Characterisation and Molecular Epidemiology of Mycobacterium chimaera isolates in Ireland
Citation:
MOK, SIMONE, Characterisation and Molecular Epidemiology of Mycobacterium chimaera isolates in Ireland, Trinity College Dublin.School of Medicine, 2019Download Item:
SimoneMokThesisHardBound2019.pdf (PhD thesis, examined and approved) 5.812Mb
Abstract:
Mycobacterium chimaera is a slow-growing nontuberculous Mycobacterium spp. that is now recognized as a separate species within the Mycobacterium avium Complex (MAC). In the past, M. chimaera was mainly associated with respiratory tract colonization or infections in patients with underlying structural lung disease. More recently, it has become recognized as the cause of invasive cardiovascular infections associated with open heart surgery (OHS). Cases of invasive M. chimaera infections have been linked to contaminated heater-cooler unit devices which are used for cardiopulmonary bypass during OHS. Following the global outbreak alert of invasive M. chimaera infections, efforts have been made internationally to assess the risks posed by these infections and to identify the sources of M. chimaera. In Ireland, a national investigation of M. chimaera infections was initiated by the Irish Health Service Executive and Health Protection Surveillance Centre in 2015. M. chimaera is an understudied pathogen and the overall aim of this project was to gain greater insight into the identification, epidemiology, antibiotic susceptibility and virulence of M. chimaera as a human pathogen.
Most commercial diagnostic assays cannot differentiate between M. chimaera and M. intracellulare within the MAC. The initial aim of this study was to re-identify an archival collection of clinical MAC isolates in the Irish Mycobacteria Reference Laboratory (IMRL) using 16S rRNA and ITS sequencing and to evaluate the use of a commercial assay ?GenoType NTM-DR? for identifying M. chimaera. The second aim of this study was to facilitate the national investigation of M. chimaera infections by identifying clinical and environmental M. chimaera isolates in conjunction with the IMRL and Public Health Laboratory Dublin, and to investigate the genomic relationship of these isolates with the use of whole genome sequencing (WGS) to find further evidence of molecular epidemiological links to those that have been reported internationally. The molecular epidemiology of respiratory M. chimaera isolates has not been studied extensively and it is now evident that M. chimaera is often recovered from respiratory specimens. The third aim was to investigate the genomic diversity of respiratory M. chimaera isolates using WGS. Invasive M. chimaera infections are particularly associated with poor clinical responses with approximately 50% mortality rate, and the optimal antibiotic treatment regimen for these infections is unknown. The fourth aim of this study was to characterise the antibiotic susceptibility profiles of clinical and environmental M. chimaera isolates by performing in vitro antimicrobial susceptibility testing to antimicrobial agents that are commonly used for treatment of mycobacterial infections.
In collaboration with the TB Immunology research laboratory, Trinity Translational Medicine Institute, the final aim of this study was to perform a preliminary study to gain insight into the host immune response to M. chimaera with the use of a THP-1 macrophage model to investigate cell viability and the production of pro-inflammatory cytokines.
There was a high proportion of M. chimaera isolates not previously identified by a commercial assay used in the IMRL. Evaluation of the GenoType NTM-DR has shown that this method can identify M. chimaera with 100% specificity and sensitivity and would also be useful for diagnostic laboratories microbiology where gene sequencing is not available. Accurate and rapid identification of M. chimaera is important due to the global outbreak of invasive cardiovascular infections and it is expected that more cases may be identified in the future due to the long incubation periods. M. chimaera contamination is mainly associated with Sorin/LivaNova devices and it is likely that these devices were contaminated at the manufacturing site rather than by local water sources in Ireland. WGS results from this study were consistent with those that have been reported internationally, which suggests that there is a low genetic diversity between M. chimaera isolates associated with OHS and Sorin/LivaNova HCU devices. These isolates were highly clonal to the global outbreak strain 1.1. By contrast, M. chimaera isolates from Maquet devices and unrelated respiratory M. chimaera isolates were genetically distinct. The molecular epidemiology of respiratory M. chimaera isolates is associated with diverse subgroups which are unrelated to those associated with OHS. This demonstrates that M. chimaera is an emerging respiratory pathogen and further investigation will be useful for identifying which strains are associated with colonization or clinical infection. Of the antibiotics tested, clarithromycin, amikacin and rifabutin had best activity against M. chimaera isolates, while susceptibility rates were lower for ethambutol and rifampicin. There was a high prevalence of isolates not susceptible to moxifloxacin or linezolid. In vitro antimicrobial susceptibility testing should help inform on the choice of antimicrobial agents as part of the overall therapeutic strategy. This work represents the first attempt to investigate the host immune response to M. chimaera infection. M. chimaera does not appear to induce high levels of cell death and the host defence mechanism appears to vary in response to the different doses of M. chimaera.
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APPROVED
Author: MOK, SIMONE
Advisor:
Rogers, ThomasQualification name:
Doctor of Philosophy (Ph.D.)Publisher:
Trinity College Dublin. School of Medicine. Discipline of Clinical MicrobiologyType of material:
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