Finally, we evaluated alternative E.faecalis biofilm treatment strategies. We isolated lytic bacteriophages with activity against ST55 E.faecalis and evaluated the use of phages and antimicrobial peptides LL-37 and PR-39 against E. faecalis biofilm, alone, and in combination with antimicrobials. Our results identified that bacteriophages successfully decreased biofilm produced by ST55 and ST4 E. faecalis isolates and should be evaluated further for treatment of animal and human enterococcal-associated biofilm infections.by Mia Tova Rock Lieberman.Ph. D